Publications

Research Publications

Research Publications	Publication Date
Paukert, C., E. Kleekamp, and R. Tingley. 2020. Identifying Candidate Reference Reaches to Assess the Physical and Biological Integrity of Wadeable Streams in Different Ecoregions and Stream Sizes. Ecological Indicators 111. https://doi.org/10.1016/j.ecolind.2019.105966	April 2020
Şen, B., C. Che-Castaldo, H. J. Lynch, F. Ventura, M. A. LaRue and S. Jenouvrier. 2024. Detecting stochasticity in population time series using a non-parametric test of intrinsic predictability. Methods in Ecology and Evolution 15:1834–1846. https://doi.org/10.1111/2041-210X.14423. \| Abstract \| Download \| Publisher Website	August 2024	1. Many ecological systems dominated by stochastic dynamics can produce complex time series that inherently limit forecast accuracy. The ‘intrinsic predictability’ of these systems can be approximated by a time series complexity metric called weighted permutation entropy (WPE). While WPE is a useful metric to gauge forecast performance prior to model building, it is sensitive to noise and may be biased depending on the length of the time series. Here, we introduce a simple randomized permutation test (rWPE) to assess whether a time series is intrinsically more predictable than white noise.<br><br>2. We apply rWPE to both simulated and empirical data to assess its performance and usefulness. To do this, we simulate population dynamics under various scenarios, including a linear trend, chaotic, periodic and equilibrium dynamics. We further test this approach with observed abundance time series for 932 species across four orders of animals from the Global Population Dynamics Database. Finally, using Adélie (<i>Pygoscelis adeliae</i>) and emperor penguin (<i>Aptenodytes forsteri</i>) time series as case studies, we demonstrate the application of rWPE to multiple populations for a single species.<br><br>3. We show that rWPE can determine whether a system is significantly more predictable than white noise, even with time series as short as 10 years that show an apparent trend under biologically realistic stochasticity levels Additionally, rWPE has statistical power close to 100% when time series are at least 30 time steps long and show chaotic or periodic dynamics. Power decreases to ~10% under equilibrium dynamics, irrespective of time series length. Among four classes of animal taxa, mammals have the highest relative frequency (28%) of time series that are both longer than 30 time steps and indistinguishable from white noise in terms of complexity, followed by insects (16%), birds (16%) and bony fishes (11%).<br><br>4. rWPE is a straightforward and useful method widely applicable to any time series, including short ones. By informing forecasters of the inherent limitations to a system's predictability, it can guide a modeller's expectations for forecast performance.
Zydlewski, J. (2021). Book Review: “From catastrophe to recovery: stories of fisheries management successes” edited by Krueger, Taylor and Youn. Fisheries. DOI: 10.1002/fsh.10604 \| Download	June 2021
Zydlewski, J., Bailey, M. Roy, S., Sheehan, T., Sprankle, K. Stich, D. (2021) What have we lost? American shad’s impounded history. Frontiers in Marine Science. Volume 8:734213. doi: 10.3389/fmars.2021.734213 \| Download	October 2021
Zydlewki, J. (2023) American Eel. Chapter (Species Essay) in “Our Maine”, edited by Aram Calhoun, Mac Hunter and Kent Redford.	July 2023
Zulian, V, K Pacifici, NM Bacheler, JA Buckel, WF Patterson III, BJ Reich, KW Shertzer, NJ Hostetter. 2024. Applying mark-resight, count, and telemetry data to estimate effective sampling area and fish density with stationary underwater cameras. Canadian Journal of Fisheries and Aquatic Sciences. https://doi.org/10.1139/cjfas-2023-0373 \| Abstract	August 2024	Accurate estimates of abundance and density within geographically open populations must account for sampling gear effective sampling area (ESA). We describe a Marked N-Mixture model to estimate ESA and density (number of individuals/unit area) from repeated counts of unmarked and marked individuals, integrating mark-resight, camera counts, and telemetry data of red snapper (<i>Lutjanus campechanus</i>)<i> </i>at a 1.6 km<sup>2</sup> reef off North Carolina, USA. Cameras recorded observations of unmarked and marked individuals, whereas telemetry data indicated the number of tagged fish present on the reef. We estimated density (95 individuals/km<sup>2</sup>, 95%CI.:58–149), ESA (which was lower when current direction was towards the camera), detection probability (0.06, 95%CI.: 0.03–0.09), and covariate relationships. Simulation studies under different scenarios of data quality and space use identified positive bias in density estimates from N-mixture models due to fish movement, while the Marked N-Mixture model returned unbiased estimates of density and ESA. Our approach allowed the estimation of density, improved precision, and reduced the bias of parameter estimates, even under scenarios of poor data and animal movement, and can be applied to other geographically open populations where count and telemetry overlap in space and time.
Zuckerman, G. et al. Diverse migratory portfolios drive inter-annual switching behavior of elk across the Greater Yellowstone Ecosystem	December 2023
Zipkin, E.F., & G. V. DiRenzo. 2022. Biodiversity is decimated by the cascading effects of the amphibian-killing fungus. PLoS Pathogens, 18(7), e1010624. DOI: 10.1371/journal.ppat.1010624.	July 2022
Zipkin, E. F., DiRenzo, G. V., Rossman, S., Ray, J. M, & K. R. Lips. 2020. Tropical snake community collapses following pathogen-induced amphibian loss. Science 367: 814-816. DOI: 10.1126/science.aay5733 \| Abstract \| Download \| Publisher Website	December 2020	Biodiversity is declining at unprecedented rates worldwide. Yet cascading effects of biodiversity loss on other taxa are largely unknown because baseline data are often unavailable. We document the collapse of a Neotropical snake community after the invasive fungal pathogen <i>Batrachochytrium dendrobatidis</i> caused a chytridiomycosis epizootic leading to the catastrophic loss of amphibians, a food source for snakes. After mass mortality of amphibians, the snake community contained fewer species and was more homogeneous across the study site, with several species in poorer body condition, despite no other systematic changes in the environment. The demise of the snake community after amphibian loss demonstrates the repercussive and often unnoticed consequences of the biodiversity crisis and calls attention to the invisible declines of rare and data-deficient species.
Zimmerman, G. S., B. A. Milsap, F. Abadi, J. V. Gedir, W. L. Kendall, and J. R. Sauer. 2022. An integrated population model to inform exploitation management for bald eagles. Journal of Wildlife Management 86:e22158, https://doi.org/10.1002/jwmg.22158. \| Abstract	January 2022	Effectively managing take of wildlife resulting from human activities poses a major challenge for applied conservation. Demographic data essential to decisions regarding take are often expensive to collect and are either not available or based on limited studies for many species. Therefore, modeling approaches that efficiently integrate available information are important to improving the scientific basis for sustainable take thresholds. We used the prescribed take level (PTL) framework to estimate allowable take for bald eagles (Haliaeetus leucocephalus)in the conterminous United States. We developed an integrated population model (IPM) that incorporates multiple sources of information and then use the model output as the scientific basis for components of the PTL framework. Our IPM is structured to identify key parameters needed for the PTL and to quantify uncertainties in those parameters at the scale at which the United States Fish and Wildlife Service manages take. Our IPM indicated that mean survival of birds >1 year old was high and precise (0.91, 95% CI = 0.90–0.92), whereas mean survival of first‐year eagles was lower and more variable(0.69, 95% CI = 0.62–0.78). We assumed that density dependence influenced recruitment by affecting the probability of breeding, which was highly imprecise and estimated to have declined from approximately 0.988 (95% CI = 0.985–0.993) to 0.66 (95% CI = 0.34–0.99) between 1994 and 2018. We sampled values from the posterior distributions of the IPM for use in the PTL and estimated that allowable take (e.g., permitted take for energy development, incidental collisions with human made structures, or removal of nests for development) ranged from approximately 12,000 to 20,000 individual eagles depending on risk tolerance and form of density dependence at the scale of the conterminous United States excluding the Southwest. Model‐based thresholds for allowable take can be inaccurate if the assumptions of the underlying framework are not met, if the influence of permitted take is under‐estimated, or if undetected population declines occur from other sources. Continued monitoring and use of the IPM and PTL frameworks to identify key uncertainties in bald eagle population dynamics and management of allowable take can mitigate this potential bias, especially where improved information could reduce the risk of permitting non‐sustainable take.
Zhao, Q., A.K. Fuller, and J.A. Royle. 2022. Spatial dynamic N-mixture models with interspecific interactions. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13936	July 2022
Zhang, Y., Y. Feng, S. Wang, Z. Tang, Z. Zhai, R. Viegut, E. Webb, A. Raedeke and Y. Shang. Deep Learning Models for Waterfowl Detection and Classification in Aerial Images. Information \| Abstract	March 2024	Waterfowl populations monitoring is essential for wetland conservation. Lately, deep 1 learning techniques have shown promising advancements in detecting waterfowl in aerial images. In 2 this paper, we present performance evaluation of several SOTA supervised and semi-supervised deep 3 learning models for waterfowl detection in aerial images using four new image datasets containing 4 197,642 annotations. The best-performing model, Faster R-CNN, achieved 95.38% accuracy in terms 5 of mAP. Semi-supervised learning models outperformed supervised models when the same amount 6 of labeled data were used for training. Additionally, we present performance evaluation of several 7 deep learning models on waterfowl classifications on aerial images using a new real-bird classification 8 dataset consisting of 6,986 examples and a new decoy classification dataset consisting of about 10,000 9 examples per category of 20 categories. The best model achieved accuracy of 91.58 % on the decoy 10 dataset and 82.88% on the real-bird dataset.
Zhang, Q., J. Jin, P. Budy, S.E. Null, and X. Wang. 2021. Predicting the response of Arctic lake thermal processes to a whole-lake warming manipulation. Geophysical Research Letters, 48, e2021GL092680. https://doi.org/10.1029/2021GL092680. USGS FSP IP-127181. \| Abstract	December 2021	We investigated how lake thermal processes responded to whole-lake warming manipulation in a lake in the Alaskan Arctic through observations and numerical modeling. The warming manipulation was conducted by artificially heating the epilimnion as a proxy for climate warming. We performed numerical modeling and used an improved lake scheme based on the Community Land Model (CLM). We simulated a control run (CTL) without warming and a warming manipulation simulation (WARM). Results indicated the WARM simulation accurately captured observed lake temperature profiles where water stratification was extended in time, and water stability was strengthened. Two additional sensitivity tests with different warming onset dates and of the same warming duration showed that earlier onsets of warming are predicted to make the lake water column more stable and less easily mixed relative to a later onset of warming. The results of this study provide a more complete understanding of lake thermal processes in arctic freshwater lake systems and how they will respond to predicted future warming.
Zentner, D., D. Shoup, and S.K. Brewer. 2023. Effects of Sucker Gigging on Fish Populations in Oklahoma Scenic Rivers. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-151-2023, Washington, D.C. https://doi.org/10.3996/css882119	July 2023
Zentner, D. L., S. L. Wolf, S. K. Brewer and D. E. Shoup. 2021. A review of factors affecting PIT-tag detection using mobile arrays and use of mobile antennas to detect PIT-tagged suckers in a wadeable Ozark stream. North American Journal of Fisheries Management 41: 697-710.	February 2021
Zentner, D. L., J. J. Spurgeon, S. E. Lochmann, C. L. Graham. 2021. Tag type and location-dependent retention impart varied levels of bias on mark-recapture parameter estimates. North American Journal of Fisheries Management 41:474-483.	November 2020
Zeller, K.A., D.W. Wattles, J.M. Bauder, and S. DeStefano. 2020. Forecasting seasonal connectivity in a developing landscape. Land 9:233. \| Abstract \| Download \| Publisher Website	April 2020	Connectivity and wildlife corridors are often key components to successful conservation and management plans. Connectivity for wildlife is typically modeled in a static environment that reflects a single snapshot in time. However, it has been shown that, when compared with dynamic connectivity models, static models can underestimate connectivity and mask important population processes. Therefore, including dynamism in connectivity models is important if the goal is to predict functional connectivity. We incorporated four levels of dynamism (individual, daily, seasonal, and interannual) into an individual-based movement model for black bears (Ursus americanus) in Massachusetts, USA. We used future development projections to model movement into the year 2050. We summarized habitat connectivity over the 32-year simulation period as the number of simulated movement paths crossing each pixel in our study area. Our results predict black bears will further colonize the expanding part of their range in the state and move beyond this range towards the greater Boston metropolitan area. This information is useful to managers for predicting and addressing human–wildlife conflict and in targeting public education campaigns on bear awareness. Including dynamism in connectivity models can produce more realistic models and, when future projections are incorporated, can ensure the identification of areas that offer long-term functional connectivity for wildlife.
Zebro, L.R., J.T. Mrnak, S.L. Shaw, S.R. Chipps, and G.G. Sass. 2022. Density-Dependent, Cannibalism, and Environmental Influences on Juvenile Walleye Survivorship in Northern Wisconsin Lakes. Fisheries Management and Ecology 29:897-910. \| Abstract	October 2022	Walleye (<i>Sander vitreus</i>) natural recruitment has declined in many populations within the Ceded Territory of Wisconsin (CTWI) over the past twenty years. Using CTWI age-0 and age-1 walleye relative abundance (CPE) data during 1990-2019, we tested for abiotic and biotic (density dependence, cannibalism) factors influencing age-0 to age-1 walleye mortality. Age-0 to age-1 walleye mortality was strongly density-dependent. Juvenile walleye mortality was always elevated at high age-0 CPE and highly variable at low age-0 CPE. Cannibalism effects did not influence age-0 to age-1 walleye mortality. Mixed effects modeling results suggested that age-0 CPE (positive), May surface water temperature (positive), and peak surface water temperature (negative) were the strongest predictors of age-0 to age-1 walleye mortality. Our results suggest that density-dependence and environmental factors influencing spawning and ontogenetic phenology (climate change, variable ice-off dates), trophic mismatches, and metabolic and consumptive demand may dictate age-0 to age-1 walleye mortality. Our results also showed elevated age-0 to age-1 walleye mortality at low age-0 CPE, which supports previous findings of depensatory recruitment dynamics in CTWI walleye populations. Given observed natural recruitment declines observed in CTWI walleye populations over time, stocking has been primarily used to rehabilitate stocks. Our findings suggest that stocking on top of natural recruitment would further increase density-dependent juvenile walleye mortality rates. Additional research is needed to specifically address elevated juvenile walleye mortality at low adult stock sizes and/or with declining natural recruitment to inform conservation management decisions.
Zatkos L., Murphy C.A., Pollock A., Penaluna B.E., Olivos J.A., Mowlds E., Moffitt C., Manning M., Linkem C., Holst L., Cárdenas B., and Arismendi I. 2020. AFS Roots: Dr. Emmeline Moore, All Things to All Fishes. Fisheries 45(8). DOI: 10.1002/fsh.10501	August 2020
Zaidel, P.A., A.H. Roy, K.M. Houle, B. Lambert, B.H. Letcher, K.H. Nislow, and C. Smith. 2020. Impacts of small dams on stream temperature. Ecological Indicators. https://doi.org/10.1016/j.ecolind.2020.106878 \| Publisher Website	September 2020
Yurek S, Eaton MJ, Lavaud R, Laney RW, DeAngelis D, Pine III, WE, La Peyre MK, Martin J, Frederick P, Wang H, Lowe MR, Johnson F, Camp EV, Mordecai R. 2021 Modeling structural mechanics of oyster reef self-organization including environmental constraints and community interactions. Ecological Modelling 440:109389 \| Abstract \| Download	January 2021	Self-organization in reef-building systems is a process of establishing reef morphology on aquatic landscapes from substrate generated by the population, and reinforcing these structures through interactions between internal processes and external factors. In oyster reefs, internal dynamics include production of calcareous shell, which serves as settlement substrate for larval recruits. External factors include environmental conditions and predation, which regulate overall population size through growth and mortality, but also regulate settlement dynamics by exposing interior shell surfaces through mortality. Oyster reefs are also highly spatially constrained by aquatic conditions, thus their efficiency for producing settlement habitat under these constraints may be critical to self-organization and long term persistence. We developed an individual based model that simulates engineering of oyster reefs through individual contributions of shell, which slowly degrade and consolidate to form reef structure. Reef habitat has two aspects in this model, one for elevating the population above the benthos, and another for making exposed shell surfaces available for settlement. We applied the model to examine how these two aspects relate to the live population as a coupled system with complex feedbacks. In particular, we examined how temporal dynamics of the reef proceed through time as the size structure of the live population and relative composition of shell types change through time. To represent these dynamics, we simulated single restoration events and tracked ensuing dynamics over subsequent decades without additional enhancement, for an example study site in South Carolina (USA). To estimate uncertainty in restoration performance, we followed a biological ensemble modeling approach, varying selected model parameters over five scenarios of predator community composition. Our goal was to identify trends that were robust across simulations, which could serve as hypotheses and predictions for future field studies. The overall temporal pattern of simulations was three distinct phases: initial transient dynamics of the stocked population, followed by growth and saturation of the life population, and then saturation of settlement habitat several years later. All simulations incurred considerable loss of shell biomass during the transient phase when the live population was establishing and shell degradation exceeded production. Simulations with predators were able to recover from this decline through production of live oysters, while simulations without predators continued to decline throughout simulation runs. These results indicate that reefs can be productive with respect to the live population, but decline overall in reef substrate. We conclude with hypotheses relating the efficiency of generation of settlement habitat to measures of biomass and individual density, which suggest levels that may lead to reef self-organization.
Young, J.K, A.R. Butler, J.D. Holbrook, H. Shamon, and R. C. Lonsinger. 2023. Mesocarnivores of western landscapes in LB McNew, DK Dahlgren, and JL Beck, editors. Rangeland Wildlife Ecology and Conservation. https://doi.org/10.1007/978-3-031-34037-6_16. \| Abstract	September 2023	This book chapter reviews the current state of knowledge on mesocarnivores in working landscapes of western North America, including, natural history of mesocarnivores, the ecological role of mesocarnivores, and the influence or ranching, harvest, and predator control on mesocarnivores. This chapter will be included in the book Wildlife Ecology in Working Landscapes of the West
Yiu, S-W., N. Owen-Smith, and J.W. Cain III. 2022. How do lions move at night when they hunt? Journal of Mammalogy 103:855-864 \| Download	August 2022
Yarra, A.N. and D.D. Magoulick. 2020. Effect of stream permanence on predation risk of lotic crayfish by riparian predators. Southeastern Naturalist 19:673-691. doi.org/10.1656/058.019.0407	November 2020
Yang, Y., S. E. Hobbie, R. R. Hernandez, D. Tilman, S. M. Grodsky, Y-G. Zhu, Y. Luo, T. M. Smith, J. Fargione, J. M. Jungers, M. Yang, W-Q Chen. 2020. Restoring abandoned farmland to mitigate climate change on a full Earth. One Earth. 3:176–186. doi:10.1016/j.oneear.2020.07.019.	August 2020
Yackel Adams AA, NJ Hostetter, WA Link, and SJ Converse. 2024. Identifying Pareto-efficient eradication strategies for invasive populations. Conservation Letters: e13051.	September 2024
Y. Yang, J. Zhenong, N. D. Mueller, R. R. Hernandez, S. M. Grodsky, L. Sloat, M. Chester, Y. G. Zhu, and D. Lobell. 2022. Climate feedbacks from irrigation inform sustainable adaptation. Nature Food.	September 2023
Xu, W., L.C. Gigliotti, R. Royauté, H. Sawyer, and A.D. Middleton. 2023. Fencing amplifies individual differences in movement with implications on survival for two migratory ungulates. Journal of Animal Ecology 92(3): 677-689. https://doi.org/10.1111/1365-2656.13879	March 2023
Xu, L., Z. Feiner, P. Frater, G. Hansen, R. Ladwig, C. Paukert, M. Verhoeven, L. Wszola, and O Jensen. 2024. Small wins, big losses: asymmetric impacts of climate change on preferred thermal habitat of inland lake fishes. Nature Communications 15:10273. https://doi.org/10.1038/s41467-024-54533-2	November 2024
Wu, H., Flynn, C., Hall, C., Che-Castaldo, C., Samaras, D., Schwaller, M. and Lynch, H.J. (2024). Penguin colony georegistration using camera pose estimation and phototourism. PLoS ONE, 19(10), pp.e0311038–e0311038. doi:https://doi.org/10.1371/journal.pone.0311038. \| Abstract \| Download \| Publisher Website	October 2024	Satellite-based remote sensing and uncrewed aerial imagery play increasingly important roles in the mapping of wildlife populations and wildlife habitat, but the availability of imagery has been limited in remote areas. At the same time, ecotourism is a rapidly growing industry and can yield a vast catalog of photographs that could be harnessed for monitoring purposes, but the inherently ad-hoc and unstructured nature of these images make them difficult to use. To help address this, a subfield of computer vision known as phototourism has been developed to leverage a diverse collection of unstructured photographs to reconstruct a georeferenced three-dimensional scene capturing the environment at that location. Here we demonstrate the use of phototourism in an application involving Antarctic penguins, sentinel species whose dynamics are closely tracked as a measure of ecosystem functioning, and introduce a semi-automated pipeline for aligning and registering ground photographs using a digital elevation model (DEM) and satellite imagery. We employ the Segment Anything Model (SAM) for the interactive identification and segmentation of penguin colonies in these photographs. By creating a textured 3D mesh from the DEM and satellite imagery, we estimate camera poses to align ground photographs with the mesh and register the segmented penguin colony area to the mesh, achieving a detailed representation of the colony. Our approach has demonstrated promising performance, though challenges persist due to variations in image quality and the dynamic nature of natural landscapes. Nevertheless, our method offers a straightforward and effective tool for the georegistration of ad-hoc photographs in natural landscapes, with additional applications such as monitoring glacial retreat.
Wu, Donghai; Steven M. Grodsky; Wenfang Xu; Naijing Liu; Rafael M. Almeida; Liming Zhou; Lee M. Miller; Xiang Zhao; Somnath Baidya Roy; Geng Xia; Anurag A. Agrawal; Benjamin Z. Houlton; Alexander S. Flecker; Xiangtao Xu. 2023. Large wind farms reduce grassland productivity and carbon sequestration via atmospheric drying. Science Bulletin.	July 2023
Wszola, L.S., L.N. Messinger, L.F. Gruber, E.F. Stuber, C.J. Chizinski, and J.J. Fontaine. 2020. Use and expenditures on public access hunting lands. Journal of Outdoor Recreation and Tourism 29:100256.	December 2020
Wszola, L., N. A. Sievert, A. J. Lynch, H. S. Embke, A. L. Kaz, M. D. Robertson, S. R. Midway, C. P. Paukert. Lake temperature and morphometry shape the thermal composition of recreational fishing catch. 2024. Transactions of the American Fisheries Society. 2024:1-17. IP-154515. BAO Approval 07/12/2024.DOI: 10.1002/tafs.10481	June 2024
Wszola, L. S., A. L. Madsen, E. F. Stuber, C. J. Chizinski, J. J. Lusk, J. S. Taylor, K. L. Pope, and J. J. Fontaine. 2020. Public access for pheasant hunters: understanding an emerging need. Journal of Wildlife Management 84:45-55. \| Download	January 2020
Wright, A., Bernard, R. F., Mosher, B. A., O'Donnell, K., Braunagel, T., DiRenzo, G. V., Fleming, J., Shafer, C., Brand, A., Zipkin, E., Grant, E. H. C. 2020. Moving from decision to action in conservation science. Biological Conservation 249: 108698. https://doi.org/10.1016/j.biocon.2020.108698 \| Abstract \| Download \| Publisher Website	December 2020	Biodiversity loss is a major threat to the integrity of ecosystems and is projected to worsen, yet the path to successful conservation remains elusive. Decision support frameworks (DSFs) are increasingly applied by resource managers to navigate the complexity, uncertainty, and differing socio-ecological objectives inherent to conservation problems. Most published conservation research that uses DSFs focuses on analytical stages (e.g., identifying an optimal decision), making it difficult to assess and learn from previous examples in a conservation practice context. Here, we (1) evaluate the relationship between the application of decision science and the resulting conservation outcomes, and (2) identify and address existing barriers to the application of DSFs to conservation practice. To do this, we develop a framework for evaluating conservation initiatives using decision science that emphasizes setting attainable goals, building momentum, and obtaining partner buy-in. We apply this framework to a systematic review of amphibian conservation decision support projects, including a follow-up survey of the pertinent conservation practitioners, stakeholders, and scientists. We found that all projects identified optimal solutions to reach stated objectives, but positive conservation outcomes were limited when implementation challenges arose. Further, we identified multiple barriers (e.g., dynamic and hierarchical leadership, scale complexity, limited resource availability) that can inhibit the progression from decision identification to action implementation (i.e., ‘decision-implementation gap’), and to successful conservation outcomes. Based on these results, we provide potential actionable steps and avenues for future development of DSFs to facilitate the transition from decision to action and the realization of conservation successes.
Wood, J.M., A.K. Tegeler, and B.E. Ross. Vegetation management on private forestland can increase avian species richness and abundance.	August 2020
Wood, C.M., S.T. McKinney, C.S. Loftin, and Z. Loman. 2020. Testing prediction accuracy in a short-term ecological study. Basic and Applied Ecology 43:77-85.	March 2020
Woo, I, MJ Davis, SEW De La Cruz, L Windham-Myers, JZ Drexler, KB Byrd, EJ Stuart-Haëntjens, FA Anderson, BA Bergamaschi, G Nakai, CS Ellings, and S Hodgson. 2021. Carbon flux, storage, and wildlife co-benefits in a restoring estuary: case study at the Nisqually River Delta, Washington, USA. In K Krauss, Z Zhilang, and C Stagg (eds.) Wetland Carbon and Environmental Management. Wiley Publishers. https://doi.org/10.1002/9781119639305.ch5 \| Publisher Website	October 2021
Wolfson, D.W., J.R. Fieberg, and D.E. Andersen. 2020. Juvenile sandhill cranes exhibit wider ranging and more exploratory movements than adults during the breeding season. Ibis 162:556-562 DOI:10.1111/ibi.12786.	October 2020
Wolfson, D.W., D.E. Andersen, and J.R. Fieberg. Using piecewise regression to identify biological phenomena in biotelemetry datasets. Journal of Animal Ecology 91:1755–1769. https://doi.org/10.1111/1365-2656.13779 \| Publisher Website	September 2022
Wolfenkoehler, W., J.M. Long, R. Gary, R.A. Snow, J.D. Schooley, L. A. Bruckerhoff, and R.C. Lonsinger. 2023. Viability of side-scan sonar to enumerate Paddlefish, a large pelagic freshwater fish, in rivers and reservoirs. Fisheries Research 261:106639. https://doi.org/10.1016/j.fishres.2023.106639	January 2023
Wolf, S., D. Swedberg, E. Tanner, S. Fuhlendorf, and D. Brewer. 2022. Using fiber-optic distributed temperature sensing in fisheries applications: An example from the Ozark Highlands. Fisheries Research, https://doi.org/10.1016/j.fishres.2022.106542	November 2022
Wolf, S. and S. K. Brewer. 2021. Survival and movement patterns of Rainbow Trout stocked in a groundwater-influenced warmwater stream. North American Journal of Fisheries Management. https://doi.org/10.1002/nafm.10566	January 2021
Wohner,W.J, A. Duarte, J. Wikert, B. Cavallo, S.C. Zeug, and J.T Peterson. Integrating monitoring and optimization modeling to inform flow decisions for Chinook salmon smolts. Ecological Modeling \| Abstract	July 2022	Monitoring is usually among the first actions taken to help inform recovery planning for declining species, but these data are rarely used formally to inform conservation decision making. For example, Central Valley Chinook salmon were once abundant, but anthropogenic activities have led to widespread habitat loss and degradation resulting in significant population declines. Juvenile Chinook salmon survival through the southern Sacramento-San Joaquin River Delta in particular, may be a limiting factor for juveniles outmigrating from the San Joaquin River and tributaries. However, survival and routing monitoring data have not been formally used to inform water management. Here, we illustrate how estimates derived from monitoring data can be used to inform water management and as a basis for developing adaptive management for flows. Specifically, we conducted a meta-analysis of Chinook salmon smolt survival and routing estimates through the south Delta. We then used the resulting parameter estimates to develop a survival and routing simulation model to estimate optimal flows for the San Joaquin River during smolt outmigration from February–May. We found that large flow pulses at predictable times during the spring are projected to be optimal for increasing Chinook salmon smolt survival to the Bay and that optimal scenarios differed somewhat with water year type. Sensitivity analysis revealed temperature and smolt outmigration timing are driving optimal pulse distribution and that water allocation changes little with parameter uncertainty. This case study highlights the utility of the decision-analytic framework for solving conservation problems.
Wohner, PJ, SA Laymon, JE Stanek, SL King, RJ Cooper. 2021. Challenging our understanding of western Yellow-billed Cuckoo habitat needs and accepted management practices. Restoration Ecology 29(3): e13331. https://doi.org/10.1111/rec.13331 \| Abstract	March 2021	<b>Riparian restoration in the southwestern United States frequently involves planting cottonwood (<i>Populus</i> spp.) and willow (<i>Salix</i> spp.) cuttings or seedlings. In the absence of flooding and gap-forming disturbance, planted forests often senesce without further young tree recruitment. This has largely been the case in riparian systems in California that historically supported state endangered western Yellow-billed Cuckoo (<i>Coccyzus americanus</i>; Cuckoo). Associated with riparian forest maturation has been around an 85% decline in Cuckoo population numbers in approximately the past thirty years. Other riparian species of concern show a concomitant decline, indicating the problem is not specific to Cuckoo. Although varying hypotheses exist for the recent decline, alternative management practices have not been sufficiently explored to rule out breeding ground habitat quality as a major contributing factor. Few intensive Cuckoo datasets currently exist to test hypotheses about breeding habitat quality due to extremely low populations in the remaining occupied sites. We used a historical (1986–1996) spot mapping dataset from the South Fork Kern River Valley, California to identify vegetation characteristics related to Cuckoo and five other sensitive riparian bird territory densities. We found Cuckoo densities were positively associated with increased vertical vegetative structure 1–5 m above ground with a threshold for mean tree height. Sensitive species densities were also related to vertical structure and started to decline with stand height greater than 6–8 m. Low and mid canopy vertical structure started declining after about age eight. Naturally regenerated sites had higher densities of most sensitive bird species than planted sites. We provide ideas for restoring mature forest with little low to mid canopy vertical structure.</b>
Wohner, P.J., R.F. Thurow, and J.T. Peterson. 2024. Evaluating streamflow and temperature effects on migration and survival of a cold-water fish with spatial capture-recapture models. Transactions of the American Fisheries Society153(3): 326-346. https://doi.org/10.1002/tafs.10464 \| Publisher Website	April 2024
Wohner, P.J., P.D. Scheerer, M.H. Meeuwig, and J.T. Peterson. 2023. A comprehensive multi-state conditional occupancy model for evaluating interactions of non-native and native species. Frontiers in Ecology and Evolution 10, p.1288. \| Abstract	January 2023	A major challenge in ecology is disentangling interactions of non-native, potentially invasive species on native species. Conditional two-species occupancy models are used to examine the effects of dominant species (e.g., non-native) on subordinate species (e.g., native) while considering the possibility that occupancy of one species may affect occupancy and/ or detection of the other. Although conditional two-species models are useful for evaluating the influence of one species on presence of another, it is possible that species interactions are density dependent. Therefore, we developed a novel two-species occupancy model that incorporates multiple abundance states (i.e., absent, present, abundant) of the native species. We showcase the utility of this model that has the capacity to incorporate random effects and covariates on both occupancy and detection and that can help disentangle species interactions given varying occupancy and detection in different abundance states. As a case study, we use snorkel survey data from the Umpqua basin, Oregon, where it is hypothesized that smallmouth bass <i>Micropterus dolomieu</i>, a non-native piscivore, exclude Umpqua chub <i>Oregonichthys kalawatseti</i>, a small endemic minnow. Our conditional two-species multi-state (2SMS) model allowed us to conclude that in general, average occupancy was low for both fishes, and that when non-native bass were present, overall native chub occupancy in the present (0.18 ± 0.05 SD) and abundant (0.19 ± 0.03) states was higher than when non-natives were absent (0.14 ± 0.02/ 0.08 ± 0.02), indicating the non-native was not excluding the native species. By incorporating a species interaction factor into the model, we found a positive association (6.75 ± 5.54 SD) between native chub and non-native bass. The covariates strongly related to occupancy were elevation, algae, and land cover type (urban and shrub). Detection probability was relatively high for both species (0.21–0.82) and was most strongly related to the covariates day of year, water temperature, gravel substrate, and stream order/ magnitude. Incorporation of detection probability and covariates enabled interpretation of interactions between the two species that may have been missed without their inclusion in the modeling process. Our new 2SMS occupancy model can be used by scientists and managers with a broad range of survey and covariate data to disentangle species interactions problems to help them inform management decisions.
Wohner, P.J., A. Duarte, and J.T. Peterson. 2024. An integrated analysis for estimation of survival, growth, and movement of unmarked juvenile anadromous fish. Ecological Modeling 495, p.110780. https://doi.org/10.1016/j.ecolmodel.2024.110780 \| Abstract \| Publisher Website	September 2024	Managers invest substantial resources to promote recovery of declining anadromous fish stocks. Recovery strategies are manifold and often include management actions intended to stimulate somatic growth, increase in-river survival, and motivate juvenile outmigration during favorable environmental conditions. Evaluating the efficacy of these management actions is difficult, however, because monitoring data that explicitly track individuals from egg deposition to juvenile outmigration are typically lacking. We developed an integrated population model that links two different and often collected types of anadromous fish monitoring data: spawning ground surveys and rotary screw trap juvenile catch data. The integrated model accounts for incomplete detection and uses the two sources of data to estimate juvenile demographic parameters in a multistate framework. We evaluated the model’s performance using simulated data under a range of conditions typically encountered in similar surveys. Simulation results indicated that the model estimated juvenile survival, growth, and movement with no-to-minimal bias (i.e., ≥ 50% of simulations ± 0–0.05). As an example case study, we fit the model to empirical fall-run Chinook Salmon (<i>Oncorhynchus tshawytscha</i>) monitoring data collected in California’s Central Valley, U.S.A. In doing so, we evaluated the influence of environmental conditions (e.g., discharge, water temperature) and habitat availability on juvenile demographic rates. We demonstrated that through our integrated approach we could estimate state transition probabilities that are typically inestimable for naturally produced, unmarked juvenile fish when using traditional statistical approaches to analyze these types of monitoring data. Furthermore, the structure of our model can serve as a useful foundation for decision-support models within adaptive management programs by directly linking management actions, decision-support-model predictions, and monitoring.
Winship A.J., Thorson J., Clarke E., Coleman H., Costa B., Georgian S., Gillett D., Grüss A., Henderson M., Hourigan T.F., Huff D., Kreidler N., Pirtle J., Olson J.V., Poti M., Rooper C.N., Sigler M.F., Viehman S., and Whitmire C.E. in review . Good practices for species distribution modeling of deep-sea corals and sponges: data collection, analysis, validation, and communication. Submitted to Frontiers in Marine Science. \| Abstract	May 2020	Resource managers in the United States and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on habitat-forming invertebrates, including deep-sea corals and sponges (DSCS). Related management decisions require information about where DSCS occur and in what densities. Species distribution modeling (SDM) provides a cost-effective means of identifying potential DSCS habitat over large areas to inform these management decisions and data collection. Here we provide recommendations of good practices for DSCS SDM, especially in the context of data collection and management applications. Managers typically need information regarding DSCS encounter probabilities, densities, and sizes, defined at sub-regional to basin-wide scales and validated using subsequent, targeted data collections. To realistically achieve these goals, we recommend integrating available data sources in SDMs including fine-scale visual sampling and broad-scale resource surveys (e.g., fisheries trawl surveys). When possible, we recommend models fitted to presence-absence and density data rather than models fitted only to presence data, which are difficult to validate and can confound estimated probability of occurrence or density with sampling effort. Ensembles of models can provide robust predictions, while multi-species models leverage information across taxa and facilitate community inference. We also recommend that analysts include environmental predictor variables representing multiple spatial scales, model residual spatial autocorrelation, and quantify prediction uncertainty. To facilitate the use of models by managers, predictions should be expressed in units that are widely understood and should be validated at an appropriate spatial scale using a sampling design that provides strong statistical inference. We present three case studies for the Pacific Ocean that illustrate good practices with respect to data collection, modeling, and validation; these case studies demonstrate it is possible to implement our recommendations in real-world settings.
Winemiller KO, Keppeler FW, Bower LM, Cunha ER, Quintana Y, Saenz DE, Lopez‐Delgado EO, Bokhutlo T, Arantes CC, Andrade MC, Robertson CR, Mayes KB. Can spatial food web subsidies associated with river hydrology and lateral connectivity be detected using stable isotopes? Food Webs. 2023. \| Abstract	March 2023	Hydrology, lateral connectivity and stable isotope ratios of fishes and mussels in the Guadalupe River, Texas, were analyzed for evidence of spatial food web subsidies between the active channel and oxbow lakes in the floodplain. During and following lateral connections, aquatic organisms residing in the channel may assimilate material from sources imported from oxbows, and oxbow residents may consume and assimilate material imported from the channel. During surveys conducted between March 2016 and April 2017, fish, mussel, algae, and riparian plants samples were collected in and around two oxbows and adjacent channel sites for analysis of stable isotope ratios. Biplots of d<sup>13</sup>C and d<sup>15</sup>N were graphed for basal sources and specimens of Longnose Gar <i>Lepisosteus osseus, </i>Gizzard Shad <i>Dorosoma cepedianium, </i>Threadfin Shad <i>Dorosoma petenense, </i>Bullhead Minnow <i>Pimephales vigilax, </i>Smallmouth Buffalo <i>Ictiobus bubalus, </i>White Crappie <i>Pomoxis annularis</i>, sunfishes (<i>Lepomis</i> species combined), and two mussel species (combined) captured from oxbows and the channel. Within each graph, a source polygon was drawn to indicate the space occupied by animals that could have assimilated feasible combinations of source materials from the oxbows or river channel. Based on positions of animals within source polygons, riparian plants were the most important source of organic matter supporting biomass of fishes and mussels both within the channel and oxbows during every survey period, with algae contributing minor percentages. Most organisms had isotopic signatures consistent with assimilation of <i>in situ</i> sources, or else were inconclusive with regard to cross-habitat exchanges. Between-habitat food web subsidies were indicated for 7.6% of 314 organisms from oxbows and 11.2% of 231 from the channel, and these cases followed high flow pulses that connected oxbows for extended periods. Several issues that compromise inferences from stable isotope analysis were identified, and attempts to estimate spatial food web subsidies in fluvial systems could be enhanced by analyzing additional biomarkers, such as isotopic ratios of other elements and compound-specific stable isotopes, as well as additional sources, time-specific biotracers, and experimental approaches that directly track movement of sources and organisms in spatially structured food webs.
Wineland, S. M., R. Fovargue, B. York, A. J. Lynch, C. P. Paukert, and T. M. Neeson. 2020. Is there enough water? How bearish and bullish outlooks shape decision-maker perspectives on environmental flows. Journal of Environmental Management 280. https://doi.org/10.1016/j.jenvman.2020.111694	November 2020
Wilson, R. E., and S. A. Sonsthagen. Species-specific responses to landscape features shaped genomic structure within Alaska galliformes. IUCN Galliformes Specialists Group Newsletter	July 2022
Wilson, R. E., S. W. Boyd, S. A. Sonsthagen, D. H. Ward, P. Clausen, K. M. Dickson, B. S. Ebbinge, G. A. Gudmundsson, G. K. Sage, J. R. Rearick, D. V. Derksen, and S. L. Talbot. 2024. Where east meets west: phylogeography of the high Arctic North American brant goose. Ecology and Evolution.14: e11245. doi.org/10.1002/ece3.11245	April 2024
Wilson, R. E., S. M. Matsuoka, L. L. Powell, J. A. Johnson, D. Demarest, D. Stralberg, and S. A. Sonsthagen. 2021. Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: the rusty blackbird. Diversity. 13:103.	February 2021
Wilson, R. E., S. A. Sonsthagen, P. Lavretsky, A. Majewski, E. Arnason, K. Halldórsdóttir, A. W. Einarsson, K. Wedemeyer, and S. L. Talbot. 2022. Low levels of hybridization between sympatric cold-water adapted Arctic cod and Polar cod in Beaufort Sea confirms genetic distinctiveness. Arctic Science. doi.org/10.1139/AS-2021-0030	February 2022
Wilson, R. E., S. A. Sonsthagen, N. Sme, A. J. Gharett, A. Majewski, K. Wedemeyer, R. J. Nelson, and S. L. Talbot. 2020. Mitochondrial genome diversity and population mitogenomics of Polar cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biology. 43:979–994.	June 2020
Wilson, R. E., S. A. Sonsthagen, J. M. DaCosta, M. D. Sorenson, A. D. Fox, M. Weaver, D. Skalos, A. Kondratyev, K. T. Scribner, A. Walsh, C. R. Ely, and S. L. Talbot. 2022. As the goose flies: Migration routes and timing of strategies influence genetic diversity patterns of a circumpolar goose. Diversity. 14:1067. doi.org/10.3390/d14121067	December 2022
Wilson, L., G. Lonsdale, J.D. Curlis, E.A. Hunter, and C.L. Cox. 2022. Predator-based selection and the impact of edge sympatry on components of coral snake mimicry. Evolutionary Ecology https://doi.org/10.1007/s10682-021-10143-8.	January 2022
Williams, J. R., C. S. Guy, T. M. Koel, P. Bigelow. 2020. Targeting aggregations of telemetered lake trout to increase gillnetting suppression efficacy. North American Journal of Fisheries Management 40:225-231.	January 2020
Williams, J. R., C. S. Guy, P. E. Bigelow, and T. M. Koel. 2021. Quantifying the spatial structure of invasive lake trout (Salvelinus namaycush) in Yellowstone Lake to improve suppression efficacy. North American Journal of Fisheries Management 42:50-62 DOI: 10.1002/nafm.10712.	December 2021
Will, A., H. McFarland, C. Latty, and A. Powell. 2024. Geolocators, stable isotopes, and citizen science identify migratory timing, route, and spring molt of Smith’s Longspurs. Avian Conservation and Ecology 19(1):13. [online] URL: https://www.ace-eco.org/vol19/iss1/art13 \| Abstract	April 2024	Climate change is disproportionately impacting the Arctic. For Arctic breeding birds, basic knowledge of their annual cycle, specifically the timing, route, and movement behavior of migration, is needed to understand when and where populations may experience threats. We use a combination of geolocators and stable isotope analysis to identify route and timing of migration in Smith’s Longspurs (<i>Calcarius pictus</i>) that breed in Alaska’s Brooks Range. We trapped males on their breeding grounds in 2011-2014 and collected head feathers for stable isotopes of hydrogen (δ<sup>2</sup>H). We deployed 22 geolocators on a subset of individuals and retrieved four, which all overwintered in southern Texas. Individual start dates for fall migration based on geolocators were more variable than for the spring, and individuals were highly mobile while on their wintering grounds. Geolocators and stable isotope values were comparable across years and indicated that birds from the Brooks Range undergo their pre-nuptial molt in central Canada. We compared geolocator and stable isotope inferred locations to observations submitted to e-Bird and found that longspurs were distributed farther south during the winter months, but farther north during the spring than most eBird observations. Concurrent deployments of geolocator tags across Smith’s longspur’s breeding range would clarify whether migratory behaviors and routes are population specific or shared widely across breeding locations.
Wilkinson, Christine E., Alex McInturff, Maggi Kelly, and Justin S. Brashares. "Quantifying wildlife responses to conservation fencing in East Africa." Biological Conservation 256 (2021): 109071. \| Abstract	April 2021	The fencing of protected areas is increasing worldwide. However, the implementation of fences for conservation has outpaced scientific assessment of their effectiveness, non-target impacts, and long-term costs. We assessed landscape predictors of fence crossing sites and employed camera traps over a one-year period to investigate wildlife responses to a conservation fence around Lake Nakuru National Park, Kenya. Specifically, we measured the impact of the fence on wild mammal movement, and the temporal impacts of fence maintenance on wildlife crossings and behavior. Cameras captured more than 65,000 detections of animals approaching fences, with 3626 observed crossings over 2818 trap nights at 19 sites. Using these data, we developed a guide to classifying fence-specific mammal behaviors. Thirty-eight wild mammal species approached known weak points in the fence, and 27 species were recorded crossing the fence. No single environmental variable predicted detection or fence crossing points for all species, but seasonality, human activity, habitat visibility, and proximity to an adjacent protected area were each correlated with species-specific crossing locations. Additionally, breaches of repaired fence-crossing locations occurred within days of maintenance. We conclude that popular, ‘one-size-fits-all’, conservation fence designs may be ineffective and costly for restraining movement of many wildlife species. We recommend that those deploying conservation fences start with clearly articulated management goals, that fence maintenance be informed by taxa-specific tendencies to breach fences, and that managers consider the strategic creation of wildlife corridors, overpasses, or ungulate-proof fences to link fenced protected areas with surrounding habitat.
Wilkinson, B.P., and P.G.R. Jodice. Support for the fasting endurance hypothesis of partial migration in Brown Pelicans. 2023. Ecosphere 2023;14:e4365. https://doi.org/10.1002/ecs2.4365 \| Abstract \| Download	February 2023	Partial migration occurs when only a certain fraction of a population or species migrates instead of all individuals. Considered an evolutionary precursor, understanding why some individuals choose to undertake migration while others do not may serve to inform general migratory theory. While several hypotheses currently exist for explaining the maintenance of partial migration, empirical support for many is limited. To address this gap, we analyzed telemetry data acquired from individual brown pelicans (<i>Pelecanus occidentalis</i>; <i>n</i> = 74), a partially migratory seabird, nesting on six colonies in the South Atlantic Bight over the course of four autumn migrations using a Cox’s proportional hazards model. We estimated that approximately 74% of pelicans nesting within the study area may be migratory on an annual basis, with the remainder staying within the surrounding marine ecoregion year-round. Mean date of migration initiation was 9 November, although movements occurred from September – December. Modeling results indicated significant effects of rising sea-surface temperatures and decreased body condition on migration rate. We suggest that the ontogenetic migration of the primary forage species of brown pelicans from estuarine to pelagic environments causes a seasonal reduction in prey, and that individuals in poor body condition are unable to meet the energetic demands potentially associated with this decrease in prey availability (i.e., the fasting endurance hypothesis of partial migration). Although we did not find evidence for a density-dependent migratory response, the effects of intraspecific competition on migration in pelicans appears to warrant consideration.
Wilkinson, B.P., and P.G.R. Jodice. 2022. Interannual colony exchange among breeding Eastern Brown Pelicans. J. Field Ornithology. 93(1) 5. https://doi.org/10.5751/JFO-00074-930105 \| Download	April 2022
Wilkinson, B.P., A.R. Robuck, R. Lohmannm, H.M., Packard, P.G.R. Jodice. 2022. Urban proximity while breeding is not a predictor of perfluoroalkyl substance contamination in the eggs of brown pelicans. Science of the Total Environment 803 (2022) 150110 \| Download	September 2021
Wilkinson, B.P., A.M. Haynes-Sutton, L. Meggs, and P.G.R Jodice. 2020. High spatial fidelity among foraging trips of Masked Boobies from Pedro Bank, Jamaica. PLoOS ONE 15(4): e0231654. https://doi.org/10.1371/journal.pone.0231654 \| Download	April 2020
Wilkins, K., Pejchar, L., Carroll, S. L., Jones, M. S., Walker, S. E., Shinbrot, X. A., ... & Reid, R. S. (2021). Collaborative conservation in the United States: A review of motivations, goals, and outcomes. Biological Conservation, 259, 109165. https://doi.org/10.1016/j.biocon.2021.109165 \| Abstract \| Publisher Website	July 2021	For centuries, communities around the globe have worked together to manage resources—a process often referred to as community-based conservation. More recently in the US, diverse stakeholders have partnered to address complex environmental issues that span land ownership or administrative boundaries, calling these efforts collaborative conservation. Reviews of community-based and collaborative conservation have historically focused on developing countries. To synthesize published information on U.S.-focused groups, we conducted a literature review with the following objectives: 1) characterize geographic distribution, types of participants, and sources of funding for these groups; 2) assess issues motivating group formation, goals, activities to achieve those goals, and outcomes; 3) identify whether these goals, activities, and outcomes were biophysical, social, and/or economic. To accomplish these objectives, we searched for relevant peer-reviewed journal articles, book chapters, and reports in online databases from 1800's-2017. Our review resulted in 245 documents describing 296 collaborative conservation groups across all 50 states (primarily the Western U.S.) and the District of Columbia. The top three issues motivating collaborative group formation included impacts of land and resource degradation on livelihoods, water quality and management, and managing land and resources across ownership boundaries. We found that there was little published information on the outcomes of group activities (16% of groups). For the limited number of groups for which the literature reported outcomes, there was no relationship between positive outcomes and group characteristics. Our findings suggest that renewed efforts to evaluate the impact of collaboration on conservation are warranted and could support learning and improved action.
Wilder, Benjamin T; Amanda T. Becker, Adrian Munguia-Vega, Melanie Culver. 2021. Tracking the desert's edge with a Pleistocene relict. Journal of Arid Environments, DOI.org/10.1016/j.jaidenv.2021.104653 \| Abstract	October 2021	A series of 900–1200 m desert peaks surrounded by arid lowlands occur throughout the southwestern U.S. and northwestern Mexico where temperate affiliated species occur at highest elevations. The presence of disjunct long-lived plant taxa on under-explored summits, especially Isla Tiburón at 29º latitude in the Gulf of California, suggests a more southerly extent of Ice Age woodlands than previously understood. The phylogeography of the desert edge species <i>Canotia holacantha</i> (Celastraceae) was investigated to test the hypothesis that insular desert peak populations represent remnants of Pleistocene woodlands rather than recent dispersal events. Sequences of four chloroplast DNA regions totaling 2,032 bp were amplified from 74 individuals of 14 populations across the entire range of <i>C. holacantha</i> as well as nine individuals that represented the other two species in its clade (<i>C. wendtii</i> and <i>Acanthothamnus aphyllus</i>) and two outgroups. Results suggest that a <i>Canotia</i> common ancestor occurred on the landscape, which underwent a population contraction ca. 15 kya. The Isla Tiburón <i>C. holacantha</i> population and the Chihuahuan Desert microendemic <i>C. wendtii</i>have the greatest genetic differentiation, are sister to one another, and basal to all other <i>Canotia</i> populations. Three haplotypes within <i>C. holacantha</i> were recovered, which correspond to regional geography and thus identified as the Arizona, Sonora, and Tiburón haplotypes, within which <i>Acanthothamnus aphyllus</i> is nested rather than as a related genus. These results indicate a once broad distribution of <i>Canotia </i>/<i> Acanthothamnus</i> during the Pleistocene, now present in relict populations on the fringes of the southern desert, in the Chihuahuan Desert, with scattered populations on desert peaks and a common or abundant distribution at the norther ecotone of the Sonoran Desert. These results suggest <i>Canotia</i> has tracked the shift of the desert’s edge both in latitude and elevation since the end of the last Ice Age.
Wiens, JD, KM Dugger, M Higley, DB Lesmeister, AB Franklin, KA Hamm, GC While, KE Dilione, DC Simon, RR Bown, PC Carlson, CB Yackulic, JD Nichols, JE Hines, RJ Davis, DW Lamphear, C McCafferty, TL McDonald, and SG Sovern. 2021. Invader removal triggers competitive release in a threatened avian predator. Proceedings of the National Academy of Science 118 (31): e2102859118. https://doi.org/10.1073/pnas.2102859118	July 2021
Whittum, K., Zydlewski, J., Coghlan, Jr., S., Hayes, D., Watson, J., and Kiraly, I. (2023) Fish Assemblages in the Penobscot River: A Decade after Dam Removal. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 15:e10227. DOI: 10.1002/mcf2.10227 \| Download	January 2023
Whittier, J., J. Westhoff, C. Paukert, and R. Rotman. 2020. Use of multiple temperature logger models can alter conclusions. Water2(3), 668; doi.org/10.3390/w12030668	March 2020
Whitlock, S.L., T.M. Lewis, and J.T. Peterson. 2020. Using a Bayesian Multistate Occupancy Model to Assess Seabird and Shorebird Status in Glacier Bay, Alaska. Wildlife Society Bulletin https://doi.org/10.1002/wsb.1100	October 2020
Whitlock, S.L, J.N. Womble, and J.T. Peterson. Modelling Pinniped Abundance and Distribution Using Counts at Terrestrial Sites and In-Water Sightings. Ecological Modelling	March 2020
Whitesell, M.J., E.A. Hunter, D.C. Rostal, and J.M. Carroll. 2022. Direct and indirect pathways for environmental drivers of hatching success in the loggerhead sea turtle (Caretta caretta). Marine Ecology Progress Series 701: 119-132.	November 2022
White, S.L., M.S. Eackles, T. Wagner, M. Schall, G. Smith, J. Avery, and D.C. Kazyak. 2021. Optimization of a suite of flathead catfish (Pylodictis olivaris) microsatellite markers for understanding the population genetics of introduced populations in the northeast United States. BMC Research Notes 14:314.	August 2021
White, S.L., J. Keagy, S. Batchelor, J. Langlois, N. Thomas, and T. Wagner. 2024. Movement beyond the mean: decoupling sources of individual variation in brook trout movement across seasons.Environmental Biology of Fishes 106:2205-2218. https://doi.org/10.1007/s10641-023-01501-2	January 2024
White, S.L., E.M. Hanks, and T. Wagner. 2020. A novel quantitative framework for riverscape genetics. Ecological Applications. https://doi-org.ezaccess.libraries.psu.edu/10.1002/eap.2147	May 2020
White, S.L., D.A. DeMario, L.R. Iwanowicz, V.S. Blazer, and T. Wagner. 2020. Tissue distribution and immunomodulation in channel catfish (Ictalurus punctatus) following dietary exposure to polychlorinated biphenyl Aroclors and food deprivation. Int J Environ Res Public Health: 17(4). pii: E1228. doi: 10.3390/ijerph17041228	February 2020
White, S.L. and T. Wagner. 2020. Behavior at short temporal scales drives dispersal dynamics and survival in a metapopulation of brook trout (Salvelinus fontinalis). Freshwater Biology.	November 2020
White, S., E. Faulk, C. Tzilkowski, A.S. Weber, M. Marshall, and T. Wagner. 2020. Predicting fish species richness and habitat relationships using Bayesian hierarchical multispecies occupancy models. Canadian Journal of Fisheries and Aquatic Sciences 77:602-610.	January 2020
White, S., D. DeMario, L. Iwanowicz, V. Blazer, and T. Wagner. 2020. Tissue distribution and immunomodulation in channel catfish (Ictalurus punctatus) following dietary exposure to polychlorinated biphenyl Aroclors and food deprivation. Int J Environ Res Public Health: 17(4). pii: E1228. doi: 10.3390/ijerph17041228	February 2020
White, L.M., S.J. Gifford, G. Kaufman, E. Gese, M.A. Peyton, R.R. Parmenter, and J.W. Cain III. 2024. Seroprevalence, blood chemistry, and patterns of canine parvovirus, distemper virus, plague, and tularemia in free-ranging coyotes (Canis latrans) in northern New Mexico, USA. Journal of Wildlife Diseases 60:14–25. \| Download	January 2024
White, K. M., J. D. Stafford, and R. C. Lonsinger. 2023 The first documented interaction between a long-tailed weasel (Mustela frenata) and a plains spotted skunk (Spilogale interrupta) carcass. Ecology and Evolution 13(1):e9758. https://doi.org/10.1002/ece3.9758 \| Abstract \| Download	January 2023	A novel interaction between a long-tailed weasel (<i>Mustela frenata</i>) and a plains spotted skunk (<i>Spilogale interrupta</i>) carcass is detailed. In November 2020, a farmer in Edmunds County in north-central South Dakota sent in a video recording of a long-tailed weasel with a spotted skunk carcass. Location of the event, carcass condition, and recorded behavior of the long-tailed weasel offers probable, but unconfirmed, evidence that the spotted skunk was killed by the long-tailed weasel.
White, K. M., A. M. Cheeseman, J. D. Stafford, and R. C. Lonsinger. 2024. Pasture and diurnal temperature are key predictors of regional Plains Spotted Skunk (Spilogale interrupta) distribution. Journal of Mammalogy 105(6): 1278–1288. https://doi.org/10.1093/jmammal/gyae063 \| Abstract	June 2024	The plains spotted skunk (<i>Spilogale interrupta</i>) is a small carnivore native to central North America that has experienced significant population reductions, and there is a lack of information about the species that could inform conservation efforts. Our study aimed to address knowledge gaps about the distribution and habitat associations of the species in South Dakota using species distribution modeling. We used species location data collected from state natural resource managers, trappers, and members of hunting and wildlife social groups, environmental predictors, and six predictive modeling algorithms (i.e., artificial neural networks, artificial classification tree analysis, generalized boosting models, maximum entropy, multivariate adaptive regression splines, and random forests) to develop climate and landcover ensemble distribution models. The most important climate and landcover predictors were mean temperature diurnal range and proportion of area classified as pasture. Ensemble model concordance identified approximately 31,300 km<sup>2</sup> of potential plains spotted skunk habitat primarily in eastern South Dakota and between the watersheds of the Missouri and James River. Our results offer insights that can guide conservation efforts and inform effective management strategies for conserving plains spotted skunk populations in the northern Great Plains. The promotion of low-intensity agricultural practices, such as maintaining pastures, farm buildings, and fences rows and the management of woodland encroachment may improve habitat suitability and facilitate the recovery of plains spotted skunks in the region.
White, J.S., Peterson, J.T., Stratton Garvin, L.E., Kock, T.J., and Wallick, J.R., 2022, Assessment of habitat availability for juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the Willamette River, Oregon: U.S. Geological Survey Scientific Investigations Report 2022–5034, 44 p., https://doi.org/10.3133/sir20225034 \| Abstract	March 2022	The Willamette River, Oregon, is home to two salmonid species listed as threatened under the Endangered Species Act (ESA), Chinook salmon and steelhead trout. Streamflow along the Willamette River is largely controlled by upstream dams, 13 of which are operated by the U.S. Army Corps of Engineers (USACE) as part of the Willamette Valley Project. In 2008, these dams were found to have a deleterious effect on ESA-listed salmonids (NOAA Fisheries, 2008), resulting in USACE taking mitigatory actions. Included in these actions was setting seasonal streamflow targets at various locations along the river to improve survival and migration of juvenile salmonids. Though these targets were established with the best available information at the time, recent data and models have advanced understanding of river dynamics and allow a more robust analysis of the affect of streamflow on downstream habitat. This study leverages these recent datasets to build high-resolution models of useable habitat for juvenile Chinook Salmon and steelhead trout to assess how this habitat varies with streamflow. Habitat models rely on hydraulic models developed in White and Wallick, 2021, and temperature models developed in Stratton Garvin and others, 2021b, both paired with literature supplied data on habitat preferences. Findings a non-uniform response to streamflow, where habitat in some reaches of the Willamette consistently increases with additional streamflow, while other reaches see habitat decrease when streamflows increase from low to moderate flows. These differences are explained by local geomorphology in each reach, particularly the transition of the river from a relatively dynamic, multi-threaded river to a simpler and more confined river downstream. The upstream reaches generally have more habitat available per unit stream distance than their counterparts, but all reaches display greatest amounts of habitat at the highest streamflows. Finally, results show that water temperature in summer greatly reduces the amount of habitat available to the focal species, particularly downstream of Corvallis. Together, these findings serve to inform flow management by providing a quantitatve assessment of the affects of streamflow on habitat.
White, C. LeAnn, Lankton, Julia S., Walsh, Daniel P., Sleeman, Jonathan M., Stephen, Craig. 2020. An ecological and conservation perspective. One health: The theory and practice of integrated health approaches (2nd edition) : 25-38.	January 2020
Whitby, M. D., T. J. Kieran, T. C. Glenn, and C. Allen. 2020. Agricultural pests consumed by common bat species in the United States corn belt: The importance of DNA primer choice. Agriculture, Ecosystems & Environment 303:107105.	August 2020
Whelan, G.E., D.M. Day, J. Casselman, L. Gephart, C.J. Hall, J. Lichatowich, M. Matylewich, L.E. Miranda, L. Roulson, P.D. Shirey, N. Mercado-Silva, J. Waldman, and D. Winters. 2020. Tracking fisheries through time: The American Fisheries Society as an historical lens. Fisheries 45:392-426. https://doi.org/10.1002/fsh.10457 \| Abstract	May 2020	The historical context of current environmental conditions offers vital guidance to North American fisheries professionals as they strive to develop effective management plans and policies. Through this retrospective we highlight the remarkable historic fisheries resources and causative reasons for establishing public fisheries agencies and the American Fisheries Society (AFS). Through a review of primary historical documents and literature for North America, this paper identifies: factors contributing to the founding of AFS and public fish commissions; shows how selected resource issues evolved; and documents how and why selected fisheries and aquatic habitat policies changed in response to those issues. Overexploitation, landscape-scale habitat alterations, mining, and dams were the causative agents for emergence of fisheries agencies and the AFS, and these factors remain relevant today. Beginning in the 1960s, North Americans grew tired of degraded waters and fisheries and forced policy changes that have directly and indirectly affected the fisheries we manage today. The historical events and resulting corrective legislation are taken for granted by those unaware that AFS has actively participated in developing policies to address these environmental issues. Further, AFS continues to play a vital role in identifying key issues, providing conduits for information to cope with impairments, and advocating for policies to conserve intact habitats and improve degraded systems. The struggles documented in this paper offer crucial lessons as we continue to be challenged by legacy resource issues and face emerging environmental stressors such as climate change as well as regression in long-standing environmental protection policies.
Wheeler, M.E., J.A. Barzen, S.M. Crimmins, and T.R. Van Deelen. 2021. Population responses to harvest depend on harvest intensity, demographics, and mate replacement in sandhill cranes. Global Ecology and Conservation 30: e01778 https://doi.org/10.1016/j.gecco.2021.e01778	August 2021
Wheeler, K., Kuhn, E., Bruckerhoff, L., Udall, B., Wang, J., Gilbert, L., Goeking, S., Kasprak, A., Mihalevich, B., Neilson, B. and Salehabadi, H., 2021. Alternative Management Paradigms for the Future of the Colorado and Green Rivers. Center for Colorado River Studies, White Paper, (6), pp.1-85. https://qcnr.usu.edu/coloradoriver/files/WhitePaper6.pdf	January 2021
Westhoff, J.T., Berkman ,L.K., Klymus, K.E., Thompson, N.L. and Richter, C.A. 2022. A comparison of eDNA and visual survey methods for detection of Longnose Darter Percina nasuta in Missouri. Fishes 2022, 7, 70. https://doi.org/10.3390/fishes7020070 \| Abstract	March 2022	The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA further upstream in the mainstem St. Francis River than previously reported and in a tributary for the first time. Our multi-scale occupancy approach compared models where detection was constant against a model that allowed detection to vary by survey method. The constant model received the most support indicating survey method was not a strong predictor and detection was estimated at 0.70 (0.45–0.86; 95% CI) across both methods. Our study produced effective longnose darter eDNA primers and demonstrated the application of eDNA for sampling small-bodied, cryptic fish. We detected longnose darter eDNA 27 km upstream of their known range and determined that snorkel surveys are the most efficient sampling method if water clarity allows. We recommend target sample sizes to achieve various detection goals for both sample methods and our results inform future design of distributional and monitoring efforts.
Westhoff, J. T., H. A. Abdelrahman, and J. A. Stoeckel. 2023. Upper thermal tolerance of two native and one invasive crayfish in Missouri, USA. Freshwater Crayfish 28:27-36. https://doi.org/10.5869/fc.2023.v28-1.27 \| Abstract	December 2023	The spread of invasive crayfish requires invaded habitats to be thermal suitable and differences in thermal tolerances among species could provide refugia for native crayfish affected by the invader. We estimated upper thermal tolerance for the invasive <i>Faxonius hylas</i> and native <i>F. peruncus</i> and <i>F. quadruncus</i> using critical thermal maxima (CTM) methodology to determine if there are ecologically exploitable differences in estimates among species and if there are areas within their distributional ranges that exceed their thermal maximums. We found no differences in CTM estimates among species or sexes but did observe significant differences in CTM estimates among acclimation temperatures. Additionally, crayfish size had a small, yet significant effect on CTM estimates whereby smaller individuals had lower CTM estimates than larger individuals. The similarity among CTM estimates suggests that for at least upper thermal tolerance, areas thermally available to the native species will also be thermal suitable for the invasive. We did not observe water temperatures in the field that exceeded CTM estimates for any species. However, areas within the mainstem St. Francis River did have warming tolerance estimates of less than 5 °C suggesting spread of the invasive through the mainstem could be limited by water temperature.
West L, K Rafiq, SJ Converse, AM Wilson, NR Jordan, KA Golabek, JW McNutt, and B Abrahms. 2024. Droughts reshape apex predator space use and intraguild overlap. Journal of Animal Ecology 93:1785-1798.	October 2024
Werdel, T. J., C. W. Piper, A. M. Ricketts, M. S. Peek, D. S. Sullins, and A. A. Ahlers. 2023. Strategic grassland conservation for swift foxes in multi-use landscapes. Biological Conservation 277:109864. DOI: 10.1016/j.biocon.2023.109864.	October 2023
Wenger, S.J., E.S. Stowe, K.B. Gido, M.C. Freeman, Y. Kanno, N.R. Franssen, J.D. Olden, N.L. Poff, A.W. Walters, P.M. Bumpers, M.C. Mims, M.B. Hooten, and L. Lu. Accepted. Simple statistical models can be useful for testing hypotheses with population time series data. Ecology and Evolution http://dx.doi.org/10.1002/ece3.9339	September 2022
Wenger, A.S., E. Gómez Juárez, J. Thomas, T. Amaya, C. Corbin, J. Edmond, K. Falinski, J. Hill, A. Jenkins, S.D. Jupiter, C.D. Kuempel, J.B. Lamb, E.M. Nalley, S. Omwenga, T. Oza, E.N. Perez, L.J. Tuttle Raz, S. Sarkozy-Banoczy, A. Wakwella. 2023. A guide for integrated conservation and sanitation programs and approaches. Wildlife Conservation Society. Pp. 1-143. https://doi.org/10.19121/2023.Report.49832 \| Abstract \| Publisher Website	October 2023	Human and ecosystem health are inextricably linked, yet strategies to improve both are addressed in siloed ways (Wakwella et al., 2023). For instance, the water, sanitation, and hygiene (WASH) sector focuses on the provision of services for safe drinking water, sanitation, and hygiene to improve human health and wellbeing. However, although there is substantial evidence to show that unsafely managed sanitation degrades ecosystems and makes them more vulnerable to climate change (Wear et al., 2023), and that ecosystem loss and degradation negatively impacts human health (Herrera et al., 2017; Wakwella et al., 2023), the sanitation and conservation sectors rarely work in a coordinated and strategic way to achieve their interconnected goals. The Science for Nature and People Partnership (SNAPP) Improving Coastal Health working group formed in 2020 to develop resources to help marine conservation and sanitation practitioners work together on integrated conservation and sanitation programs. Informed by the outcomes of a needs assessment launched in 2021 to better understand the challenges and opportunities related to integrated programs, we created this document as a first step towards providing advice on implementing integrated conservation and sanitation programs. The purpose of this guide is: -Create awareness among stakeholders about the impacts of poor sanitation and wastewater pollution on ocean health and the importance of more integrated solutions. -Outline the benefits of an integrated approach for achieving human and ecosystem health goals and simultaneously improving climate resilience. -Provide guidance to the conservation and sanitation sectors on how to work in partnership. The information contained in this guide is primarily aimed at actors who could participate in the sanitation-conservation interface, including practitioners from both sectors, investors, governments, research scientists, and private businesses. We focus on domestic wastewater pollution impacts on tropical coastal marine ecosystems, including mangroves, seagrass, and coral reefs, although we reference other coastal systems when relevant. This resource is also flexible enough for the guidance to be adapted for other coastal and marine environments. Freshwater ecosystems are considered in this guide in their role as transportation of diffuse pollution, but the specific impacts of wastewater pollution on freshwater aquatic life are not included. Other land-based sources of pollution, including from agriculture and development (e.g., agrochemicals, chemical contaminants, sediments) are also outside the scope of this guide, as there are already several resources on addressing these sources of pollution. We hope this is the first of many resources to help guide collaboration and coordination across sectors to achieve human and ecosystem health goals.
Welsh, S.A., K.J. Zipfel, A.W. Peters, D.C. Hoffman and C.M. Layne. 2024. Paddlefish movement and dam passage in the Ohio and Kanawha Rivers, West Virginia. West Virginia Academy of Science 96:12-19.	October 2024
Weller, F.W., W.S. Beatty, E.B. Webb, D.C. Kesler, D.G. Krementz, K. Asante, L.W. Naylor. Environmental drivers of autumn migration departure decisions in midcontinental mallards. Movement Ecology \| Abstract	January 2022	<i><u>Background</u><br>The timing of autumn migration in ducks is influenced by a range of environmental conditions that may elicit individual experiences and responses from individual birds, yet most studies have investigated relationships at the population level. We used data from individual satellite-tracked mallards (<i>Anas platyrhynchos</i>) to model the timing and environmental drivers of autumn migration movements at the landscape scale.<br><u>Methods</u> <br>We combined two sets of location records (2004-2007, and 2010-2011) from satellite-tracked mallards migrating to winter in the Mississippi Alluvial Valley, and identified records that indicated the start of long-range (≥ 30 km) southward movements during the migration period. We developed candidate models to predict the departure date, conditional on daily mean environmental covariates (temperature, snow and ice cover, wind conditions, precipitation, cloud cover, and pressure), at a 32×32 km resolution. We modeled selection of departure date by individual mallards using a discrete choice model accounting for heterogeneity in individual preferences. We ranked model performance with the Bayesian Information Criterion (BIC).<br><u>Results</u> <br>Departure was best predicted (60% precision) by a “winter conditions” model containing temperature and snow cover depth and duration. Models conditional on wind speed, precipitation, pressure variation, and cloud cover received lower support. Number of days of snow cover, recently experienced (snow days), and current snow cover had the strongest positive effect on departure likelihood, followed by experienced days of freezing temperature (frost days) and current low temperature. Distributions of dominant drivers and of correct vs incorrect prediction along the movement tracks indicate that these responses applied throughout the latitudinal range of migration. Among recorded departures, most were driven by snow days (65%) followed by current temperature (30%). <br><u>Conclusions</u> <br>Our results indicate that the dominant environmental driver of departure decision in autumn-migrating mallards was the onset of snow conditions, and secondarily the onset of temperatures close to, or below, the freezing point. Mallards are likely to relocate southwards quickly when faced with foraging that is impeded by snow, and could use declining temperatures as a more graduated early cue for departure. Our findings provide further insights into the functional response of mallards to weather and climate factors during the migration period that ultimately determine distribution.</i>
Weller, F.G., E.B. Webb, W.S. Beatty and D.C. Kesler. Agent-based modeling of movements and habitat selection of mid-continent mallards. Final report	September 2022
Weller, F.G., E.B. Webb, S. Fogenburg, W. S. Beatty, D. Kesler, R.H. Blenk, K.M. Ringelman, M.L. Miller and J.M. Eadie. An agent-based model to quantify energetics, movements and habitat selection of mid-continent mallards in the Mississippi Alluvial Valley. Ecological Modeling \| Abstract	September 2023	The dynamics of wintering waterfowl populations at the landscape scale are the result of complex interactions of environmental, behavioral and energetic drivers. Agent-based models provide a method to directly link these factors in a spatially explicit framework and allow the emergence of subtle or non-linear patterns from the aggregation of individual agent actions. We adapted the Spatially-explicit Waterbird Agent-based Model Program (SWAMP), originally developed for waterbirds in central California, to simulate a basin-scale population of mallards (<i>Anas platyrhynchos</i>) wintering in the Mississippi Alluvial Valley over a four-month period (November–February). Simulated agents move within the landscape, foraging on areas made available conditional on a probabilistic inundation status, and depleting food resources. The model uses a high-resolution map of eastern Arkansas waterfowl habitats and incorporates a hierarchical habitat selection system that enables mallards to relocate at increasing scales in response to changing food availability. We validated the performance of modeled mallard body condition and behavioral metrics under different environmental conditions against expected outcomes, and found that the simulation produced realistic representations of changes in flight distances, energy expenditure, lipid storage, and foraging habitat use in response to depleting food resources over time. We discuss the model's applicability as a tool to quantify waterfowl response to a range of environmental conditions and evaluate scenarios of landscape composition and configuration in the context of waterfowl population management.
Wegleitner, E., J. Raabe, D. Dembkowski, N. Legler, and D. Isermann. In Press. Wild juvenile salmonid abundance in Wisconsin tributaries indicates limited contributions to Lake Michigan fisheries. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2021.10.005	December 2021
Wedgeworth, M.,R. Mollenhauer, and S. K. Brewer. 2023. Spatial and temporal dynamics of successful Prairie Chub spawning in the upper Red River basin. North American Journal of Fisheries Management 43: 1246-1259, https://doi.org/10.1002/nafm.10842	August 2023
Webster AJ, Douglas TA, Regier P, Scheuerell MD, Harms TK. Multi-scale temporal patterns in stream biogeochemistry indicate linked permafrost and ecological dynamics of boreal catchments. Ecosystems 25: 1189–1206 \| Abstract	October 2021	Temporal patterns in stream chemistry provide integrated signals describing the hydrological and ecological state of whole catchments. However, stream chemistry integrates multi-scale signals of processes occurring in both the catchment and stream. Deconvoluting these signals could identify mechanisms of solute transport and transformation and provide a basis for monitoring ecosystem change. We applied trend analysis, wavelet decomposition, multivariate autoregressive state-space modeling, and analysis of concentration-discharge relationships to assess temporal patterns in high-frequency (15 min) stream chemistry from permafrost-influenced boreal catchments in Interior Alaska at diel, storm, and seasonal time scales. We compared catchments that varied in spatial extent of permafrost and fire history to identify biogeochemical signals characteristic of these regimes. An unburned catchment with high spatial extent (54%) of permafrost was characterized by increasing nitrate concentration through the thaw season, an abrupt increase in nitrate and fluorescent dissolved organic matter (fDOM) and declining specific conductivity in late summer, and flushing of nitrate and fDOM during summer rain storms. In contrast, these patterns were absent, of lower magnitude, or reversed in catchments with lower permafrost extent (<19%) and recent fire. Solute dynamics revealed a positive influence of permafrost on fDOM export and the role of shallow, seasonally dynamic flowpaths in delivering solutes from high-permafrost catchments to streams. Lower spatial extent of permafrost resulted in static delivery of nitrate and limited transport of fDOM to streams. Shifts in concentration-discharge relationships and seasonal trends in stream chemistry toward less temporally dynamic patterns might therefore indicate reorganized catchment hydrology and biogeochemistry due to permafrost thaw.
Webb, M. A. H., C. S. Guy, H. B. Treanor, K. W. Wilson, C. D. Mellon, P. Abate, H. J. Crockett, J. Hofmeier, C. Pasbrig, P. Isakson. 2023. Prioritizing imperiled native aquatic species for conservation propagation. Journal of Fish and Wildlife Management. https://doi.org/10.3996/JFWM-22-040.	October 2023
Webb, E.B., E.B. Hill, K.M. Malone and D. Mengel. Use of a dynamic occupancy model to evaluate secretive marsh bird habitat associations at spring migration stopover sites. Journal of Wildlife Management \| Abstract	March 2022	Despite several secretive marsh bird (SMB) species being listed as “Critically Imperiled” throughout the mid-continent of North America, there is limited information on SMB distribution and habitat use within primary migratory corridors, resulting in uncertainty on contributions of wetlands in mid-latitude states toward SMB annual cycle needs. Our objectives were to quantify patterns of SMB wetland occupancy during spring migration at a mid-latitude state and evaluate the relationships between SMB colonization probability and water-level management practices, as well as the resulting habitat conditions during spring migration. We conducted a two year dynamic occupancy study (2013-2014) that included six rounds of repeated call-back surveys to detect the presence of five SMB species (Virginia rail (<i>Rallus limicola</i>), sora (<i>Porzana carolina</i>), King rail (<i>R. elegans</i>), least bittern (<i>Ixobrychus exilis</i>) and American bittern (<i>Botaurus lentiginosus</i>)) during spring and summer (April-July) on 107 wetlands across 8 Conservation Areas and 4 National Wildlife Refuges throughout Missouri. Sora were detected most frequently, followed by Least Bittern, American Bittern, Virginia Rail, and King Rail. Colonization probability for all species was positively associated with emergent vegetation cover and negatively associated with amount of open water. Open water was the most important factor for American Bittern site colonization, to which they were negatively associated. Virginia Rail colonization had a strong positive association with vegetation height, whereas Least Bittern and Sora site colonization were influenced positively by water depth and agriculture, respectively. Based on the habitat associations within and among SMB species identified in this study, wetland managers can tailor management strategies to optimize spring migration habitat for single- or multi-species objectives.
Webb, E. B. and M. Brasher. 2021. Changing Distributions of Migrating and Wintering Waterfowl? Studies contribute to a growing understanding of changes in waterfowl patterns during fall and winter. Ducks Unlimited Magazine	December 2021
Weaver, D., Sigourney, D., Delucia, M., Zydlewski, J. (2021) Characterizing Downstream Migration Timing of American Eels Using Commercial Catch Data in the Penobscot and Delaware Rivers. Marine and Coastal Fisheries, 13(5): 534-547. \| Download	October 2021
Waterhouse, Lynn, Scott A. Heppell, Christy V. Pattengill-Semmens, Croy McCoy, Phillippe Bush, Bradley C. Johnson, and Brice X. Semmens. 2020. Recovery of critically endangered Nassau grouper (Epinephelus striatus) in the Cayman Islands following targeted conservation actions. Proceedings of the National Academy of Sciences 117(3): 1587-1595. https://doi.org/10.1073/pnas.1917132117 \| Abstract \| Publisher Website	January 2020	Many large-bodied marine fishes that form spawning aggregations, such as the Nassau grouper (<i>Epinephelus striatus</i>), have suffered regional overfishing due to exploitation during spawning. In response, marine resource managers in many locations have established marine protected areas or seasonal closures to recover these overfished stocks. The challenge in assessing management effectiveness lies largely in the development of accurate estimates to track stock size through time. For the past 15 y, the Cayman Islands government has taken a series of management actions aimed at recovering collapsed stocks of Nassau grouper. Importantly, the government also partnered with academic and nonprofit organizations to establish a research and monitoring program (Grouper Moon) aimed at documenting the impacts of conservation action. Here, we develop an integrated population model of 2 Cayman Nassau grouper stocks based on both diver-collected mark–resight observations and video censuses. Using both data types across multiple years, we fit parameters for a state–space model for population growth. We show that over the last 15 y the Nassau grouper population on Little Cayman has more than tripled in response to conservation efforts. Census data from Cayman Brac, while more sparse, show a similar pattern. These findings demonstrate that spatial and seasonal closures aimed at rebuilding aggregation-based fisheries can foster conservation success.
Waterhouse, L., White, J., See, K., Murdoch, A., and B. X. Semmens. 2020. A Bayesian nested patch occupancy model to estimate steelhead movement and abundance. Ecological Applications 30(8):e02202. https://doi.org/10.1002/eap.2202 \| Abstract \| Publisher Website	June 2020	Anthropogenic impacts on riverine systems have, in part, led to management concerns regarding the population status of species using these systems. In an effort to assess the efficacy of restoration actions, and in order to improve monitoring of species of concern, managers have turned to PIT (passive integrated transponder) tag studies with in-stream detectors to monitor movements of tagged individuals throughout river networks. However, quantifying movements in a river network using PIT tag data with incomplete coverage and imperfect detections presents a challenge. We propose a flexible Bayesian analytic framework that models the imperfectly detected movements of tagged individuals in a nested PIT tag array river network. This model structure provides probabilistic estimates of up-stream migration routes for each tagged individual based on a set of underlying nested state variables. These movement estimates can be converted into abundance estimates when an estimate of abundance is available for a location within the river network. We apply the model framework to data from steelhead (<i>Oncorhynchus mykiss</i>) in the Upper Columbia River basin and evaluate model performance (precision/variance of simulated population sizes) as a function of population tagging rates and PIT tag array detection probability densities within the river system using a simulation framework. This simulation framework provides both model validation (precision) and the ability to evaluate expected performance improvements (variance) due to changes in tagging rates or PIT receiver array configuration. We also investigate the impact of different network configurations on model estimates. Results from such investigations can help inform decisions regarding future monitoring and management.
Waterhouse, L., L. Ailloud, R. Austin, W. J. Golet, A. Pacicco, A. Andrews, K. Diouf, Y. Ndiour, K. Krusic-Golub, G. da Silva, and J. M. Hoenig. 2022. Updated Integrated Growth Model for Bigeye Tuna (Thunnus obesus) in the Atlantic Ocean. Fisheries Research. https://doi.org/10.1016/j.fishres.2022.106317 \| Abstract \| Download	December 2022	The International Commission for the Conservation of Atlantic Tunas (ICCAT) concluded the Atlantic Ocean tropical Tuna Tagging Programme (AOTTP) in 2021. This project had the objectives of enhancing food security, stimulating economic growth, and improving management through research on tropical tuna resources in the Atlantic Ocean, including bigeye tuna (Thunnus obesus). Here, we combine tagging data and otolith data from the AOTTP program, Panama City Lab and the Pelagic Fisheries Lab at the University of Maine with historical tagging data and otolith data from ICCAT and other sources to fit integrated growth models with the goal of providing the most complete growth curve (in terms of data inclusion and validation of age-at-length) for bigeye tuna in the Atlantic Ocean. Both Richards and von Bertalanffy growth models were fitted. A variety of models were fitted to subsets of the data to investigate the consistency of growth information. In all cases for the integrated model, the Richards and von Bertalanffy models were very similar with the von Bertalannfy model being preferred for parsimony. The preferred model, based on fit to old fish, was the von Bertalanffy curve based on length-age pair data from multiple sources. The addition of tagging data to create an integrated model showed patterns of lack of fit to both the tagging and otolith data suggesting conflict between the tagging and otolith data. The preferred model (length-age pair data only) gave the estimates: asymptotic length L∞ (fork length) equals 161.21 cm (95% bootstrap CI 154.39, 166.84), growth parameter K equals 0.392 yr− 1 (95% bootstrap CI 0.355, 0.441), and the time-axis intercept t0 equals − 0.239 yr (95% bootstrap CI –0.306, − 0.175). For the best fitting integrated model, the asymptotic length L∞(fork length, in cm) was estimated to be 185.78 (SD 6.298), the growth parameter K was 0.252 yr− 1 (SD 0.014), and the time-axis intercept t0 was − 0.524 yr (SE 0.025). The value for asymptotic length L∞ from the integrated model was larger than the lengths of all the old fish in the sample whereas the value for the curve based on otoliths passes through the cloud of points for old fish.
Warlick, AJ, Johnson, D., Gelatt, T., Converse, SJ. 2022. Environmental drivers of demography and potential factors limiting the recovery of an endangered marine top predator. Ecosphere 13:e4325. \| Abstract	December 2022	Understanding what drives changes in wildlife demography over time is fundamental to the conservation and management of depleted or declining populations, though making inference about the intrinsic and extrinsic factors that influence survival and reproduction is challenging as they can change over time and space. Here we use almost 20 years of mark-resight data from 2000-2018 to examine the effects of environmental variability on age-specific survival and natality for the endangered western distinct population segment of Steller sea lions (<i>Eumetopias jubatus</i>) in Alaska, USA. Though this population has been studied extensively over the last four decades, the causes of divergent abundance trends that have been observed across the range of this population remain unknown. We developed a Bayesian multi-event mark-resight model that accounts for female reproductive state uncertainty. Results indicated that survival rates for male pups (0.44; 0.36-0.53), female yearlings (0.63; 0.49-0.73), and male yearlings (0.62; 0.51-0.71) born in the western portion of the range, estimated here for the first time, were lower than those estimated for male pups (0.69; 0.65-0.74), female yearlings (0.76; 0.71-0.81), and male yearlings (0.71; 0.65-0.78) born in the eastern portion of the range. Additionally, pup mass had a positive effect on pup survival in the eastern portion of the range and a negative effect in the western portion of the range. Local and basin-scale oceanographic features such as the Aleutian Low, the Arctic Oscillation Index, the North Pacific Gyre Oscillation, chlorophyll concentration, upwelling, and wind in certain seasons exhibited correlations with vital rates. However, strong inference is challenging given that relationships between ocean conditions and an adaptive top predator in a highly dynamic ecosystem are exceedingly complex. This study provides the first demographic rate estimates for the western portion of the population range where abundance estimates continue to decline. This work can inform ongoing research and management and will advance efforts to identify factors driving regionally divergent abundance trends with implications for population-level responses to future climate variability.
Warlick AJ, GK Himes Boor, TL McGuire, KEW Shelden, EK Jacobson, C Boyd, PR Wade, AE Punt, SJ Converse. 2024. Identifying demographic and environmental drivers of population dynamics and viability in an endangered top predator using an integrated model. Animal Conservation 27:240-252. \| Abstract	April 2024	Knowledge about the demographic and environmental factors underlying population dynamics is fundamental to designing effective conservation measures to recover depleted wildlife populations. However, sparse monitoring data or persistent knowledge gaps about threats make it difficult to identify the drivers of population dynamics. In situations where small, depleted populations show continued evidence of decline for unknown reasons, integrated population models can improve our understanding of demography, provide fundamental insights into factors that may be limiting recovery, and support conservation decisions. We used mark-resight and aerial survey data from 2004-2018 to build an integrated population model for the Cook Inlet population of beluga whales (<i>Delphinapterus leucas</i>), which is listed as endangered under the U.S. Endangered Species Act. We examined the relationships between beluga vital rates and prey availability and environmental conditions and conducted a population viability analysis to predict extinction risk across a range of hypothetical changes in beluga survival and reproduction. Our results indicated that while survival of breeding females (0.97; 95% CrI 0.95-0.99) and young calves (0.92; 0.80-0.98) was relatively high, survival of non-breeders (0.94; 0.91-0.97) and fecundity (0.27; 0.21-0.35) may be depressed. Furthermore, our analysis indicates that if vital rates and environmental variability remain similar to estimates from the latter part of the study period, the population will likely continue to decline, with a 19-32% probability of extinction in 150 years. Our model framework highlights the utility of integrated population modeling for identifying factors contributing to the failure of protected populations to recover.
Warlick AJ, DS Johnson, KL Sweeney, TS Gelatt, and SJ Converse. 2023. Examining the effect of environmental variability on the viability of endangered Steller sea lions using an integrated population model. Endangered Species Research 52:343-361.	December 2023
Ward, N. K., A. J. Lynch, E. A. Beever, J. Booker, K. L. Bouska, H. Embke, et al. 2023. Reimagining large river management using the Resist–Accept–Direct (RAD) framework in the Upper Mississippi River. Ecological Processes 12:48. https://doi.org/10.1186/s13717-023-00460-x \| Abstract \| Publisher Website	October 2023	<i>Background</i>: Large-river decision-makers are charged with maintaining diverse ecosystem services through unprecedented social-ecological transformations as climate change and other global stressors intensify. The interconnected, dendritic habitats of rivers, which often demarcate jurisdictional boundaries, generate unique management challenges. Here, we explored how the Resist-Accept-Direct (RAD) framework may enhance large-river management by promoting coordinated and deliberate responses to social-ecological trajectories of change. The RAD framework identifies the full decision space, wherein managers may <i>resist </i>change to maintain historical conditions, <i>accept </i>change toward different conditions, or <i>direct </i>change to a specified future with novel conditions. In the Upper Mississippi River System, managers are facing ecosystem transformations from more frequent and extreme high-water events. We illustrate how RAD-informed basin-, reach-, and site-scale decisions could: 1) provide river continuum and cross-spatial scale framing; <i>and</i> 2) open the entire decision space of possible approaches; <i>to</i> 3) enhance coordinated inter-jurisdictional management in response to the trajectory of the Upper Mississippi River hydrograph.<br><i>Results</i>: The RAD framework helps identify plausible long-term trajectories in different reaches (or subbasins) of the river and how the associated social-ecological transformations could be managed by altering site-scale conditions. Strategic reach-scale objectives may reprioritize how, where, and when site conditions (e.g., habitat connectivity, diversity, redundancy) could be altered to contribute to the basin goal, given the basin’s plausible trajectories of change, and vice versa.<br><i>Conclusions</i><b>: </b> When faced with long-term systemic transformations (e.g., > 50 years), RAD helps explicitly consider whether or when the basin vision or goals may no longer be achievable, and <i>direct </i>options may open yet unconsidered potential for the basin. Embedding RAD in hierarchical decision making clarifies that the selection of actions in space and time should be derived from basin-wide goals and reach-scale objectives to ensure that site-scale actions contribute effectively to the larger river habitat mosaic. Embedding RAD thinking in large-river decisions can provide the necessary conduit to link flexibility and innovation at the site scale with stability at larger scales for adaptive governance of changing social-ecological systems.
Ward, M.J. and S.R. Chipps. 2020. Availability and timing of Fathead Minnow supplementation influence Largemouth Bass survival and production in rearing ponds. Open Journal of Animal Science 10:337-345.	May 2020
Ward EJ, Marshall KN, Scheuerell MD. Regularizing priors for Bayesian VAR applications to large ecological datasets. PeerJ \| Abstract	December 2022	Using multi-species time series data has long been of interest for estimating inter-specific interactions with vector autoregressive models (VAR) and state space VAR models (VARSS); these methods are also described in the ecological literature as multivariate autoregressive models (MAR, MARSS). To date, most studies have used these approaches on relatively small food webs where the total number of interactions to be estimated is relatively small. However, as the number of species or functional groups increases, the length of the time series must also increase to provide enough degrees of freedom with which to estimate the pairwise interactions. To address this issue, we use Bayesian methods to explore the potential benefits of using regularized priors , such as Laplace and regularized horseshoe, on estimating interspecific interactions with VAR and VARSS models. We first perform a large-scale simulation study, examining the performance of alternative priors across various levels of observation error. Results from these simulations show that for sparse matrices, the regularized horseshoe prior minimizes the bias and variance across all inter-specific interactions. We then apply the Bayesian VAR model with regularized priors to a output from a large marine food web model (37 species) from the west coast of the USA. Results from this analysis indicate that regularization improves predictive performance of the VAR model, while still identifying important inter-specific interactions.
Waraniak, J. M.S. Eackles, J. Keagy, G.D. Smith, M. Schall, S. Stark, S.L. White, D.C. Kazyak, T. Wagner. 2024. Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US mid-Atlantic rivers. https://doi.org/10.1111/jfb.15888	August 2024
Wampole. E, Farris, Z, and Gerber, BD. 2021. A synthesis of life-history, functionaltraits, and consequences of anthropogenic pressures on Madagascar’s threatened carnivorans,Eupleridae. Mammal Review, 51: 402-419 https://doi.org/10.1111/mam.12234 \| Download	January 2021
Wampole, EM, Gerber, BD, Farris, ZJ, Razafimahaimodison, JC, Andrianarisoa, MH, Ralazampirenena, CJ, Wright, PC, et al. 2022. Madagascar Terrestrial Camera Survey Database 2021: A collation of protected forest camera surveys from 2007-2021. Ecology, 103:e3687. https://doi.org/10.1002/ecy.3687	March 2022
Wampole, E.M., Farris, Z.J., Razafy, P. and Gerber, B.D. (2023), Forest carnivores living on the edge with invasive predators. Animal Conservation. https://doi.org/10.1111/acv.12926 \| Download	December 2023
Walther, E.J., Zimmerman, M.S., Falke, J.A., and P.A.H. Westley. Species distributions and the recognition of risk in restoration planning: A case study of salmonid fishes in the Chehalis River, Washington, USA.	August 2022
Walters, A.W., N.G. Clancy, T.P. Archdeacon, S. Yu, J.S. Rogosch, and E.A. Rieger. Early view. Development of a refuge identification framework that promotes fish persistence during climate-related drought. Fish and Fisheries doi/10.1111/faf.12860	September 2024
Walters, A.W., N.G. Clancy, T.P. Archdeacon, S. Yu, J.S. Rogosch, and E.A. Rieger. Early view. Development of a refuge identification framework that promotes fish persistence during climate-related drought. Fish and Fisheries doi/10.1111/faf.12860	September 2024
Walter, W.D., A. Fameli, K. Russo-Petrick, J.E. Edson, C.S. Rosenberry, K.L. Schuler, M.J. Tonkovich. Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to chronic wasting disease. Ecology and Evolution 14, e11347. https://doi.org/10.1002/ece3.11347. \| Abstract	May 2024	Chronic wasting disease (CWD) can be spread by direct and indirect transmission with direct transmission easier to predict and assess using landscape genetics. Identifying subpopulations of a wild large herbivore allows identification of focal areas to target for effective intervention. Our aim was to assess population structure of white-tailed deer (<i>Odocoileus virginianus</i>) in the northeastern United States at a regional scale to inform managers of gene flow throughout the region. We used ten microsatellites to genotype 5,701 samples collected from wild deer in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022. We conducted a spatial principal component analysis to assess distribution of genetic variability and assessed population genetic structure using two methods: non-spatial Bayesian clustering algorithm (BCA) and spatial BCA. We used results of these clustering methods to create simulated populations of 500 individuals representing each cluster and also created simulated populations representing a captive deer population, among other anthropogenically-derived spatial units to conduct genetic assignment tests. We conducted genetic assignment tests using these simulated reference populations as potential sources, calculating the probability of samples being assigned to their corresponding genetic cluster, state, or physiographic province. Non-spatial BCA identified widespread gene flow with only 2 clusters across the region, while spatial BCA suggested further partitioning into a maximum of nine clusters. Our assignment tests were able to correctly assign deer to captive or wild origin in most cases (94%), as reported in a previous study, but performance varied when trying to assign wild deer to spatial units. Assignments to genetic clusters performed well where the potential sources represented clusters inferred with non-spatial BCA, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. This indicates that differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for unequivocally inferring geographic origin of deer using 10 microsatellites. However, genetic distinction between clusters is still important to consider when managing for disease. Future research on what landscape barriers may be leading to these divisions and species-specific single-nucleotide polymorphisms will further our understanding of potential subpopulations in the region.
Walter, W. D., B. Hanley, C. E. Them, C. I. Mitchell, J. Kelly, D. Grove, N. Hollingshead, R. C. Abbott, and K. L. Schuler. 2024. Predicting the odds of chronic wasting disease with Habitat Risk software. Spatial and Spatio-temporal Epidemiology 49:100650. \| Abstract	April 2024	Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (<i>Odocoileus virginianus</i>) populations across the US and Canada. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies have employed epidemiological models to understand long-term environmental risk. However, continued rapid spread of CWD into new regions of the continent has underscored the need for extension of these models into broader tools applicable for wide use by wildlife agencies. Additionally, efforts to semi-automate models will facilitate access of technical scientific methods to broader audiences. We introduce software (<i>Habitat Risk</i>) designed to link a previously published epidemiological model with spatially referenced environmental and disease testing data enabling agency personnel to make up-to-date, localized, data-driven predictions regarding the odds of CWD infection in surrounding areas after an outbreak is discovered. <i>Habitat Risk</i> requires pre-processing publicly available environmental datasets and standardization of disease testing (surveillance) data, after which an autonomous computational pipeline terminates in a user interface that displays an interactive map of disease risk. We demonstrated the use of the <i>Habitat Risk </i>software with surveillance data of white-tailed deer from Tennessee, US. Software to pre-process environmental data is openly available at <i>doi.org/10.7298/2tt1-yy48</i>, while <i>Habitat Risk</i> software is available at <i>doi.org/10.7298/rcz8-nw50</i>.
Walsworth, T. and P. Budy. 2021. Hydrologic controls on abundance and distribution of a highly imperiled desert fish. Canadian Journal of Fisheries and Aquatic Sciences Volume 78. doi.org/10.1139/cjfas-2020-0353. USGS FSP IP-121942. \| Abstract	May 2021	Increasing water demand, water development, and on-going climate change have driven extensive changes to the hydrology, geomorphology and biology of arid-land rivers globally, driving an increasing need to understand how annual hydrologic conditions affect the distribution and abundance of imperiled desert fish populations. We analyzed the relationship between annual hydrologic conditions and the endangered Rio Grande silvery minnow in the Middle Rio Grande, New Mexico, USA, using hurdle models to predict both presence and density as a function of integrated annual hydrologic metrics. Both presence and density were positively related to spring high flow magnitude and duration and negatively related to summer drying, as indicated by an integrated flow metric. Simulations suggest hydrologic conditions near the wettest observed in the data set would be required to meet recovery goals in a single year in all reaches. We demonstrate how the models developed herein can be used to examine alternative water management strategies, including strategies that may currently be socially and logistically infeasible to implement, to identify strategies minimizing trade-offs between conservation and other management goals.
Walsh, H.L., V.S. Blazer and P.M. Mazik. 2022. Development of a multiplex fluorescence in situ hybridization to identify coinfections in young-of-the-year smallmouth bass. Journal of Aquatic Animal Health 34:12-19 https://doi.org/10.1002/aah.10144	January 2022
Walsh, H.L., V.S. Blazer and P.M. Mazik. 2021. Identification of Aphanomyces invadans, the cause of epizootic ulcerative syndrome, in smallmouth bass (Micropterus dolomieu) from the Cheat River, West Virginia, USA. Journal of Fish Diseases 44:1639-1641.	August 2021
Wallin, T. and C.A. Caldwell. Comparative assessment of laboratory-derived thermal maxima of Gila Trout (Oncorhynchus gilae) with current stream temperatures. The Southwestern Naturalist 66(4):317-326. \| Abstract	February 2022	Gila Trout (<i>Oncorhynchus gilae</i>) represents an iconic species of the American Southwest. The salmonid has survived extensive logging, livestock grazing, and mining, and is currently threatened by climate change, wildfire, and extended drought. Long term conservation and recovery of the species and its unique lineages rely on stocking and translocation into historically inhabited streams. Thus, the fish’s thermal tolerance is essential in determining suitable habitat and potential vulnerability to a warming climate. We compared laboratory-derived temperature metric, critical thermal maximum (CTMax), in hatchery-reared Gila Trout from three lineages (Main Diamond, South Diamond, and Whiskey Creek) to determine if CTMax differed among the lineages. The average initial (28.9, SD = 0.81°C) and final (29.2, SD = 0.74°C) loss of righting responses did not differ across the lineages. We compared the CTMax values with stream temperatures across three drainages representative of extant Gila Trout populations from spring 2015 to fall 2018. The East Fork Gila River drainage was represented by more extreme stream temperatures. The maximum daily maximum temperature (i.e., single highest temperature) varied from 24.1 to 33.4°C, exceeding CTMax in four of the five streams. The maximum daily temperature range varied from 12.1 to 28.6°C, and the mean weekly maximum temperature varied from 19.9 to 31.1°C. Mean weekly maximum temperature in Lower Diamond Creek exceeded CTMax on eleven occasions. Stream temperatures were cooler within the Middle and the West Fork Gila River drainages and did not exceed CTMax. Intermittency loggers within the East Fork Gila River Drainage, which supports Main Diamond and South Diamond lineages of Gila Trout, recorded over 300 days of intermittency during a drought. Continued long term monitoring of stream temperature and comparison to CTMax of Gila Trout could assist with decisions of which streams in the Gila Drainage are suitable for Gila Trout recovery, stocking, and translocation.
Wallin, T. and C.A. Caldwell. Comparative assessment of laboratory-derived thermal maxima of Gila Trout (Oncorhynchus gilae) with current stream temperatures. The Southwestern Naturalist 66(4):317-326. \| Abstract	February 2022	Gila Trout (<i>Oncorhynchus gilae</i>) represents an iconic species of the American Southwest. The salmonid has survived extensive logging, livestock grazing, and mining, and is currently threatened by climate change, wildfire, and extended drought. Long term conservation and recovery of the species and its unique lineages rely on stocking and translocation into historically inhabited streams. Thus, the fish’s thermal tolerance is essential in determining suitable habitat and potential vulnerability to a warming climate. We compared laboratory-derived temperature metric, critical thermal maximum (CTMax), in hatchery-reared Gila Trout from three lineages (Main Diamond, South Diamond, and Whiskey Creek) to determine if CTMax differed among the lineages. The average initial (28.9, SD = 0.81°C) and final (29.2, SD = 0.74°C) loss of righting responses did not differ across the lineages. We compared the CTMax values with stream temperatures across three drainages representative of extant Gila Trout populations from spring 2015 to fall 2018. The East Fork Gila River drainage was represented by more extreme stream temperatures. The maximum daily maximum temperature (i.e., single highest temperature) varied from 24.1 to 33.4°C, exceeding CTMax in four of the five streams. The maximum daily temperature range varied from 12.1 to 28.6°C, and the mean weekly maximum temperature varied from 19.9 to 31.1°C. Mean weekly maximum temperature in Lower Diamond Creek exceeded CTMax on eleven occasions. Stream temperatures were cooler within the Middle and the West Fork Gila River drainages and did not exceed CTMax. Intermittency loggers within the East Fork Gila River Drainage, which supports Main Diamond and South Diamond lineages of Gila Trout, recorded over 300 days of intermittency during a drought. Continued long term monitoring of stream temperature and comparison to CTMax of Gila Trout could assist with decisions of which streams in the Gila Drainage are suitable for Gila Trout recovery, stocking, and translocation.
Walker, R.H., G.D. Smith, S.B. Hudson, S.S. French, and A.W. Walters. 2020. Warmer temperatures interact with salinity to weaken physiological facilitation to stress in freshwater fishes. Conservation Physiology https://doi.org/10.1093/conphys/coaa107	December 2020
Walker, R.H., C.E. Girard, S.L. Alford, and A.W. Walters. 2020. Individual and interactive effects of hydrology and surface disturbance on fish populations. Journal of Applied Ecology 57: 149-159. doi:10.1111/1365-2664.13517	January 2020
Walker, R.H., A.C. Belvin, J.B. Mouser, A. Pennino, S. Plont, C.D. Robinson, L.B. Smith, J. Thapa, C.E. Zipper, P.L. Angermeier, and S.A. Entrekin. 2023. Global review reveals how disparate study motivations, analytical designs, and focal ions limit understanding of salinization effects on freshwater animals. Science of the Total Environment 20:892:164061. \| Abstract	September 2023	Global salinization of freshwaters is adversely affecting biotic communities and ecosystem processes. We reviewed six decades (1960–2020) of literature published on animal responses to increased salinities across different taxonomic and ecological contexts and identified knowledge gaps. From 585 articles, we characterized 5924 responses of mollusks, macro-crustaceans, zooplankton, non-arthropod invertebrates (NAI), insects, fishes, and amphibians to salinization. Insects and fishes were the most studied taxa; Na<sup>+</sup> and Cl<sup>-</sup> were the most studied ions<sup>-</sup>. Collectively, concentrations of examined ions typically spanned five orders of magnitude. Species’ invasiveness was a key motivation for studying mollusks, macro-crustaceans, and fishes; threats of urbanization and road salts were key motivations for studying NAI, zooplankton, and amphibians. Focal life stages in laboratory studies varied widely but juveniles and adults were represented similarly in field studies. Studies of mollusks, NAI, and macro-crustacean focused on adults; studies of zooplankton, insects, fishes, and amphibians focused on juveniles. Organismal- and population-level responses measuring solute uptake, internal chemistry, body condition, or ion concentrations predominated laboratory studies; population- and assemblage-level responses measuring abundance, spatial distribution, or assemblage composition predominated field studies. Negative responses to salinization predominated but positive and unimodal responses were apparent across all taxa and organizational levels. Key topics for further research include: a) salinity responses by more taxa, b) responses to especially toxic ions (i.e., K<sup>+</sup>, HCO<sub>3</sub><sup>-</sup>, SO<sub>4</sub><sup>2-</sup>, Mg<sup>2+</sup>), c) mechanisms causing positive and unimodal responses, d) traits underpinning responses, e) effects transcending organizational levels, f) ion-specific response thresholds, and g) interactions between salinity and other stressors. Our review suggests inter-taxa variation in salinization sensitivity reflects occurrence of certain biological traits, including gill-breathing, semi-permeable skin, multiple life stages, and limited mobility. We propose a traits-based framework to predict salinization sensitivity from shared traits. This evolutionary approach could inform management aimed at preventing or reducing adverse impacts of freshwater salinization.
Walker, Nelson, Hefley, Trevor J., Ballmann, Anne, Russell, Robin E., Walsh, Daniel P. 2021. Recovering individual-level spatial inference from aggregated binary data. Spatial Statistics, 44: https://doi.org/10.1016/j.spasta.2021.100514 \| Abstract	January 2021	Binary regression models are commonly used in disciplines such as epidemiology and ecology to determine how spatial covariates influence individuals. In many studies, binary data are shared in a spatially aggregated form to protect privacy. For example, rather than reporting the location and result for each individual that was tested for a disease, researchers may report that a disease was detected or not detected within geopolitical units. Often, the spatial aggregation process obscures the values of response variables, spatial covariates, and locations of each individual, which makes recovering individual-level inference difficult. We show that applying a series of transformations, including a change of support, to a bivariate point process model allows researchers to recover individual-level inference for spatial covariates from spatially aggregated binary data. The series of transformations preserves the convenient interpretation of desirable binary regression models that are commonly applied to individual-level data. Using a simulation experiment, we compare the performance of our proposed method under varying types of spatial aggregation against the performance of standard approaches using the original individual-level data. We illustrate our method by modeling individual-level probability of infection using a data set that has been aggregated to protect an at-risk and endangered species of bats. Our simulation experiment and data illustration demonstrate the utility of the proposed method when access to original non-aggregated data is impractical or prohibited.
Waldrop, T., S. Summerfelt, P. Mazik, P.B. Kenney and C. Good. The effects of swimming exercise and dissolved oxygen on growth performance, fin condition and survival of rainbow trout, Oncorhynchus mykiss. Aquaculture Research https://doi.org/10.1111/are.14600h	July 2020
Walden, M.A., K.J. Loope, E.A. Hunter, S.J. Divers, J.R. Comolli, T.C. Esque, K.T. Shoemaker. 2023. Testosterone identifies hatchling sex for Mojave desert tortoises (Gopherus agassizii). Scientific Reports 13: 14818.	May 2023
Wagner, T., P. McLaughlin, K.E. Faunce, S. Austin, K. Smalling. 2024. The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA. Environmental Toxicology and Chemistry. https://doi.org/10.1002/etc.5849	March 2024
Wagner, T., McLaughlin, P., Smalling, K., Breitmeyer, S., Gordon, S., and Noe, G.B., 2021. The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed, USA. Science of the Total Environment 812:152435. https://doi.org/10.1016/j.scitotenv.2021.152435	December 2021
Wagner, T., G.J.A. Hansen, E. Schliep, B. Bethke, A. Honsey, P. Jacobson, B.C. Kline, and S.L. White. 2020. Improved understanding and prediction of freshwater fish communities through the use of joint species distribution models. Canadian Journal of Fisheries and Aquatic Sciences 77(9): 1540-1551. https://doi.org/10.1139/cjfas-2019-0348	August 2020
Wagner, T., E.M. Schliep, J.S. North, H. Kundel, J.K. Ruzich, C.A. Custer, and G.J.A. Hansen. 2023. Predicting climate change impacts on poikilotherms using physiologically guided species abundance models. Proceedings of the National Academy of Sciences: 15: e2214199120 https://doi.org/10.1073/pnas.2214199120	April 2023
Wade, M., K. Moore-O'Leary, S. M. Grodsky, and M. Meek. 2022. Of Mojave milkweed and mirrors: The population genomics of a species impacted by solar energy planning. Conservation Science and Practice.	June 2023
Waddle, J.H., Grear, D.A., Mosher, B.A., E. H. Campbell Grant, M. J. Adams, A. R. Backlin, W. J. Barichivich, A. B. Brand,G. M. Bucciarelli, D. L. Calhoun, T. Chestnut, J. M. Davenport, A. E. Dietrich, R. N. Fisher, B. M. Glorioso, B. J. Halstead, M. P. Hayes, R. K. Honeycutt, B. R. Hossack, P. M. Kleeman, J. A. Lemos-Espinal, J. M. Lorch^,B. McCreary, E. Muths, C. A. Pearl, K. L. D. Richgels, C. W. Robinson, J. C. Rowe, B. H. Sigafus, I. Stasiak, S. Sweet, S. C. Walls, G. J. Watkins-Colwell, C. L. White, L. A. Williams,M. E. Winzeler. Batrachochytrium salamandrivorans (Bsal) not detected in an intensive survey of wild North American amphibians. Sci Rep 10, 13012 (2020). https://doi.org/10.1038/s41598-020-69486-x \| Abstract \| Publisher Website	August 2020	The salamander chytrid fungus (<i>Batrachochytrium salamandrivorans</i> [Bsal]) is causing massive mortality of salamanders in Europe. The potential for spread via international trade into North America and the high diversity of salamanders has catalyzed concern about Bsal in the U.S. Surveillance programs for invading pathogens must initially meet challenges that include low rates of occurrence on the landscape, low prevalence at a site, and imperfect detection of the diagnostic tests. We implemented a large-scale survey to determine if Bsal was present in North America designed to target taxa and localities where Bsal was determined highest risk to be present based on species susceptibility and geography. Our analysis included a Bayesian model to estimate the probability of occurrence of Bsal given our prior knowledge of the occurrence and prevalence of the pathogen. We failed to detect Bsal in any of 11,189 samples from 594 sites in 223 counties within 35 U.S. states and one site in Mexico. Our modeling indicates that Bsal is highly unlikely to occur within wild amphibians in the U.S. and suggests that the best proactive response is to continue mitigation efforts against the introduction and establishment of the disease and to develop plans to reduce impacts should Bsal establish.
Voss, N. S., R. Al-Chokhachy, A. J. Sepulveda, C. E. Verhille, M. P. Ruggles, and A. V. Zale. 2022. The importance of phenology and thermal exposure to early life history success of non-native Smallmouth Bass in the Yellowstone River. Transactions of the American Fisheris Society 151:527-542. DOI: 10.1002/tafs.10364 \| Abstract	July 2022	Knowledge of the potential spread of an introduced species is critical to direct management efforts to where they will provide the greatest benefits. The Smallmouth Bass <i>Micropterus dolomieu</i>, is an example of a fish that has been introduced globally, often spreads following introduction, and has substantial predatory impacts on fish assemblages. We evaluated Smallmouth Bass spread in the free-flowing Yellowstone River, Montana, where this non-native fish has expanded from warmer, downstream sections of river into colder, upstream sections. We hypothesized that progressively colder upstream climates would limit age-0 growth and overwinter survival in the Yellowstone River, thereby curbing potential upstream spread. We documented the phenology, growth, and overwinter survival of age-0 Smallmouth Bass across a gradient of temperature and population densities. Age-0 individuals were rare or absent throughout the uppermost upstream distribution of adults, suggesting that something limits or discourages reproduction farther upstream. However, we found no support for colder water temperatures alone as the limiting factor. Age-0 body size at the onset of winter did not differ significantly among the uppermost 200 km of their distribution. Rather, the earlier hatching timing exhibited by some age-0 individuals in colder, upstream sections allowed them to experience longer growing seasons than many individuals in warmer, downstream sections. This counter-intuitive hatching phenology mediated much of the negative effect of colder upstream climates on growth. Furthermore, evidence of successful overwinter survival and simulations of age-0 starvation mortality indicated that age-0 individuals at the upstream extent of their distribution successfully recruited to the age-1 year-class in four consecutive years. Taken together, our results suggest that Smallmouth Bass have not yet reached the thermal limit of their upstream distribution in the Yellowstone River, and that further spread will probably be driven by complex interactions between density dependence, spawn timing, and ambient thermal and hydrologic regimes.
Voss, N. S., J. L. McCormick, W. J. Lubenau, B. J. Bowersox, T. Copeland, and M. C. Quist. 2024. Retention of T-bar anchor tags by adult steelhead during their upstream migration. North American Journal of Fisheries Management 44:1385-1391.	January 2025
Voss, N. S., B. J. Bowersox, and M. C. Quist. 2023. Reach-scale associations between introduced Brook Trout and juvenile and stream-dwelling Bull Trout in Idaho. Transactions of the American Fisheries Society 152:835-848.	November 2023
Volski, L., McInturff, A., Gaynor, K. M., Yovovich, V., & Brashares, J. S. (2021). Social Effectiveness and Human-Wildlife Conflict: Linking the Ecological Effectiveness and Social Acceptability of Livestock Protection Tools. Frontiers in Conservation Science, 42. \| Abstract	August 2021	Human-wildlife interactions are embedded within socio-ecological systems (SES), in which animal behavior and human decision-making reciprocally interact. While a growing body of research addresses specific social and ecological elements of human-wildlife interactions, including conflicts, integrating these approaches is essential for identifying practical and effective solutions. Carnivore predation on livestock can threaten human livelihoods, weaken relationships among stakeholders, and precipitate carnivore declines. As carnivores have received greater protection in recent decades, researchers and managers have sought non-lethal tools to reduce predation and promote coexistence between livestock producers and carnivores. For these tools to be successful, they must effectively deter carnivores, and they must also be adopted by producers. Relatively few studies examine the practical and context-specific effectiveness of non-lethal tools, and even fewer simultaneously consider their social acceptability among producers. To address this gap, we suggest that a tool's ecological effectiveness and social acceptability be analyzed concurrently to determine its <i>social effectiveness</i>. We thus paired an experimental study of a carnivore predation deterrent called Foxlights<sup>®</sup> with qualitative interviews of livestock producers in Northern California. We placed camera traps in sheep pastures to measure the response of coyotes (<i>Canis latrans</i>) to experimentally deployed Foxlights and interviewed livestock producers before and after the experiment. Our experiment revealed weak evidence for reducing coyote activity with Foxlights, but interviews revealed that the potential adoption of tools had as much to do with their social acceptability and implementation feasibility as with evidence-based measurements of tool effectiveness. Interviewees viewed Foxlights as potentially effective components of husbandry systems, despite the data suggesting otherwise, demonstrating that scientific reductionism may lag behind producer practices of systems-thinking and that isolated demonstrations of a tool's ecological effectiveness do not drive tool adoption. Future empirical tests of non-lethal tools should better consider producers' perspectives and acknowledge that data-based tests of ecological effectiveness alone have a limited place in producer decision-making. Iteratively working with producers can build trust in scientific outputs through the research process itself.
Volkel, S., K.F. Robinson, D.B. Bunnell, M. Connerton, D. Hondorp, J. Holden, B. Weidel. 2021. Slimy sculpin depth distribution shifts and habitat squeeze following round goby invasion in the Laurentian Great Lakes. Journal of Great Lakes Research 47:1793-1803. DOI: 10.1016/j.jglr.2021.08.017	December 2021
Vogel, S., Jansujwicz, J., Sponarski, C and Zydlewski, J. (2020) Science in action or science inaction? Evaluating the implementation of "best available science" in hydropower relicensing. Energy Policy 143:1-10. DOI: 10.1016/j.enpol.2020.111457 \| Download	August 2020
Vitale, N., J. Brush, and A. Powell. 2021. Factors limiting reproductive success of American Oystercatchers (Haematopus palliatus) in Florida’s Southern Big Bend. Waterbirds 44(4): 449-462.	December 2021
Vitale, N., Brush, J. and A. Powell. 2021. Loss of coastal islands along Florida’s Big Bend Region: Implications for breeding American Oystercatchers. Estuaries and Coasts 44:1173–1182. https://doi.org/10.1007/s12237-020-00811-3	September 2020
Vilella, F.J., and R. Gonzalez. 2023. Multi-resolution habitat models of the Puerto Rican Nightjar Antostromus noctitherus. Bird Conservation International. Bird Conservation International 33:e74 https://doi.org/10.1017/S0959270923000278 \| Abstract \| Download	September 2023	The Puerto Rican Nightjar <i>Antrostomus </i><i>noctitherus</i> is an endemic Caprimulgid found in dry coastal and lower montane forests of southwestern Puerto Rico. Information on the species (abundance, nesting biology) has been mostly restricted to forest reserves (i.e., Guánica Forest, Susúa Forest) with limited information available from private lands. We collected stand-level vegetation structure and geographic information to model habitat suitability and distribution for the Nightjar. Results of the stand-level model indicated forest type and midstory vegetation density best predicted Nightjar habitat. Our spatial model predicted considerably more Nightjar habitat (17,819.64ha) was located outside protected areas than previously reported. Further, the model highlighted several localities of importance for the species across southern Puerto Rico, all located within private lands. We used a patch occupancy approach to assess regions identified by the landscape-level model as suitable for the Nightjar and documented presence of the species in 32 of 55 sites, located in 12 of 18 municipalities across southern Puerto Rico. The protection and restoration of forest across the southern coast of Puerto Rico would help ensure the long-term persistence of the Nightjar across a considerable portion of its range. Addressing habitat needs may be the single most effective mechanism to achieve recovery of the species.
Vilella, F.J., and R. Gonzalez. 2023. Multi-resolution habitat models of the Puerto Rican Nightjar Antostromus noctitherus. Bird Conservation International. Bird Conservation International 33:e74 https://doi.org/10.1017/S0959270923000278 \| Abstract \| Download	September 2023	The Puerto Rican Nightjar <i>Antrostomus </i><i>noctitherus</i> is an endemic Caprimulgid found in dry coastal and lower montane forests of southwestern Puerto Rico. Information on the species (abundance, nesting biology) has been mostly restricted to forest reserves (i.e., Guánica Forest, Susúa Forest) with limited information available from private lands. We collected stand-level vegetation structure and geographic information to model habitat suitability and distribution for the Nightjar. Results of the stand-level model indicated forest type and midstory vegetation density best predicted Nightjar habitat. Our spatial model predicted considerably more Nightjar habitat (17,819.64ha) was located outside protected areas than previously reported. Further, the model highlighted several localities of importance for the species across southern Puerto Rico, all located within private lands. We used a patch occupancy approach to assess regions identified by the landscape-level model as suitable for the Nightjar and documented presence of the species in 32 of 55 sites, located in 12 of 18 municipalities across southern Puerto Rico. The protection and restoration of forest across the southern coast of Puerto Rico would help ensure the long-term persistence of the Nightjar across a considerable portion of its range. Addressing habitat needs may be the single most effective mechanism to achieve recovery of the species.
Vilella, F.J., J.A. Cruz-Burgos, R.M. Kamisnki, H.R. Murkin, J.B. Davis, S.L. Weitzel, and F. Vizcarra. 2020. Avian community response to vegetation and water level management in restored wetlands at the Humacao Nature Reserve, Puerto Rico. Caribbean Naturalist 72:1-24. \| Abstract \| Download	February 2020	Coastal wetlands of the Caribbean have been greatly reduced in area and quality, and information on wildlife responses to management is lacking. We applied wetland management practices (disking, water level management) in a site historically disturbed by <i>Saccharum spp.</i> L. (sugarcane) cultivation at the Humacao Nature Reserve, southeastern Puerto Rico, and evaluated avian community response. We conducted weekly bird surveys and nest searches on disked and non-disked plots within recently constructed impoundments. The avian community shifted from 16 upland dominated species pre-restoration, to 67 wetland-dependent species at the end of our study (2001-2002). Ordination analysis indicated avian guild use of plots varied with environmental variables. Bird species diversity was not influenced by treatment, month, or salinity levels but was influenced by water depth and vegetation cover. Bird abundance was influenced by water depth, but not by treatment, month, salinity or vegetation cover. Furthermore, water depths of 0.10 – 0.20 m and salinity ≤ 15 ppt promoted habitat conditions suitable for a diverse wetland avian community. We located 268 nests of 8 wetland bird species and observed adults with young of various other waterbirds, including species of conservation concern such as <i>Dendrocygna arborea</i> (West Indian Whistling Duck) and <i>Porzana flaviventer</i> (Yellow-breasted Crake). Bird community responses suggest that management practices (i.e., water level management and soil disturbance) can improve wetland biodiversity in abandoned sugarcane fields of Puerto Rico. Moreover, these practices may benefit wetland biodiversity in other Caribbean islands with a similar history of land use and habitat degradation.
Vilchez, M., J. Dattilo, and S. K. Brewer. 2024. Length-weight relationships of big-river fishes in the lower Red River catchment, USA. Journal of Applied Ichthyology https://doi.org/10.1155/2024/5578825	September 2024
Viegut, R.A., E.B. Webb, A.H. Raedeke, Z. Tang, Y.Zhang and Y. Shang. Nonbreeding waterfowl behavioral response to crewed and uncrewed aerial surveys on conservation areas in Missouri. Journal of the Southeastern Association of Fish and Wildlife Agencies \| Abstract	June 2024	Monitoring waterfowl populations provides the basis for improving habitat quantity and quality, establishing harvest regulations, and ensuring sustainable waterfowl populations through components of state natural-resource management objectives, joint-venture objectives, and the North American Waterfowl Management Plan. Waterfowl biologists currently use a variety of population and habitat monitoring methods ranging from informal ground observations to more systematic approaches, including low-level crewed aerial surveys. Although uncrewed aerial systems (UAS) may provide safer and more precise alternatives to traditional aerial survey techniques that are less disturbing to waterfowl and safer for people and waterfowl, there is limited information on how waterfowl in winter respond to UAS. We compared the behavioral responses of waterfowl to helicopters and UAS on Missouri Department of Conservation wetland conservation areas flown during waterfowl surveys October – February 2021-2022. Helicopter surveys were flown using an Airbus H125 helicopter at heights of 100 – 350 meters, with UAS surveys flown using a DJI Mavic 2 Pro UAS at 15 – 90 meters. Waterfowl behavior was categorized using flock-scan surveys recorded for 10-minute periods before, during, and after the surveys. Behaviors were categorized as alert, swim, fly, or abandonment and the proportion of time flocks spent in each behavior during- or post-survey were compared to pre-survey behaviors. Waterfowl behavior increased time spent swimming, flying, and abandonment in response to helicopter flights, whereas UAS flights did not influence waterfowl behavior regardless of survey height, guild or hunting season (open or closed). UAS may be a good alternative to traditional survey methods and are not likely to affect waterfowl distributions or energy expenditures during the survey periods.
Viegut, R.A., E.B. Webb, A.H. Raedeke, Z. Tang, Y. Zhang, Z. Zhai, Z Liu, S. Wang J. Zheng and Y. Shang. Detection probability and bias in machine-learning-based unoccupied aerial system non-breeding waterfowl surveys. Drones \| Abstract	February 2024	Unoccupied aerial systems (UAS) may provide cheaper, safer, and more accurate and precise alternatives to traditional waterfowl survey techniques while also reducing disturbance to waterfowl. We evaluated availability and perception bias on machine-learning-based nonbreeding waterfowl count estimates derived from aerial imagery collected using a DJI Mavic Pro 2 on Missouri Department of Conservation intensively managed wetland Conservation Areas within the Upper Mississippi River Conservation Priority Area across Missouri, USA. UAS imagery was collected using a proprietary software for automated flight path planning in a back-and-forth transect flight pattern at 10 m/s, no earlier than two hours after sunrise and ending by 1:00 pm at 15 - 90 m in altitude above ground level (AGL) (ground sampling distance 0.38-2.29 cm/pixel). Waterfowl in images were labeled using LabelMe by trained labelers. These same images were simultaneously analyzed using a computer algorithm developed to detect and classify waterfowl in aerial images by species and sex. We developed and evaluated three generalized linear mixed models with Bernoulli distributions: one to model the probability that a bird present in the image area was visible in the image (availability), one to model the probability that a bird visible in the image was detected by the algorithm, and one to model the probability that a machine-learning generated detection was actually a false-positive and not an actual bird. Variation in waterfowl availability was best explained by the interaction of vegetation cover type, sky condition, survey altitude, and individual bird characteristics of species and sex, with more complex and taller vegetation cover types reducing availability by up to 70 percent at higher survey altitudes. The probability of the algorithm correctly detecting available birds showed no pattern within vegetation cover type, survey altitude, or sky condition, with the algorithm correctly detecting 85 percent of available birds. The probability of the algorithm generating incorrect false-positive detections was best explained by vegetation cover types with features similar in size and shape to the birds, especially lotus (<i>Nelumbo lutea</i>), with up to 58 percent of detections being false-positive detections in lotus cover types. Overall, the algorithm achieved counts an average of 6.70 percent greater than the human labeled counts, and upon applying correction factors using a modified Horvitz-Thompson estimator, the corrected estimates were an average of 5.59 percent lower than the human labeled counts. Our results indicate that vegetation cover type, sky condition, and survey altitude influence the availability and detection of waterfowl in UAS surveys; however, using well-trained machine learning algorithms may produce accurate counts per image under a variety of survey conditions.
Vhay, M.P., D.A. Haukos, D.S. Sullins, and M.B. Rice. 2024. Landscape-scale changes in lesser prairie-chicken habitat. PLoS ONE	June 2024
Vhay, M. P., D. A. Haukos, D. S. Sullins, and M.B. Rice. 2024. Broad-scale changes in lesser prairie-chicken habitat. Plos one 19: e0304452. DOI: 10.1371/journal.pone.0304452	May 2024
Vest, J.L., D.A. Haukos, N.D. Niemuth, C.M. Setash, J.H. Gammonley, J.H. Devries, and D.K. Dahlgren. 2023. Waterfowl and wetland birds. Chapter 13 in L.B. McNew, D.K. Dahlgren, and J.L. Beck, editors. Rangeland Wildlife Ecology and Conservation. Springer Publishing, New York, New York, USA.	September 2023
Verheijen, B.H.F., E.B. Webb, M.G. Brasher and H.M. Hagy. 2024. Spatiotemporal dynamics of waterfowl harvest distributions in the Central and Mississippi Flyways from 1960–2019. The Journal of Wildlife Management	February 2024
Verheijen, B.H.F., E.B. Webb, M.G. Brasher and H.M. Hagy. 2024. Long-term changes in autumn-winter harvest distributions vary among duck species, months, and subpopulations. Ecology and Evolution	June 2024
Verheijen, B.H.F., D.M. Varner, and D.A. Haukos. 2020. Future losses of playa wetlands decrease network structure and connectivity of the Rainwater Basin, Nebraska. Landscape Ecology 35:453–467. https://doi.org/10.1007/s10980-019-00958-w	January 2020
Verheijen, B. H. F., R. T. Plumb, C. K. J. Gulick, C. A. Hagen, S. G. Robinson, D. S. Sullins, and D. A. Haukos.2021. Breeding space use by lesser prairie-chickens varies among ecoregions and breeding stages. American Midland Naturalist 185: 149–174. DOI: 10.1674/0003-0031-185.1.149.	January 2022
Verheigen, B.H.F., R.T. Plumb, C.K.J. Gulick, C.A. Hagen, S.G. Robinson, D.S. Sullins, and D.A. Haukos. 2021. Breeding season space use by lesser prairie-chickens (Tympanuchus pallidicinctus) varies among ecoregions and breeding stages. American Midland Naturalist 185:149-174. \| Abstract	April 2021	Large-scale declines of grasslands ecosystems in the conterminous United States since European settlement have led to substantial loss and fragmentation of lesser prairie-chicken (<i>Tympanuchus pallidicinctus</i>) habitat and decreased their occupied range and population numbers by ~85%. Breeding season space use is an important component of lesser prairie-chicken conservation, because it could affect both dynamics and carrying capacity of local populations. Previous estimates of breeding season space use are largely limited to one of the four currently occupied ecoregions, but potential extrinsic drivers of breeding space use, such as landscape fragmentation, vegetative structure and composition, and density of anthropogenic structures, can show large spatial variation. Moreover, habitat needs vary greatly among the lekking/prelaying, nesting, brooding, and postbreeding stages of the breeding season, but space use by female lesser prairie-chickens during these stages remain relatively unclear. We tested whether home range area and daily displacement of female lesser prairie-chickens varied among ecoregions and breeding stages at four study sites in Kansas and Colorado, USA, representing three of the four currently occupied ecoregions. We equipped females with very-high-frequency (VHF, <i>n</i> = 39) or GPS transmitters (<i>n</i> = 157), and estimated home range area with kernel density estimators or biased random bridge models, respectively. Across all ecoregions, breeding season home range area averaged 190.4 ha (± 19.1 ha SE) for birds with VHF and 283.6 ha (± 23.1 ha) for birds with GPS transmitters, while daily displacement averaged 374.8 m (± 14.3 m). Average home range area and daily displacement were greater in the Short-Grass Prairie/CRP Mosaic Ecoregion (VHF: 233.0 ± 34.7 ha, GPS: 420.8 ± 52.8 ha, 468.5 ± 29.4 m) compared to sites in the Mixed-Grass Prairie Ecoregion (VHF: 146.4 ± 16.4, 158.6 ± 25.2 ha, GPS: 183.9 ± 21.2, 183.3 ± 13.9 ha, 281.0 ± 16.0, 319.5 ± 13.8 m). Home range area and daily displacement were greatest during lekking/prelaying (252.8 ± 23.0 ha, 539.7 ± 223.0 m) and smallest during the brooding stage (81.4 ± 11.5 ha, 221.3 ± 63.7 m), when female movements are restricted by mobility of chicks. Ecoregion- and breeding stage-specific estimates of space use by lesser prairie-chickens will help managers determine the spatial configuration of breeding stage-specific habitat on the landscape. Furthermore, ecoregion- and breeding stage specific estimates are crucial when estimating the amount of breeding habitat needed for lesser prairie-chicken population to persist.
Veon, J.T., E. Lassiter, E. Johansson, M. Shaw, L. McTgue, R. Gibson, A. Massey, and B.A. DeGregorio. 2023. Influence of Human Development and Predator Abundance on Virginia Opossum Occupancy, Abundance, and Activity Patterns. Journal of Zoology. doi:10.1111/jzo.13111 \| Abstract \| Download	August 2023	As human development increases across the globe, wildlife are either pushed out of developed areas or adapt to survive in these novel, human-dominated landscapes. Many mammalian mesopredators, such as the Virginia opossum (<i>Didelphis virginiana</i>), have adapted to living alongside human development in order to take advantage of human-subsidized food, water, and shelter and may also benefit from being “shielded” by humans from their natural predators if those predator species are less able to coexist with humans or if they alter their behavior when living in proximity to humans (the human shield hypothesis). The human shield hypothesis has been used to explain the co-existence of dominant and subordinate mesopredators in some of North America’s largest cities. Our objective was to evaluate if patterns of Virginia opossum occupancy, abundance, and activity conformed to patterns consistent with the presence of a human shield. We used data from a coordinated continent-wide camera trapping study, Snapshot USA to estimate Virginia opossum occupancy, abundance, and activity and relate these measures to surrounding landscape and urbanization variables. We found that opossum occupancy was positively associated with an index of human activity (anthropogenic sound), although at very high levels of sound, opossum occurrence decreased. Furthermore, opossum in heavily forest areas were more likely to be detected in areas with nearby anthropogenic sound indicating a preference towards settling near humans. In areas with a high density of human housing, opossum relative abundance and predator abundance both increased suggesting that opossum were shielded from predators, whereas at low or moderate levels of housing density, opossum abundance did not increase although predator abundance did. We found that opossum were strictly nocturnal (99% of detections) and that they shifted their activity to being active earlier in the evening in the presence of high predator abundance. We found evidence that Virginia opossum are likely shielded by humans from their predators and this was most apparent when examining abundance and to some extent occupancy. These results help to explain why the Virginia opossum is such a successful urban-exploiter.
Veon, J.T., D.G. Krementz, L.W. Naylor, B.A. DeGregorio. 2023. Effects of landscape composition on winter mallard (Anas platyrhnchos) body condition in Eastern Arkansas. Journal of Wildlife Management \| Abstract \| Download	November 2023	Overwintering waterfowl with a higher body condition index are thought to be more likely to survive the winter and have increased productivity during the following breeding season. Body condition index in waterfowl should reflect the resources available to them locally. Here, we analyze the relationship of landscape composition on mallard (<i>Anas platyrhynchos</i>)<i> </i>body condition using a mass by wing length index (BCI) within the Lower Mississippi Alluvial Valley of Arkansas. We measured hunter-harvested mallards during the 2019-2020 and 2020-2021 duck hunting seasons. We found that mallards collected from areas with high proportions of water cover, woody wetlands, and open water within a 30-km radius had higher BCI. Conversely, we found that mallards collected from areas with higher proportions of herbaceous wetlands or human disturbance had lower BCI. Management actions focused on maintaining water levels for waterfowl to access food resources, while providing ample habitat that allows for resting, loafing, and other life cycle events free of human disturbance, will most likely increase BCI in mallards wintering in the Lower Mississippi Alluvial Valley.
Veon, J.T., B.A. DeGregorio, L.W. Naylor, K.J. Reinecke, B.C. Dabbert, D.W. Demarest, K.M. Hartke, and D.G. Krementz. 2023. Body mass dynamics in wintering mallards (Anas platyrhynchos) in the lower mississippi alluvial valley. Global Ecology and Conservation 41: e02368 \| Download	January 2023
Veggerby K, Scheuerell MD, Sanderson B, Kiffney P. Stable isotopes reveal intertidal fish and crabs use bivalve farms as foraging habitat in Puget Sound, Washington. \| Abstract	January 2024	Bivalves such as oysters and clams have been farmed in the Puget Sound region of the Salish Sea for thousands of years. Indigenous peoples have traditionally used systems called clam gardens to modify stretches of shoreline habitat to create ideal conditions for edible bivalves. More recently, oysters, clams, and other bivalves have been grown by both First Nation and non-First Nation farmers using a variety of gear types in intertidal zones across Puget Sound and the coast of Washington. These gear types create complex vertical structure and attachment points for aquatic epiphytes and invertebrates which increases habitat structural complexity, but may alter eelgrass cover in areas where bivalve farms and eelgrass meadows overlap. Eelgrass meadows are highly productive and ecologically foundational nearshore habitats that provide valuable ecosystem services including sediment deposition and stabilization, and the provision of nursery, refuge, and foraging habitat throughout much of the Puget Sound. Eelgrass meadows overlap with bivalve farming activities across many intertidal areas of Washington State. Many nearshore species of fish and crab inhabit both bivalve farm and eelgrass habitats, but how they are using the farm habitat and the importance of bivalve farm habitat for foraging and predator refuge relative to unfarmed eelgrass meadows is unclear. We used stable isotope mixing models to estimate, for several species of nearshore fish and crab in two areas of North Puget Sound, Washington, the percent diet originating from eelgrass meadows, pelagic planktonic sources, and oyster farm habitats. Our results indicate that several species of nearshore fish derive a significant proportion of their diets from farm areas, while others derive most of their diets from eelgrass habitat or planktonic sources. The results indicate that foraging habitat uses are species specific, and that modifying habitat will likely change both species composition and species usage of an area. Having an adequate amount of habitat diversity is needed to support the community of fishes and invertebrates that inhabit these intertidal areas.
Veggerby K, Scheuerell MD, Sanderson B, Kiffney P, Ferriss B. Shellfish aquaculture farms as foraging habitat for nearshore fishes and crabs.	March 2024
Vega-Castillo, S. I., J. A. Collazo, A. R. Puente-Rolón, and E. Cuevas. 2020. Influence of habitat structure and prey abundance on occupancy and abundance of two anoles ecomorphs, Anolis cristatellus and Anolis krugi, in Secondary Karst Forests in Northern Puerto Rico. J. of Herpetology 54(1) : 107-117. doi.org/10.1670/19-009	March 2020
Vargas K, Kraberger S, Custer JM, Paietta EN, Culver M, Munguia-Vega A, Dolby GA and A Varsani 2023. Identification of novel polyomavirus in wild Sonoran Desert rodents of the family Heteromyidae. Archives of Virology, 168:253. doi: 10.1007/s00705-023-05877-5. \| Abstract	October 2023	Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and are often found in close association with humans, domestic animals, and wildlife. Although rodents are known to be reservoirs of zoonotic viruses and a significant amount of research has focused in this area, there has been less emphasis on viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate the DNA virome of wild rodent from Baja California Peninsula, Mexico using fecal samples. As part of this study, we identified a novel polyomavirus (PyV) in fecal samples from two rodent species, a spiny pocket mouse (<i>Chaetodipus spinatus</i>), and a Dulzura kangaroo rat (<i>Dipodomys simulans</i>). These two polyomaviruses represent a new species in the genus <i>Betapolyomavirus</i>. Sequences of this polyomavirus phylogenetically cluster with other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the respiratory tract of young humans. Through our continued work on seven species of rodents, we endeavor to explore viral diversity associated with wild rodents in Baja California Peninsula and expand on current knowledge of their ecology and evolution.
VanderBloemen, S. L.E. Miranda, G.G. Sass, M. Colvin, and N. Faucheux. 2023. Influence of invasive bigheaded carps on Gizzard Shad in the Tennessee River. Transactions of the American Fisheries Society. https://doi.org/10.1002/tafs.10442 \| Abstract	August 2023	The Tennessee River basin and its cascade of reservoirs are home to some of the most diverse fish assemblages in the world. This unique system is threatened by the ongoing invasion of Silver Carp <i>Hypophthalmichthys molitrix</i> and Bighead Carp <i>H. nobilis</i>, hereafter bigheaded carps. Bigheaded carps may directly compete for food resources with native clupeid species such as Gizzard Shad <i>Dorosoma cepedianum</i>, and this potential interaction could have damaging ecological and economic consequences. High relative abundances of Gizzard Shad are crucial to the Tennessee River food web and associated fisheries because of their role as a forage base for piscivorous species. We analyzed an extensive dataset of annual gillnetting and electrofishing data extending from 1990 to 2017, to test whether Gizzard Shad relative abundances have changed in Tennessee River reservoirs since the invasion of bigheaded carps. Our analyses indicate that Gizzard Shad abundances have been declining and were already declining prior to the discovery of bigheaded carps in the Tennessee River. The Tennessee River system needs to be continually monitored for any signs of possible interactions between bigheaded carps and Gizzard Shad.
Vanausdall, R. A., W. L. Kendall, D. P. Collins, and Q. R. Hays. 2024. Time of year and weather influence departure decisions of sandhill cranes at a primary stopover. Frontiers in Ecology and Evolution 12:1279279, doi: 10.3389/fevo.2024.1279279.	March 2024
Van Vleet, N. P., Ward, D. M., Som, N. A., Barton, D. C., Anderson, C., & Henderson, M. J. (2024). It's about time: A multistate semicontinuous time mark–recapture model to evaluate seasonal survival and movement rates of juvenile Coho Salmon in a small coastal watershed. Transactions of the American Fisheries Society, 153, 541–1. https://doi.org/10.1002/tafs.10471 \| Abstract	August 2024	It is important to have an accurate understanding of species habitat use and demographics as managers prioritize restoration efforts and develop recovery plans for depleted salmon populations. Previous research on threatened populations of Coho Salmon has suggested that overwinter survival is a major limiting factor for population recovery in some watersheds, but these survival estimates are often confounded with emigration to alternative rearing habitats, such as estuaries. Furthermore, emigration to alternative rearing habitats can occur continuously throughout the fall and winter, which is ignored by most types of mark-recapture models. To refine previous survival estimates, we developed a multi-state mark-recapture model that allows separately estimated emigration and survival rates throughout the year. To do this, we used weekly time-varying occasions paired with discrete spatial states. We conducted extensive simulation trials to validate the use of a multi-state model on an existing 4-year PIT tag dataset in a northern California watershed. Results from our model suggest that overwinter survival rate for fish that overwinter in stream habitat and migrate as spring smolts ranged from 0.72-0.83, which is higher than expected for Coho Salmon in this region. We estimate that a substantial proportion of smaller juveniles (0.21-0.28 annually) are emigrating from upstream rearing habitat before the spring smolt migration. This implies that previous estimates of low overwinter survival of Coho Salmon could be due to high emigration rates to alternative rearing locations. Given the apparent juvenile life-history diversity of Coho Salmon, multiple emigration patterns should be considered in the design of future research, monitoring, and restoration projects.
Van Tatenhove, A.M., Neill, J., Norvell, R.E., Stuber, E.F. and Rushing, C.S., 2024. Scale‐dependent population drivers inform avian management in a declining saline lake ecosystem. Ecological Applications, p.e3021.	September 2024
Van Ee, J.J. C.A. Hagen, D.C. Pavlacky Jr., D.A. Haukos , A.J. Lawrence, A.M. Tanner, B.A. Grisham, K.A. Fricke, L.G. Rossi, G.M. Beauprez, K.E. Kuklinski, R. Martin, M.D. Koslovsky, T.B. Rintz, M.B. Hooten. 2024. Melded integrated population models. Journal of Agricultural, Biological, and Environmental Statistics doi.org/10.1007/s13253-024-00620-2	May 2024
Van Doren, B.M., Willard, D.E., Hennen, M., Horton, K.G., Stuber, E.F., Sheldon, D., Sivakumar, A.H., Wang, J., Farnsworth, A. and Winger, B.M., 2021. Drivers of fatal bird collisions in an urban center. Proceedings of the National Academy of Sciences, 118(24). https://doi.org/10.1073/pnas.2101666118	April 2021
Van Buskirk, A., C. S. Rosenberry, B. D. Wallingford, E. J. Domoto, M. E. McDill, P. Drohan, and D. R. Diefenbach. 2021. Modeling how to achieve localized areas of reduced white-tailed deer density. Ecological Modelling 442:109393 DOI: 10.1016/j.ecolmodel.2020.109393 \| Download	February 2021
Valentine GP, Lu X, Childress ES, Dolloff CA, Hitt NP, Kulp MA, Letcher BH, Pregler KC, Rash JM, Hooten MB, Kanno Y. 2024. Spatial asynchrony and cross-scale climate interactions in populations of a coldwater stream fish. Global Change Biology. 30:e17029. doi: https://doi.org/10.1111/gcb.17029	January 2024
Valente, J.J., V. Jirinec, and M. Leu. 2024. Thinking beyond the closure assumption: designing surveys for estimating biological truth with occupancy models. Methods in Ecology and Evolution 15:2289-2300.	December 2024
Valente JJ, Gannon D, Hightower J, Kim H, Leimberger K, Macedo R, Rousseau J, Weldy M, Zitomer R, Fahrig L, Fletcher R, Wu J, Betts MG. 2023. Toward conciliation in the habitat fragmentation and biodiversity debate. Landscape Ecology. 38, 2717-2730. https://doi.org/10.1007/s10980-023-01708-9. \| Abstract \| Download \| Publisher Website	September 2023	Landscape-scale conservation planning is urgent given the extent of anthropogenic land-use change and its pervasive impacts on Earth’s biodiversity. However, such efforts are hindered by disagreements over the effects of habitat fragmentation on biodiversity that have persisted since the mid-1970s. We contend that nearly 50 years later, these disagreements have become a locked-in debate characterized by polarized, unproductive discourse and a lack of consistent guidance for landscape managers and policy makers. Here, we highlight the need for a unified set of principles regarding conservation in fragmented landscapes, identify potential reasons for disparate conclusions in fragmentation research, and suggest ways for the ecological community to advance research that leads to consensus rather than the perpetuation of disagreement. Explicit efforts to develop and test multiple competing hypotheses, inter-laboratory collaborations, and acknowledgement of multiple interacting effects will be vital for moving the fragmentation debate forward. We argue that we in the ecology community should be responsible for helping to reconcile different views across scales, systems, and methodological approaches to advance conservation planning within a landscape ecology framework.
Valente JJ, Adrean LJ, Nelson SK, Betts MG, Roby DD, and Rivers JW. 2024. Presence-absence surveys yield spatially imprecise information about nesting sites of an endangered, forest-nesting seabird. PLoS ONE 19:e0315531.	December 2024
Vaisvil, A., D. Shoup, and S.K. Brewer. 2023. Striped Bass Exploitation in Tailwater Habitats of East-Central Oklahoma. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-152-2023, Washington, D.C. https://doi.org/10.3996/css83805350	October 2023
Vaisvil, A., C.A. Caldwell, and E. Frey. Effects of water-level fluctuations and water temperature on young-of-year Largemouth Bass in a southwest Irrigation reservoir. Journal of Fish and Wildlife Management 12(2):534-543. \| Abstract	August 2022	The effects of a warming climate will alter the hydrological cycles of arid southwestern U.S. reservoirs which primarily support agricultural needs, provide flood control, and generate hydroelectric power while secondarily supporting fish communities and sport fishing opportunities. The success of littoral spawning fishes depends on the timing and variability of water levels. The onset of drought between 2017 and 2018 provided an opportunity to evaluate the timing of hatch dates and relative abundance of young-of-year Largemouth Bass<i> Micropterus salmoides </i>across two water years of varying water temperatures and water levels in a southwestern U.S. reservoir. A retrospective analysis of otoliths in young-of-year Largemouth Bass revealed similar hatch dates in 2017 (14 April–29 May) and 2018 (13 April–28 May) despite differences in water temperature and water level rate-of-change. Median water temperature during hatch dates was greater in 2017 (median 19.0°C, range 14.3–24.4°C) than 2018 (17.6°C, range 13.5–21.7°C). Water level rate-of-change during hatch dates in 2017 was positive (+3.1– +13.1 cm/d), which reflected reservoir filling. In contrast, water level rate-of-change during hatch dates in 2018 was negative (-8.5– -0.6 cm/d), which reflected reservoir receding. Relative abundance of young-of-year fish was greater in 2017 (21.7 fish/h) when the reservoir was filling compared to relative abundance in 2018 (6.8 fish/h) when the reservoir was receding. The median growth rate was greater in 2017 (1.02 mm/d) when the reservoir was filling than in 2018 (0.82 mm/d) when the reservoir was receding. Despite differences in water temperature and contrasting reservoir levels between the two water years, the Largemouth Bass population in a southwest U.S. reservoir exhibited similar hatch dates reported for the species in southeastern and northeastern U.S. reservoirs. While water demand in the 21<sup>st</sup> century may exceed availability, the opportunity exists to collaborate with water managers to benefit Largemouth Bass populations in southwestern reservoirs.
Ureta, J. C., Ureta, J. U., Bower, L. M., Peoples B. K, & Motallebi, M. (2024). The value of improving freshwater ecosystem services: South Carolina residents’ willingness-to-pay for improved water quality. Journal of Ecological Economics. \| Publisher Website	February 2024
Ungulate Migrations of the Western United States, Volume 4. Kauffman et al.	April 2024
Ulrich, T. L., and S. A. Bonar. 2020. Inexpensive, Underwater Filming of Rare Fishes in High Definition. Fisheries 45:121-130.	March 2020
Ulaski, M. E., and M. C. Quist. 2021. Filling knowledge gaps for a threatened species: age and growth of Green Sturgeon of the southern Distinct Population Segment. Journal of Fish and Wildlife Management 12:234-240.	August 2021
Ulaski, M. E., S. E. Blackburn, Z. J. Jackson, and M. C. Quist. 2022. Management goals for conserving White Sturgeon in the Sacramento-San Joaquin River basin. Journal of Fish and Wildlife Management 13:334-343.	January 2023
Ulaski, M. E., J. L. McCormick, M. C. Quist, and Z. J. Jackson. 2023. Leveraging angler effort to inform fisheries management: using harvest and harvest rate to estimate abundance of White Sturgeon. Journal of Fish and Wildlife Management 14:324-336.	December 2023
Tábora-Sarmiento, S., Patiño, R., Portillo-Quintero, C., Coldren, C. 2022. Air, land, and water variables associated with the first appearance and current spatial distribution of toxic Prymnesium parvum blooms in reservoirs of the Southern Great Plains, USA. Science of the Total Environment 836, 155567. https://doi.org/10.1016/j.scitotenv.2022.155567 \| Publisher Website	May 2022
Twining, JP, Zalewski, A, Cove, MV, Birks, J, Wearn, O, Haysom, J, Wereszczuk, A,Manzo, E, Bartolommei, P, Mortelli, A, Evans, B, Gerber, BD, McGreevy, TJ,Ganoe, L, Masseloux, J, Mayer, A, Wierzbowska, I, Akins, J, Drummey, D, McShea,W, Kays, R, Schuttler, S, Pardo, L, Boyce, A, Trujillo, AJV, L´opez-Gonz´alez, C, Lara-D´ıaz, NE, Sukmasuang, R, Whatton, M, Cosby, O, Giman, B, Ragai, RB, Li, S, Bu,H, Wang, D, Wang, F, Waggershauser, C, Bamber, J, Stewart, F, Fisher, J, Fuller,A, Perkins, K, Sutherland, C, and Powell, RA. In Press. Sociality in unexpected places: Using global remote camera data to evaluate the drivers of social complexity.Proceedings of the National Academy of Science. 121, e2312252121. \| Abstract \| Download \| Publisher Website	March 2024	The social system of animals involves a complex interplay between physiology, natural history, and the environment. Long relied upon discrete categorizations of “social” and “solitary” inhibit our capacity to understand species and their interactions with the world around them. Here, we use a globally distributed camera trapping dataset to test the drivers of aggregating into groups in a species complex (martens and relatives, family <i>Mustelidae</i>, Order <i>Carnivora</i>) assumed to be obligately solitary. We use a simple quantification, the probability of being detected in a group, that was applied across our globally derived camera trap dataset. Using a series of binomial generalized mixed-effects models applied to a dataset of 16,483 independent detections across 17 countries on four continents we test explicit hypotheses about potential drivers of group formation. We observe a wide range of probabilities of being detected in groups within the solitary model system, with the probability of aggregating in groups varying by more than an order of magnitude. We demonstrate that a species’ context-dependent proclivity toward aggregating in groups is underpinned by a range of resource-related factors, primarily the distribution of resources, with increasing patchiness of resources facilitating group formation, as well as interactions between environmental conditions (resource constancy/winter severity) and physiology (energy storage capabilities). The wide variation in propensities to aggregate with conspecifics observed here highlights how continued failure to recognize complexities in the social behaviors of apparently solitary species limits our understanding not only of the individual species but also the causes and consequences of group formation.
Twining, J.P., V.L. Springer, E.G. Cooch, and A.K. Fuller. Landscape-scale drivers of tayra abundance in the Ecuadorian Andes. Biodiversity and Conservation.https://doi.org/10.1007/s10531-023-02636-5	June 2023
Twining, J.P., J.L. Brazeal, P.G. Jensen, and A.K. Fuller. 2024. Intraguild interactions and abiotic conditions mediate occupancy of mammalian carnivores: co-occurrence of coyotes-fishers-martens. Oikos. https://doi.org/10.1111/oik.10577	March 2024
Twining, J.P., Fuller, A.K., Sun, C.C., Calderon-Acevedo, C., Schlesinger, M.D., Berger, M., Kramer, D., Frair, J.L. 2024. Integrating presence-only and detection/non-detection data to estimate distributions and expected abundance of difficult-to-monitor species on a landscape-scale. Journal of Applied Ecology. DOI: 10.1111/1365-2664.14633	March 2024
Twining, J.P., D. Kramer, K.A. Perkins, and A.K. Fuller. 2024. Landscape-scale population trends in the occurrence and abundance of wildlife populations using long term camera-trapping data. Biological Conservation.	January 2024
Twining, J.P., B.C. Augustine, J.A. Royle, and A.K. Fuller. Abundance-mediated species interactions. Ecology. https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.4468 \| Abstract	December 2024	Species interactions shape biodiversity patterns, community assemblage, and the dynamics of wildlife populations. Ecological theory posits that the strength of interspecific interactions is fundamentally underpinned by the population sizes of the involved species. Nonetheless, prevalent approaches for modelling species interactions predominantly centre around occupancy states. Here, we use simulations to illuminate the inadequacies of modelling species interactions solely as a function of occupancy, as is common practice in ecology. We demonstrate erroneous inference into species interactions due to bias in parameter estimates when considering species occupancy alone. To address this critical issue, we propose, develop, and demonstrate an occupancy-abundance model designed explicitly for modelling abundance-mediated species interactions involving two or more species. We present Markov chain Monte Carlo (MCMC) samplers tailored for diverse ecological scenarios, including intraguild predation, disease or predator mediated competition, and trophic cascades. Illustrating the practical implications of our approach, we compare inference from modelling the interactions in a three-species network involving coyotes<i>, </i>fisher, and American marten in North America as a function of occupancy states, and as a function of abundance. When modelling interactions as a function of abundance rather than occupancy, we uncover previously unidentified interactions. Our study emphasizes that accounting for abundance-mediated interactions rather than simple co-occurrence patterns can fundamentally alter our comprehension of system dynamics. Through an empirical case study and comprehensive simulations, we demonstrate the importance of accounting for abundance when modelling species interactions, and we present a statistical framework equipped with MCMC samplers to achieve this paradigm shift in ecological research.
Twining, J.P. C. Sutherland, A. Zalewski, M.V. Cove, J. Birks, O.R. Weaarn, J. Haysom, A. Wereszcuk, E. Manzo, P. Bartolommei, A. Mortelliti, B. Evans, B.D. Gerber, T.J. McGreevy, L.S. Ganoe, J. Masseloux, A. Mayer, I. Wierzbowska, J. Loch, J. Akins, D. Frummey, W. McShea, R. Kays, S. Manke, L. Pardo, A. Boyce. S. Li, R.B. Ragai, A.J.V. Trujiilo, C. Lopez-Gonzalez, N. Lara-Diaz, O. Cosby, C. Waggershauser, J. Bamber, F. Stewart, J. Fisher, A.K. Fuller, K. Perkins, and R.A. Powell. Using global remote camera data of a "solitary" species complex to evaluate the drivers of group formation. Proceedings of the National Academy of Sciences. DOI 10.1073/pnas.2312252121 www.pnas.org/doi/10.1073/pnas.2312252121	March 2024
Twardek, W. M., I.G. Cowx, N. Lapointe, C. P. Paukert, T. D. Beard, E. M. Bennett, D. Browne, A. K. Carlson, K. D. Clarke, Z. Hogan, K. Lorenzen, A. J. Lynch, P. B. McIntyre, P. Pompeu, M. Rogers, A. Sakas, W. W. Taylor, T. D.Ward, Z. Basher, and S. J.Cooke. 2022. Bright spots for inland fish and fisheries to guide future hydropower development. Water Biology and Security .https://doi.org/10.1016/j.watbs.2022.100009.	February 2022
Twardek, W. M., I. G. Cowx, N. Lapointe, C. Paukert, T. D. Beard, E. M. Bennett, D. Browne, A. K. Carlson, K. D. Clarke, Z. Hogan, K. Lorenzen, A. J. Lynch, P. B. McIntyre, P. Pompeu, M. Rogers, A. Sakas, W. W. Taylor, T. D. Ward, Z. Basher, and S.J. Cooke^. Bright spots for inland fish and fisheries to guide future hydropower development. Water Biology and Security 1(1):100009. https://doi.org/10.1016/j.watbs.2022.100009	February 2022
Tuttle, LJ, and MJ Donahue. 2022. Effects of sediment exposure on corals: a systematic review of experimental studies. *Environmental Evidence*. 11(4). https://doi.org/10.1186/s13750-022-00256-0	February 2022
Tuttle, LJ, RW Lamb, and AL Stringer. 2021. Differential learning by native versus invasive predators to avoid distasteful cleaning mutualists. *Functional Ecology*. 35(7): 1481-1490. https://doi.org/10.1111/1365-2435.13806	April 2021
Tuttle, LJ, C Johnson, S Kolinski, D Minton, and MJ Donahue. 2020. How does sediment exposure affect corals? A systematic review protocol. *Environmental Evidence*. 9: 17. https://doi.org/10.1186/s13750-020-00200-0	August 2020
Tuttle Raz, L. J., T. B. Grabowski, and R. Masse. 2024. Analysis and Review of Fishery-Dependent Data for Hawaiian Nearshore Noncommercial Fisheries. Report to State of Hawai'i Department of Land and Natural Resources, Division of Aquatic Resources. 97 p.	January 2024
Turnley, M. T. , T. A. Hughes, R. T. Larsen, K. R. Hersey, M. S. Broadway, M. C. Chitwood, W. S. Fairbanks, R. C. Lonsinger, and B. R. McMillan. 2024. A fine-scale examination of parturition timing in temperate ungulates. Ecology and Evolution 14(7): e11703. https://doi.org/10.1002/ece3.11703 \| Abstract	July 2024	1. Parturition timing has long been a topic of interest in ungulate research. However, few studies have examined parturition timing at fine scale (e.g., <1 day). Predator activity and environmental conditions can vary considerably with diel timing, which may result in selective pressure for parturition to occur during diel times that maximize the likelihood of neonate survival.<br>2. We monitored parturition events and early-life survival of elk (<i>Cervus canadensis</i>) and mule deer (<i>Odocoileus hemionus</i>) in Utah, USA to better understand diel timing of parturition in temperate ungulates.<br>3. Diel timing of parturition was highly synchronous among conspecifics and influenced by environmental variables on the date of parturition. For elk, parturition events were most common during the morning crepuscular period and generally occurred later (i.e., closer to 12:00) when a relatively large proportion of the moon was illuminated. For mule deer, parturition events were most common during the diurnal period and generally occurred later (i.e., closer to 15:00) on cold, wet dates.<br>4. Diel timing of parturition did not influence neonate survival, but larger data sets may be required to verify the apparent lack of influence.<br>5. Although additional work could evaluate alternative variables that might affect parturition timing, our data provide an improved and finer-scale understanding of reproductive ecology and phenology in ungulates.
Turner, W.C., S. Périquet, C.E. Goelst, K. Vera, E.Z. Cameron, K.A. Alexander, J.L. Belant, C.C. Cloete, P. du Preez, W.M. Getz, R.S. Hetem, P.L. Kamath, M. Kasaona, M. Mackenzie, J. Mendelsohn, J.K.E. Mfune, J.R. Muntifering, R. Portas, H.A. Scott, W. M. Strauss, W. Versfeld, B. Wachter, G. Wittemyer, and J.W. Kilian. 2022. Africa’s drylands in a changing world: Challenges for wildlife conservation under climate and land-use changes in the Greater Etosha Landscape. Global Ecology and Conservation, https://doi.org/10.1016/j.gecco.2022.e02221. \| Abstract \| Publisher Website	July 2022	Proclaimed in 1907, Etosha National Park in northern Namibia is an iconic dryland system with a rich history of wildlife conservation and research. A recent research symposium on wildlife conservation in the Greater Etosha Landscape (GEL) highlighted increased concern of how intensification of global change will affect wildlife conservation based on participant responses to a questionnaire. The GEL includes Etosha and surrounding areas, the latter divided by a veterinary fence into large, private farms to the south and communal areas of residential and farming land to the north. Here, we leverage our knowledge of this ecosystem to provide insight into the broader challenges facing wildlife conservation in this vulnerable dryland environment. We first look backward, summarizing the history of wildlife conservation and research trends in the GEL based on a literature review, providing a broad-scale understanding of the socioecological processes that drive dryland system dynamics. We then look forward, focusing on eight key areas of challenge and opportunity for this ecosystem: climate change, water availability and quality, vegetation and fire management, adaptability of wildlife populations, disease risk, human-wildlife conflict, wildlife crime, and human dimensions of wildlife conservation. Using this model system, we summarize key lessons and identify critical threats highlighting future research needs to support wildlife management. Research in the GEL has followed a trajectory seen elsewhere reflecting an increase in complexity and integration across biological scales over time. Yet, despite these trends, a gap exists between the scope of recent research efforts and the needs of wildlife conservation to adapt to climate and land-use changes. Given the complex nature of climate change, in addition to locally existing system stressors, a framework of forward-thinking adaptive management to address these challenges, supported by integrative and multidisciplinary research could be beneficial. One critical area for growth is to better integrate research and wildlife management across land-use types. Such efforts have the potential to support wildlife conservation efforts and human development goals, while building resilience against the impacts of climate change. While our conclusions reflect the specifics of the GEL ecosystem, they have direct relevance for other African dryland systems impacted by global change.
Turner, W.C., P.L. Kamath, H. van Heerden, Z. Barandongo, Y.-H. Huang, S.A. Bruce and K. Kausrud. 2021. The roles of environmental variation and parasite survival in virulence-transmission relationships. Royal Society Open Science, 8: 210088. https://doi.org/10.1098/rsos.210088 \| Abstract \| Publisher Website	June 2021	Disease outbreaks are a consequence of interactions among the three components of a host-parasite system: the infectious agent, the host, and the environment. While virulence and transmission are widely investigated, most studies of parasite life history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host-parasite coevolution. Here we review research on how environmental context alters virulence-transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related “approaches” that have dominated the study of the evolution of virulence and transmission for different host-parasite systems: i) evolutionary trade-off theory, ii) parasite local adaptation, and iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence-transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life history evolution, phylogenetics, adaptive dynamics, and comparative genomics, we can improve our understanding of virulence-transmission relationships across a diversity of host-parasite systems that have eluded experimental study of parasite life history.
Turner, R.M., C. Loftin, A. Revello, L.R. Kline, M.A. Lewis, and S.Y. Sekeh. 2021. Modeling and Using Context, vol. 21 no. 4 (CONTEXT-21 Special Issue).	July 2021
Tuma, M. E. and A. N. Powell. 2021. The southeastern U.S. as a complex of use sites for nonbreeding rufa Red Knots: fifteen years of band-encounter data. Wader Study 128(3): 265-273. doi:10.18194/ws.00256 \| Abstract	December 2021	Shorebirds have been banded for decades and monitoring programs have helped to accumulate large band-encounter datasets from across the globe; however, many of these datasets are left largely unused, particularly those collected by citizen scientists. These datasets can provide valuable insight into<br>the migration and movement strategies of shorebirds and the threats they face throughout their migratory cycle. We used long-term (2003–2018) band-encounter data of Red Knots Calidris canutus rufa in North America to determine: (1) the spatiotemporal distribution during the nonbreeding season, (2) site fidelity to nonbreeding sites, and (3) migratory connectivity of knots using the southeastern United States (Southeast), an important overwintering and stopover area for this subspecies. Annual mean site fidelity ranged from 0% to 86% across 24 sites. We found movement between sites across the Southeast during migratory and wintering periods, indicating that knots are using the region as interconnected sites, as opposed to relying on a single site or a cluster of adjacent sites. We identified ‘hop migration’ as a common strategy for knots in the region, and showed regular within-year movement between sites in South Carolina, Georgia,<br>and Florida. The Southeast is an understudied part of the rufa range; our results show the importance of the region to the subspecies both as a stopover and wintering area. Despite the inherent biases in the data and imperfect detection due to inconsistent survey effort, the data showed large-scale movements and confirmed the region as a complex of sites connected by knots.
Tucker, A.M., C.P McGowan, B.L. Nuse, J.E. Lyons, C.T. Moore, D.R. Smith, J.A. Sweka, K.A. Anstead, A. DeRose-Wilson, and N.A. Clark. 2023. Estimating recruitment rate and population dynamics at a migratory stopover site using an integrated population model. Ecosphere. \| Abstract	February 2023	Consideration of the full annual cycle population dynamics can provide useful insight for conservation efforts but collecting data needed to estimate demographic parameters is often logistically difficult. For species that breed in remote areas, monitoring is often conducted during migratory stopover or at nonbreeding sites and the recruitment rate of new breeding adults can be difficult to estimate directly. Here we present an integrated population model that uses mark-resight and count data collected during migratory stopover to estimate population growth rate and recruitment rate for an Arctic-breeding shorebird of conservation concern, the red knot (<i>Calidris canutus rufa</i>), from data collected during spring stopover in Delaware Bay, USA from 2005-2018. At this site, red knot feed primarily on the eggs of spawning horseshoe crabs (<i>Limulus polyphemus</i>), a legally harvested species. We used this model to estimate the relationship between horseshoe crab abundance and red knot demographics, which informed a recent revision to framework used to establish horseshoe crab harvest regulations. Our analysis indicates that the red knot population was most likely stable from 2005-2018 (average l = 1.04, 95% CRI: 0.997, 1.07) despite low recruitment rates (average = 0.093, 95% CRI: 0.036, 0.015). Adult survival probability was positively associated with horseshoe crab abundance (β = 0.35, 95% CRI: 0.09, 0.63), but we found no effect of horseshoe crab abundance on recruitment (β = -0.08, 95% CRI: -0.41, 0.38). Our approach demonstrates the utility of integrated population models for understanding full annual cycle population dynamics, even when data are only available from one point of the annual cycle.
Tucker, A.M. and M.C. Runge. 2021. Optimal strategies for managing wildlife harvest under system change. Journal of Wildlife Management, 85(5): 847-854. https://doi.org/10.1002/jwmg.22047	April 2021
Tucker et al. and 150 others. Changes in human presence during COVID-19 lockdowns altered the spatial behavior of terrestrial mammals	June 2023
Tucker AM, McGowan CP, Mulero E, Angeli N, Zegarra JP. 2020. A demographic projection model to support conservation decision making for an endangered snake with limited monitoring data. Animal Conservation 24 (2): 291-301. https://doi.org/10.1111/acv.12641	October 2020
Tucker AM, McGowan CP, Lyons JE, Derose-Wilson A, Clark NA. 2021. Species-specific demographic and behavioral responses to food availability during migratory stopover. Population Ecology. https://doi.org/10.1002/1438-390X.12094	July 2021
True, M.C., R.W. Perry and W.M. Ford. 2021. Forecasting the Distribution of a Range-Expanding Bat Reveals Future Response to Climate Change and Habitat. Acta Chiropterlogica 23(1) : 139-152	July 2021
True, M.C., R.J. Reynolds and W.M. Ford. 2021. Monitoring and Modeling Tree Bat (Genera: Lasiurus, Lasionycteris) Occurrence Using Acoustics on Structures Off the Mid-Atlantic Coast—Implications for Offshore Wind Development. Animals 11(11), 3146; https://doi.org/10.3390/ani11113146	November 2021
True, M.C., K.M. Gorman, H. Taylor, R.J. Reynolds and W.M. Ford. 2023. Fall migration, oceanic movement, and site residency patterns of the eastern red bats (Lasiurus borealis) on the mid-Atlantic Coast. Movement Ecology 2023) 11:35https://doi.org/10.1186/s40462-023-00398-x	June 2023
Triano, B., K. M. Kappenman, T. E. McMahon, M. Blank, K. C. Heim, A. E. Parker, A. V. Zale, and K. Plymesser. 2022. Attraction, entrance, and passage efficiency of Arctic Grayling, trout, and suckers at Denil fishways in the Big Hole River Basin, Montana. Transactions of the American Fisheries Society 151:453-473. https://doi.org/10.1002/tafs.10362 \| Abstract	May 2022	The Big Hole River basin in southwest Montana supports the only indigenous, self-sustaining fluvial population of Arctic Grayling <i>Thymallus arcticus</i> in the conterminous United States. Denil fishways were installed at 63 low-head irrigation diversion dams in the basin to provide grayling and other fishes year-round access to critical habitats; however, their efficiency has not been evaluated comprehensively. We quantified all components of fishway efficiency (approach, attraction, entrance, and passage) for hatchery-reared grayling, wild trout (Brook Trout <i>Salvelinus fontinalis </i>and Brown Trout <i>Salmo trutta</i>), and wild suckers (White Sucker <i>Catostomus commersonii</i> and Longnose Sucker <i>C. catostomus</i>) during 14 field trials conducted at six Denil fishways over a representative range of fishway slopes and hydraulic conditions using passive integrated transponder telemetry. Attraction (60.4-84.3%) and entrance (44.3-78.6%) efficiencies were variable across test conditions and reduced overall fishway efficiencies (19.1-55.8%). In contrast, upon entry, passage efficiencies were high (96.2-97.0%) for all taxa across all test conditions. Attraction of hatchery-reared grayling was limited at fishways with shallow upstream depths (low fishway discharges) and low attraction flows, but wild fish were less limited by these conditions. Entrance of grayling and trout was limited at deep upstream depths (high fishway discharges) and fishways with steep slopes, especially when plunging entrance conditions associated with shallow downstream depths were present. However, both grayling and trout were more likely to enter fishways with deep downstream depths than those with shallow downstream depths, and deep downstream depths demonstrated promise for increasing entrance at fishways with high discharges and steep slopes. Our results indicate that Denil fishways have enhanced aquatic connectivity for fishes in the Big Hole River basin, and maintaining high attraction flows and deep downstream depths could increase attraction and entrance, thereby improving overall fishway efficiency.
Treanor, H. B., C. S. Guy. J. E. Ilgen, W. M. Sealey, A. T. Dove, and M. A. H. Webb. 2024. Survival and growth of larval pallid sturgeon are improved by a live diet. North American Journal of Aquaculture http://doi.org/10.1002/naaq.10340	March 2024
Tracy, E. E., M. J. Brouder, A. C. Iles, C. N. Teal and S. A. Bonar. 2024. Indices for Common North American Fishes. Pages 441 to 786 in S. A. Bonar, N Mercado-Silva, and K. L. Pope, editors. Standard methods to sample North American freshwater fishes. American Fisheries Society, Bethesda, Maryland.	September 2024
Tracy, E. E, C. N. Teal, S. J. Ingram, C. J. Jenney, J. D. Grant, and S. A. Bonar. 2021. The Impact of COVID-19 on Freshwater Fisheries Fieldwork and Data Collection. Fisheries. https://doi.org/10.1002/fsh.10636	July 2021
Tracy, E. E, C. N. Teal, S. J. Ingram, C. J. Jenney, J. D. Grant, and S. A. Bonar. 2021. The Impact of COVID-19 on Freshwater Fisheries Fieldwork and Data Collection. Fisheries. https://doi.org/10.1002/fsh.10636	July 2021
Torvinen, E.S., Falke, J.A., Arp, C.D., Jones, B.M., Whitman, M.S., and C.E. Zimmerman. Lake trout (Salvelinus namaycush) otoliths indicate effects of climate and lake morphology on growth patterns in Arctic lakes. Ecology of Freshwater Fish.	September 2022
Torolski, H.M., J.M. Long, R.C. Lonsinger, and L.A. Bruckerhoff. 2024. Updated distribution for two freshwater mussel species of conservation concern in Oklahoma. Southeastern Naturalist 23:N44-N49.	September 2024
Tonkin, J.D., J.D. Olden, D.M. Merritt, L.V. Reynolds, J.S. Rogosch, and D.A. Lytle. 2021. Designing flow regimes to support entire river ecosystems. Frontiers in Ecology and the Environment, fee.2348. https://doi.org/10.1002/fee.2348	May 2021
Ton, R., and T. E. Martin. 2019. Nest Predation and Adult Mortality Relationships with Post-natal Metabolic Rates and Growth among Temperate and Tropical Songbirds. Journal of Experimental Biology 223: doi: 10.1242/jeb.226563. \| Abstract	September 2020	Variation in life history expression is thought to arise from selection acting through physiological mechanisms, but selection pressures may differ or even conflict between life stages. High offspring predation risk can favor fast growth rates among species that may be achieved by faster post-natal metabolic rates. Faster metabolism, on the other hand, may create costs for adults, such that species with low adult mortality rates may be expected to minimize such adult costs through slower metabolism. Thus, mortality at the two different life stages may differentially influence offspring metabolism. We tested these possibilities among 43 songbird species studied on three continents. We found that nest predation risk and adult mortality probability were indeed interactive in their association with offspring metabolic rates across species. Our results provide a rare example of ecological sources of mortality during different life stages being correlated with post-natal metabolic rate as a mechanism underlying offspring growth.
Toews, D.P.L., G.R. Kramer, A.W. Jones, C.L. Brennan, B.E. Cloud, D.E. Andersen, I.J. Lovette, and H. Streby. 2020. Genomic identification of intergeneric hybrids in New World wood-warblers (Aves: Parulidae). Biological Journal of the Linnean Society 131:183–191. doi10.1093/biolinnean/blaa085 \| Publisher Website	July 2020
Todd Zaragoza MI, AJ DuVall, JA Howard, DM Mazurkiewicz, and SJ Converse. 2023. Laying sequence and oceanographic factors affect egg size in Scripps's Murrelets Synthliboramphus scrippsi at Santa Barbara Island. Marine Ornithology 51:1-9.	April 2023
Thurow, R.F., J.T. Peterson, G.L. Chandler, C. M. Moffitt, and T. C. Bjornn. 2020 Concealment of Juvenile Bull Trout in Response to Temperature, Light, and Substrate: Implications for Detection. PloS ONE https://doi.org/10.1371/journal.pone.0237716	September 2020
Thurner SD, SJ Converse, and TA Branch. 2021. Modeling opportunistic exploitation: increased extinction risk when targeting more than one species. Ecological Modelling 454:109611.	August 2021
Thorne, E.D., M.L. Fies and W.M. Ford. 2024. Home-Range Size and Resource Use by Eastern Spotted Skunks in Virginia. Journal of the Southeastern Association of Fish and Wildlife Agencies 11:206–214	May 2024
Thorne, E.D., K.E. Powers, R.J. Reynolds, M.E. Beckner, K.A. Ellis and W.M. Ford. 2022. Comparison of survey methods to maximize detection of a declining rodent, the Allegheny woodrat Neotoma magister, in Virginia. Journal of Fish and Wildlife Management.13:396-406	December 2022
Thorne, E.D., K.E. Powers, R.J. Reynolds, M.E. Beckner, K.A. Ellis and W.M. Ford. 2022. Comparison of survey methods to maximize detection of a declining rodent, the Allegheny woodrat Neotoma magister, in Virginia. Journal of Fish and Wildlife Management.13:396-406	December 2022
Thorne, E.D. and W.M. Ford. 2021. Contemporary *Distribution of the Eastern Spotted Skunk (Spilogale putorius) in Virginia* . Southeastern Naturalist 20:39-51	July 2021
Thompson, T.J., M.A. Briggs, P.J. Phillips, V.S. Blazer, K.L. Smalling, D.W. Kolpin, T. Wagner. 2020. Groundwater discharges as a source of phytoestrogens and other agriculturally derived contaminants to streams. Science of the Total Environment.	October 2020
Thompson, T.J., M.A. Briggs, P.J. Phillips, V.S. Blazer, K.L. Smalling, D.W. Kolpin, T. Wagner. 2020. Groundwater discharges as a source of phytoestrogens and other agriculturally derived contaminants to streams. Science of the Total Environment.	October 2020
Thompson, L. M., A. J. Lynch, E. A. Beever, A. C. Engman, J. A. Falke, S. T. Jackson, T. J. Krabbenhoft, D. J. Lawrence, D. Limpinsel, R. T. Magill, T. A. Melvin, J. M. Morton, R. A. Newman, J. Peterson, M. T. Porath, F. J. Rahel, S. A. Sethi, J. L. Wilkening. 2021. When is resistance futile? Resisting, accepting, or directing ecosystem transformation. Fisheries. 46:8-21. DOI: 10.1002/fsh.10506	January 2021
Thompson, C.J. and J.W. Cain III. 2024. Biological feasibility of introducing bighorn sheep to the Jicarilla Apache Nation. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS–159–2024, Washington, D.C. \| Download	November 2024
Thompson BK, SJ Converse and JD Olden. 2021. Mechanistic invasive species management models and their application in conservation. Conservation Science and Practice 3:e533. \| Abstract	September 2021	Management strategies to address the challenges associated with invasive species are critical for effective conservation. An increasing variety of mathematical models offer insight into invasive populations, and can help managers identify cost effective prevention, control, and eradication actions. Despite this, as model complexity grows, so does the inaccessibility of these tools to conservation practitioners making decisions about management. Here, we seek to narrow the science-practice gap by reviewing invasive species management models (ISMMs). We define ISMMs as mechanistic models used to explore invasive species management strategies, and include reaction-advection-diffusion models, integrodifference equations, gravity models, particle transport models, non-spatial and spatial discrete-time population growth models, cellular automata, and individual-based models. For each approach, we describe the model framework and its implementation, discuss strengths and weaknesses, and give examples of conservation applications. We conclude by discussing how ISMMs can be used in concert with adaptive management to address scientific uncertainties impeding action and with multiple objective decision processes to evaluate tradeoffs among management objectives. We undertook this review to support more effective decision-making involving invasive species by providing conservation practitioners with the information they need to identify tools most useful for their applications.
Thomas-Walters, L., Cologna, V., de Lange, E., Ettinger, J., Selinske, M. & Jones, M.S. (2024). Reframing conservation audiences from individuals to social beings. Conservation Letters. https://doi.org/10.1111/conl.13064 \| Abstract	October 2024	Environmental practitioners often develop communications and behavior change interventions that conceptualize individuals as consumers, or other limited, standalone persona. This view neglects the role of the conservation audiences as social beings with complex social relationships and networks, potentially resulting in lost opportunities to increase the effectiveness of conservation interventions. We offer a reframing of individuals as members of social networks who can influence societal structures through their many different relationships. This framing may help individuals recognize their potential to affect large-scale societal structures and empower them to contribute to systemic changes. In practice, conservation organizations might increase the impact and reach of their behavioral interventions by targeting social referents and leveraging interpersonal relationships. This includes encouraging individuals to make use of their networks to discuss issues such as biodiversity loss with a variety of acquaintances to normalize them as a topic of conversation. We argue that organizations can leverage the power of social networks to amplify change and promote the message that people change the world through their social ties, thereby inspiring audiences to further engage in conservation behaviors.
Themelin, M., C. A. Ribic, K. Melillo-Sweeting, and K. M. Dudzinski. 2020. A new approach to the study of relationship quality in dolphins: framework and preliminary results. Behavioural Processes 181:104260. doi.org/10.1016/j.beproc.2020.104260	December 2020
Tharp, RM, NJ Hostetter, AB Paxton, JC Taylor, JA Buckel. 2024. Artificial structure selection by economically important reef fishes at North Carolina artificial reefs. Frontiers in Marine Science 11:1373494. doi.org/10.3389/fmars.2024.1373494.	April 2024
Tetzlaff, S.J., Sperry, J.H. and DeGregorio, B.A., 2022. You can go your own way: No evidence for social behavior based on kinship or familiarity in captive juvenile box turtles. Applied Animal Behaviour Science, 248, p.105586. \| Download	February 2022
Tetzlaff, S.J., Estrada, A., DeGregorio, B.A. and Sperry, J.H., 2020. Identification of Factors Affecting Predation Risk for Juvenile Turtles Using 3D Printed Models. Animals, 10(2), p.275. \| Download	February 2020
TenHarmsel, H. J., B. B. Boley, B. J. Irwin, and C. A. Jennings. 2021. Perceived constraints and negotiations to trout fishing in Georgia based on angler specialization level. North American Journal of Fisheries Management 41:115-129. doi:10.1002/nafm.10540 \| Abstract	February 2021	Anglers face constraints that influence participation and dropout rates. Some recreational anglers may be able to negotiate constraints by altering the timing or frequency of participation, acquiring new skills, or modifying non-recreational aspects such as family or work responsibilities. We consider data collected via a mail survey from Georgia-resident trout license holders to identify both perceived constraints and strategies used to negotiate them. To capture variation among anglers, survey responses were grouped by level of angler specialization using K-means cluster analysis, which resulted in a three-cluster solution of most, moderate, and least specialized anglers. Analysis of variance (ANOVA) tests were used to detect potential differences among the three specialization clusters. Tests revealed the least specialized anglers experienced constraints more frequently (mean=1.74 on a 4-point scale) than the most (1.55) or moderately (1.64) specialized anglers. Likewise, lease specialized anglers negotiated constraints (mean=2.81 on a 5-point scale) less frequently than the most (3.00) or moderately (2.75) specialized anglers. The least specialized anglers used negotiation strategies involving overcoming perceived lack of skill more frequently than their counterparts. The most commonly experienced constraints overall were lack of time due to work or family obligations and distance of Georgia’s trout waters from home. The most frequently used negotiation strategies overall were “learn to enjoy being outside and stress less about catching fish” (mean=3.86/5) and “encourage family or friends to go fishing with me” (mean=3.61/5). This research benefits fishery managers by providing a method of identifying angling groups that perceive more constraints and are less likely to overcome these constraints through constraint negotiation strategies. With this information, managers may choose to tailor efforts towards reducing constraints for angling groups that have low participation and may drop out of the activity all together.
TenHarmsel, H. J., B. B. Boley, B. J. Irwin, and C. A. Jennings. 2021. Perceived constraints and negotiations to trout fishing in Georgia based on angler specialization level. North American Journal of Fisheries Management 41:115-129. doi:10.1002/nafm.10540 \| Abstract	February 2021	Anglers face constraints that influence participation and dropout rates. Some recreational anglers may be able to negotiate constraints by altering the timing or frequency of participation, acquiring new skills, or modifying non-recreational aspects such as family or work responsibilities. We consider data collected via a mail survey from Georgia-resident trout license holders to identify both perceived constraints and strategies used to negotiate them. To capture variation among anglers, survey responses were grouped by level of angler specialization using K-means cluster analysis, which resulted in a three-cluster solution of most, moderate, and least specialized anglers. Analysis of variance (ANOVA) tests were used to detect potential differences among the three specialization clusters. Tests revealed the least specialized anglers experienced constraints more frequently (mean=1.74 on a 4-point scale) than the most (1.55) or moderately (1.64) specialized anglers. Likewise, lease specialized anglers negotiated constraints (mean=2.81 on a 5-point scale) less frequently than the most (3.00) or moderately (2.75) specialized anglers. The least specialized anglers used negotiation strategies involving overcoming perceived lack of skill more frequently than their counterparts. The most commonly experienced constraints overall were lack of time due to work or family obligations and distance of Georgia’s trout waters from home. The most frequently used negotiation strategies overall were “learn to enjoy being outside and stress less about catching fish” (mean=3.86/5) and “encourage family or friends to go fishing with me” (mean=3.61/5). This research benefits fishery managers by providing a method of identifying angling groups that perceive more constraints and are less likely to overcome these constraints through constraint negotiation strategies. With this information, managers may choose to tailor efforts towards reducing constraints for angling groups that have low participation and may drop out of the activity all together.
Teitelbaum, C.S. (2024). Species diversity links land consolidation to rodent disease. Nature Ecology & Evolution 9:17-18. http://dx.doi.org/10.1038/s41559-024-02584-5	November 2024
Teige, E.C., N.J. Parker, M.P. Vhay, and D.A. Haukos. 2022. Durability and longevity of Tympanuchus pallidicinctus (Lesser Prairie-Chicken) fence tags in Kansas and Colorado. Ecological Restoration 40:83-87. doi:10.3368/er.40.2.83	June 2022
Teige, E.C., L.A. Berigan, C.S.H. Aulicky, J.H. Reitz, D.A. Haukos, D.S. Sullins, K.A. Fricke, K.A. Schultz, and L.G. Rossi. 2023. Assessment of lesser prairie-chicken translocation through survival and lek counts. Wildlife Society Bulletin 2023:e1493.	October 2023
Teige, E. C., L. A. Berigan, C. Aulicky, J. H. Reitz, D. A. Haukos, D. S. Sullins, K. A. Fricke, K. A. Schultz, L. G. Rossi. 2023. Assessment of lesser prairie-chicken translocation through survival and lek surveys. Wildlife Society Bulletin 47:e1493. DOI: 10.1002/wsb.1493.	October 2023
Teal, C.N., Schill, D.J., Bauder, J.M., Fogelson, S.B., Fitzsimmons, K., Stewart, W.T., Culver, M. and Bonar, S.A., 2024. The effects of estradiol‐17β on the sex reversal, survival, and growth of Red Shiner and its use in the development of YY individuals. North American Journal of Aquaculture, 86(1), pp.110-129. https://doi.org/10.1002/naaq.10314	January 2024
Teal, C. N., D. Katharine Coykendall, Matthew R. Campbell, Thomas A. Delomas, Daniel L. Eardley, John A. Erwin, Daniel J. Schill, Javan M. Bauder, Scott A. Bonar and Melanie Culver. 2023. The development of genetic sex identification markers and evidence of a male heterogametic sex determination system in Red Shiner Cyprinella lutrensis. North American Journal of Aquaculture 85:(1)74-86.	October 2022
Teal, C. N., D. J. Schill, S. B. Fogelson, C. M. Roberts, K. Fitzsimmons, J. M. Bauder, W. T. Stewart and S. A. Bonar. 2023. The effects of estradiol-17β on the sex reversal, survival, and growth of green sunfish Lepomis cyanellus. Aquaculture. 562, 738853	January 2023
Teal, C. N., D. J. Schill, S. B. Fogelson, C. M. Roberts, K. Fitzsimmons and S. A. Bonar 2022. Development of Aquaculture Protocols and Gonadal Differentiation of Green Sunfish (Lepomis cyanellus). Aquaculture 547 (2022) 737515	January 2022
Teal, C. N., D. J. Schill, S. B. Fogelson, C. M. Roberts, K. Fitzsimmons and S. A. Bonar 2022. Development of Aquaculture Protocols and Gonadal Differentiation of Green Sunfish (Lepomis cyanellus). Aquaculture 547 (2022) 737515	January 2022
Teal, C. N., D. J. Schill, S. B. Fogelson and S. A. Bonar. 2021. Development of aquaculture protocols and gonadal differentiation of Red Shiner (Cyprinella lutrensis). North American Journal of Aquaculture. Early View.	January 2021
Taylor, W. W., C. P. Ferreri, A. K. Carlson, and A. Bennett. 2020. Preface. In: Lessons in Leadership: Integrating Courage, Vision, and Innovation for the Future of Sustainable Fisheries. American Fisheries Society, Bethesda, Maryland. https://doi.org/10.47886/9781934874608	August 2020
Taylor, W. W., A. K. Carlson, A. Bennett, and C. P. Ferreri, editors. 2020. Lessons in Leadership: Integrating Courage, Vision, and Innovation for the Future of Sustainable Fisheries. American Fisheries Society, Bethesda, Maryland. 418 pages.	August 2020
Taylor, R. B., Mather, M. E., Smith, J. M., Gerber-Boles, K. 2021. Can identifying discrete behavioral groups with individual-based acoustic telemetry advance the understanding of fish distribution patterns? Frontiers in Marine Science (section Global Change and the Future Ocean). https://doi.org/10.3389/fmars.2021.723025 \| Abstract	October 2021	Complex relationships between human and natural ecosystems in human-dominated coastalscapes can be negotiated through science-based, data-driven conservation. To be effective for biodiversity and other issues, however, conservation needs to address processes related to field-based patterns of organismal distribution. Organismal distribution patterns in geographically-large, spatially-heterogeneous, and temporally-dynamic field environments can be challenging to identify using existing approaches. Here we show how dynamic-distribution telemetry data<b> </b>can provide a detailed temporal record of how individuals are distributed that provides new directions for a range of basic and applied questions beyond those issues traditionally explored by telemetry. To illustrate the advantages that accrue from this approach, we explored the connection between discrete groups of coexisting, same-species, same-size individuals and patterns of field distribution. We quantified locations of 59 acoustically-tagged striped bass (<i>Morone saxatilis) </i>within a 26-stationary unit telemetry receiver estuarine array in Plum Island Estuary. We then used cluster analyses on spatial and temporal-spatial metrics from this dataset to (1) assess if distinct groups of individuals coexisted, (2) quantify group characteristics, and (3) test associations between groups and distribution (e.g., physical site types and regions). Four discrete, co-occurring groups of similar-sized, individual striped bass were defined by different patterns of spatio-temporal use of physical habitat types and estuarine regions. Thus, our approach provides a different view of spatial distribution patterns, in a geographic area adjacent to dense human settlements, that has relevance to a wide range of ecological, evolutionary, behavioral, and conservation questions relevant to human-dominated coastalscapes.
Taylor, J.M., N.M. Roberts, and S.M. Crimmins. 2022. Assessing Winter Habitat by River Otters Using Aerial Surveys. Wildlife Society Bulletin 46:e1349 https://doi.org/10.1002/wsb.1349.	September 2022
Taylor, D.A.R., R.W. Perry, W.M. Ford and D.A. Miller. 2020. Bats and forest management. Bat Conservation International, Austin, TX and U.S. Fish and Wildlife Service White-nose Syndrome Program, Hadley, MA. 25 p.	November 2020
Taylor, C., La Peyre MK, Sable S., Kiskadon E, Baustian M. 2020. Gear Comparison Study for Sampling Nekton in Barataria Basin Marshes. 66 pp. https://thewaterinstitute.org/reports	June 2020
Taylor, AT, MR Bangs, and JM. Long. 2021. Sibship reconstruction from single-nucleotide polymorphisms illuminates the scope of a cryptic aquatic species invasion. Biological Invasions 23:569-580. doi:10.1007/s10530-020-02384-5	November 2020
Taylor, A.T., T. Hafen, C.T. Holley, A. Gonzalez, and J.M. Long. 2020. Spatial sampling bias and model complexity in stream-based species distribution models: a case study of Paddlefish (Polyodon spathula) in the Arkansas River basin, U.S.A. Ecology and Evolution 10:705-717. DOI: 10.1002/ece3.5913	January 2020
Taylor, A.T., J.M. Long, R.A. Snow, and M.J. Porta. 2020. Hybridization and population genetics of Alligator Gar in Lake Texoma. North American Journal of Fisheries Management 40:544-554.	June 2020
Taylor, A.T., A.M. Peeper, B. Chapagain, O. Joshi, and J.M. Long. 2022. Modern reporting methods for angler tag-return studies: trends in data quality, choice of method, and future consideration. North American Journal of Fisheries Management 42:189-199. DOI: 10.1002/nafj.10738	January 2022
Taylor, A. T., and J. M. Long. 2022. Assessment of invasion extent of Asian Swamp Eels in ponds and backwater marshes adjacent to the Chattahoochee River, with consideration of management and control strategies. Natural Resource Report NPS/CHAT/NRR—2022/2357. National Park Service, Fort Collins, Colorado.	February 2022
Taylor CB, Nyman JA, La Peyre MK. 2022. Effects of freshwater inflow on nekton assemblages and blue crab, Callinectes sapidus, populations in southeastern Louisiana. Aquatic Biology DOI: https://doi.org/10.3354/ab00748 \| Abstract	January 2022	High fisheries production within estuaries is associated with coastal upwelling, tidal mixing, and land-based runoff including river inflows that vary from climate and human activities. Understanding how estuarine nekton respond to changing river flows remains critical to manage these systems to maintain fisheries production. To compare effects of different river inflows on nekton, we quantified nekton assemblages in marsh edge and open water sites within an active and inactive delta system. Crustaceans dominated assemblages with Palaemonid shrimp contributing 44% to 65% of total catch, differing only by season, and not delta; summer and fall generally supporting higher densities. In contrast, fish density and assemblages differed seasonally between deltas with the largest differences occurring during extended and high spring river discharge into the active delta. During this period, the active delta experienced lowered salinity, temperature, submerged aquatic vegetation (SAV) biomass, and reduced fish densities and richness compared to the inactive delta. Active delta sites supported greater biomass of <i>Callinectes sapidus</i> during the fall at marsh edge sites compared to other season and delta combinations. Nekton densities and habitat use patterns across deltas and seasons reflect a combination of life history characteristics of dominant species and habitat conditions. The high spring river discharge in 2019 impacted habitat availability (reduced SAV biomass), habitat quality (decreased temperatures and salinity), and potentially displaced nekton to un-sampled habitat areas (i.e., interior marsh surface) within the active delta. Understanding how altered inflow impacts environmental and habitat variables supporting estuarine nekton production remains critical to support management.
Tang, Z., Y. Zhang, Y. Wang, Y. Shang, R. Viegut, E. Webb, A. Raedeke and J. Sartwell. Drones and Machine Learning Integration in Waterfowl Population Surveys. Proceedings of the IEEE International Conference on Tools With Artificial Intelligence \| Abstract	December 2021	The rapid technological development of drones has led to an increase in capabilities of aerial image collection and analysis for wildlife monitoring. Historically, wildlife abundance estimates were based on manual counts from the ground or from the air using fix-winged aircraft over the regions, both of which are expensive and potentially dangerous methods. However, drones can help easily collect aerial images with a limited budget and increased flexibility, as it creates less disturbance to the wildlife, allowing us to get closer to the target animals and providing clearer images. In this paper, we propose a new, integrated system of drones and machine learning for waterfowl population surveys, which provides a user-friendly interface for data collection and integrates data post-processing using deep learning methods to detect and count waterfowl automatically. Our system has proved to be an efficient and accurate approach of collecting, analyzing, and providing outputs of waterfowl abundance estimates using drones and machine learning.
Takahashi, F., F. Sanders, and P.G.R. Jodice. 2021. Spatial and Temporal Overlap between Foraging Shorebirds and Spawning Horseshoe Crabs (Limulus polyphemus) in the Cape Romain - Santee Delta Region of the U.S. Atlantic Coast. Wilson Journal of Ornithology. https://doi.org/10.1676/21-00009 \| Download	October 2021
Tabak, Michael A., Norouzzadeh, Mohammad S., Wolfson, David W., Newton, Erica J., Boughton, Raoul K., Ivan, Jacob S., Odell, Eric, Newkirk, Eric S., Conrey, Reesa Y., Stenglein, Jennifer L., Iannarilli, Fabiola, Erb, John, Brook, Ryan K., Davis, Amy J., Lewis, Jesse S., Walsh, Daniel P., Beasley, James C, Vercauteren, Kurt C., Clune, Jeff, Miller, Ryan S. 2020. Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2. Ecology and Evolution 10: 10374-10383. https://doi.org/10.1002/ece3.6692	January 2020
T Mitchell, B Folt, J Hall. 2021. Dumpsters and other anthropogenic structures as habitat for invasive African rock agama lizards in Florida. Biological Invasions 23: 2689–2693. https://doi.org/10.1007/s10530-021-02537-0	April 2021
Şen, B., C. Che-Castaldo and H. R. Akçakaya. 2024. The potential for species distribution models to distinguish source populations from sinks. Journal of Animal Ecology, 00:1–11. https://doi.org/10.1111/1365- 2656.14201 \| Abstract \| Download \| Publisher Website	October 2024	1. While species distribution models (SDM) are frequently used to predict species occurrences to help inform conservation management, there is limited evidence evaluating whether habitat suitability can reliably predict intrinsic growth rates or distinguish source populations from sinks. Filling this knowledge gap is criti- cal for conservation science, as applications of SDMs for management purposes ultimately depend on these typically unobserved population or metapopulation dynamics.<br><br>2. Using linear regression, we associated previously published population level es- timates of intrinsic growth and abundance derived from a Bayesian analysis of mark-recapture data for 17 bird species found in the contiguous United States with SDM habitat suitability estimates fitted here to opportunistic data for these same species. We then used the area under the ROC curve (AUC) to measure how well SDMs can distinguish populations categorized as sources and sinks. We built SDMs using two different approaches, boosted regression trees (BRT) and generalized linear models (GLM), and compared their source/sink predictive per- formance. Each SDM was built with presence points obtained from eBird (a web- available database) and 10 environmental variables previously selected to model intrinsic growth rates and abundance for these species.<br><br>3. We show that SDMs built with opportunistic data are poor predictors of species demography in general; both BRT and GLM explained very little spatial variation of intrinsic growth rate and population abundance (median R2 across 17 species was close to 0.1 for both SDM methods). SDMs, however, estimated higher suit- ability for source populations as compared to sinks. Out of 13 species which had both source and sink populations, both BRT and GLM had AUC values greater than 0.7 for 7 species when discriminating between sources and sinks.<br><br>4. Habitat suitability have the potential to be a useful measure to indicate a popula- tion's ability to sustain itself as a source population; however more research on a diverse set of taxa is essential to fully explore this potential. This interpreta- tion of habitat suitability can be particularly useful for conservation practice, and identification of explicit cases of when and how SDMs fail to match population demography can be informative for advancing ecological theory.
Sévêque, A., R. C. Lonsinger, L. P. Waits, K. E. Brzeski, L. M. Komoroske, C. N. Ott-Conn, S. L. Mayhew, D. C. Norton, T. R. Petroelje, J. D. Swenson, and D. J. Morin. In Review. Sources of bias in applying close-kin mark–recapture to terrestrial game species with different life histories. Ecology. https://doi.org/10.1002/ecy.4244 \| Abstract	January 2024	1. Close-kin mark–recapture (CKMR) is a method analogous to traditional mark–recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify proportions of related individuals detected in a single sampling occasion. An advantage of this novel method is that it enables the opportunistic use of samples from harvested wildlife. While the CKMR framework is mathematically straightforward, meeting key model assumptions is required to yield reliable results. Thus, it is important to explore the strengths and limitations of this emerging method under a range of scenarios to reveal potential obstacles and evaluate implications of violating model assumptions.<br>2. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among long-lived game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. We conclude with a simulated example using a harvested Michigan black bear <i>Ursus americanus</i> population.<br>3. Our simulations show that CKMR can yield non-trivial biases in both survival and abundance estimates if deviations from the core assumptions are not explicitly incorporated in the modeling framework. The number of related kin pairs observed in the sample, in combination with the type of close kin estimator used (parent-offspring pairs or half-sibling pairs), can affect the precision and accuracy of the estimates. The Michigan black bear population exemplifies our findings, with biases in estimated population abundance ranging from -12% to +99%.<br>4. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analyses continue to decline. However, our work highlights the importance of evaluating and accounting for all relevant parameters linked to the species of interest and the protocol through which individuals were sampled. Population simulations will be key to developing and validating increasingly complex models and making CKMR applicable to a greater number of species and systems.
Syslo, J. M., T. O. Brenden, C. S. Guy, T. M. Koel, P. E. Bigelow, P. D. Doepke, J. L. Arnold, and B. E. Ertel. 2020. Could ecological release buffer suppression efforts for non-native lake trout (Salvelinus namaycush) in Yellowstone Lake, Yellowstone National Park? Canadian Journal of Fisheries and Aquatic Sciences 77:1010-1025.	June 2020
Sweka, J.A. and T. Wagner. 2021. Influence of seasonal extreme flows on Brook Trout recruitment. Transactions of the American Fisheries Society. https://doi.org/10.1002/tafs.10347	December 2021
Sweet, A.D., R. Wilson, J. Reakoff, S. Sonsthagen, C. Hurst, and S. Pirro. The Complete Genome Sequence of Splendidofilaria pectoralis (Onchocercidae, Rhabditida, Chromadorea, Nematoda). Biodiversity Genomes. doi: 10.56179/001c.126786	December 2024
Sweet, A. D., R. E. Wilson, S. A. Sonsthagen, and K. P. Johnson. 2020. Lousy grouse: Comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions. Ecology and Evolution. 10:8379–8393.	July 2020
Swedberg, D., R. Mollenhauer, and S. K. Brewer. 2023. Factors driving spring associated species in naturally isolated ecoregions. Ecology and Evolution 13, e10701. https://doi.org/10.1002/ece3.10701	December 2023
Swearingen, T.C., Klaver, R.W., Anderson, C.R. and Jacques, C.N. (2023). Influence of camera model and alignment on the performance of paired camera stations. Wildlife Society Bulletin, 47(2). doi:https://doi.org/10.1002/wsb.1422.	November 2022
Swam LM, La Peyre MK, Couvillion B, Callam B, La Peyre JF. 2022 Defining oyster resource zones across coastal Louisiana for restoration and aquaculture. Ocean and Coastal Management \| Abstract	April 2022	Eastern oysters (<i>Crassostrea virginica</i>) are a critical ecological and commercial resource in the northern Gulf of Mexico facing changing environmental conditions from river management and climate change. In Louisiana, USA, development of restored reefs, and off-bottom aquaculture would benefit from the identification of locations supportive of sustainable oyster populations (<i>i.e.,</i> metapopulations) and high consistent production. This study defines four oyster resource zones across coastal Louisiana based on environmental conditions known to affect oyster survival, growth, and reproduction. Daily data from 2015 – 2019 were interpolated to generate salinity and temperature profiles across Louisiana’s estuaries, which were then used to classify zones based on monthly and annual salinity mean and variance. Zones were classified as supportive of (1) broodstock sanctuary reefs (i.e., support reproductive populations), (2) productive reefs during dry (salty) years, (3) productive reefs during wet (fresh) years, and (4) off-bottom aquaculture development. Of the 38,000 km<sup>2</sup> investigated, over 11,000 km<sup>2</sup> of potential oyster zone area was identified across the Louisiana coast. The Broodstock Sanctuary Zone was the smallest (~540 km<sup>2</sup>), as salinity variance limited this zone in many areas, as it is driven largely by riverine inputs across many estuaries. Located up-estuary (Dry Restoration Zone) and down-estuary (Wet Restoration Zone) of the Broodstock Sanctuary Zone, Dry and Wet Restoration Zone areas covered ~2,400 km<sup>2</sup> and ~3,900 km<sup>2</sup>, respectively. Existing mapped reefs in Louisiana currently exist largely within the Dry Restoration zones, suggesting a potential strategy to focus reef development in Wet Restoration zones to ensure reef network sustainability through years with high precipitation and river inflow. The off-bottom Aquaculture Zone was the largest (~6,400 km<sup>2</sup>) zone identified, with much of this area located more down-estuary and off-shore. Accounting for variable water quality conditions enables the development of a network of reefs resilient to environmental variability, and more stable areas for consistent off-bottom aquaculture production. Spatial planning and identification of oyster resource zones reduces focus on individual reef success and supports management of oyster metapopulation outcomes, while identifying zones supportive of off-bottom aquaculture.
Swam L, Marshall D, La Peyre MK. 2022. Five years of monitoring of bio-engineered living shoreline oyster reef development. Cooperator Science Series 139-2022.	February 2022
Swam L, La Peyre MK, Callam B, La Peyre JF. 2022 Local populations of eastern oyster from Louisiana differ in their tolerance to low salinity. North American Journal of Aquaculture. \| Abstract	July 2022	Eastern oysters support a critical commercial industry and provide many ecosystem services to coastal estuaries yet are currently threatened by changing estuarine conditions. A changing climate alongside river and coastal management strategies are affecting freshwater inflows into productive oyster areas, causing more frequent and extreme salinity exposure. Although oysters are tolerant to a wide range of salinity means and variation, more frequent and extreme exposure to low salinity (< 5) impacts oyster populations and aquaculture operations. This study assessed four Louisiana, USA oyster stocks to explore population-specific responses to low salinity exposure. Hatchery-produced progeny (< 25 mm) were deployed in baskets kept off-bottom on longline systems in a low salinity (mean ± 1 SEM daily salinity of 8.7 ± 0.2, ranging 1.2 – 19.0) and a moderate salinity (mean ± 1 SEM daily salinity of 16.8 ± 0.3, ranging 4.8 – 30.0) environment for one year with growth and mortality determined monthly. Significant differences in cumulative mortality between stocks at the end of the study were found at the low salinity site, with the greatest increase in cumulative mortality occurring mid-July to mid-August. Mortality differences between stocks suggest that discrete oyster populations may be better suited to low salinity or low salinity events than others. This difference may be attributed to similarity between site of origin and grow out site conditions and/or to greater salinity variability and therefore higher phenotypic plasticity in some oyster populations compared to others. The identification of oyster stocks able to survive under extreme low salinity conditions would facilitate the development of “low salinity tolerant” broodstock to support aquaculture in areas experiencing and predicted to experience low salinity events.
Suraci, Justin P., et al. "Disturbance type and species life history predict mammal responses to humans." Global change biology 27.16 (2021): 3718-3731. \| Abstract	August 2021	Human activity and land use change impact every landscape on Earth, driving declines in many animal species while benefiting others. Species ecological and life history traits may predict success in human-dominated landscapes such that only species with “winning” combinations of traits will persist in disturbed environments. However, this link between species traits and successful coexistence with humans remains obscured by the complexity of anthropogenic disturbances and variability among study systems. We compiled detection data for 24 mammal species from 61 populations across North America to quantify the effects of (1) the direct presence of people and (2) the human footprint (landscape modification) on mammal occurrence and activity levels. Thirty-three percent of mammal species exhibited a net negative response (i.e., reduced occurrence or activity) to increasing human presence and/or footprint across populations, whereas 58% of species were positively associated with increasing disturbance. However, apparent benefits of human presence and footprint tended to decrease or disappear at higher disturbance levels, indicative of thresholds in mammal species’ capacity to tolerate disturbance or exploit human-dominated landscapes. Species ecological and life history traits were strong predictors of their responses to human footprint, with increasing footprint favoring smaller, less carnivorous, faster-reproducing species. The positive and negative effects of human presence were distributed more randomly with respect to species trait values, with apparent winners and losers across a range of body sizes and dietary guilds. Differential responses by some species to human presence and human footprint highlight the importance of considering these two forms of human disturbance separately when estimating anthropogenic impacts on wildlife. Our approach provides insights into the complex mechanisms through which human activities shape mammal communities globally, revealing the drivers of the loss of larger predators in human-modified landscapes.
Sun, C.C., J.E. Hurst, and A.K. Fuller. 2021. Citizen science data collection for integrated wildlife population analyses. Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2021.682124	June 2021
Sullivan, L., Jones, M. S., Jimenez, M. F., Dodgson, K. R., & Storrs, E. L. (2022). Justice discourses in the mainstream environmental movement, 30 years after the SWOP letter. Environmental Justice. https://doi.org/10.1089/env.2022.0025 \| Abstract \| Publisher Website	November 2022	Calls for the mainstream environmental movement to engage more closely with the work of social justice have been pervasive for over three decades, marked by demands for large environmental organizations to diversify their staff and center the voices of those living in frontline communities. These calls, first made prominent by the Southwest Organizing Project (SWOP) in 1990, have grown in intensity in recent years as rampant inequalities compound environmental crises, illustrating that environmental protection cannot be decoupled from social justice. In this paper, we draw on public statements released by large environmental organizations in the wake of the 2020 Black Lives Matter protests to examine how their use of language around racial and social justice today reflects early calls for the environmental movement to address its own problematic legacies and align its aims with the work of environmental justice. Our findings suggest that organizations are leaning into four distinct discourses around justice that evoke ideas of <i>solidarity, heroism, internal reform, and redress of problematic legacies</i>, but also indicate a relative lack of attention to ideological or structural change within the movement. We explore the historical context of these findings, paying particular attention to the ways in which the neoliberalization of the non-profit sector over the last 30 years may have limited opportunities for more emancipatory discourses to emerge. We conclude with a call for mainstream environmental organizations to revisit the SWOP letter and explore new ways to couple internal cultural change with deeper institutional reform.
Sullivan, C.J., K.E. Whitlock, J.F. Hansen, and D.A. Isermann. 2020. Assessing the potential to mitigate climate-related expansion of largemouth bass populations using angler harvest. Canadian Journal of Fisheries and Aquatic Sciences 77:520-533. https://doi.org/10.1139/cjfas-2019-0035	January 2020
Sullivan, C. J., M. J. Weber, C. L. Pierce, and C. A. Camacho. A comparison of Grass Carp (Ctenopharyngodon idella) population characteristics upstream and downstream of Lock and Dam 19 of the Upper Mississippi River. Journal of Fish and Wildlife Management 11(1):99-111. https://doi.org/10.3996/062019-JFWM-046.	June 2020
Sullins, D.S., D. A. Haukos, J. D. Kraft, J. M. Lautenbach, J. D. Lautenbach, R. T. Plumb, S. G. Robinson, J. M. Shawn Hutchinson, M. B. Rice, and B. K. Sandercock. 2019. Strategic regional conservation for lesser prairie-chickens among landscapes of varying anthropogenic influence. Biological Conservation 238:108213. (Shortlisted for The Wildlife Society's best journal article of 2020)	December 2021
Sullins, D. S., W. C. Conway, D. A. Haukos, and C. E. Comer. 2019. Using pointing dogs and hierarchical models to evaluate American woodcock winter habitat. Proceedings of the American Woodcock Symposium 11:154–167. No DOI available.	October 2020
Sullins, D. S., M. Bogaerts, B. H. F. Verheijen, D. E. Naugle, T. Griffiths, and C. A. Hagen. 2021. Increasing durability of voluntary conservation through strategic implementation of the Conservation Reserve Program. Biological Conservation 259:109177. DOI: 10.1016/j.biocon.2021.109177	November 2022
Suarez B & TB Grabowski. 2021. Estimating detection and occupancy coefficients for the Pacific Islands coral reef fish species. Hawaii Cooperative Fishery Research Unit Technical Report Series HCFRU-001. University of Hawaii at Hilo. Available online at: hdl.handle.net/10790/5553 \| Abstract \| Download \| Publisher Website	January 2021	The data-limited stock assessment models used to monitor the status of coral reef fish species in the Western Pacific region are dependent upon accurate estimates of standing stock biomass generated from underwater visual surveys of reefs. However, the imperfect detection of and variable occupancy of habitat by reef fishes are not currently accounted for in these estimates. Therefore, the objective of this project was to estimate detection and occupancy coefficients for the species listed in the Western Pacific Regional Fishery Management Council’s Fishery Ecosystem Plans by analyzing the Pacific Island Fishery Science Center-Coral Reef Ecosystem Program Reef Fish Dataset. These detection and occupancy coefficients would then be applied to refine standing stock biomass estimates. In general, species with higher detection probabilities and/or lower occupancy rates tended to exhibit the greatest differences in the estimates of standing stock biomass calculated with and without accounting for detection and occupancy. The standing stock biomass of most reef fish species seem to be underestimated when detection and occupancy are not accounted for. However, the standing stock biomass of larger-bodied targeted species, such as jacks, snappers, and groupers, seem to be over-estimated relative to the estimates generated when accounting for occupancy and detection. Based on the re-estimated standing stock biomass. While there are still issues to resolve regarding how well the current data collection methods meet the underlying assumptions of the detection and occupancy modeling approach, the inclusion of detection and occupancy coefficients seems likely to improve estimates of standing stock biomass of coral reef fish species.
Stuber, EF, BC Carlson, and B Jesmer. 2022. Many avenues for spatial personality research: a response to comments on Stuber et al. 2022. Behavioral Ecology 33(3): 492-3 DOI: 10.1093/beheco/arac018 \| Abstract	June 2022	NA
Stuber, E.F., O. Robinson, E.R. Bjerre, M.C. Otto, B.A. Millsap, G.S. Zimmerman, M. G. Brasher, K. M. Ringelman, A.M.V. Fournier, A. Yetter, J.E. Isola, V. Ruiz-Gutierrez. The potential of semi-structured citizen science data as a supplement for conservation decision-making: Validating the performance of eBird against targeted avian monitoring efforts. 270, p.109556. https://doi.org/10.1016/j.biocon.2022.109556	June 2022
Stuber, E.F., Gruber, L.F. 2020. Recent Methodological Solutions to Identifying Scales of Effect in Multi-scale Modeling. Current Landscape Ecology Reports 5, 127–139. https://doi.org/10.1007/s40823-020-00055-8	January 2020
Stuber, E., B. Carlson, and B. Jesmer. Spatial Personalities: a meta-analysis of consistent individual differences in spatial behavior. Behavioral Ecology. 33(3): 477-86. DOI: 10.1093/beheco/arab147 \| Abstract	June 2022	Individual variation in behavior, particularly consistent among-individual differences (i.e., personality), has important ecological and evolutionary implications for population and community dynamics, trait divergence, and patterns of speciation. Nevertheless, individual variation in spatial behaviors, such as home range behavior, movement characteristics, or habitat use has yet to be incorporated into the concepts or methodologies of ecology and evolutionary biology. To evaluate evidence for the existence of consistent among-individual differences in spatial behavior – which we refer to as “spatial personality” – we performed a meta-analysis of 200 repeatability estimates of home range size, movement metrics, and habitat use. We found that the existence of spatial personality is a general phenomenon, with consistently high repeatability (r) across classes of spatial behavior (r = 0.67 - 0.82), taxa (r = 0.31 - 0.79), and time between repeated measurements (r = 0.54 - 0.74). These results suggest: (1) repeatable spatial behavior may either be a cause or consequence of the environment experienced and lead to spatial personalities that may limit the ability of individuals to behaviorally adapt to changing landscapes; (2) interactions between spatial phenotypes and environmental conditions could result in differential reproduction, survival, and dispersal, suggesting that among-individual variation may facilitate population-level adaptation; (3) spatial patterns of species’ distributions and spatial population dynamics may be better understood by shifting from a mean field analytical approach towards methods that account for spatial personalities and their associated fitness and ecological dynamics.
Strickfaden, K.M., M.L. Behan, A.M. Marshall, L.K. Svancara, D.E. Ausband, and T. Link. 2023. Virtual snow stakes: a new method for snow depth measurement at remote camera stations. Wildlife Society Bulletin. 47: e1481. \| Abstract	August 2023	Remote cameras are used to study demographics, ecological processes, and behavior of wildlife populations. Cameras have also been used to measure snow depth with physical snow stakes. However, concerns that physical instruments at camera sites may influence animal behavior limit installation of instruments to facilitate collecting such data. Given that snow depth data are inherently contained within images, potential insights that could be made using these data are lost. To facilitate camera‐based snow depth observations without additional equipment installation, we developed a method implemented in an R package called edger to superimpose virtual measurement devices onto images. The virtual snow stakes can be used to derive snow depth measurements. We validated the method for snow depth estimation using camera data from Latah County, Idaho, USA in winter 2020–2021. Mean bias error between the virtual snow stake and a physical snow stake was 5.8 cm; the mean absolute bias error was 8.8 cm. The mean Nash Sutcliffe Efficiency score comparing the fit of the 2 sets of measurements within each camera was 0.748, indicating good agreement. The edger package provides researchers with a means to take critical measurements for ecological studies without the use of physical objects that could alter animal behavior, and snow data at finer scales can complement other snow data sources that have coarser spatial and temporal resolution.
Strickfaden, K.M., A. Marshall, L. Svancara, D.E. Ausband, and T. Link. 2023. Identifying snow refugia in complex forested terrain using camera data. Environmental Research Letters. 18:044014. https://doi.org/10.1088/1748-9326/acbb90. \| Abstract	March 2023	Knowledge of snow cover properties on fine scales is imperative both for estimation of hydrologic processes and for habitat management for wildlife species that rely on snow cover. Identification of snow refugia, or places with relatively late snow disappearance dates compared to surrounding areas, are especially important as climate change continues to alter snow cover timing and duration. However, many snow data products are either too coarse-scale to capture variations in snow cover or are too expensive or logistically challenging to collect over broad spatial extents. The purpose of this study was to use remote cameras to collect snow data at fine spatial and temporal scales in a complex forested terrain for the identification of snow refugia. We built generalized linear models to relate the snow disappearance dates (SDDs) at the camera sites to their topographic and vegetation characteristics. We built a model to describe SDDs of camera sites which contained elevation, aspect, and an interaction between canopy cover and cold-air pooling potential. This model could predict SDDs to within 2 weeks and to within 1 week of true SDD for 93% and 71% of the camera sites, respectively. This model contains only data which are readily available as spatially distributed datasets, which allowed for mapping of SDDs across the entire study site. This model and map can be used to guide forest management for the retention of snow, increase the accuracy of hydrologic models, and inform habitat management for snow-dependent wildlife species.
Streker, R.A., J.S. Lamb, J. Dindo, and P.G.R. Jodice. 2021. Fine-scale weather patterns drive reproductive success in the Brown Pelican. Waterbirds 44:153-166. \| Download	January 2022
Stratton, M.E., Finkle, H., Falke, J.A., and P.A.H. Westley.Tracking adult Coho Salmon (Oncorhynchus kisutch) to investigate the presence of stock structure and extent of premature migration in the Buskin River Watershed, Alaska. North American Journal of Fisheries Management.	July 2021
Stout, J.B., M.M. Conner, P. Budy, P. Mackinnon, and M. McKinstry. 2020. Keeping it classy: Classification of live fish and ghost PIT tags detected with a mobile PIT tag interrogation system using an innovative analytical approach. Canadian Journal of Fisheries and Aquatic Sciences 77:1564-1573. \| Abstract	June 2020	The ability of PIT tag data to improve demographic parameter estimates has led to the rapid advancement of PIT tag systems. However, ghost tags create uncertainty about detected tag status (i.e. live fish or ghost tag) when using mobile interrogation systems. We developed a method to differentiate between live fish and ghost tags using a random forest classification model with a novel data input structure based on known fate PIT tag detections in the San Juan River, NM, CO, and UT, USA. We used our model to classify detected tags with an overall error rate of 6.8% (1.6% ghost tags error rate and 21.8% live fish error rate). The important variables for classification were related to distance moved and response to flood flows; however, habitat variables did not appear to influence model accuracy. Our results and approach allow the use of mobile detection data with confidence and allow for greater accuracy in movement, distribution, and habitat use studies, potentially helping identify influential management actions improving our ability to conserve and recover endangered fish.
Stoczynski, L., Scott, M. C., Bower, L., & Peoples, B. Effects of environment and metacommunity delineation on multiple dimensions of stream fish beta diversity. Frontiers in Ecology and Evolution, 11, 182. \| Abstract	March 2023	In a metacommunity context, beta diversity is driven by the interplay between abiotic factors and dispersal as represented by spatial distance among communities. Most existing studies have considered only ‘natural’ abiotic factors and have ignored anthropogenic factors such as land cover change and pollution. Most studies have focused only on taxonomic beta diversity, and few have considered functional or phylogenetic beta diversity. Including anthropogenic factors and multiple dimensions of biodiversity may explain additional variation in beta diversity, providing new insight into how metacommunities are structured across the landscape. In this study, we used a 350 site stream fish abundance dataset from South Carolina, USA to quantify variation in beta diversity explainable by dispersal, as well as natural and anthropogenic abiotic variables. We investigated metacommunity drivers along three spatial delineations by breaking up the dataset into a metacommunity at the whole state level, two geomorphologically distinct metacommunities of the upstate and lowlands, and four natural watershed metacommunities. Within each of these metacommunities we calculated taxonomic, functional, and phylogenetic beta diversity and used variation partitioning to determine explained variation. We explained 25-81% of beta diversity for stream fish metacommunities. We observed differing importance of spatial, natural, or anthropogenic factors based on the spatial delineation and diversity dimension. We detected distinct structuring of stream fish communities in South Carolina occurring between the upstate and the lowlands. When accounting for the geomorphic differences the fall line creates, we observed a significant anthropogenic signal in the upstate and lowland metacommunities. Spatial, environmental, and anthropogenic factors explained slightly more variation in beta diversity for the taxonomic dimension compared to the functional and phylogenetic dimensions. Our study highlights the importance of including anthropogenic factors when trying to determine mechanisms for stream fish community structure and the significance of spatial delineation in how researchers interpret their results.
Stock, B.C., Heppell, S. A., Waterhouse, L., Dove, I. C., Pattengill-Semmens, C. V., McCoy, C. M., Bush, P. G., Ebanks-Petrie, G., and B. X. Semmens. 2021. Pulse recruitment and recovery of Cayman Islands Nassau Grouper (Epinephelus striatus) spawning aggregations revealed by in situ length-frequency data. ICES Journal of Marine Science 78(1): 277-292. https://doi.org/10.1093/icesjms/fsaa221 \| Abstract \| Publisher Website	January 2021	Fish spawning aggregations (FSAs) are vulnerable to overexploitation, yet quantitative assessments of FSA populations are rare. We document an approach for how to conduct such an assessment, evaluating the response of Critically Endangered Nassau Grouper (<i>Epinephelus striatus</i>) to protections in the Cayman Islands. We assessed pre-protection status on all islands using length data from fishery catch. We then used 17 years of noninvasive length-frequency data, collected via diver-operated laser calipers, to estimate recruitment and spawning biomass of Nassau Grouper on Little Cayman following protection. Bimodal length distributions in 2017–2019 indicated a large recruitment pulse (4–8× average) derived from spawning in 2011. Biomass recovered to 90–106% of the pre-exploitation level after 16 years, largely driven by the strong 2011 year class. Length distributions were also bimodal in 2017–2019 on nearby Cayman Brac, implying a synchronous recruitment pulse occurred on both islands. Our results demonstrate that: (i) <i>in situ</i> length data can be used to monitor protected FSAs; (ii) spatiotemporal FSA closures can be effective, but success takes time if population recovery depends upon sporadic recruitment; and (iii) FSA fishery management targets may need to be higher than commonly recommended (i.e. spawning potential ratio >0.6 instead of 0.4).
Stillman, A.N., P.E. Howell, G.S. Zimmerman, E.R. Bjerre, B.A. Millsap, O.J. Robinson, D. Fink, E.F. Stuber, V. Ruiz-Gutierrez. Leveraging the strengths of citizen science and structured surveys to achieve scalable inference on population size.	November 2023
Stiller, J.C., W.F. Siemer, K.A. Perkins, and A.K. Fuller. 2022. Choosing an optimal duck season: Integrating hunter values and duck abundance. Wildlife Society Bulletin. https://doi.org/10.1002/wsb.1313 \| Abstract	June 2022	State wildlife agencies have long struggled to identify optimal hunting season dates for migratory game bird species that meet the diverse and often competing interests of stakeholders. Many approaches have been used to ensure the regulated community is involved in the decision-making process, including public hearings, hunter season-date preference surveys, and hunter task forces or committees. Although these approaches include portions of the regulated community (i.e., typically the most avid) they may not necessarily reflect the opinions and values of all stakeholders. Additionally, these approaches rely heavily on limited anecdotal observations that may be unduly influenced by hunter avidity (e.g. days spent afield), hunter density, species preferences, and property access. To address these challenges, we used a structured decision-making framework that included a duck hunter survey to elucidate values of a representative sample of the regulated community in each duck hunting zone in New York State. Rather than asking duck hunters about their specific duck hunting season date preferences, we asked them to rank 6 objectives describing what they value in their hunting experience (e.g., maximizing the opportunity to see mallards [<i>Anas platyrhynchos</i>] and black duck [<i>Anas rubripes</i>], maximizing the number of weekend days, etc.). Four of the 6 objectives described duck species availability (i.e., abundance or immigration). We used spatiotemporal abundance models derived from eBird citizen science data to estimate abundance and immigration rates of ducks in each waterfowl zone. We evaluated up to 9 unique season date alternatives developed by duck hunter task forces to determine which season date alternative best satisfied the competing objectives of duck hunters in each zone. The approach we developed allowed for selection of optimal duck hunting season dates and successfully involved avid duck hunters in the development stages, while ensuring that the values of a representative sample of all stakeholders were directly considered through a clear and transparent decision-making process.
Stewart, D.R., T. Hafen, D.A. Hendrickson, A.T. Taylor, A. Varela-Romero, D.H. Mason, J.C. Dysthe, T.W. Franklin, M.K. Young, K.S. McKelvey, M.K. Schwartz, and J.M. Long. 2024. Development and application of environmental DNA (eDNA) markers to assess factors affecting occupancy of the endangered Yaqui Catfish and non-native Channel Catfish in the Yaqui River basin, Mexico. Endangered Species Research 53:569-586. https://doi.org/10.3354/esr01320	April 2024
Stewart, D. R., K. M. Broms, K. G. Gerow, M. A. Allen, and M. C. Quist. 2024. Statistical analysis. Pages 285-338 in S. Bonar, N. Mercado-Silva, and K. Pope, editors. Standard methods for sampling North American freshwater fishes, second edition. American Fisheries Society, Bethesda, Maryland.	September 2024
Stevens, J.N., C.E. Barshinger, J.J. Spurgeon, M.A. Eggleton, and S.E. Lochmann. 2024. Comparison of two otolith processing methods for Silver Carp age estimation. Journal of the Southeastern Association of Fish and Wildlife Agencies. \| Abstract	April 2024	Accurate age estimates are critical in the development, implementation, and assessment of silver carp (<i>Hypophthalmichthys molitrix</i>) management plans. Lapilli otoliths are the most commonly used hard structures for silver carp age estimation, though data regarding the precision of two established preparation methods (i.e., grind-and-burn, thin-section) are lacking. To compare the two methods, we assessed within-reader, between-reader, and between-method precision for 125 silver carp collected from six rivers throughout the Lower Mississippi River Basin (Arkansas, Cache, Mississippi, St. Francis, White, and Yazoo). Additionally, we compared the effort and material costs associated with each method. Overall, the grind-and-burn method (mean age ± SE = 5.97 ± 0.18 years) resulted in younger estimated ages than the thin-section method (mean age ± SE = 6.90 ± 0.18 years), particularly in older individuals. The thin-section method (average coefficient of variation = 7.964) displayed slightly greater between-reader precision than the grind-and-burn method (average coefficient of variation = 8.072), but raw data plots revealed lower precision at older ages relative to younger ages. This discrepancy between methods may be a result of misidentification of annuli near the otolith margin as both readers reported that sectioned otoliths offered clearer views than burned and ground otoliths. Processing times and material costs were similar for the two methods and are likely not limiting when choosing an aging protocol. Our results indicate that managers may be able to use the grind-and-burn method to estimate silver carp age in younger populations where older fish are uncommon. However, the thin-section method for silver carp age estimation may lead to less biased age estimates for established populations with greater abundances of older individuals.
Stevens, B. S., and C. J. Conway. 2021. Mapping habitat quality and threats for eastern black rails. Waterbirds 44:245-256.	October 2021
Stevens, B. S., and C. J. Conway. 2020. Mapping habitat suitability at range-wide scales: spatially-explicit distribution models to inform conservation and research for marsh birds. Conservation Science and Practice 2:e178. doi: 10.1111/csp2.178	February 2020
Stevens, B. S., S. B. Roberts, C. J. Conway, and D. K. Englestead. 2023. Effects of large-scale disturbance on animal space use: Functional responses by sage-grouse after megafire. Ecology and Evolution 13:ece3.9933.	April 2023
Stevens, B. S., C. J. Conway, K. Sawyer, and L. Kershek. 2024. Developing a range-wide sampling framework for endangered species: a case study with light-footed Ridgway’s rail. Biodiversity and Conservation 33:3703-3726. 10.1007/s10531-024-02919-5	August 2024
Stevens, B. S., C. J. Conway, K. Luke, A. Weldon, C. Hand, A. Schwarzer, F. Smith, C. Watson, and B. D. Watts. 2022. Large-scale distribution models for optimal prediction of Eastern black rail habitat within tidal ecosystems. Global Ecology and Conservation 38:e02222.	July 2022
Stevens, B. S., C. J. Conway, J. M. Knetter, S. B. Roberts, and P. Donnelly. 2023. Multi-scale effects of land cover, weather, and fire on Columbian sharp-tailed grouse. Journal of Wildlife Management 87:e22349. https://doi.org/10.1002/jwmg.22349	January 2023
Stevens, B. S., C. J. Conway, C. Tisdale, K. Denny, A. Meyers, and P. Makela. 2023. Backpack satellite transmitters reduce survival but not nesting propensity or success of greater sage-grouse. Ecology and Evolution 13:e10820.	December 2023
Sterrett, S., A. Roy, P. Hazelton, B. Swartz, E. Nedeau, J. Carmignani, and A. Skorupa. 2022. Standard Operating Protocol for Mark and Recapture Monitoring of Brook Floater in Streams. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-142-2022, Washington, D. C. https://doi.org/10.3996/css67282137 \| Publisher Website	July 2022
Sterling, E., Sigouin, A., Betley, E., Zavaleta Cheek, J., Solomon, J., Landrigan, K., . . . Jones, M. (2021). The state of capacity development evaluation in biodiversity conservation and natural resource management. Oryx, 1-12. doi:10.1017/S0030605321000570 \| Abstract \| Publisher Website	December 2021	Capacity development is critical to long-term conservation success, yet we lack a robust and rigorous understanding of how well its effects are being evaluated. A comprehensive summary of who is monitoring and evaluating capacity development interventions, what is being evaluated and how, would help in the development of evidence-based guidance to inform design and implementation decisions for future capacity development interventions and evaluations of their effectiveness. We built an evidence map by reviewing peer-reviewed and grey literature published since 2000, to identify case studies evaluating capacity development interventions in biodiversity conservation and natural resource management. We used inductive and deductive approaches to develop a coding strategy for studies that met our criteria, extracting data on the type of capacity development intervention, evaluation methods, data and analysis types, categories of outputs and outcomes assessed, and whether the study had a clear causal model and/or used a systems approach. We found that almost all studies assessed multiple outcome types: most frequent was change in knowledge, followed by behaviour, then attitude. Few studies evaluated conservation outcomes. Less than half included an explicit causal model linking interventions to expected outcomes. Half of the studies considered external factors that could influence the efficacy of the capacity development intervention, and few used an explicit systems approach. We used framework synthesis to situate our evidence map within the broader literature on capacity development evaluation. Our evidence map (including a visual heat map) highlights areas of low and high representation in investment in research on the evaluation of capacity development.
Stephenson, M.D., L.A Schulte, R. W. Klaver, and J. Niemi. 2021. Miniature temperature data loggers increase precision and reduce bias when estimating the daily survival rate for bird nests. Journal of Field Ornithology 92:492-505 \| Abstract \| Download	November 2021	Demographic studies of many bird species are challenging because their nests are cryptic, resulting in few nests being found. To maximize statistical power, methods are needed that minimize disturbance while yielding as much information per nest as possible. One way to meet these objectives is to use miniature thermal data loggers to precisely date nest fates. Our objectives, therefore, were to (1) examine the possible effect of thermal data loggers on nest success through hatching by grass- and shrub-nesting songbirds that differed in their parasite egg-accepting and -rejecting behavior, (2) examine the effect of using daily temperature data versus less frequent nest-visit data on statistical power, bias, and precision when estimating the daily survival rate (DSR) for nests, and (3) compare these two approaches using a simulation study and field data. We monitored the survival of nests located in agricultural landscapes and used a binomial logistic regression with main effects for data-loggers and parasite-accepting or -rejecting status and their interaction. We also compared maximum likelihood–derived DSR for differences in estimated rates, precision, and sample sizes with both data collected in the field and simulated with varying sample sizes and visit frequencies. We found no evidence that thermal data loggers had any effect on hatching rates either for all species or for parasite egg-accepting and -rejecting species, separately. Both our simulation and analysis of real nest data indicated that use of data loggers increased the statistical power from each nest studied by increasing effective sample sizes and precision of DSR estimates compared to in-person visits. We also found a negative bias in DSR estimates with longer visit intervals, which use of data-loggers removed. Both the results of simulated- and field-data analyses suggest that future studies of nest survival can be improved by automated nest monitoring by removing a source of bias and providing more time to find additional nests
Stephenson, M. D., L. A. Schulte, and R. W. Klaver. 2024. The relative contributions of habitat area, configuration, and vegetative diversity on snake and lizard presence in agricultural landscapes. Conservation Science and Practice:16.	May 2024
Stephenson, M. D., K. L. Yuza, L. A. Schulte, and R. W. Klaver. 2024. Habitat amount and edge effects, not perch proximity, nest exposure, or vegetation diversity affect cowbird parasitism in agricultural landscapes. Landscape Ecology 39:69-69.	March 2024
Stell, E.G., S. K. Brewer, L. M. Horne, R. A. Wright, and D. R. DeVries. 2023. Using the electron transport system as an indicator of organismal thermal tolerance and respiratory exploitation. Canadian Journal of Zoology 102(2): 155-165. https://doi.org/10.1139/cjz-2023-0027.	August 2023
Steffensmeier, Z.D., M. Wedgeworth, L. Yancy, N. Santee, S. K. Brewer, and J. S. Perkin. 2022. Paradigm versus paradox on the prairie: Testing competing stream fish movement frameworks using a highly imperiled Great Plains minnow. Movement Ecology 10, https://doi.org/10.1186/s40462-022-00306-9.	August 2022
Steffensmeier, Z., S. K. Brewer, M. Wedgeworth, T.A. Starks, A. Rodger, E. Nguyen, and J. Perkin. 2023. Conservation at the Nexus of Niches: Multidimensional Niche Modelling to Improve Management of Prairie Chub. North American Journal of Fisheries Management 43: 1205-1224. https://doi.org/10.1002/nafm.10860	September 2023
Stears, K., M.H. Schmitt, W.C. Turner, D.J. McCauley, E.A. Muse, H. Kiwango, D. Matheyo and B.M. Mutayoba. Hippopotamus movements structure the spatiotemporal dynamics of an active anthrax outbreak, Ecosphere, 12(6):e03540. https://doi.org/10.1002/ecs2.3540 \| Abstract \| Publisher Website	June 2021	Anthrax outbreaks across Africa pose serious threats to people, livestock, and wildlife and can be exacerbated by environmental change. However, little is known about how the quantitative spatial dynamics of host movement and environmental change may affect the spread of <i>Bacillus anthracis</i> – the causative agent of anthrax. Here, we use real-time observation and high-resolution tracking data from a population of common hippopotamus (<i>Hippopotamus amphibius</i>) to explore the relationship between changing river hydrology, <i>H. amphibius</i> movement, and the spatiotemporal dynamics of an active anthrax outbreak. We found that changes in water availability indirectly facilitated the spread of <i>B. anthracis</i> by modulating <i>H. amphibius</i> movements. Our findings reveal that anthrax spread upstream in the Great Ruaha River, which followed the movement patterns of infected <i>H. amphibius</i>, who moved upstream as the river dried in search of remaining aquatic refugia. Moreover, infection by <i>B. anthracis</i> did not appear to influence <i>H. amphibius</i> movement behaviours. Contact rates between <i>H. amphibius </i>and <i>B. anthracis-</i>infected river pools are heterogeneous and the frequency and duration of contacts increase the probability of mortality. While difficult to obtain, the quantitative insights that we gathered during a real-time anthrax outbreak are critical to better understand, predict, and manage future outbreaks.
Starkloff, N. C., W. C. Turner, A. M. FitzGerald, M. C. Oftedal, E. S. Martinsen, and J. J. Kirchman. 2021. Disentangling the effects of host relatedness and elevation on haemosporidian parasite turnover in a clade of songbirds. Ecosphere. 12(5):e03497 \| Abstract \| Publisher Website	May 2021	The persistence of a parasite species in an ecological community is determined together by its environmental tolerance and host breadth. The relative contribution of these niche characteristics to parasite community structure is challenging to parse because host persistence is also a consequence of extrinsic environmental factors. We investigated haemosporidian parasites (genera Plasmodium, Leucocytozoon and Haemoproteus) in a clade of avian hosts in eastern North America. This clade of Catharus thrushes contains species that occupy specific elevational bands in a non-phylogenetically determined manner. This allowed us to tease apart the effects of host relatedness and elevation on parasite diversity, community structure and infection prevalence. We screened blood and tissue samples from 414 birds from four mountain ranges in the Appalachian Highlands for blood parasites using a cytochrome-b nested PCR protocol and identified parasite lineages by sequencing. We found an overall infection prevalence of 88.4% and identified a total of 38 parasite lineages including seven novel lineages. Host relatedness rather than elevational zone predicted the beta turnover and phylobetaturnover of Leucocytozoon parasites, where closely related host species had more similar parasites. While this pattern was not seen in Plasmodium parasites, the diversity of this parasite genus varied considerably in the high elevational zones among mountain ranges, i.e. a sky-island effect. Additionally, the alpha diversity of Haemosporidians did not vary by host species or elevational zone, Plasmodium and Leucocytozoon infection prevalence was determined by one or two of these predictors, respectively. Haemoproteus parasites were rare in this study system. Our study suggests that the mechanisms that underlie the community structuring vary between haemosporidian genera due to differences in the degree of host sharing among lineages.
Stark, S., M.K. Schall, G.D. Smith, A.P. Maloy, J.A. Coombs, T. Wagner, J. Avery. 2024. Feeding Habits and Ecological Implications of the Invasive Flathead Catfish, Pylodictis olivaris, in the Susquehanna River Basin, Pennsylvania. Transactions of the American Fisheries Society 153:591-610. https://doi.org/10.1002/tafs.10480	August 2024
Stantial, M.L., A.M.V. Fournier, A.J. Lawson, B.G. Marcot, M.S. Woodrey, J.E. Lyons. 2024. RE-ARMing Salt Marshes: A Resilience-Experimentalist Approach to Prescribed Fire and Bird Conservation in High Marshes of the Gulf of Mexico. Frontiers in Conservation Science 5: 1426646. doi: 10.3389/fcosc.2024.1426646 \| Publisher Website	August 2024
Stantial, M.L., A.J. Lawson, A.M.V. Fournier, P.J. Kappes, C.S. Kross, M.C. Runge, M.W. Woodrey, and J.E. Lyons. 2023. Qualitative value of information provides a transparent and repeatable method for identifying critical uncertainty. Ecological Applications:e2824. \| Abstract \| Publisher Website	February 2023	Conservation decisions are often made in the face of uncertainty because the urgency to act can preclude delaying management while uncertainty is resolved. In this context, adaptive management is attractive, allowing simultaneous management and learning. An adaptive program design requires the identification of critical uncertainties that impede the choice of management action. Quantitative evaluation of critical uncertainty, using the expected value of information, may require more resources than are available in the early stages of conservation planning. Here, we demonstrate the use of a new qualitative index to the value ofinformation (QVoI) to prioritize which sources of uncertainty to reduceregarding the use of prescribed fire to benefit Eastern Black Rails(Laterallus jamaicensis jamaicensis), Yellow Rails (Coterminous noveboracensis), and Mottled Ducks (Anas fulvigula; hereafter, focal species) in high marshes of the U.S. Gulf of Mexico. Prescribed fire has been used as a management tool in Gulf of Mexico high marshes throughout the last 30+ years; however, effects of periodic burning on the focal species and the optimal conditions for burning marshes to improve habitat remain unknown. We followed a structured decision making framework to develop conceptual models, which we then used to identify sources of uncertainty and articulate alternative hypotheses about prescribed fire in high marshes. We used QVoI to evaluate the sources of uncertainty based on their magnitude, relevance for decision making, and reducibility. We found that hypotheses related to the optimal fire return interval and season were the highest priorities for study, whereas hypotheses related to predation rates and interactions among management techniques were lowest. These results suggest that learning about the optimal fire frequency and season to benefit the focal species might produce the greatest management benefit. In this case study, we demonstrate that QVoI can help managers decide where to apply limited resources to learn which specific actions will result in a higher likelihood of achieving the desired management objectives. Further, we summarize the strengths and limitations of QVoI and outline recommendations for its future use for prioritizing research and to reduce uncertainty about system dynamics and the effects of management actions.
Stahlecker, D.W., Z.P. Wallace, D.G. Mikesic, C.W. Boal, R.K. Murphy, W.H. Howe, and M.B. Ruehmann. 2022. Golden Eagle Breeding Distribution in Wind Energy Landscapes of the Southern Great Plains. Journal of Raptor Research 54:1-11. \| Abstract	September 2022	Abstract.–– Deaths of four Golden Eagles (<i>Aquila chrysaetos</i>) due to collision trauma at a new wind energy facility in east central New Mexico during 2004–2005 prompted concerns about the species’ population status in the encompassing Southern Great Plains region, primarily because its breeding distribution there was poorly documented and wind energy was expanding. Therefore, we conducted aerial searches for Golden Eagle nests across northeastern New Mexico, northwestern Texas and western Oklahoma, and adjacent portions of Colorado and Kansas during 2006–2009 and 2015–2020. We delineated five Golden Eagle Nest Search Areas (NSAs) with unique physiographic/geological origins. Individual NSAs were searched partly or entirely for up to 8 yr. Collectively, we identified 123 breeding areas (BAs) occupied by Golden Eagles ≥1 yr, 95 (77.2%) of which were in northeastern New Mexico. The most BAs (40) were in the 11,720-km<sup>2</sup> Highlands NSA. Greatest BA density (126.6 km<sup>2</sup>/BA) and shortest BA nearest neighbor distance (7.4 km) were in the 3,533-km<sup>2</sup> Northern Caprock NSA. Wind energy was developing rapidly in the region. Wind turbines existed near (within 3.2 km) 21 nests distributed among six of 28 BAs in the Northern Caprock and were planned for siting near another BA. Elsewhere, only planned turbines were near nests and only within six BAs. Our findings indicate that the Southern Great Plains supports many Golden Eagle pairs at the eastern margin of the species’ breeding range in western North America. Our data provide a solid basis for protecting breeding habitat from potential threats, particularly those posed by wind and fossil-fuel energy development, and provides a foundation for long-term population monitoring.
Stacy, J., R.L. Ryan, A.H. Roy, and A. Milman. 2021. Homeowners' willingness to adopt environmentally beneficial landscape practices in an urbanizing watershed. Cities and the Environment 14(1). DOI: 10.15365/cate.2021.140102 \| Publisher Website	July 2021
Stachelek, J. W. Weng, C.C. Carey, A.R. Kemanian, K.M. Cobourn, T. Wagner, K.C. Weathers, P.A. Soranno. 2020. Granular measures of agricultural land-use influence lake nitrogen and phosphorus differently at macroscales. Ecological Applications 30, e02123.	April 2020
Spurgeon, J.J. 2022. Defining habitat: implications for management of altered freshwater systems. Lakeline 42: 6-9.	April 2022
Spurgeon, J., J. Kaiser, C. Graham, and S. Lochmann. 2022. Trout responses to stocking rates and river discharge within a southeast U.S. hydropeaking tailwater. North American Journal of Fisheries Management 42:926-938.	April 2022
Spurgeon, J. J., M. A. Pegg, K. L. Pope, and L. Xie. 2020. Ecosystem-specific growth responses to climate pattern by a temperate freshwater fish.Ecological Indicators 112:106130. \| Download	January 2020
Spurgeon, J, M. Rhodes, J. W. Neal, and K. Evans. 2021. Aquatic habitat changes within the channelized and impounded Arkansas River, Arkansas, USA. River Research and Applications 37:462-474.	December 2020
Sorensen, G.E., D.W. Kramer, J.W. Cain III, C.A. Taylor, P.S. Gibson, M.C. Wallace, R.D. Cox, and W.B. Ballard. 2020. Mule deer habitat selection following vegetation thinning treatments in New Mexico. Wildlife Society Bulletin 44:122-129. \| Download	March 2020
Sorensen, A.E., J. Brown, A. Alred, J.J. Fontaine, and J.M. Dauer. 2020. Student representations and conceptions of ecological versus social sciences in a conservation course. Journal of Environmental Studies and Sciences 2020:1-11.	December 2020
Sorel MH, RW Zabel, DS Johnson, AM Wargo Rub, and SJ Converse. 2021. Estimating population-specific predation effects on Chinook salmon via data integration. Journal of Applied Ecology 58:371-381. https://doi.org/10.1111/1365-2664.13772 \| Abstract	February 2021	1) Recent success in the conservation of many marine mammals has resulted in new management challenges due to increasing conflict with fisheries. Increasing predation by pinnipeds on threatened salmon is of particular concern. Seemingly, pinniped conservation is now in conflict with the recovery of threatened salmon, creating a dilemma for managers. <br><br>2) We use the Lower Columbia River as a case study for examining the relationship between seasonal California sea lion (<i>Zalophus californianus</i>) abundance and survival of threatened salmon. To quantify mortality associated with increasing sea lion abundance, we examined the effect of seasonal sea lion abundance on adult Chinook salmon<i> </i>(<i>Oncorhynchus tshawytscha</i>)<i> </i>survival during migrations through the Lower Columbia River. We integrated data on survival with data on population-specific migration timing, allowing quantification of the relationship between sea lion abundance and survival in 18 populations of spring-summer Chinook salmon listed as Threatened or Endangered under the U.S. Endangered Species Act.<br><br>3) Of the 18 populations examined, earlier migrating populations experienced lower survival in association with increased exposure to higher sea lion abundance. We estimated that in years with high sea lion abundance, the nine earliest-migrating populations experienced an additional 21.1% (16.3, 26.1) mortality compared to years with baseline sea lion abundance, while the nine latest migrating populations experienced an additional 10.1% (7.5, 13.0). <br><br>4)<i> Synthesis and Application.</i> Integrating datasets on seasonal survival and migration timing made it possible for us to estimate population-specific mortality associated with increased sea lion abundance in the Lower Columbia River. This information could not be produced from any one data set, highlighting the utility of data integration approaches. The mortality experienced by early migrating Chinook salmon suggests the potential for demographic and evolutionary consequences. Management actions such as hazing, relocating, or removing individuals that are frequent predators on salmon have been proposed. Identifying the management actions that will allow for socially and legally acceptable tradeoffs between multiple conservation and other social values will be facilitated by development of explicit multi-species management frameworks. Continued monitoring will help to reduce the substantial uncertainty about the effect of pinnipeds on salmon and the predicted outcomes of alternative management actions.
Sorel MH, JC Jorgensen, RW Zabel, MD Scheuerell, AR Murdoch, CM Kamphaus, and SJ Converse. 2024. Incorporating life history diversity in an integrated population model to inform viability analysis. Canadian Journal of Fisheries and Aquatic Sciences 81:535-548.	March 2024
Sorel MH, AR Murdoch, RW Zabel, JJ Jorgensen, CM Kamphaus, and SJ Converse. 2023. Juvenile life history diversity is associated with lifetime demographic heterogeneity in a migratory fish. Ecosphere 14:e4366. \| Abstract	January 2023	Differences in the life history pathways of juvenile animals are often associated with differences in demographic rates in later life stages. For migratory animals, different life-history pathways often result in animals from the same population occupying distinct habitats subjected to different environmental drivers. Understanding how demographic rates differ among animals expressing different life history pathways may reveal fitness tradeoffs that drive the expression of alternative life history pathways and enable better prediction of population dynamics in a changing environment. To understand how demographic outcomes and their relationships with environmental variables differ among animals with different life history pathways, we analyzed a long-term mark-recapture dataset for Chinook salmon (<i>Oncorhynchus tshawytscha</i>) from the Wenatchee River, Washington, USA. Distinct life history pathways represented in this population include either remaining in the natal stream until emigrating to the ocean as a one-year-old (<i>natal-reach rearing</i>) or emigrating from the natal stream and rearing in downstream habitats for several months before completing the emigration to the ocean as a one-year-old (<i>downstream rearing</i>). We found that downstream-rearing fish emigrated to the ocean 19 days earlier on average and returned as adults from the ocean at higher rates. We detected a positive correlation between rate of return from the ocean by downstream-rearing fish and coastal upwelling in their spring of outmigration, whereas for natal-reach-rearing fish we detected a positive correlation with sea surface temperature during their first marine summer. Different responses to environmental variability should lead to asynchrony in adult abundance among juvenile life history pathways. A higher proportion of downstream-rearing fish returned at younger ages compared to natal-reach-rearing fish, which contributed to more variability in age at reproduction and greater mixing across generations. Our results provide an example of how diversity in juvenile life history pathways is associated with heterogeneity in demographic rates during subsequent life stages. This demographic heterogeneity can in turn affect variance in the aggregate population abundance and population response to environmental change. Our findings underscore the importance of considering life history diversity in demographic analyses and lay the foundation for the development of population models that account for different life history pathways.
Sorel MH, AR Murdoch, RW Zabel, CM Kamphaus, ER Buhle, MD Scheuerell, and SJ Converse. 2023. Effects of population density and environmental conditions on life-history prevalence in a migratory fish. Ecology and Evolution 13:e11087. \| Abstract	May 2023	Individual variation in life-history traits can have important implications for the ability of populations to respond to environmental variability and change. In migratory animals, flexibility in the timing of life-history events, such as juvenile emigration from natal areas, can influence the effects of population density and environmental conditions on population dynamics. We evaluated the functional relationships between population density and environmental covariates and the abundance of juveniles expressing different life-history pathways in a migratory fish, Chinook salmon (<i>Oncorhynchus tshawytscha</i>), in a river basin in Washington State, USA. We found that the abundance of younger emigrants from natal streams was best described by an accelerating or near-linear function of spawners, whereas the abundance of older emigrants was best described by a decelerating function of spawners. This supports the hypothesis that emigration timing varies in response to density in natal areas, with younger-emigrating life-history pathways comprising a larger proportion of emigrants when densities of conspecifics are high. We also observed positive relationships between winter stream discharge and abundance of younger emigrants, supporting the hypothesis that habitat conditions can also influence the expression of different life-history pathways. Our results suggest that early emigration, and a resultant increase in the use of downstream rearing habitats, may increase if winter precipitation increases in the future as is projected due to climate warming. Characterizing relationships between life-history expression and environmental conditions is a necessary first step in understanding the dynamics of species with diverse life-history strategies. As environmental conditions change – due to climate change, management, or other factors – resultant life-history changes are likely to have important demographic implications that will be challenging to predict if life-history diversity is not accounted for in population models.
Soranno, P.A., K.S. Cheruvelil, B. Liu, Q. Wang, P-N. Tan, J. Zhou, K.B.S. King, I.M. McCullough, J. Stachelek, M. Bartley, C.T. Filstrup, E.M. Hanks, J-F. Lapierre, N.R. Lottig, E.M. Schliep, T. Wagner, K.E. Webster. 2020. Ecological prediction at macroscales using big data: Does sampling design matter? Ecological Applications 30:e02123.	September 2020
Sonsthagen, S. A., T. Swem, S. Ambrose, M. Flamme, C. M. White, G. K. Sage, and S. L. Talbot. 2022. The DDT-induced decline influenced genetic diversity in two naturally recovered populations of peregrine falcons nesting within the Alaska Arctic and eastern Interior. The Ibis. 164:1265-1272. doi.org/10.1111/ibi.13095	July 2022
Sonsthagen, S. A., R. E. Wilson, and S. L. Talbot. 2022. Species-specific responses to landscape features shaped genomic structure within Alaska galliformes. Journal of Biogeography, 49:261-273. doi.org/10.1111/jbi.14294	January 2022
Sonsthagen, S. A., R. E. Wilson, R. Turner, M.-J. Fortin, G. Gilchrist, and V. Friesen. 2024. Wintering grounds leave their mark: where birds winter influences genomic structure in Arctic nesting common eiders. Conservation Genetics. doi.org/10.1007/s10592-024-01654-2	November 2024
Sonsthagen, S. A., C. Jay, R. S. Cornman, A. Fischbach, J. Grebmeier, and S. L. Talbot. 2020. DNA metabarcoding to infer summer diet of Pacific walrus. Marine Mammal Science. 36:1196-1211.	July 2020
Sonsthagen, S. A., C. Haughey, M. G. Sexson, D. V. Solovyeva, M. R. Petersen, and A. Powell. 2020. Temporal variation in genetic structure within the threatened spectacled eider. Conservation Genetics. 21:175–179.	January 2020
Song, C, O’Malley, A., Zydlewski,J., and Mo, W (2020) Balancing fish-energy-cost tradeoffs through strategic basin-wide dam management. Resources, Conservation & Recycling.Resources, Conservation & Recycling 161:1-12. DOI: 10.1016/j.resconrec.2020.104990 \| Download	April 2020
Somers, LN, DH Jackson, KM Dugger, and JD Burco. 2023. A mixture of Nalbuphine, Azaperone, and Medetomidine for Immobilizing Ringtail (Bassariscus astutus). Journal of Wildlife Diseases. Journal of Wildlife Diseases 59(4):610-615. DOI: 10.7589/JWD-D-23-00006. \| Download	October 2023
Som, N.A. 2024. Applications of a disease-induced mortality model to inform regulatory compliance of the Klamath Project. \| Download	March 2024
Solokas, M., Z. Feiner, R. Al-Chokhachy, P. Budy, J. Tyrell DeWeber, J. Sarvala, G.G. Sass, S.A. Tolentino, T. Walsworth, and O.P. Jensen. 2023. Shrinking body size and climate warming: Many freshwater salmonids do not follow the rule. Global Change Biology 2023;29:2478–2492. USGS FSP under Al-Chockhachy, IP-146706. \| Abstract	January 2023	Declining body size is believed to be a universal response to climate warming andhas been documented in numerous studies of marine and anadromous fishes. TheSalmonidae are a family of coldwater fishes considered to be among the most sensitivespecies to climate warming; however, whether the shrinking body size responseholds true for freshwater salmonids has yet to be examined at a broad spatial scale.We compiled observations of individual fish lengths from long-termsurveys acrossthe Northern Hemisphere for 12 species of freshwater salmonids and used linearmixed models to test for spatial and temporal trends in body size (fish length) spanningrecent decades. Contrary to expectations, we found a significant increase in lengthoverall but with high variability in trends among populations and species. More thantwo-thirdsof the populations we examined increased in length over time. Secondaryregressions revealed larger-bodiedpopulations are experiencing greater increases inlength than smaller-bodiedpopulations. Mean water temperature was weakly predictiveof changes in body length but overall minimal influences of environmentalvariables suggest that it is difficult to predict an organism's response to changingtemperatures by solely looking at climatic factors. Our results suggest that decliningbody size is not universal, and the response of fishes to climate change may be largelyinfluenced by local factors. It is important to know that we cannot assume the effectsof climate change are predictable and negative at a large spatial scale.
Soller, J.M., D.E. Ausband, and M.S. Gunther. 2020. The curse of observer experience: error in noninvasive genetic sampling. PLOS ONE. 15(3): e0229762. https://doi.org/10.1371/journal.pone.0229762	March 2020
Sofaer, HR, CS Jarnevich, EK Buchholtz, BS Cade, JT Abatzoglou, CL Aldridge, PJ Comer, D Manier, LE Parker, and JA Heinrichs. 2022. Potential cheatgrass abundance within lightly invaded areas of the Great Basin. Landscape Ecology 37, 2607–2618. doi.org/10.1007/s10980-022-01487-9 \| Abstract \| Publisher Website	October 2022	<b>Context: </b>Anticipating where an invasive species could become abundant can help guide prevention and control efforts aimed at reducing invasion impacts. Information on potential abundance can be combined with information on the current status of an invasion to guide management towards currently uninvaded locations where the threat of invasion is high.<br><b>Objectives: </b>We aimed to support management by developing predictive maps of potential cover for cheatgrass (<i>Bromus tectorum</i>), a problematic invader that can transform plant communities. We integrated our predictions of potential abundance with mapped estimates of current cover to quantify invasion potential within lightly invaded areas.<br><b>Methods: </b>We used quantile regression to model cheatgrass abundance as a function of climate, weather, and disturbance, treating outputs as low to high invasion scenarios. We developed a species-specific set of covariates and validated model performance using spatially and temporally independent data.<br><b>Results: </b>Potential cheatgrass abundance was higher in areas that had burned, at low elevations, and when fall germination conditions were more favorable. Our results highlight the extensive areas across the Great Basin where cheatgrass abundance could increase to levels that can alter fire behavior and cause other ecological impacts.<br><b>Conclusions:</b> We predict potential cheatgrass abundance to quantify relative invasion risk. Our model results provide high and low scenarios of cheatgrass abundance to guide resource allocation and planning efforts across shrubland ecosystems of the Great Basin that remain relatively uninvaded. Combining information on an invasive species’ current and potential abundance can yield spatial predictions to guide resource allocation and management action.
Snyder, S., C.S. Loftin, and A.S. Reeve. 2023. Predicting the presence of Groundwater Influenced Ecosystems in the northeastern United States with ensembled correlative distribution models. Water. 15, 4035. https://doi.org/10.3390/w15234035	November 2023
Snyder, S., C.S. Loftin, A.S. Reeve. Vulnerability assessment of groundwater influenced ecosystems in the Northeastern United States. Water, 2024, 16, 1366. https://doi.org/10.3390/w16101366	May 2024
Snow, R.A., J.M. Long, and M.J. Porta. 2020. Marking otoliths of Alligator Gar by immersion in oxytetracycline. North American Journal of Fisheries Management 40:669-674.	June 2020
Snow, R.A., D.R. Stewart, M.J. Porta, and J.M. Long. 2020. Feeding ecology of age-0 gar at Lake Texoma inferred from analysis of stable isotopes. North American Journal of Fisheries Management 40:638-650. DOI: 10.1002/nafm.10436	June 2020
Snavely, B.M., and R.C. Lonsinger. 2023. The Factors Affecting Female Black Bear Harvest Rates in Pennsylvania. Final Report to the Pennsylvania Game Commission: Cooperative Agreement #4000024645. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-150-2023, Washington, D. C. https://doi.org/10.3996/css88880882 .	July 2023
Smith, Kyle, A.C. Landon, D.C. Fulton. A self-determination approach to understanding leisure identity salience among lapsed hunters. Leisure Science. \| Abstract	June 2023	This study extended a framework based on self-determination theory (SDT) to study hunting identity salience in lapsed hunters. SDT suggests that multiple forms of motivation can influence levels of self-determination and subsequent behavioral intentions and addresses how social-contextual factors support or thwart individual satisfaction of needs. In the context of hunting, SDT posits that individuals initially interested in the activity will habitually seek out positive hunting experiences and, when supported, will integrate deer hunting as part of their identity. Data were drawn from a survey of lapsed hunters in Minnesota, United States conducted during the winter of 2021. Results suggested that socio-contextual constraints were negatively associated with intrinsic motivation and support amotivation. Subsequently, these differing forms of motivation had a variable influence on identity salience. These findings have implications for recruitment, retention, and reactivation (R3) efforts and highlight the need to understand the influence of social-contextual factors and individual motivation in the context of continued hunting participation.
Smith, K., S.A. Schroeder, A.C. Landon, L.J. Cornicelli, D.C. Fulton, and L.E. McInenly. (2020). A replication of proximity to chronic wasting disease, perceived risk, and social trust in managing between hunters in Minnesota and Illinois. Human Dimensions of Wildlife (published online without volume/page numbers). DOI: 10.1080/10871209.2020.1860270	December 2020
Smith, K., A. Landon, D.C. Fulton, and G. Kyle. 2024. Self-determination theory as an alternate conceptual foundation for motivation in natural resource recreation. Human Dimensions of Wildlife. \| Abstract	March 2024	Motivation is a topic that receives substantial interest across the social sciences. However, in the human dimensions literature, scholars have primarily treated motivation as a unitary construct defined by the individual's desired goal state. In contrast, self-determination theory (SDT) suggests that multiple forms of motivation can influence levels of self-determination, integration of identities, and subsequent behavioral intentions, and has been utilized in multiple realms to understand human behaviors. SDT forms a consistent and well-understood mechanism for human psychological development and optimal function and allows for the formulation of out-of-sample prediction, a cornerstone of science. In this manuscript, we review the basic theories that make up SDT and provide insight for its application to human dimensions of wildlife research.
Smith, G.D., Massie, D.L., Perillo, J., Wagner, T. and Pierce, D., 2021. Range expansion and factors affecting abundance of invasive Flathead Catfish in the Delaware and Susquehanna rivers, Pennsylvania, USA. North American Journal of Fisheries Management 41:S205-S220. http://dx.doi.org/10.1002/nafm.10628	April 2021
Smith, G.D., Massie, D.L., Perillo, J., Wagner, T. and Pierce, D., 2021. Range expansion and factors affecting abundance of invasive Flathead Catfish in the Delaware and Susquehanna rivers, Pennsylvania, USA. North American Journal of Fisheries Management 41:S205-S220. http://dx.doi.org/10.1002/nafm.10628	April 2021
Smith, D.M., S.A. Welsh, and C. HIlling. 2021. Seasonal Movement Patterns and Distribution of Walleye in a Central Appalachian Hydropower Reservoir. Pages 209-237 in J. Bruner and R. DeBruyne (eds.) Biology, Management, and Culture of Walleye, Sauger, and Yellow Perch: Status and Needs, Springer	November 2021
Smith, D.M., S.A. Welsh, C.D. Hilling. Environmental correlates of spawning related movements of walleye in an Appalachian hydropower reservoir. Journal of the Southeastern Association of Fish and Wildlife Agencies 10:36-44.	January 2023
Smith, D., Newhard, J., McGowan, C. and Butler, A., 2020. The Long-Term Effect of Bleeding for Limulus Amebocyte Lysate on Annual Survival and Recapture of Tagged Horseshoe Crabs. Frontiers in Marine Science, 7, p.1133.	December 2020
Smith, D. M., C. D. Hilling, S. A. Welsh, and D. I. Wellman, Jr. 2022. Differences in population characteristics and modeled response to harvest regulations in reestablished Appalachian Walleye populations. North American Journal of Fisheries Management 46:612–629.	June 2022
Smith, C.R., V.S. Blazer, C.A. Ottinger, H.L. Walsh and P.M. Mazik. 2023. Immune function of wild smallmouth bass collected from sites within the Chesapeake Bay watershed, 2016-2021. U.S. Geological Survey Data Release, https://doi.org/10.5066/P9FTUPPX \| Abstract	June 2023	<b>Abstract: </b>The utility of a functional immune assay for wild smallmouth bass (<i>Micropterus dolomieu</i>) was evaluated in context with other aspects of host and environmental health. The mitogenesis assay utilized imaging flow cytometry with advanced machine learning for cell cycle analyses, 5-ethynyl-2’-deoxyuridine (EdU) incorporation into replicating DNA for detection of proliferation and an anti-smallmouth bass IgM monoclonal antibody to distinguish lymphocyte type. The assay was field-tested with fish collected from three sites, in two river drainages within West Virginia, as part of fish health assessments occurring in spring (pre-spawn; April – May) and fall (recrudescence; October – November). Leukocytes were isolated from anterior kidney tissue and exposed to lipopolysaccharide (LPS) from <i>E.coli</i> O111:B4 or mitogen-free media, which served as the negative control and a measure of unstimulated background lymphocyte proliferation as a baseline for wild fish. Mitogenic responses were dependent upon the collection site and season in which the fish were collected. Factors such as sex, age, tissue parasites, and macrophage aggregates were also evaluated. The differences in lymphocyte mitogenesis among smallmouth bass populations emphasizes the need for integrated assessments to determine not only environmental stressors but also infectious agents that may modulate the immune response in immunotoxicological studies.
Smith, C.R., Ottinger, C.A., Walsh, H.L., Mazik, P.M. & Blazer, V.S. 2023. Application of a lipopolysaccharide (LPS)-stimulated mitogenesis assay in Smallmouth Bass (Micropterus dolomieu) to augment wild fish health studies. Fishes, 8(3), 159. https://www.mdpi.com/2410-3888/8/3/159 \| Abstract	June 2023	A mitogenesis assay was developed for smallmouth bass (<i>Micropterus dolomieu</i>) which distinguishes between proliferation of immunoglobulin M (IgM<sup>+</sup> and IgM<sup>-</sup>) lymphocytes and utilizes imaging flow cytometry and advanced machine learning for cell cycle analyses. Mitogenesis was detected by 5-ethynyl-2’-deoxyuridine (EdU) incorporation into replicating DNA and lymphocytes were differentiated with an anti-smallmouth bass IgM monoclonal antibody. The assay was field tested in fish collected from three sites, in two river drainages within West Virginia, as part of fish health assessments occurring in spring before spawning and fall during recrudescence. Leukocytes were isolated from anterior kidney tissue and exposed to the mitogens concanavalin A (Con A), phytohemagglutinin (PHA-P) and lipopolysaccharide (LPS) from <i>E.coli</i> O111:B4 for the mitogenesis assay. Mitogenic responses were dependent upon specific mitogen used, collection site, and season in which the fish were collected. To provide a better understanding of factors affecting these responses, tissue parasites and macrophage aggregates were quantified. Wild fish are inherently exposed to stressors, including disease, parasites, and fluctuations in environmental parameters such as temperature, water quality and contaminants. The differences in lymphocyte mitogenesis among smallmouth bass populations observed in this study validate the utility of this improved method for future ecotoxicological studies and fish health assessments. It also emphasizes the need for integrated assessments to determine not only environmental parameters but also infectious agents that may modulate the immune response.
Smit, R. B., Goodman, D. H., Boyce, J., & Som, N. A. 2024. Effects of 2D hydrodynamic model resolution on habitat estimates for rearing Coho Salmon in contrasting channel forms. River Research and Applications 40(10): 1912-1924. https://doi.org/10.1002/rra.4341	July 2024
Smalling, K.L., Romanok, K.M., Bradley, P.M, Morriss, M.C., Gray, J.L., Kanagy, L.K., Gordon, S.E., Williams, B.W., Breitmeyer, S.E., Jones, D.K., DeCicco, L.A., Eagles-Smith, C.A., and Wagner, T., 2023, Per- and Polyfluoroalkyl Substances (PFAS) in United States Tapwater: Comparison of Underserved Private-Well and Public-Supply Exposures and Associated Health Implications, Environment International, p. 108033, https://doi.org/10.1016/j.envint.2023.108033	June 2023
Smalling, K.L., O.H. Devereux, S. Gordon, P. Phillips, V.S. Blazer, M.L. Hladik, D.W. Kolpin, M.T. Meyer, A. Sperry, and T. Wagner. 2021. Environmental and anthropogenic drivers of contaminants in agricultural watersheds with implications for land management. Science of the Total Environment 145687.	February 2021
Slevin, M. C., E. E. Bin Soudi, and T. E. Martin. 2020. Breeding Biology of Mountain Wren-Babbler (Gypsophila crassus). Wilson Journal of Ornithology 132(1):124-133.	January 2020
Sleugh, T., McCoy, C.M., Pattengill-Semmens, C.V. et al. 2023. Migratory behavior of aggregating male Tiger Grouper (Mycteroperca tigris) in Little Cayman, Cayman Islands. Environ Biol Fish 106, 1195–1206 (2023). https://doi.org/10.1007/s10641-023-01399-w \| Abstract \| Download \| Publisher Website	March 2023	Tiger Grouper (<i>Mycteroperca tigris</i>) form fish spawning aggregations (FSAs) around the winter full moons (typically January through April) in the central Caribbean. Males defend territories to attract mates in a lek-like reproductive strategy. Prior studies have documented rapid declines in populations with FSA associated fisheries. This study examines the migratory behavior and spatial ecology of adult male Tiger Grouper in Little Cayman, Cayman Islands, to better understand the localized impacts of aggregation fishing. As part of the Grouper Moon Project, we acoustically tagged ten spawning male Tiger Grouper at the western end of Little Cayman in February 2015. Using an array of hydrophones surrounding the island, we tracked the movements of the ten tagged fish over a 13-month period. We observed 3 migratory strategies: resident fish (n = 2) that live at the FSA site, neighboring fish (n = 5) that live within 4 km of the site, and commuter fish (n = 3) that travel over 4 km for spawning. Fish began aggregating two days before the full moon and typically left between ten and twelve days after the full moon, January through May. Regardless of migratory strategy, all tagged fish that returned to spawn in2015 after the February tagging effort came back to the west-end FSA. However, in January2016, one fish appeared to attend a different FSA closer to its presumed home territory. Unlike other larger-bodied grouper, it appears that Tiger Grouper establish multiple FSAs around Little Cayman, and males attend FSAs near their home territories. Protracted spawning seasons, FSA site infidelity, and putative FSA catchments should all be brought into management consideration to ensure sustainable fisheries for this important species.
Sleezer, L.J., P.L. Angermeier, E.A. Frimpong, and B.L. Brown. 2021. A new composite abundance metric detects stream fish declines and community homogenization during six decades of invasions. Diversity and Distributions 27: 2136-2156. http://doi.org/10.1111/ddi.13393	September 2021
Skorupa, A.J., D. Perkins, A.H. Roy, and J.E. Ryan. 2023. Watershed selection to support freshwater mussel restoration: An open-loop decision guide. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/149-2023, Washington, DC. https://doi.org/10.3996/css85533320 \| Publisher Website	May 2023
Skorupa, A.J., A.H. Roy, P.D. Hazelton, D. Perkins, and T. Warren. 2022. Evaluation of host fishes for the Brook Floater (Alasmidonta varicosa) from populations in Massachusetts and Maine. Freshwater Mollusk Biology and Conservation 25:91-102. DOI:10.31931/fmbc-d-21-00011 \| Download \| Publisher Website	November 2022
Skorupa, A.J., A.H. Roy, P.D. Hazelton, D. Perkins, T. Warren, and B.S. Cheng. 2024. Food and water quality impact in situ growth of a freshwater mussel: implications for population restoration. Freshwater Science 43(2):107-123. \| Download	April 2024
Skorupa, A.J., A.H. Roy, P.D. Hazelton, D. Perkins, T. Warren, and A. Fisk. 2024. Abundance of five sympatric stream dwelling mussels varies with physical habitat. Aquatic Conservation: Marine and Freshwater Ecosystems 2024:e4069. https://doi.org/10.1002/aqc.4069 \| Download \| Publisher Website	January 2024
Sirén, A.P.K., Michael Hallworth, J. Kilborn, C.A. Bernier, N.L. Fortin, K.D. Gieder, R. Patry, R.M. Cliché, L.S. Prout, S. Gifford, S. Wixsom, T.L. Morelli, T.L. Wilson. 2024. Monitoring animal populations with cameras using open, multistate, N-mixture models. Ecology and Evolution: e70583. https://doi.org/10.1002/ece3.70583 \| Abstract	December 2024	Remote cameras have become a mainstream tool for studying wildlife populations. For species whose developmental stages are identifiable in photographs, there are opportunities for tracking population changes and estimating demographic rates. Recent developments in hierarchical models allow for the estimation of ecological states and rates over time for unmarked animals whose stages are known. However, this powerful class of models has been underutilized as they are computationally intensive and model outputs can be difficult to interpret. Here, we use simulation to show how camera data can be analyzed with open, multistate, N-mixture (hereafter multistate DM) models to estimate abundance, survival, and recruitment. We evaluated 4 commonly encountered scenarios arising from camera trap data (low and high abundance and 25% and 50% missing data) each with 18 different sample size combinations (camera sites = 40, 250; surveys = 4, 8, 12; and years = 2, 5, 10) and evaluated the bias and precision of abundance, survival, and recruitment estimates. We also analyzed our empirical camera data on moose (<i>Alces alces</i>) with multistate DM models and compared inference with telemetry studies from the same time and region to assess the accuracy of camera studies to track moose populations. Most scenarios recovered the known parameters from our simulated data with higher accuracy and increased precision for scenarios with more sites, surveys, and/or years. Large amounts of missing data and fewer camera sites, especially at higher abundances, reduced accuracy and precision of survival and recruitment. Our empirical analysis provided biologically realistic estimates of moose survival and recruitment and recovered the known pattern of moose abundance across the region. Multistate DM models can be used for estimating demographic parameters from camera data when developmental stages are clearly identifiable. We discuss several avenues for future research and caveats for using these models for large-scale population monitoring.
Sirén, A.P.K., J. Berube, L.A. Clarfeld, C.F.Sullivan, B. Simpson, T.L. Wilson. 2024. Accounting for missing ticks: Use (or lack thereof) of hierarchical models in tick ecology studies. Ticks and Tickborne Diseases 15:102342. DOI: 10.1016/j.ttbdis.2024.102342. \| Abstract \| Publisher Website	April 2024	Ixodid (hard) ticks play important ecosystem roles and have significant impacts on animal and human health via tick-borne diseases and physiological stress from parasitism. Tick occurrence, abundance, activity, and key life-history traits are highly influenced by host availability, weather, microclimate, and landscape features. As such, changes in the environment can have profound impacts on ticks, their hosts, and the spread of diseases. Researchers recognize that spatial and temporal factors influence activity and abundance and attempt to account for both by conducting replicate sampling bouts spread over the tick questing period. However, common field methods notoriously underestimate abundance, and it is unclear how (or if) tick studies model the confounding effects of factors influencing activity and abundance. This step is critical as unaccounted variance in detection can lead to biased estimates of occurrence and abundance. We performed a descriptive review to evaluate the extent to which studies account for the detection process while modeling tick data. We also categorized the types of analyses that are commonly used to model tick data. We used hierarchical models (HMs) that account for imperfect detection to analyze simulated and empirical tick data, demonstrating that inference is muddled when detection probability is not accounted for in the modeling process. Our review indicates that only 5 of 412 (1 %) papers explicitly accounted for imperfect detection while modeling ticks. By comparing HMs with the most common approaches used for modeling tick data (e.g., ANOVA), we show that population estimates are biased low for simulated and empirical data when using non-HMs, and that confounding occurs due to not explicitly modeling factors that influenced both detection and abundance. Our review and analysis of simulated and empirical data shows that it is important to account for our ability to detect ticks using field methods with imperfect detection. Not doing so leads to biased estimates of occurrence and abundance which could complicate our understanding of parasite-host relationships and the spread of tick-borne diseases. We highlight the resources available for learning HM approaches and applying them to analyzing tick data.
Sirch, M.W., D.S. Sullins, N.J. Parker, D.A. Haukos, J.D. Kraft, C.A. Hagen, and K.A. Fricke. 2022. Woody species mortality due to a megafire within the mixed-grass prairie. Prairie Naturalist 54:11-23. https://www.eaglehill.us/prna-pdfs-regular/prna-54/prna-008-Sirch.pdf \| Abstract	July 2022	Lack of fire in contemporary grasslands has contributed to the invasion of woody plants that often survive low- to moderate-intensity fire upon maturity. Knowledge of the effect of megafires (>40,000 ha) on grassland tree mortality and role of megafires in maintaining large grasslands is limited. We first quantified severity and spatial extent of a megafire using remote sensing techniques and then evaluated the effect of the megafire on woody canopy cover and tree mortality within the mixed-grass prairie of Clark County, Kansas, USA. We also used remote sensing techniques to estimate woody cover change and performed ground surveys to estimate woody species mortality, top-kill rates of woody species, size of remaining woody vegetation, postfire herbaceous composition, and the influence of herbicide and wildfire interaction on non-native saltcedar (<i>Tamarix ramosissima </i>Ledeb.). The megafire killed 33 ± 2% of saltcedar and 18 ± 1% (mean ± SD) of all other trees, including all eastern redcedar (<i>Juniperus virginiana</i> L.), and another 54 ± 2% of trees were top-killed and resprouted. Herbicide treatments in the burned area before the fire did not reliably increase saltcedar mortality. We conclude that further postfire management may be required to limit woody encroachment following megafire.
Sirch, M. W.*, D. S. Sullins, N. J. Parker, D. A. Haukos, J. D. Kraft, C. A. Hagen, and K. A. Fricke. 2022. Woody species mortality due to a megafire within the mixed-grass prairie. Prairie Naturalist 54: 11–23. No DOI available.	November 2022
Sipe HA, IN Keren, and SJ Converse. 2023. Integrating community science and agency-collected monitoring data to expand monitoring capacity at large spatial scales. Ecology and Evolution 14: e4585. \| Abstract	June 2023	Monitoring species to better understand their status, ecology, and management needs is a major expense for agencies tasked with biodiversity conservation. Community science data have the potential to improve monitoring for minimal cost, given appropriate analytical frameworks are established. We describe a framework for integrating data from the eBird community science platform with agency-collected monitoring data using a multi-state occupancy model. Our novel occupancy model accounts for the structural differences in eBird data and agency-collected monitoring data and allows for estimation of both occupancy and breeding probabilities. The framework was applied to Common Loons (Gavia immer) in Washington State. Common Loons are state listed in Washington as Sensitive and identified as a species of greatest conservation need, and little is known about their breeding distribution beyond the locations of known nesting pairs. Based on our model, we predicted that only 6.5% (95% Bayesian credible interval, BCI = 1.6%, 50.9%) of the 2324 sites in our sampling frame were occupied by Common Loons, though Common Loons were predicted to be breeding at 95% (95% BCI = 71.2%, 99.9%) of the lakes they occupied. We identified only 1 abiotic covariate – elevation – that was a useful predictor of occupancy or reproduction probabilities in Common Loons; improvements in the predictive power of our model might be achieved with information on difficult-to-monitor biotic covariates, such as fish community metrics. We found that state agency biologists were 16 times more likely to detect breeding Common Loons during a visit than were eBird users (94.2%, 95% BCI = 77.9%, 98.9% for agency biologists vs. 8.2%, 95% BCI = 6.3%, 10.4% for eBird users). However, the amount of effort expended by eBird users meant that they confirmed Common Loons at 94 sites while agency biologists confirmed them at just 24 sites. Importantly, though, certain information – namely, evidence of reproduction – was only contributed by agency biologists. Our results provide a better understanding of the distribution of Common Loons in Washington, while further demonstrating that community science data can be a valuable complement to agency-collected data, if appropriate frameworks are developed to integrate these data sources.
Sink, CE, KM Dugger, CA Hagen and JN Vradenburg. 2024. Living on the edge: identifying demographic bottlenecks in an isolated sage-grouse population. Wildlife Biology 2024: e01242, https://doi.org/10.1002/wlb3.01242.	September 2024
Simonsen, V., E. Stuber, and J.J. Fontaine. (2022) Examining the effects of patch size and nest density on artificial nest survival. The Wilson Journal of Ornithology -* 134(2): 182–192. https://doi.org/10.1676/19-00063	May 2022
Silver-Georges, I., S. A. Ceriani,M. Ware, M. Lamb, M. Lamont, J. Becker, R.R. Carthy, C, Matechik, J. Mitchell, R. Pruner, M. Reynolds, B. Smith, C. Snyder, and M. M. P. B. Fuentes. 2021. Using systems thinking to inform management of imperiled species: a case study with sea turtles. Biological Conservation 260: 109201 \| Abstract \| Publisher Website	June 2021	Management of imperiled species facing spatiotemporally dynamic threats is difficult. Systems thinking can inform their management by quantifying the impacts that they face. We apply systems thinking to the Northern Gulf of Mexico (NGM) loggerhead (Caretta caretta) Recovery Unit (RU), one of the smallest subpopulations of loggerheads nesting in the USA. We characterized disturbances to nests, management actions, and hatchling production across 12 nesting beaches used by this RU to explore how hatchling production would increase if disturbances were mitigated. Annual hatchling production at sites ranged from 470 to 18,191 hatchlings/year. Wash overs (19.3% nests/year), washouts (17.9% nests/year), and predation (13% nests/year) were the most common annual disturbances across sites. Focusing on the most impactful disturbances at just five sites could increase annual NGM RU hatchling production by 2.2–6.7%. Efforts to mitigate wash overs and washouts are ongoing in Alabama, but these may be futile against tropical cyclones, which accounted for >80% of washouts in the present study, and further require careful examination of associated adverse side-effects. Efforts to mitigate predation are common throughout this RU, but require improved knowledge of predator ecology to reach full potential. Systems thinking allowed us to create a simple model for assessing disturbances and management strategies in terms of hatchling sea turtles. This model can be augmented to run dynamic simulations of how disturbances and management actions impact hatchling production, and can be applied to other species with similar reproductive strategies.
Sievert, N., C. P. Paukert, J. B. Whittier, W. Daniel, D. M. Infante, and J. Stewart. 2022. A broad-scale stream fish community risk assessment based on predicted changes in climate in the Northeastern and Midwestern United States. Ecological Indicators 144. https://doi.org/10.1016/j.ecolind.2022.109493	November 2022
Sievert, N. A., C. P. Paukert, and J. B. Whittier. 2020. A Framework to Incorporate Established Conservation Networks into Freshwater Conservation Planning. Frontiers in Environmental Science: https://doi.org/10.3389/fenvs.2020.515081	December 2020
Sievert, N. A., A. J. Lynch, H. S. Embke, A. Robertson, M. Lang, A. L. Kaz, M. D. Robertson, S. R. Midway, L. Wszola, C. P. Paukert. 2023. CreelCat, a Catalog of United States Inland Creel and Angler Survey Data. Scientific Data 10: 762 (2023). https://doi.org/10.1038/s41597-023-02523-2. IP-152029. BAO Approval 8/13/2023.	November 2023
Siemiantkowski, M. J., C. S. Guy, T. M. Koel, L. M. Tronstad, C. R. Fredenberg, and L. R. Rosenthal. 2022. Combination of acoustic telemetry and side-scan sonar advances suppression efforts for invasive lake trout Salvelinus namaycush in a submontane lake. North American Journal of Fisheries Management. https://doi.org/10.1002/nafm.10855	December 2022
Siemer, W.F., T. Bruce Lauber, Stedman, R.C., Hurst, J.E., Sun, C.C., Fuller, A.K., Hollingshead, N., Belant, J.L. and Kellner, K.F. (2023). Perception and trust influence acceptance for black bears more than bear density or conflicts. Frontiers in conservation science, 4. doi:https://doi.org/10.3389/fcosc.2023.1041393.	January 2023
Siegel, J.V., S.A. Welsh, N.D. Taylor, and Q.E. Phelps. Size Structure, Age, Growth, and Mortality of Flathead Catfish in the Robert C. Byrd Pool of the Ohio and Kanawha Rivers. Journal of the Southeastern Association of Fish and Wildlife Agencies 10:10-16.	January 2023
Shi, Y., J.J. Homola, P.T. Euclide, D.A. Isermann, D.C. Caroffino, M.V. McPhee, and W.A. Larson. 2022. High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan. Evolutionary Applications. https://doi.org/10.1111/eva.13475	August 2022
Shi, Y., Dick, C.M., Karpan, K., Baetscher, D., Henderson, M.J., Sethi, S.A., McPhee, M.V., Larson, W.A. Towards absolute abundance for conservation applications: estimating the number of contributors via microhaplotype genotyping of mixed-DNA samples. submitted to Molecular Ecology Resources. \| Abstract	May 2023	Molecular methods including metabarcoding and qPCR have shown promises for estimating species abundance by quantifying the concentration of genetic material in field samples. However, the relationship between specimen abundance and detectable concentrations of genetic material is often variable in practice. DNA mixture analysis represents an alternative approach to quantify specimen abundance based on the identity of unique alleles in a sample. The DNA mixture approach provides novel opportunities to inform ecology and conservation by estimating the absolute abundance of target taxa through molecular methods; yet, challenges with genotyping many highly variable markers in mixed-DNA samples have prevented its widespread use. To advance molecular approaches for abundance estimation we explored the utility of microhaplotypes for DNA mixture analysis by applying a 125-marker panel to 1,179 Chinook salmon (<i>Oncorhynchus tshawytscha</i>) smolts from the Sacramento-San Joaquin Delta. We assessed the accuracy of DNA mixture analysis through a combination of mock mixtures containing DNA from up to 20 smolts and a trophic ecological application enumerating smolts in predator diets. Mock DNA mixtures of up to 10 smolts could reliably be resolved using microhaplotypes and increasing the panel size would likely facilitate identification of more individuals. However, while analysis of predator gastrointestinal tract contents indicated DNA mixture analysis could discern the presence of multiple prey items, poor DNA quality prevented accurate genotyping and abundance estimation. Our results indicate that DNA mixture analysis can perform well with high-quality DNA, but methodological improvements in genotyping degraded DNA are necessary before this approach can be used on marginal quality samples.
Shepard, B. B., P. Clancey, M. L. Nelson, C. G. Kruse, R. T. Al-Chokhachy, D. Drinan, M. L. Taper, and A. V. Zale. 2021. Evaluation of remote site incubators to incubate wild- and hatchery-origin Westslope Cutthroat Trout embryos. North American Journal of Fisheries Management 41:844-855. https://doi.org/10.1002/nafm.10588 \| Download	June 2021
Sheffer, R.J., S.R. Hogler, and D.A. Isermann. Submitted. Mark-recapture models accurately predict growth trajectories of known-age muskellunge in Green Bay, Lake Michigan. North American Journal of Fisheries Management. https://doi.org/10.1002/nafm.10757	February 2022
Sheehan, K.R. and S.A. Welsh. 2021. Comparison of geographically weighted regression of benthic substrate modeling accuracy on large and small wadeable streams. Journal of Geographic Information System 13:194-209. DOI: 10.4236/jgis.2021.132011	April 2021
Shashank Poudel, Twining, J.P., Stedman, R.C., Shravan Kumar Ghimire and Fuller, A.K. (2023). Ecological and anthropogenic drivers of leopard (Panthera pardus fusca) attack occurrence on humans in Nepal. People and nature, 5(6), pp.1977–1988. doi:https://doi.org/10.1002/pan3.10536. \| Abstract	August 2023	In Nepal, human-leopard conflict manifests primarily as livestock depredation and attack on humans, creating an important social, ecological, and management issue. In this study, we estimate the probability of leopard attack occurrence on humans and assess the influence of social and environmental variables on these attacks by analyzing reported cases of conflict. The data collected from online news and articles on incidents of leopard attack on humans were used in an occupancy model to evaluate the effect of the proportion of vegetation (forest, shrubs, and bushes), livestock density, and human population density on the probability of attack occurrence on humans. We searched online news reports from 2015-2019 for leopard attacks on humans in 59 districts across Nepal that generated 72 reports of leopard attacks (n = 49 human injury, 23 human death). The proportion of shrubs and bushes (other wooded lands) within a district was positively associated with the probability of leopard attack occurrence ψ (SE) = 0.58 (0.12). This could be a result of migration induced land abandonment in the hills which has led to the succession of farmlands to shrubs and bushes, which now offers habitat to wild animals. Leopards using shrub habitat potentially encounter humans collecting fodder and grazing livestock which could escalate conflict. Understanding leopard ecology and human dimension inquiry regarding conflict across different leopard habitat types will be crucial for achieving the goals of mitigating conflict and leopard conservation in Nepal.<i> </i>
Shamon, Hila. Et Al. 2024. Snapshot USA 2021: A third coordinated national camera trap survey of the United States - first trends. Ecology.doi.org/10.1002/ecy.4318 \| Abstract \| Download	May 2024	SNAPSHOT USA is a multi-contributor camera trap survey designed to survey mammals across the United States. The growing Snapshot dataset is useful for tracking wildlife populations responses to changes in land use, land cover, and climate across spatial and temporal scales. Here we present the SNAPSHOT USA 2021 dataset, the third national camera trap survey across the U.S. Data were collected across 109 camera trap arrays and consists of 1715 camera sites, 1849 camera deployments, the effort equaled 73,959 camera trap nights, and resulted in 172,957 observations of free-ranging mammals, birds, and humans. As an example of the potential uses, we analyze all 3 years of survey data to examine the proportion of change in occupancy of two sympatric common carnivores and two sympatric common ungulates: red fox (Vulpes vulpes), coyote (Canis latrans), mule deer (Odocoileus hemionus), and white-tailed deer (Odocoileus virginianus). We considered annual arrays to be comparable if separated by < 10 km and represented similar habitat. White-tailed deer occupancy remained stable across all years (mean proportion 2021/2019: 1.03 ± 0.38 SD). Occupancy proportions (mean proportion 2021/2019) between years for the other species appear stable for mule deer (0.93 ± 0.8 SD), increasing for coyote (1.34 ± 0.56 SD), and decreasing for red fox (0.74 ± 0.79 SD), but in each case the variability between regions precludes significance at the national level. Data collected across years can detect changes in species occurrence, but assessment at the national level require examination of occurrence in relation to land cover and climate gradients.
Shamon, Hila, Roi Maor, Michael V. Cove, Roland Kays, Jessie Adley, Peter D. Alexander, David N. Allen, et al. 2024. “ SNAPSHOT USA 2021: A Third Coordinated National Camera Trap Survey of the United States.” Ecology e4318. https://doi.org/10.1002/ecy.4318	May 2024
Shamaskin, A.V., M.E. Colvin, L.E. Miranda. 2023. Evaluating regional length limits in freshwater fisheries. Canadian Journal of Fisheries and Aquatic Sciences. http://dx.doi.org/10.1139/cjfas-2022-0179 \| Abstract	April 2023	Length limits are often used in recreational fisheries management to prevent overharvest and manipulate fish size distributions. These regulations are ideally customized to meet water-specific stock dynamics and fishery objectives. However, in districts with numerous discrete waters, fisheries are commonly managed with a universal regional regulation. Evaluating alternative regional length limits requires consideration of management objectives that may not be important at the single-system level, but that emerge as relevant at the regional scale, such as uniformity of regional harvest, diversity of average catch sizes, and opportunity to harvest. We developed a flexible tool for evaluating regional length limits. The tool joins the well-established Beverton-Holt yield-per-recruit model with elements of decision-support methods. The model quantifies regional management objectives as utility functions that are weighted and summed into a single value used to evaluate alternative length limits. The flexibility of the tool stems from its capacity to consider a mixture of stock parameters and associated uncertainty to evaluate multiple length limits, weighing an array of regional fishery objectives quantified by various performance metrics. This adjustability affords flexibility to consider a diversity of options that can stimulate innovation in setting regional length limits. We demonstrate the model by evaluating varying length limits on fishery objectives related to the management of hypothetical Yellow Perch populations and real Black Crappie populations.
Shaftel, R., Mauger, S., Falke, J., Rinella, D., Davis, J., and L. Jones. Thermal diversity of salmon streams in the Matanuska-Susitna Basin, Alaska. Journal of the American Water Resources Association 56(4) 630-646. https://doi.org/10.1111/1752-1688.12839.	August 2020
Severud, W.J., D.Wolfson, J. Fieberg, and D.E. Andersen. 2022. Sandhill crane colt survival in Minnesota. Journal of Fish and Wildlife Management https://doi.org/10.3996/JFWM-21-097 \| Abstract	April 2022	Age-structured population models require reliable estimates of cohort-specific survival rates, yet vital rates of younger age classes are often difficult to estimate because of the logistical challenges of monitoring young animals. As part of a study of sandhill cranes <i>Antigone canadensis </i>in the zone of contact between breeding distributions of the Eastern Population and Mid-continent Population in Minnesota, United States, we monitored first summer survival of 34 sandhill cranes (hereafter, “colts”) using VHF and/or GPS-GSM transmitters. We estimated daily survival probabilities from 19 to 120 days post-hatch using a generalized linear model accounting for interval censoring, resulting in an estimated period survival rate of 0.52 (90% confidence interval 0.36–0.71) over summer (100 days). Estimated daily probabilities of survival increased as colts became older and fledged (at 70–75 days post-hatch), when they presumably became less vulnerable to predation. Causes of mortality were mostly unknown aside from one case of a collision with a vehicle. There is a scarcity of published colt survival rate estimates for sandhill cranes and what is available varies widely by study site. Region-specific sandhill crane colt survival rate estimates can inform future management efforts and inform population dynamics research and overall natural history knowledge of sandhill cranes.
Sethi, S. A., A. J. Poulton, A. Koeberle, D. Linden, D. R. Diefenbach, F. E. Buderman, M. J. Casalena, K. Duren. 2024. Multistage time-to-event models improve survival inference by partitioning mortality processes of tracked organisms. Scientific Reports 14:14628. https://doi.org/10.1038/s41598-024-64653-w \| Download	June 2024
Sethi SA, Carey MP, Gerken J, Harris B, Cunningham C, Wolf N, Restrepo F, Ashline J (2022) Juvenile salmon habitat use drives variation in growth and highlights vulnerability to river fragmentation. Ecosphere 13:e4192. \| Abstract	July 2022	Widespread stream network fragmentation from dams and culverts has altered habitat connectivity in river ecosystems and presents an acute threat to migratory fish. To support watershed management for an iconic migratory fish group, we assessed juvenile salmon growth outcomes across habitat use strategies and characterized how these life histories may be impacted by stream connectivity loss. Juvenile coho salmon (<i>Oncorynchus kisutch</i>) in the Big Lake drainage, Alaska, U.S.A., were individually tracked over 2012-2013 and categorized into habitat use behaviors, with fish either remaining in streams throughout freshwater residency or migrating seasonally to overwinter in lake habitats. Size, growth rate, and body condition of smolts (n=1,113) were compared across habitat use strategies. Juvenile coho salmon that moved seasonally to lake overwintering habitats, the most frequently observed strategy, grew faster and were significantly larger as smolts compared to their counterparts who remained in streams exclusively (spring age 1 fish: 18% larger by weight, 9% faster growth rate; spring age 2+ fish: 26% heavier, 11% faster growth). Environmental data from a subset of overwinter lakes indicate that greater foraging opportunity and lower energy costs may be implicated in growth advantages conferred by lentic overwintering strategies. Habitat use strategies requiring seasonal migrations, however, increased exposure to stream connectivity loss, and fish blocked from accessing a potential overwinter headwater lake by a culvert and dam had lowest body condition among study groups. Stream network fragmentation restricts access to preferred overwinter habitats, and our findings suggest this may constrain freshwater rearing strategies associated with strong juvenile coho salmon growth. As size at smolt has been implicated as a driver of salmon survival through ocean residency, reduced freshwater habitat connectivity during juvenile stages may have deleterious impacts on later marine life stages. Consequently, conservation of stream connectivity across lentic and lotic habitats represents an important watershed management priority for juvenile salmon.
Sethi SA, Ashline J, Harris B, Gerken J, Restrepo F. (2021) Connectivity between lentic and lotic freshwater habitats identified as a conservation priority for coho salmon. Aquatic Conservation: Marine and Freshwater Ecosystems, 31:1791-1801. \| Abstract	July 2021	1. Juvenile Pacific salmon exhibit diverse habitat use and migration strategies to navigate high environmental variability and predation risk during freshwater residency. Increasingly, urbanization and climate-driven hydrological variability present further stressors for these anadromous species, emphasizing a need to conserve freshwater habitat integrity to support life history diversity as a buffer against ongoing ecosystem changes.<br>2. To inform catchment management for salmon, information on the distribution and movement dynamics of juvenile fish throughout the annual seasonal cycle is needed. While a number of studies have assessed the ecology of juvenile coho salmon (<i>Oncorhynchus kisutch</i>) during summer and fall seasons, catchment use by this species throughout the annual cycle is less well characterized, particularly in high latitude systems.<br>3. Here, <i>n</i> = 3,792 tagged juvenile coho salmon were tracked throughout two complete annual cycles to assess basin-wide distribution and movement behavior of this species in a subarctic, ice-bearing catchment.<br>4. Juvenile coho salmon in the Big Lake, Alaska, basin exhibited multiple habitat use and movement strategies across seasons; however, summer rearing in lotic mainstem environments followed by migration to lentic overwinter habitats was identified as a prominent behavior, with two thirds of tracked fish migrating en masse to concentrate in a small subset of upper catchment lakes for the winter. In contrast, the most significant tributary overwintering site (8% of tracked fish) occurred below a culvert and dam blocking juvenile fish passage to a headwater lake, indicating these fish may have been restricted from reaching preferred lentic overwinter habitats.<br>5. These findings emphasize the importance of maintaining aquatic connectivity to lentic habitats as a conservation priority for coho salmon during freshwater residency.
Setash, C. M., W. L. Kendall, and D. Olson. 2020. Nest site selection influences cinnamon teal nest survival in Colorado. Journal of Wildlife Management 84:542-552.	January 2020
Setash, C. M., W. L. Kendall, and D. Olson. 2020. Nest attendance patterns during incubation influence reproductive success of a ground-nesting bird. Ibis DOI: 10.1111/ibi.12838.	March 2020
Serota, M.W., K.J. Barker, L.C. Gigliotti, S.M.L. Maher, A.L. Shawler, G.R. Zuckerman, W. Xu, G. Verta, E. Templin, C. Andreozzi, and A.D. Middleton. 2023. Incorporating human dimensions improves wildlife translocation outcomes. Nature Communications 14(1): 2119.	April 2023
Sergeant, C.J., Falke, J.A., Bellmore, J.R., Bellmore, R.A., and R.L. Crumley. 2020. A classification of streamflow patterns across the coastal Gulf of Alaska. Water Resources Research. e2019WR026127. https://doi.org/10.1029/2019WR026127.	February 2020
Sergeant, C.J., Bellmore, J.R., Bellmore, R.A., Falke, J.A., Mueter, F.J., Westley, P.A.H. 2023. Hypoxia vulnerability in the salmon watersheds of Southeast Alaska. Science of the Total Environment. dx.doi.org/10.1016/j.scitotenv.2023.165247	October 2023
Sepulveda, A., R. Al-Chokhachy, M. B. Laramie, K. Crapster, L. Knotek, B. Miller, A. V. Zale, and D. S. Pilliod. 2021. It’s complicated…environmental DNA as a predictor of trout and char abundance in streams. Canadian Journal of Fisheries and Aquatic Sciences 78:422-432. doi.org/10.1139/cjfas-2020-0182. \| Download	April 2021
Sells, S.N., M.S. Mitchell, K.M. Podruzny, D.E. Ausband, D.J. Emlen, J.A. Gude, T.D. Smucker, D.K. Boyd, and K.E. Loonam. 2022. Competition, prey, and mortalities influence gray wolf group size. Journal of Wildlife Management. 86: e22193.	February 2022
Sells, S.N., M.S. Mitchell, D.E. Ausband, A.D. Luis, D.J. Emlen, K.M Podruzny, and J.A. Gude. 2022. Economical defense of resources structures territorial space use in a cooperative carnivore. Proceedings of the Royal Society, B. 289: 20212512. \| Abstract	January 2022	Ecologists have long sought to understand space use and mechanisms underlying patterns observed in nature. We developed an optimality landscape and mechanistic territory model for gray wolves (<i>Canis lupus</i>) to understand mechanisms driving space use and how wolves structure territories. In the model, simulated packs selected territories to economically meet resource requirements by selecting patches with greatest net value, accounting for benefits, costs, and tradeoffs of defending and using space on the optimality landscape. Economical territory selection successfully predicted the population’s distribution, territory sizes of packs, and how spatial requirements are influenced by local ecosystems, prey density, competitor density, and human-caused mortality risk. Economical territory selection is a mechanistic bridge between space use and animal distribution on the landscape. This knowledge can inform conservation.
Sells, S. N., and M. S. Mitchell. In press. The economics of territory selection. Ecological Modelling.	October 2020
Sells, S. N., C. M. Costello, P. M. Lukacs, L. L. Roberts, & M. A. Vinks. 2023. Predicted connectivity pathways between grizzly bear ecosystems in Western Montana. Biological Conservation, Volume 284, 110199, ISSN 0006-3207, https://doi.org/10.1016/j.biocon.2023.110199 \| Abstract \| Download	July 2023	Habitat and corridor mapping are key components of many conservation programs. Grizzly bear populations in the continental US are fragmented and connectivity among federal recovery areas is a conservation goal. Building on recent work, we modeled movements to predict areas of connectivity, using integrated step selection functions (iSSFs) developed from GPS-collared grizzly bears (F = 46, M = 19) in the Northern Continental Divide Ecosystem (NCDE). We applied iSSFs in a >300,000 km<sup>2</sup> area including the NCDE, Cabinet–Yaak (CYE), Bitterroot (BE), and Greater Yellowstone (GYE) Ecosystems. First, we simulated directed movements (randomized shortest paths with 3 levels of exploration) between start and end nodes across populations. Second, we simulated undirected movements from start nodes in the NCDE, CYE, or GYE (no predetermined end nodes). We summarized and binned results as iSSF classes (1 = lowest relative predicted use; 10 = highest relative predicted use) and evaluated predictions using 127 outlier grizzly bear locations. Connectivity pathways were primarily associated with mountainous areas and secondarily with river and stream courses in open valleys. Values at outlier locations indicated good model fit and mean iSSF classes at outlier locations (≥7.4) and Spearman rank correlations (≥0.87) were highest for undirected simulations and directed simulations with the highest level of exploration. Our resulting predictive maps will facilitate on-the-ground application of this research for prioritizing habitat conservation, human-bear conflict mitigation, and transportation planning. Additionally, our overall modeling approach has direct utility for myriad species and conservation applications.
Sells SN, Costello CM (2024) Predicting future grizzly bear habitat use in the Bitterroot Ecosystem under recolonization and reintroduction scenarios. PLOS ONE 19(9): e0308043. https://doi.org/10.1371/journal.pone.0308043 \| Abstract \| Download	September 2024	Many conservation actions must be implemented with limited data. This is especially true when planning recovery efforts for extirpated populations, such as grizzly bears (<i>Ursus arctos</i>) within the Bitterroot Ecosystem (BE), where strategies for reestablishing a resident population are being evaluated. Here, we applied individual-based movement models developed for a nearby grizzly bear population to predict habitat use in and near the BE, under scenarios of natural recolonization, reintroduction, and a combination. All simulations predicted that habitat use by grizzly bears would be higher in the northern half of the study area. Under the natural recolonization scenario, use was concentrated in Montana, but became more uniform across the northern BE in Idaho over time. Use was more concentrated in east-central Idaho under the reintroduction scenario. Assuming that natural recolonization continues even if bears are reintroduced, use remained widespread across the northern half of the BE and surrounding areas. Predicted habitat maps for the natural recolonization scenario aligned well with outlier and GPS collar data available for grizzly bears in the study area, with Spearman rank correlations of ≥0.93 and mean class values of ≥9.1 (where class 10 was the highest relative predicted use; each class 1 – 10 represented 10% of the landscape). In total, 52.4% of outlier locations and 79% of GPS collar locations were in class 10 in our predicted habitat maps for natural recolonization. Simulated grizzly bears selected habitats over a much larger landscape than the BE itself under all scenarios, including multiple-use and private lands, similar to existing populations that have expanded beyond recovery zones. This highlights the importance of recognizing and planning for the role of private lands in recovery efforts, including understanding resources needed to prevent and respond to human-grizzly bear conflict and maintain public acceptance of grizzly bears over a large landscape.
Seguy, L. and J.M. Long. 2021. Perceived ecological threats and economic benefits of non-native black bass in the United States. Fisheries 46:56-65. DOI: 10.1002/fsh.10520	November 2020
Scott, A. M., and A. K. Carlson. 2024. A new water temperature modeling approach to predict thermal habitat suitability for nonnative cichlids in Florida rivers. Journal of Freshwater Ecology 39(1):e2405721.	October 2024
Scott L. Morford, Brady W. Allred, Dirac Twidwell, Matthew O. Jones, Jeremy D. Maestas, Caleb P. Roberts, David E. Naugle. Herbaceous production lost to woody encroachment in U.S. rangelands. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.14288 \| Abstract	October 2023	Rangelands of the United States provide ecosystem services that sustain biodiversity and rural economies. Native tree encroachment is a recognized and long-standing conservation challenge to these landscapes, but its impact is often overlooked due to the slow pace of tree invasions and the positive public perception of trees. Here we show that tree encroachment is a dominant change agent in U.S. rangelands; tree cover has increased by more than 76,000 km2 over 30 years, and more than 25% of U.S. rangelands are now experiencing sustained tree cover expansion. Further, we use machine learning methods to estimate the potential herbaceous production (forage) lost to tree encroachment. Since 1990 roughly 315 Tg of herbaceous biomass has been lost, totaling some $5 billion in foregone revenue to agricultural<br>producers. These results suggest that tree encroachment is similar in scale and magnitude to row-crop conversion, another primary cause of rangeland loss in the U.S. Prioritizing conservation efforts to prevent tree encroachment in rangelands can bolster ecosystem and economic sustainability of these landscapes, particularly among privately-owned lands threatened by land-use conversion.
Scoggins, M., D.B. Booth, M. Fork, R. Hale, R.J. Hawley, A.H. Roy, E.E. Bilger, N. Bond, M.J. Burns, T. Fletcher, A. Gonzalez, K.G. Hopkins, K.H. Macneale, E. Marti, S.K. McKay, M.W. Neale, M.J. Pail, B. Rios-Touma, K.L. Russell, R.F. Smith, S. Wenger, and S. Wagner. 2022. Community-powered urban stream restoration: A framework for sustainable and resilient urban ecosystems. Freshwater Science 41: 404-419. https://doi.org/10.1086/721150 \| Publisher Website	September 2022
Schweiger, B.R., J.K. Frey, and J.W. Cain III. 2021. A case for multiscale habitat selection studies of small mammals. Journal of Mammalogy 102:1249-1265. \| Download	October 2021
Schwabenlander, M.D., J.C. Bartz, M. Carstensen, A. Fameli, L. Glaser, R.J. Larsen, M. Li, R. Shoemaker, G. Rowden, S. Stone, W.D. Walter, T.M. Wolf, P.A. Larsen. 2024. Prion forensics: a multidisciplinary approach to investigate CWD at an illegal deer carcass disposal site. Prion, 18(1):72-86; DOI: 10.1080/19336896.2024.2343298. \| Abstract	April 2024	Chronic wasting disease (CWD) is confirmed in 30 US states, three Canadian provinces, and in Sweden, Norway, Finland, and South Korea. Although its geographic origin is speculative, much of the disease spread in North America over the past seven decades is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD. Regulatory agencies provide guidance and proper disposal opportunities for the control of CWD in endemic areas and to reduce the risk of introduction to new areas. Upon the discovery of an illegal carcass dumping site associated with a CWD-positive captive cervid facility, we employed a veterinary forensics approach to investigate the existence of CWD-positive materials within the site. Animal remains were examined to determine species, age, sex, relatedness, and CWD status. We utilized advanced anatomic, entomologic, genetic, and prion amplification methods to discover CWD-positive remains across multiple age classes of white-tailed deer. CWD prions were detected via RT-QuIC in 13 of 49 carcass samples with 9 of 13 from fawns, 1 of 13 from a yearling, 2 of 13 from adults, and 1 of 13 from a deer of unknown age. We also identified CWD-positive fly larvae associated with positive remains. Our multi-methods approach provides the foundation for the veterinary forensic investigation of CWD spread by means of cervid carcasses.
Schwabenlander, M.D., J.C. Bartz, M. Carstensen, A. Fameli, L. Glaser, R.J. Larsen, M. Li, R. Shoemaker, G. Rowden, S. Stone, W.D. Walter, T.M. Wolf, P.A. Larsen. 2024. Prion forensics: a multidisciplinary approach to investigate CWD at an illegal deer carcass disposal site. Prion, 18(1):72-86; DOI: 10.1080/19336896.2024.2343298. \| Abstract	April 2024	Chronic wasting disease (CWD) is confirmed in 30 US states, three Canadian provinces, and in Sweden, Norway, Finland, and South Korea. Although its geographic origin is speculative, much of the disease spread in North America over the past seven decades is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD. Regulatory agencies provide guidance and proper disposal opportunities for the control of CWD in endemic areas and to reduce the risk of introduction to new areas. Upon the discovery of an illegal carcass dumping site associated with a CWD-positive captive cervid facility, we employed a veterinary forensics approach to investigate the existence of CWD-positive materials within the site. Animal remains were examined to determine species, age, sex, relatedness, and CWD status. We utilized advanced anatomic, entomologic, genetic, and prion amplification methods to discover CWD-positive remains across multiple age classes of white-tailed deer. CWD prions were detected via RT-QuIC in 13 of 49 carcass samples with 9 of 13 from fawns, 1 of 13 from a yearling, 2 of 13 from adults, and 1 of 13 from a deer of unknown age. We also identified CWD-positive fly larvae associated with positive remains. Our multi-methods approach provides the foundation for the veterinary forensic investigation of CWD spread by means of cervid carcasses.
Schwabenlander, M.D., G. Rowden, S. Stone, R. Shoemaker, L.L. Lindsey, J.D. Oliver, L. Glaser, M. Carstensen, J.C. Bartz, W.D. Walter, R.J. Larsen, T.M. Wolf, P.A. Larsen. 2022. Implementing a veterinary forensics approach to investigate chronic wasting disease at a deer carcass disposal site. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022. \| Abstract	July 2022	Chronic wasting disease (CWD) is confirmed in 29 US states, three Canadian provinces, and in Sweden, Norway, Finland, and South Korea. Although its geographic origin is speculative, much of the disease spread in North America over the past seven decades is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD. Regulatory agencies provide guidance and proper disposal opportunities for the control of CWD in endemic areas and to reduce the risk of introduction to new areas. Upon the discovery of an illegal carcass dumping site associated with a CWD-positive captive cervid facility, we employed a veterinary forensics approach to investigate the existence of CWD-positive materials within the site. Animal remains were examined to determine species, age, sex, relatedness, and CWD status. We utilized advanced anatomic, entomologic, genetic, and prion amplification methods to discover CWD-positive remains across multiple age classes of white-tailed deer. CWD prions were detected via RT-QuIC in 13 of 49 carcass samples with 9 of 13 from fawns, 1 of 13 from a yearling, 2 of 13 from adults, and 1 of 13 from a deer of unknown age. We also identified CWD-positive fly larvae associated with positive remains. Our multi-methods approach provides the foundation for the veterinary forensic investigation of CWD spread by means of cervid carcasses.
Schuyler, E.M., C. A. Hagen, C. R. Anthony, L. J. Foster, and K. M. Dugger. 2022. Habitat recovery after large-scale wildfire leads to mismatch in space use by sagebrush obligate. Ecosphere 2022;13:e4179. https://doi.org/10.1002/ecs2.4179.	September 2022
Schuster, C.J., T. Kreul, E. Al-Samarrie, J.T. Peterson, J.L. Sanders, M.L. Kent. Progression of infection and detection of Pseudoloma neurophilia in zebrafish Danio rerio Hamilton by PCR and histology. Journal of Fish Diseases https://doi.org/10.1111/jfd.13675 \| Abstract \| Publisher Website	July 2022	<i>Pseudoloma neurophilia</i> is an important threat to the zebrafish (<i>Danio rerio</i>) model, as it is the most common infectious agent found in research facilities. This parasite can cause clinical disease, but more importantly is a causative agent of non-protocol induced variation in research utilizing zebrafish as an animal model. In this study, we tracked the progression of infection using PCR and histological diagnostic tests. The first experiment compared the application of diagnostic tools for detection of <i>P. neurophilia</i> and showed that whole-body analysis by qPCR (WB-qPCR) can be a standardized process and is comparable to previously published assays using neural tissue. We also evaluated the course of infection in experimentally infected fish, revealing that WB-qPCR is much more sensitive than histology. the parasite was detectable as early as 4 days post exposure (dpe) with WB-qPCR, whereas it was undetected by histology until 92 dpe. In this study, we also added a second slide for histologic analyses, and this increased detection in our combined data set from experiments from 24% to 26%.
Schuster, C.J., M.L. Kent, J. Peterson, and J.L. Sanders. 2022. Multi-state occupancy model estimates probability of detection of an aquatic parasite using environmental DNA: Pseudoloma neurophilia in zebrafish aquaria. Journal of Parasitology https://doi.org/10.1101/2022.02.16.480730 \| Abstract \| Publisher Website	July 2022	<i>Pseudoloma neurophilia</i> is the most common pathogen reported in zebrafish (<i>Danio rerio</i>) research facilities. Assays for prevalent zebrafish pathogens are continually expanding, however for <i>P. neurophilia</i>, the only diagnostic methods available are through lethal sampling, often requiring euthanasia of the entire population for accurate estimates of prevalence in small populations. Thus, there is a need to develop non-lethal screening methods that are both sensitive and informative. Here, we describe a nonlethal assay to detect <i>Pseudoloma neurophilia</i> in tank water using a previously developed qPCR assay that was adapted to the droplet digital PCR (ddPCR) platform. The assay detected concentrations as low as 77.5 spores/L and was specific for<i> P. neurophilia.</i> The assay was then validated by testing water from five tanks with infected zebrafish over a three-month period. Each tank was tested using three different water sampling methods: water from flowing tanks, static water, or water from static spawning events. Prevalence data and occupancy modeling revealed that samples collected in static conditions were more informative than samples from flow-through conditions, with prevalence of positive samples at 80% or higher compared to 47%, respectively. Prevalence of positive water samples correlated with prevalence of infection in fish, determined by qPCR.
Schumann, D.A., M.E. Colvin, L.E. Miranda, and D.T. Jones-Farrand. 2020. Occurrence and co-occurrence patterns of gar in river-floodplain habitats: methods to leverage species interactions to benefit distributional models. North American Journal of Fisheries Management 40:622-637. https://afspubs.onlinelibrary.wiley.com/doi/abs/10.1002/nafm.10402	June 2020
Schumann, D.A., K.N.B. Graeb, J. Pfrimmer, J.D. Stafford, and S.R. Chipps. 2021. The local responses of aquatic ecosystems to adjacent grassland conversion: can streams of dreams exist in a degraded riverscape? Aquatic Conservation: Marine and Freshwater Ecosystems 31:2481-2495.	October 2021
Schulz, J.H., A.C. Totoni, S.A. Wilhelm Stanis, C.J. Li, M. Morgan, D.M. Hall and E.B. Webb. In review. Policy comparison of lead hunting ammunition bans and voluntary nonlead programs for California condors. Wildlife Society Bulletin \| Abstract	June 2023	California condors (<i>Gymnogyps californianus</i>) are critically endangered and negatively affected by lead poisoning from spent lead-based hunting ammunition. This issue is surrounded by complex policy discussions, multiple mitigation options, and differing stakeholders’ values. Because lead poisoning is the primary factor affecting condor population growth, California Fish and Game Commission banned lead hunting ammunition during 2008 in southern California. Another regulation for a statewide lead hunting ammunition ban was adopted in 2013 and fully implemented 2019. Alternatively, Arizona Game and Fish Department instituted an outreach and awareness program encouraging voluntary use of nonlead hunting ammunition in the northern portion of the state during 2005; a similar program was initiated in Utah during 2009 and accelerated in 2012. Given the data linking condor mortality to lead bullet fragments, environmental groups petitioned several federal agencies during 2010–2016 to ban lead hunting ammunition on public lands. Federal agencies declined to regulate lead ammunition and federal courts ruled against petitioner’s requests, but advocacy from environmental groups has persisted. Currently, fragmented outreach and awareness programs encouraging voluntary use of nonlead exist around the country with little or no strategic planning. Human health is also an environmental justice issue through ingestion of lead bullet fragments in ground venison from hunter donations of game meat. Evaluating policy effectiveness in the three-state region includes monitoring condor blood lead levels, population status, and hunter awareness of the issue and use of nonlead hunting ammunition.
Schultz, J.H., S.A. Wilhelm Stanis, M. Morgan, C.J. Lie, D.M. Hall and E.B. Webb. 2021. Perspectives from natural resource professionals: Attitudes of natural resource professionals about voluntary use of nonlead hunting ammunition. Journal of Outdoor Recreation and Tourism 33:100341	March 2021
Schultz, J.H., S.A. Wilhelm Stanis, D.M. Hall and E.B. Webb. 2021. Until it's a regulation, it's just not my fight: Complexities of a voluntary nonlead hunting ammunition program. Journal of Environmental Management 277:111438 \| Abstract	January 2021	Wildlife and human health are at risk of lead exposure from lead ammunition used for deer hunting. Lead exposure persists for bald eagles due to bullet fragments in game animal gut piles and unretrieved carcasses, and is also a human health risk when venison is procured using lead ammunition. Programs encouraging the voluntary use of nonlead ammunition have become a popular approach mitigating these effects. This study explored attitudes and experiences of U.S. Fish and Wildlife Service (FWS) staff implementing an outreach program encouraging deer hunters to voluntary use nonlead ammunition on 54 National Wildlife Refuges (NWRs) in the Upper Midwest U.S. to understand factors affecting program implementation by field staff. During 2017–2019, we conducted 29 semi-structured interviews of FWS staff along with 365 responses from an open-ended question on an online survey. Twelve themes emerged from the data and grouped into three broad categories: (1) challenges of dealing with complex issues, (2) importance of messengers and messages, and (3) push-back from staff. Challenges of dealing with complex included administrative restraint and uncertainty, scope and scale of program, human health not an agency responsibility, contextual political influences, and public-private collaborations. Importance of messengers and messages included the importance of experience, and salience of human health risk. Finally, push-back from staff included skepticism of the science and motives behind the program, competing priorities for refuge staff, differing perceptions of regulatory and voluntary approaches, cost and availability of nonlead ammunition, and disregard by some about lead ammunition and human health risks. These findings suggest staff identified numerous challenges implementing a voluntary nonlead ammunition program, many of which are external factors beyond the control of the participants. Understanding the factors and their influence on program implementation may help guide a more rigorous program evaluation examining long-term efforts encouraging the voluntary use of nonlead ammunition by deer hunters.
Schultz, J.H., S.A. Wilhelm Stanis, C.J. Lie, M. Morgan and E.B. Webb. Exploring factors affecting staff support of a voluntary, nonlead ammunition outreach program. Applied Environmental Education and Communication \| Abstract	June 2021	Exposure to spent lead ammunition is a serious issue for bald eagles in the Upper Midwestern U.S. An outreach program was initiated by the U.S. Fish and Wildlife Service (USFWS) to address this concern by encouraging deer hunters to voluntarily use nonlead ammunition. This paper analyzes some factors influencing program support among USFWS staff in 2017 and 2018, including the use of nonlead ammunition and lead poisoning in wildlife. Results from pooled multiple imputation showed attitudes toward eagles’ lead risk and importance of informational materials had the strongest effect on program support, followed by an individual’s innovation score. Although previous studies have focused on influencing hunter behavior, our research explored attributes among staff and their support for the outreach program. To enhance program support, different types of staff training might be necessary, depending on perceived eagles’ lead risk, importance of informational materials, and individuals’ innovativeness. Implications of these findings are discussed.
Schroeder,S. A. D. C. Fulton, L. Cornicelli, and L.E. McInenly. 2020. Recreation conflict, coping, and satisfaction: Minnesota grouse hunters’ conflicts and coping response related to all-terrain vehicle users, hikers, and other hunters,Journal of Outdoor Recreation and Tourism,Volume 30,100282 DOIL 10.1016/j.jort.2020.100282	May 2020
Schroeder, S.A., Landon, A., Cornicellis, L, Fulton, D.C. and McInenly, L.2021. Institutional trust, beliefs and evaluation of regulations, and management of chronic wasting disease (CWD). Human Dimensions of Wildlife. 26, 228-244. DOI: 10.1080/10871209.2020.1808915	August 2020
Schroeder, S.A., A.C. Landon, D.C. Fulton, L. McInenly. 2021. Social identity, values, and trust in government: How stakeholder group, ideology, and wildlife value orientations relate to trust in a state agency for wildlife management. Biological Conservation, 261 DOI: 10.1016/j.biocon.2021.109285 \| Abstract	September 2021	Our objective was to understand how social identity and values influenced general public and stakeholder trust in a state wildlife management agency (SWMA). In particular, we wanted to examine how stakeholder group, ideology, and wildlife value orientation influenced trust in a SWMA. Data were derived from a study of state residents, hunters and livestock producers related to wolf management. Results suggest differences in agency trust correlated with all three factors and the interaction between stakeholder group and wildlife value orientation. Livestock producers reported lower levels of trust in the agency, compared to hunters and the general public. Individuals with conservative or middle-of-the-road ideologies reported less trust in the agency than liberals did. Respondents with traditional wildlife values also had less trust in the agency compared to mutualist, pluralist, and distanced respondents. Results suggested parallels in the ideologies and wildlife value orientations of livestock producers and hunters, although these groups differed significantly in their trust in the agency. Agencies face the challenge of managing common-pool resources for stakeholders who hold different values and ideologies, and who are differentially affected by management decisions.
Schroeder, S.A., A. Landon, L.J. Cornicelli, D.C. Fulton, L. McInenly. 2021. Cognitive and behavioral coping in response to wildlife disease: The case of hunters and chronic wasting disease. Human Dimensions of Wildlife (Published online 4/30/2021). DOI: 10.1080/10871209.2021.1919340 \| Abstract	April 2021	Studying recreation coping is important because some coping may provoke distress, and lead to departure from participation. The transactional stress coping model has been used to examine response to social conditions (e.g., conflict, crowding) in outdoor recreation. Building on this work, we explored how Minnesota deer hunters coped with the presence of chronic wasting disease (CWD) in the state. Results are based on a survey of 2018 firearm deer hunters. We examined hunters’ reported behavioral intentions in scenarios related to the presence of CWD, and if the disease affected human health. Results suggest that most hunters would cope using product shift (i.e., eating meat after a “CWD not detected” test result) rather than displacement (i.e. hunting elsewhere or not hunting). Hunters who may cope by quitting hunting reported lower levels of involvement and higher levels of concern about CWD. Results have implications for CWD management in the state.
Schroeder, S., L. Cornicelli, D.C. Fulton, A. Landon, L. McInenly, & S. Cordts. Explaining Support for Mandatory versus Voluntary Conservation Actions among Waterfowlers. Human Dimensions of Wildlife, 26(4): 337-355. DOI: 10.1080/10871209.2020.1830205	October 2020
Schroeder, S. A., Landon, A. C., Fulton, D. C., & McInenly, L. E. 2022. On the Multiple Identities of Stakeholders in Wolf Management in Minnesota, United States. FRONTIERS IN ECOLOGY AND EVOLUTION, 10. \| Abstract	June 2022	Social identity theory offers a means to understand attitudes about wolves, with consequences for management support. Using data from a mail survey about wolves, we explored relationships among seven identities (i.e., wolf advocate, hunter, environmentalist, nature enthusiast, farmer, trapper, conservationist) using multidimensional scaling (MDS) and principal components analysis (PCA). We examined how identities correlated with political orientation, trust in a wildlife management agency, wildlife value orientations (WVOs) and attitudes about wolves, and we evaluated whether WVOs mediated the relationship between identities and attitudes. PCA suggested two factors, while MDS and correlations found diversity beyond these factors. Hunter identity was most strongly associated with a domination WVO and conservative political ideology. Farmer identity was most strongly associated with agency distrust and negative wolf attitudes. Wolf advocate was most strongly associated with a mutualism WVO, agency trust, and positive wolf attitudes. Conservationist identity was positively correlated with all other identities. WVOs partially mediated the relationship between identities and attitudes.
Scholl, E. A., W. F. Cross, and C. S. Guy. 2022. Connecting geomorphology, biodiversity, and ecosystem function in large riverscapes. Oikos http://doi.org/10.1111/oik.09431	October 2022
Scholl, E. A., W. F. Cross, C. V. Baxter, and C. S. Guy. 2020. Uncovering process domains in large rivers: Patterns and potential drivers of benthic substrate heterogeneity in two North American riverscapes. Geomorphology. https://doi.org/10.1016/j.geomorph.2020.107524	December 2020
Scholl, E. A., W. F. Cross, C. S. Guy, A. J. Dutton, and J. R. Junker. 2023. Landscape diversity promotes stable food-web architectures in large rivers. Ecology Letters 26:1740-1751. http://doi.org/10.1111/ele.14289	July 2023
Schmidt, J.S., L.A., Bruckerhoff, H., Salehabadi, and J., Wang. 2022. Chapter 10: The Colorado River. In: Large Rivers: Geomorphology and Management. (eds) A. Gupta. Wiley-Blackwell.https://doi.org/10.1002/9781119412632.ch10	February 2022
Schmidt, J.H., W.L. Thompson, T.L. Wilson, J.H. Reynolds. 2022. Understanding the impacts of the detection process on distance sampling surveys: selecting among approaches and minimizing total error. Wildlife Monographs 210: e1070. https://doi.org/10.1002/wmon.1070 \| Abstract	July 2022	Wildlife population estimators often require formal adjustment for imperfect detection of individuals during surveys. Conventional distance sampling (CDS) and its extensions (mark‐recapture distance sampling [MRDS], temporary emigration distance sampling [TEDS]) are popular approaches for producing unbiased estimators of wildlife abundance. However, despite extensive discussion and development of distance sampling theory in the literature, deciding which of these alternatives is most appropriate for a particular scenario can be confusing. Some of this confusion may stem from an incomplete understanding of how each approach addresses the components of the detection process. Here we describe the proper application of CDS, MRDS, and TEDS approaches and use applied examples to help clarify their differing assumptions with respect to the components of the detection process. To further aid the practitioner, we summarize the differences in a decision tree that can be used to identify cases where a more complex alternative (e.g., MRDS or TEDS) may be appropriate for a given survey application. Although the more complex approaches can account for additional sources of bias, in practical applications one also must consider estimator precision. Therefore, we also review the concept of total estimator error in the context of comparing competing methods for a given application to aid in the selection of the most appropriate distance sampling approach. Finally, we detail how the use of more advanced techniques (i.e., informed priors, open‐population distance sampling models, and integrated modeling approaches) can further reduce total estimator error by leveraging information from existing and ongoing data collection .By synthesizing the existing literature on CDS, MRDS, TEDS and their extensions, in conjunction with the concepts of total estimator error and the components of the detection process, we provide a comprehensive guide that can be used by the practitioner to more efficiently, effectively, and appropriately apply distance sampling in a variety of settings.
Schmidt, J.H., T.L. Wilson, W.L. Thompson, B.A. Mangipane. 2022. Integrating distance sampling survey data with population indices to separate trends in abundance and resource use. Journal of Wildlife Management 86:e22185. https://doi.org/10.1002/jwmg.22185 \| Abstract \| Publisher Website	January 2022	Managers rely on accurate estimators of wildlife abundance and trends for management decisions. Despite the focus of contemporary wildlife science on developing methods to improve inference from wildlife surveys, legacy datasets often rely on index counts that lack information about the detection process. Data integration can be a useful tool for combining index counts with data collected under more rigorous designs (i.e., designs that account for the detection process), but care is required when datasets represent different population processes or are mismatched in space and time. This can be particularly problematic in cases where animals aggregate in response to a spatially or temporally limited resource because individuals may temporarily immigrate from outside the study area and be included in the abundance index. Abundance indices based on brown bear (<i>Ursus arctos</i>) feeding aggregations within coastal meadows in early summer in Lake Clark National Park and Preserve, Alaska, USA, are one such example. These indices reflect the target population (brown bears residing within the park) and temporary immigrants (i.e., bears drawn from outside the park boundary). To properly account for the effects of temporary immigration, we integrated the index data with abundance data collected via park-wide distance sampling surveys, the latter of which properly addressed the detection process. By assuming that the distance data provide inference on abundance and the index counts represent some combination of abundance and temporary immigration processes, we were able to decompose the relative contribution of each to overall trend. We estimated that the density of brown bears within our study area was 38–54 adults/1,000 km<sup>2</sup> during 2003–2019 and that abundance increased at a rate of approximately 1.4%/year. The contribution of temporary immigrants to overall trend in the index was low, so we created 3 hypothetical scenarios to more fully demonstrate how the integrated approach could be useful in situations where the composite trend in meadow counts may obscure trends in abundance (e.g., opposing trends in abundance and temporary immigration). Our work represents a conceptual advance supporting the integration of legacy index data with more rigorous data streams and is broadly applicable in cases where trends in index values may represent a mixture of population processes.
Schmidt, J.H., J. Putera, T.L. Wilson. 2020. Direct and indirect effects of temperature and prey abundance on bald eagle reproductive dynamics. Oecologia. 192: 391-401. https://doi.org/10.1007/s00442-019-04578-8 \| Abstract \| Publisher Website	December 2020	Understanding the mechanisms by which populations are regulated is critical for predicting the effects of large-scale perturbations. While discrete mortality events provide clear evidence of direct impacts, indirect pathways are more difficult to assess but may play important roles in population and ecosystem dynamics. Here, we use multi-state occupancy models to analyze a long-term dataset on nesting bald eagles in south-central Alaska with the goal of identifying both direct and indirect mechanisms influencing reproductive output in this apex predator. We found that the probabilities of both nest occupancy and success were higher in the portion of the study area where water turbidity was low, supporting the hypothesis that access to aquatic prey is a critical factor limiting the reproductive output of eagles in this system. As expected, nest success was also positively related to salmon abundance; however, the negative effect of spring warmth suggested that access to salmon resources is indirectly diminished in warm springs as a consequence of increased glacial melt. Together, these findings reveal complex interrelationships between a critical prey resource and large-scale weather and climate processes which likely alter the accessibility of resources rather than directly affecting resource abundance. While important for understanding bald eagle reproductive dynamics in this system specifically, our results have broader implications that suggest complex interrelationships among system components.
Schmidt, J.H., Coletti, H.A., Cutting, K.A., Wilson, T.L., Mangipane, B.A., Schultz, C.N. and Schertz, D.T. (2024). The effects of spatiotemporal variation in marine resources on the occupancy dynamics of a terrestrial avian predator. Ecosphere, 15(11). doi:https://doi.org/10.1002/ecs2.70078. \| Abstract	November 2024	Identifying relationships between population dynamics and system drivers such as weather, climate, habitat, and resource availability is critical in understanding how populations respond to changing conditions. In coastal areas, the transfer of nutrients across the marine and terrestrial interface leads to further complexity. Nesting populations of bald eagles along the Pacific coast, although terrestrial, are largely dependent on marine resources during the breeding season and therefore represent a good focal species for understanding linkages of nutrients between terrestrial and marine systems. However, coastal areas are susceptible to a variety of perturbations, from both land and sea, which can be further exacerbated by climate change. For example, the northeast Pacific Marine Heatwave (PMH) of 2014-2016 had wide-ranging impacts on the marine ecosystem, providing a convenient natural experiment for further exploring how marine conditions can impact terrestrial systems. We used a spatially-explicit multi-state occupancy modeling framework to analyze >30yrs of bald eagle nest occupancy data collected in 4 large national parks along a coastal-interior gradient in Alaska, USA. We assessed occupancy state in relation to weather conditions, salmon abundance, access to alternate prey resources, and the PMH event to help elucidate the factors affecting bald eagle occupancy dynamics over time. We found that occupancy probability was higher in areas where prey resources were concentrated (e.g., near seabird colonies, where bears facilitate access to salmon carcasses), and the probability of success was higher during warmer, drier springs with higher-than-average salmon abundance. After the onset of the marine heatwave, success declined in the areas most dependent on non-salmon marine resources. These findings confirm the importance of spring weather conditions and access to salmon resources during the critical chick-rearing period, but also reveal that marine heatwaves may have important secondary effects through a reduction in the overall quantity or quality of prey available to bald eagles. Given ongoing warming at high latitudes and the expectation that marine heatwaves will become more common, our findings are useful for understanding ongoing and future changes in the transfer of nutrients from marine to terrestrial ecosystems and how such changes may impact terrestrial species such as bald eagles.
Schmidt, AE, A Lescroël, S Lisovski, M Elrod, D Jongsomjit, KM Dugger, and G Ballard. 2023. Sea ice concentration decline in an important Adélie penguin molt area. Proceedings of the National Academy of Sciences 120 (46) e2306840120 https://doi.org/10.1073/pnas.2306840120.	November 2023
Schmidt, A.E., G. Ballard, A. Lescroël, K. M. Dugger, D. Jongsomjit, M.L. Elrod, D.G. Ainley. 2021. The influence of subcolony-scale nesting habitat on reproductive success of Adélie penguins. Scientific Reports 11:15380, https://doi.org/10.1038/s41598-021-94861-7.	August 2021
Schindler, AR, DA Haukos, CA Hagen, and BE Ross. A multi-species approach to manage effects of land cover and weather on upland game birds. Ecology and Evolution. 10:14330-14345.	December 2020
Schindler, A.R., D.A. Haukos, C.A. Hagen, B.E. Ross. 2020. A decision-support tool to prioritize candidate landscapes for lesser prairie-chicken conservation. Landscape Ecology 35:1417-1434.	May 2020
Schilder, L.J., L.J. Heintzman,N.E. McIntyre, S. Harryman, C.A. Hagen, R. Martin, C.W. Boal, and B.A. Grisham. 2022. Structural and Functional Landscape Connectivity for Lesser Prairie-Chickens in the Sand Shinnery Oak Prairie Ecoregion of the Southern High Plains. Journal of Wildlife Management 2022;86:e22146. Https://soi.org/10.1002/jwmg.22146	February 2022
Schepker, T.J., E. B. Webb, D. Tillitt and T. LaGrange . 2020. Neonicotinoid insecticides in agricultural wetlands and associations with aquatic invertebrate communities. Agriculture, Ecosystems & Environment 287:106678	January 2020
Scharhag, J.M., C. Sartini, S.M. Crimmins, S.E. Hygnstrom, and J.B. Stetz. 2021. Characteristics of non-fatal attacks by black bears: conterminous United States, 2000-2017. Human-Wildlife Interactions 15:191-202.	April 2021
Schall, M.K., G.D. Smith, V.S. Blazer, H.L. Walsh, and T. Wagner. 2024. Factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania. Journal of Fish Diseases. http://doi.org/10.1111/jfd.14033	October 2024
Schall, M.K., G.D. Smith, V.S. Blazer, H.L. Walsh, Y. Li, and T. Wagner. 2020. A fishery after the decline: The Susquehanna River Smallmouth Bass story. Fisheries 45:576-584.	August 2020
Schall, M.K., G.D. Smith, V.S. Blazer, H.L. Walsh, T. Wertz, D. Shull, and T. Wagner. 2023. Assembling the right pieces: developing an interdisciplinary team to study disease, decline, and recovery of a world-class Smallmouth Bass fishery. Fisheries. https://doi.org/10.1002/fsh.10922	May 2023
Sawyer et al. Tradeoffs with utility-scale solar development and ungulates on western rangelands.	April 2022
Satgé, Y.G., S. Janssen, E. Rupp, B. Patteson, C. Gaskin, P.G.R. Jodice. 2024. Mesopelagic diet as pathway of high mercury levels in body feathers of the endangered Diablotin Black-capped Petrel. Marine Ornithology 52:261-274. \| Download	October 2024
Satgé, Y.G., E. Rupp, A. Brown, and P.G.R Jodice. 2020. Habitat modelling locates nesting areas of the Endangered Black-capped Petrel Pterodroma hasitata on Hispaniola and identifies habitat loss. Bird Conservation International 1-18. doi:10.1017/S0959270920000490 \| Download	November 2020
Satgé, Y.G., B. Keitt, C. Gaskin, P.G.R. Jodice. 2023. Spatial segregation between phenotypes of the diablotin black-capped petrel Pterodroma hasitata during the non-breeding period. Endangered Species Research. 51:183-201. doi: 10.3352/esr01254 \| Download	July 2023
Sarah N. Sells, Cecily M. Costello, Paul M. Lukacs, Frank T. van Manen, Mark Haroldson, Wayne Kasworm, Justin Teisberg, Milan A. Vinks, Dan Bjornlie. 2023. Grizzly bear movement models predict habitat use for nearby populations. Biological Conservation, Volume 279, 109940, ISSN 0006-3207, https://doi.org/10.1016/j.biocon.2023.109940.	March 2023
Santolo, G.M., and C.W. Boal. 2024. Variation in Cooper's Hawk (Accipiter cooperii) Eggshell Thickness: DDT, Measurement Methods, and Location. Journal of Raptor Research 58:	September 2024
Sandbach, C. J.K. Young, M.M. Conner, E. Hansen, and P. Budy. 2024. Beaver Dam Analogues did not Improve Translocation Outcomes in a Desert River. Restoration Ecology. doi: 10.1111/rec.14107. USGS FSP IP-155481, BOA Date: November 7, 2023. \| Abstract	February 2024	Stream restoration programs employ beaver-related restoration techniques, including beaver translocations and installation of beaver dam analogs (BDAs), to create complex in-stream habitat. Our goal was to investigate whether BDA installations improved the probability of translocated beavers surviving and colonizing a section of degraded desert river. We translocated beavers fitted with VHF and/or PIT tags to the Price River in east-central Utah, for two years before and after BDAs were installed. We monitored survival and site fidelity of VHF-tagged beavers across all four years to estimate apparent survival, using model selection to evaluate models with BDA, flow, and other factors hypothesized to be related to apparent survival. We found similar apparent survival (<i>φ</i>) eight weeks post-release of pre-BDA beavers (<i>φ </i>= 0.50 ± 0.08 SE) and post-BDA beavers (<i>φ</i> = 0.41 ± 0.06 SE). Fifteen predation-caused mortalities occurred, and 43 beavers emigrated outside of the study site. Top models indicated apparent survival was negatively related to mean flow. Of the 70 BDAs that were constructed, we observed signs of beaver activity on two structures and the number of intact natural dams decreased due to monsoon floods. Our results suggest BDAs may not improve survival or site fidelity of translocated beavers in desert river systems. However, the negative relationship between flow and apparent survival suggests survival or fidelity may be improved if beaver translocations are timed to avoid high-flow events. Additional research is needed to understand how habitat, individual behavior, and resident conspecifics influence beaver translocation success.
Samuel, W.T., Yancy, L.E., Hinkle, E.G., and J.A. Falke. 2024. Validating morphometrics as a non-lethal tool to determine Arctic Grayling sex. North American Journal of Fisheries Management 44:70-78.	January 2024
Samuel, W.T., Yancy, L.E., Hinkle, E.G., and J.A. Falke. 2024. Validating morphometrics as a non-lethal tool to determine Arctic Grayling sex. North American Journal of Fisheries Management 44:70-78.	January 2024
Sall, I., Jarchow, C.J., Sigafus, B.H., Eby, L.A., Forzley, M.J. and Hossack, B.R. (2021), Estimating inundation of small waterbodies with sub-pixel analysis of Landsat imagery: long-term trends in surface water area and evaluation of common drought indices. Remote Sens Ecol Conserv, 7: 109-124. https://doi.org/10.1002/rse2.172 \| Abstract \| Publisher Website	July 2020	Small waterbodies are numerically dominant in many landscapes and provide several important ecosystem services, but automated measurement of waterbodies smaller than a standard Landsat pixel (0.09 ha) remains challenging. To further evaluate sub-Landsat pixel techniques for estimating inundation extent of small waterbodies (basin area: 0.06–1.79 ha), we used a partial spectral unmixing method with matched filtering applied to September 1985–2018 Landsat 5 and eight imagery from southern Arizona, USA. We estimated trends in modeled surface water area each September and evaluated the ability of several common drought indices to explain variation in mean water area. Our methods accurately classified waterbodies as dry or inundated (Landsat 5: 91.3%; Landsat 8: 98.9%) and modeled and digitized surface water areas were strongly correlated (<i>R</i><sup>2</sup> = 0.70–0.92; bias = −0.024 to −0.015 ha). Estimated surface water area was best explained by the 3-month seasonal standardized precipitation index (SPI03; July‒September). We found a wide range of estimated relationships between drought indices (e.g. SPI vs. Palmer Drought Severity Index) and estimated water area, even for different durations of the same drought index (e.g. SPI01 vs. SPI12). Mean waterbody surface area decreased by ~14% from September 1985 to September 2018, which matches declines in local annual precipitation and regional trends of reduced inundation extent of larger waterbodies. These results emphasize the importance of understanding local systems when relying on drought indices to infer variation in past or future surface water dynamics. Several challenges remain before widespread application of sub-pixel methods is feasible, but our results provide further evidence that partial spectral unmixing with matched filtering provides reliable measures of inundation extent of small waterbodies.
Sainsbury, K.A., Harshaw, H.W., Fulton, D.C. et al. What waterfowl hunters want: exploring heterogeneity in hunting trip preferences. Wetlands 44, 35 (2024). https://doi.org/10.1007/s13157-023-01744-w \| Abstract	February 2024	Canadian and American waterfowl hunters were surveyed to identify their hunting trip preferences. Respondents were individuals that were or had participated in waterfowl hunting, and most had hunted the majority of the last five years. We identified four latent classes of waterfowl hunters that varied in their preferences for harvest, access effort, length of travel, quantity of waterfowl seen, and the potential for interference/ competition. We found a diminishing return associated with the number of waterfowl harvested, and that devoted and local hunters did not perceive appreciable benefit from harvesting more birds beyond harvesting a single bird. Results highlight the importance of not only considering population size, but also the location of habitat for people and waterfowl. Our results provide waterfowl managers important insights into the heterogeneity of North American waterfowl hunters by highlighting differences in priorities for waterfowl hunting trips. Notably, to address this heterogeneity, managers could consider the balance of objectives, actions and resources designed to satisfy current waterfowl hunters to that of attracting new individuals. Managing access to improve the likelihood that hunters will see and have opportunities to harvest some waterfowl has benefit to hunters.
SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 Pandemic. 2022. Ecology. DOI: 10.1002/ecy.3775 Roland Kays^1,2, Michael V. Cove², Jose Diaz³, Kimberly Todd³, Claire Bresnan³, Matt Snider¹,Thomas E. Lee, Jr.⁴, Seth C. Crockett⁴, Anthony P. Crupi⁵, Katherine C.B. Weiss^6,7, Helen Rowe⁸, Tiffany Sprague⁸, Jan Schipper⁷, Christopher A. Lepczyk⁹, Jean E. Fantle-Lepczyk⁹, Jon Davenport¹⁰, Zach Farris¹⁰, Jacque Williamson¹¹, M. Caitlin Fisher-Reid¹², Drew Rezendes¹², Alexandra J. Bebko¹², Petros Chrysafis¹³, Alex J. Jensen¹⁴, David S. Jachowski¹⁴, Katherine C. King¹⁵, Brandon McDonald¹⁵, Daniel J. Herrera¹⁶, Marius van der Merwe¹⁷, Robert V. Horan III¹⁹, Michael S. Rentz²⁰, LaRoy S.E. Brandt²¹, Christopher Nagy²², Sean P. Maher²⁴, Andrea K. Darracq²⁵, George Hess³, Matthew E. Gompper²⁶, Stephen L. Webb²⁷, John P. Vanek²⁸, Diana J. R. Lafferty²⁹, Tru Hubbard²⁹, Jorie Favreau³¹, Jack Fogarty³¹, Steven Hammerich³³, Michelle Halbur³³, Morgan Gray³³, Christine C. Rega-Brodsky³⁴, Caleb Durbin³⁴, Elizabeth A. Flaherty³⁵, Jarred Brooke³⁵, Stephanie S. Coster³⁶, Richard G. Lathrop³⁷, Katarina Russell³⁷, Daniel A. Bogan³⁸, Hila Shamon¹, Robert C. Lonsinger⁴², M. Teague O'Mara⁴³, Justin A. Compton⁴⁴, Melinda Fowler⁴⁴, Erika L. Barthelmess⁴⁵, Katherine E. Andy⁴⁵, Jerrold L. Belant⁴⁶, Dean E. Beyer, Jr.⁴⁷, Daniel G. Scognamillo⁴⁸, Chris Schalk⁴⁸, Caroline N. Ellison⁵⁰, Chip Ruthven⁵⁰, Sarah Fritts⁵¹, Jaquelyn Tleimat⁵¹, Mandy Gay⁵¹, Christopher A. Whittier⁵², Sean A. Neiswenter⁵³, Robert Pelletier⁵³, Brett A. DeGregorio⁵⁴, Erin K. Kuprewicz⁵⁵, Miranda L. Davis⁵⁵, Carolina Baruzzi⁵⁷, Marcus A. Lashley⁵⁶, David Mason⁵⁶, Derek R. Risch⁵⁸, Maximilian L. Allen^59,60, Laura S. Whipple⁶⁰, Jinelle H. Sperry⁶¹, Patrick Wolff⁶¹, Robert H. Hagen⁶², Alessio Mortelliti⁶³, Amay Bolinjcar⁶³, Marketa Zimova⁶⁸, Sean T. Giery⁷⁰, Summer D. Higdon⁷², Ronald S. Revord⁷², Christopher P. Hansen⁷³, Joshua J. Millspaugh⁷³, Adam Zorn⁷⁴, Nathaniel H. Wehr⁷⁵, Brian D. Gerber⁷⁷, Kylie Rezendes⁷⁷, Jessie Adley⁷⁷, Jennifer Sevin⁷⁸, Austin M. Green⁷⁹, Çağan H. Şekercioğlu^79,80, Mary E. Pendergast⁸¹, Kayleigh Mullen⁸¹, Tori Bird^81b, Andrew J. Edelman⁸², Tim Hawig⁸², Joanne R. Wasdin⁸², Andrea Romero⁸³, Brian J. O'Neill^83b[KR1] , Noel Schmitz^83b, Rebecca A Vandermus⁸³, Jesse M. Alston⁸⁴, Kellie M. Kuhn⁸⁵, Damon B. Lesmeister⁸⁶, Cara L. Appel⁸⁷, Christopher Rota⁸⁸, Jennifer L. Stenglein⁸⁹, Christine Anhalt-Depies⁸⁹, Carrie Nelson⁹⁰, Robert A. Long⁹¹, Paula MacKay⁹¹, Kathryn R. Remine⁹¹, Mark J. Jordan⁹², Mark Elbroch⁹³, Dylan Bergman⁹⁴, Sara Cendejas-Zarelli⁹⁵, Kim Sager⁹⁵, Haydée Hernández-Yáñez³, William J. McShea³ \| Abstract \| Download	April 2022	<b>Abstract</b>: Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here we present the data from Snapshot USA 2020, a second annual national mammal survey of the United States of America. This project involved xx scientists setting camera traps in a standardized protocol at 1481 locations across 102 arrays in 43 states for a total of 51,988 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in two years that include data from before and during the COVID-19 Pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total we recorded 114,749 detections of 77 species of wild mammals, 9200 detections of at least 25 species of birds, 15,847 detections of seven domestic animals and 23,705 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences between years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns.
SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 Pandemic. 2022. Ecology. DOI: 10.1002/ecy.3775 Roland Kays^1,2, Michael V. Cove², Jose Diaz³, Kimberly Todd³, Claire Bresnan³, Matt Snider¹,Thomas E. Lee, Jr.⁴, Seth C. Crockett⁴, Anthony P. Crupi⁵, Katherine C.B. Weiss^6,7, Helen Rowe⁸, Tiffany Sprague⁸, Jan Schipper⁷, Christopher A. Lepczyk⁹, Jean E. Fantle-Lepczyk⁹, Jon Davenport¹⁰, Zach Farris¹⁰, Jacque Williamson¹¹, M. Caitlin Fisher-Reid¹², Drew Rezendes¹², Alexandra J. Bebko¹², Petros Chrysafis¹³, Alex J. Jensen¹⁴, David S. Jachowski¹⁴, Katherine C. King¹⁵, Brandon McDonald¹⁵, Daniel J. Herrera¹⁶, Marius van der Merwe¹⁷, Robert V. Horan III¹⁹, Michael S. Rentz²⁰, LaRoy S.E. Brandt²¹, Christopher Nagy²², Sean P. Maher²⁴, Andrea K. Darracq²⁵, George Hess³, Matthew E. Gompper²⁶, Stephen L. Webb²⁷, John P. Vanek²⁸, Diana J. R. Lafferty²⁹, Tru Hubbard²⁹, Jorie Favreau³¹, Jack Fogarty³¹, Steven Hammerich³³, Michelle Halbur³³, Morgan Gray³³, Christine C. Rega-Brodsky³⁴, Caleb Durbin³⁴, Elizabeth A. Flaherty³⁵, Jarred Brooke³⁵, Stephanie S. Coster³⁶, Richard G. Lathrop³⁷, Katarina Russell³⁷, Daniel A. Bogan³⁸, Hila Shamon¹, Robert C. Lonsinger⁴², M. Teague O'Mara⁴³, Justin A. Compton⁴⁴, Melinda Fowler⁴⁴, Erika L. Barthelmess⁴⁵, Katherine E. Andy⁴⁵, Jerrold L. Belant⁴⁶, Dean E. Beyer, Jr.⁴⁷, Daniel G. Scognamillo⁴⁸, Chris Schalk⁴⁸, Caroline N. Ellison⁵⁰, Chip Ruthven⁵⁰, Sarah Fritts⁵¹, Jaquelyn Tleimat⁵¹, Mandy Gay⁵¹, Christopher A. Whittier⁵², Sean A. Neiswenter⁵³, Robert Pelletier⁵³, Brett A. DeGregorio⁵⁴, Erin K. Kuprewicz⁵⁵, Miranda L. Davis⁵⁵, Carolina Baruzzi⁵⁷, Marcus A. Lashley⁵⁶, David Mason⁵⁶, Derek R. Risch⁵⁸, Maximilian L. Allen^59,60, Laura S. Whipple⁶⁰, Jinelle H. Sperry⁶¹, Patrick Wolff⁶¹, Robert H. Hagen⁶², Alessio Mortelliti⁶³, Amay Bolinjcar⁶³, Marketa Zimova⁶⁸, Sean T. Giery⁷⁰, Summer D. Higdon⁷², Ronald S. Revord⁷², Christopher P. Hansen⁷³, Joshua J. Millspaugh⁷³, Adam Zorn⁷⁴, Nathaniel H. Wehr⁷⁵, Brian D. Gerber⁷⁷, Kylie Rezendes⁷⁷, Jessie Adley⁷⁷, Jennifer Sevin⁷⁸, Austin M. Green⁷⁹, Çağan H. Şekercioğlu^79,80, Mary E. Pendergast⁸¹, Kayleigh Mullen⁸¹, Tori Bird^81b, Andrew J. Edelman⁸², Tim Hawig⁸², Joanne R. Wasdin⁸², Andrea Romero⁸³, Brian J. O'Neill^83b[KR1] , Noel Schmitz^83b, Rebecca A Vandermus⁸³, Jesse M. Alston⁸⁴, Kellie M. Kuhn⁸⁵, Damon B. Lesmeister⁸⁶, Cara L. Appel⁸⁷, Christopher Rota⁸⁸, Jennifer L. Stenglein⁸⁹, Christine Anhalt-Depies⁸⁹, Carrie Nelson⁹⁰, Robert A. Long⁹¹, Paula MacKay⁹¹, Kathryn R. Remine⁹¹, Mark J. Jordan⁹², Mark Elbroch⁹³, Dylan Bergman⁹⁴, Sara Cendejas-Zarelli⁹⁵, Kim Sager⁹⁵, Haydée Hernández-Yáñez³, William J. McShea³ \| Abstract \| Download	April 2022	<b>Abstract</b>: Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here we present the data from Snapshot USA 2020, a second annual national mammal survey of the United States of America. This project involved xx scientists setting camera traps in a standardized protocol at 1481 locations across 102 arrays in 43 states for a total of 51,988 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in two years that include data from before and during the COVID-19 Pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total we recorded 114,749 detections of 77 species of wild mammals, 9200 detections of at least 25 species of birds, 15,847 detections of seven domestic animals and 23,705 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences between years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns.
S.M. Deeley, W.M. Ford, N. Kalen, S. R. Freeze, M. St. Germain, M. Muthersbaugh, E.L. Barr, A.B. Kniowski, A. Silvis and J. De La Cruz. 2022. Relating echolocation call data with reproduction data in mid-Atlantic bats. Diversity 14, 319. doi.org/10.3390/d14050319	April 2022
S.C. Hedden, L.A. Bruckerhoff, and K.B. Gido. 2021. Assessing Linkages Between Small Impoundments and Long-term Trajectories of Prairie Stream Fish Assemblages. American Midland Naturalist 185 (2):187-200. https://doi.org/10.1674/0003-0031-185.2.187 \| Abstract	April 2021	Most stream fish communities have changed over time in response to common anthropogenic disturbances. Impoundments are a widespread anthropogenic stressor that can negatively impact stream fishes as they alter flow regimes, block movements, and act as fountainheads for the introduction and spread of invasive species. Recent studies, however, have reported the occurrence and reproduction of native fishes in impoundments, suggesting they might benefit some native fishes. Our primary objective was to evaluate whether impoundment construction has led to changes in fish community structure in prairie streams. To accomplish this, we compared fish occupancy in small impoundments (,5 ha) to temporal trends in stream occupancy among species to test whether species' increases in stream occupancy were related to their occupancy in impoundments. We examined stream fish communities in the Upper Cottonwood River basin, Kansas, from 1948–2018, and sampled small impoundments in 2016 and 2017. A third (32%) of fish communities in impoundments were similar to stream assemblages, whereas most impoundments (68%) were dominated by sport or bait fishes. In streams, six species showed increases in occupancy and four species showed decreases since small impoundment construction. Of the species that exhibited increased stream occupancy, five showed a positive, logistical relationship between a species' impoundment occupancy and its increase in stream occupancy. Species declining in stream occupancy experienced continued linear declines and may still be declining. Our research suggests stream fish communities have changed since impoundment construction, and are associated with locally-invasive, native species reaching a new stable state in streams accompanied by declines in other native stream fish species.
Ryan, J.E., A.H. Roy, P.D. Hazelton, D.L. Perkins, T. Warren, C. Walsh, and R. Wick. 2022 Assessing methods for mitigating fungal contamination in freshwater mussel in vitro propagation. Hydrobiologia 849:2487-2501. DOI: 10.1007/s10750-022-04865-1 \| Download	April 2022
Ruzicka, R. E., D. Rollins, W. L. Kendall, and P. F. Doherty, Jr. 2024. Effects of release strategy, source population, and age on reintroduced scaled quail reproduction. Journal of Wildlife Management, DOI: 10.1002/jwmg.22660.	August 2024
Ruzicka, R. E., D. Rollins, P. F. Doherty, Jr., and W. L. Kendall. 2023. Longer holding times decrease dispersal bur increase mortality of translocated scaled quail. Journal of Wildlife Management 2023;e22498, DOI: 10.1002/jwmg.22498.	September 2023
Ruzi, S.A., E. Youngsteadt, A. Cherveny, J. Kettenbach, H. K. Levenson, D.S. Carley, J.A. Collazo, and R.E. Irwin. 2023. Bee species richness through time in an urbanizing landscape of the southeastern USA. Global Change Biology.. \| Abstract	December 2023	Compared to non-urban environments, cities host ecological communities with altered taxonomic diversity and functional trait composition. However, we know much less about how these urban changes take shape over time. Using historical bee (Apoidea: Anthophila) museum specimens supplemented with online repositories and researcher collections, we investigated whether bee species richness tracked urban and human population growth over the past 118 years. We also determined which species were no longer collected, and whether those species shared certain traits. Additionally, we looked at collector behavior over time. We focused on Wake County, North Carolina, US where human population size has increased over 16 times along with the urban area within its largest city, Raleigh, which has increased over four times. We estimated bee species richness with occupancy models, and rarefaction and extrapolation curves to account for imperfect detection and sample coverage. To determine if bee traits correlated with when species were collected, we compiled information on native status, nesting habits, diet breadth, and sociality. We used non-metric multidimensional scaling to determine if collectors contributed different bee assemblages over time. In total, there were 328 species collected in Wake County. We found that while bee species richness varied there was no clear trend in bee species richness over time. However, recent collections (since 2003) were missing 195 species and there was a shift in trait composition over time, particularly an increase in above-ground nesters. The top collectors in the dataset differed in how often they collected bee species, but this was not consistent between historic and contemporary time periods as some contemporary collectors grouped closer than others together potentially due to focusing on urban habitats. Use of historic collections and complimentary analyses can fill knowledge gaps to help understand temporal patterns of species richness for taxonomic groups that may not have long-term data.
Rutter, J.D., A.A., Dayer, H.W. Harshaw, N.W. Cole, J.N. Duberstein, D.C. Fulton, A.H. Raedeke, and R.M. Schuster. 2021. Racial, ethnic, and social patterns in the recreation specialization of birdwatchers: An analysis of Untied State eBird registrants. Journal of Outdoor Recreation and Tourism, 35: 100400 DOI: 10.1016/j.jort.2021.100400	June 2021
Ruthven, J.S., and J. Leonard, and A.W. Walters. 2023. Assessment of invasive Brook Stickleback Culaea inconstans occupancy, habitat drivers, and overlap with native fishes in the North Platte River drainage, Wyoming. Hydrobiologia doi.org/10.1007/s10750-023-05262-y	June 2023
Ruthven, J.S., and A.W. Walters. 2023. Invasive Brook Stickleback Culaea inconstans has limited effects on the trophic ecology of native fishes in Wyoming, USA. Food Webs 35 e00275. https://doi.org/10.1016/j.fooweb.2023.e00275	June 2023
Ruther, E.V., M Asher, G. Christie, C. Gale, A. Massey, C. Massery, C.R. Middaugh, J. Veon, and B.A. DeGregorio. 2021. Northern Bobwhite Occupancy Patterns on Multiple Spatial Scales Across Arkansas. Journal of Fish and Wildlife Management 12: 502-512 \| Download	December 2021
Russell, Robin E., Walsh, Daniel P., Samuel, Michael D., Grunnill, Martin S., Rocke, Tonie E. 2021. Space matters: incorporating spatial structure into models of plague transmission. Ecological Modelling 443:. https://doi.org/10.1016/j.ecolmodel.2021.109450	January 2021
Russell, R., DiRenzo, G. V., Alger, K., Grant, E. H. C., & J. Szymanski. 2020. Principles and mechanisms of disease resistance and resilience in wildlife. Frontiers in Ecology and Evolution 8: 344. https://doi.org/10.3389/fevo.2020.569016. \| Abstract \| Download \| Publisher Website	December 2020	Emerging infectious diseases can result in species declines and hamper recovery efforts for at-risk populations. Generalizing considerations for reducing the risk of pathogen introduction and mitigating the effects of disease remains challenging and inhibits our ability to provide guidance for species recovery planning. Given the growing rates of emerging pathogens globally, we identify key principles and mechanisms for maintaining sustainable populations in the face of emerging diseases (including minimizing the risk of pathogen introductions and their future effects on hosts). Our synthesis serves as a reference for minimizing the risk of future disease outbreaks, mitigating the deleterious effects of future disease outbreaks on species extinction risk, and a review of the theoretical and/or empirical examples supporting these considerations.
Rush, S. A., K. F. Gaines, W. R. Eddleman, and C. J. Conway. 2020. Clapper Rail (Rallus crepitans), version 1.0. In Birds of the World (P. G. Rodewald, Editor). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.clarai11.01	March 2020
Runge, Michael C., Campbell Grant, Evan H., Coleman, Jeremy T. H., Reichard, Jonathan D., Gibbs, Samantha E. J., Cryan, Paul M., Olival, Kevin J., Walsh, Daniel P., Blehert, David S., Hopkins, M. Camille, Sleeman, Jonathan M. 2020. Assessing the Risks Posed by SARS-CoV-2 in and via North American Bats-Decision Framing and Rapid Risk Assessment. Open-File Report 2020-1060, 43 p. https://doi.org/10.3133/ofr20201060	January 2020
Runge, M.C., P.K. Devers, G.S. Boomer, J.E. Lyons, A.M. Tucker, Q. Zhao, and J.A. Diamond. 2023. Managing waterfowl harvest under climate change. Report to the Northeast Climate Adaptation Science Center.	September 2023
Runge MC, SJ Converse, JE Lyons, and DR Smith. 2020. Structured decision making: case studies in natural resource management. Johns Hopkins University Press, Baltimore, USA.	May 2020
Runge MC and SJ Converse. 2020. Introduction to risk analysis. Pages 149-155 in Runge MC, SJ Converse, JE Lyons, and DR Smith. Structured decision making: case studies in natural resource management. Johns Hopkins University Press, Baltimore, USA.	May 2020
Ruiz‐Gutierrez, V., Bjerre, E.R., Otto, M.C., Zimmerman, G.S., Millsap, B.A., Fink, D., Stuber, E.F., Strimas‐Mackey, M. and Robinson, O.J., 2021. A pathway for citizen science data to inform policy: A case study using eBird data for defining low‐risk collision areas for wind energy development. Journal of Applied Ecology, 58(6), pp.1104-1111. https://doi.org/10.1111/1365-2664.13870	April 2021
Ruggirello, J. E., S. A. Bonar, O. G. Feuerbacher and L. H. Simons. 2020. Use of underwater videography to quantify conditions utilized by endangered Moapa Dace while spawning. North American Journal of Fisheries Management 40:17-28.	March 2020
Ruegg, K.C. Ruegg, M. Brinkmeyer,C.M. Bossu, R. Bay,E.C. Anderson, C.W. Boal, R.D. Dawson, A. Eschenbauch, C.J.W. McClure, K.E. Miller, L. Morrow, J. Morrow, M.D. Oleyar, B. Ralph, S. Schulwitz,T. Swem, J.F. Therrien, T.B. Smith, J.A. Heath. 2021.The American Kestrel Genoscape (Falco sparverius): Implications for Monitoring, Management, and Subspecies Boundaries. Ornithology 138:1-14. DOI: 10.1093/ornithology/ukaa068. \| Abstract \| Download	April 2021	Identifying population genetic structure is useful for inferring evolutionary process as well as defining subspecies boundaries and/or conservation units that can aid in species management. The American Kestrel (<i>Falco sparverius</i>) is a widespread species with two described North American subspecies, (<i>F. s. sparverius </i>and <i>F. s. paulus</i>), the latter in the southeastern United States and the former across the remainder of its distribution. In many parts of their range, American Kestrels have been declining, but it has been difficult to interpret demographic trends without a clearer understanding of gene flow among populations. Here we sequence the first American Kestrel genome and scan the genome of 197 individuals from 12 sampling locations across the range of the two North American subspecies to identify population structure. To validate signatures of population structure and fill in sampling gaps across the breeding range we screen 192 outlier loci in an additional 376 samples from 34 sampling locations. Overall, our analyses support the existence of 5 genetically distinct lineages within American Kestrels—Eastern, Western, Texas, Florida, and Alaska.Interestingly, we find that while our genome-wide genetic data support the existence of previously described subspecies boundaries, genetic differences across the species’ range correlate more with putative migratory phenotypes (resident, long-distance, and short-distance migrants) rather than a priori described subspecies boundaries per se. Based on our results, we suggest the resulting five genetic lineages serve as the foundation for American Kestrel conservation and management in the face of future threats.
Rubin, SP, MJ Davis, EE Grossman, I Woo, SEW De La Cruz, G Nakai, and JY Takekawa. 2024. Benthic macroinvertebrate response to estuarine emergent marsh restoration across a delta-wide environmental gradient. Frontiers in Ecology and Evolution 12:xx-xx. https://doi.org/10.3389/fevo.2024.1356679	April 2024
Rubenstein, S., Peterson, E., Christman, P., and Zydlewski, J. (2022) energetic consequences to migrating Atlantic salmon (Salmo salar) delayed below dams. Canadian Journal of Fisheries and Aquatic Sciences. DOI: TBD. IP-137191, BAO approval date August 15, 2021. [C:100, D:10, I:30, W:10]. \| Download	October 2022
Roy, S., Daignault, A, Zydlewski, J., Truhlar, A., Smith, S., Jain, S., and Hart, D. (2020) Coordinated river infrastructure decisions enhance social-ecological resilience. Environmental Research Letters. On Line Aug 7.	September 2020
Roy, A.H., E. Bjerre, J. Cummings, K. Kalasz, J. Carmignani, P. Hazelton, M. Kern, D. Perkins, L. Saucier, A. Skorupa, R. Katz, and C.C. Coghlan. 2022. Brook floater restoration: Identifying locations to reintroduce or augment populations with propagated mussels. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series.FWS/CSS-141-2022. doi.org/10.3996/css40468057 \| Publisher Website	March 2022
Roug, A., E. Doden, T. Griffin, J. Young, X. Waldem, N. Norman, P. Budy, and A.J. Van Wettere. 2022. Health screening of American beavers (Castor canadensis) in Utah, USA. Journal of Wildlife Diseases, Short Communications. DOI: 10.7589/JWD-D-22-00020. USGS FSP IP-139356.	August 2022
Roth, C. J., Z. S. Beard, J. M. Flinders, and M. C. Quist. 2020. Population ecology and evaluation of suppression scenarios for introduced Utah Chub. North American Journal of Fisheries Management 40:133-144.	February 2020
Rossettie, T.S., T.W. Perry, and J.W. Cain III. 2022. Noninvasive sampling of mountain lion hair by modified foothold traps. Wildlife Society Bulletin 46:e1257. \| Download	April 2022
Ross, P, Patel, E, Ferguson, B, Ravelijaona, R, Raoloniana, G, Wampole, E, Gerber,BD, and Farris, Z. 2020. Assessment of the threatened carnivore community in the recently expanded rainforest protected area Anjanaharibe-Sud Special Reserve, Madagascar. Endangered Species Research. DOI: https://doi.org/10.3354/esr01055. \| Download	May 2020
Rosenthal, WC, EG Mandeville, AM Pilkerton, PC Gerrity, JA Skorupski, AW Walters, and CE Wagner. 2024. Influence of dams on sauger population structure and hybridization with introduced walleye. Ecology and Evolution 14(7): e11706 https://doi.org/10.1002/ece3.11706	July 2024
Rosenthal, W.R., J.M. Fennell, E.G. Mandeville, J.C. Burckhardt, A.W. Walters, and C.E. Wagner. 2022. Effects of reproductive fitness in a hybridizing trout population. Molecular Ecology http://doi.org/10.1111/mec.16578	June 2022
Rosenfield, R.N., S.A. Sonsthagen, W.E. Stout, T.G. Driscoll, A.C. Stewart, P.N. Frater, and S.L. Talbot. Combined high rates of alternative breeding strategies unexpectedly found among populations of a solitary nesting raptor. Ecology and Evolution. 14: e70190 doi.org/10.1002/ece3.70190	August 2024
Rosenfield, R. N., S. A. Sonsthagen, A. E. Riddle-Berntsen, and E. Kuhel. 2021. Record fledging count from a seven-egg clutch in the Cooper’s hawk (Accipiter cooperii). The Wilson Journal of Ornithology. 132:460-463.	November 2020
Rosenblatt, E., R. Mickey, S. Creel, K. Gieder, J. Murdoch, and T. Donovan. 2023. Advances in wildlife abundance estimation using pedigree reconstruction. Ecology and Evolution 13(10):e10650. \| Abstract \| Download \| Publisher Website	October 2023	The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density measures. Traditional methods of estimating abundance and related metrics represent trade-offs in effort and precision of estimates. Pedigree reconstruction is an emerging, attractive alternate approach because its use of one-time, noninvasive sampling of individuals to infer the existence of unsampled individuals. However, advances in pedigree reconstruction could improve its utility, including forming a measure of precision for the method, establishing required spatial sampling effort for accurate estimates, ascertaining the spatial extent of abundance estimates derived from pedigree reconstruction, and assessing how population density affects the estimator's performance. Using established relationships for a stochastic, spatially explicit simulated moose (<i>Alces americanus</i>) population, pedigree reconstruction provided accurate estimates of the adult moose population size and trend. Novel bootstrapped confidence intervals performed as expected with intensive sampling but underperformed with moderate sampling efforts that could produce abundance estimates with low bias. Adult population estimates more closely reflected the total number of adults in the extant population, rather than number of adults inhabiting the area where sampling occurred. Increasing sampling effort, measured as the proportion of individuals sampled and as the proportion of a hypothetical study area, yielded similar asymptotic patterns over time. Simulations indicated a positive relationship between animal density and sampling effort required for unbiased estimates. These results indicate that pedigree reconstruction can produce accurate abundance estimates and may be particularly valuable for surveying smaller areas and low-density populations.
Rosenblatt, E., K. Gieder, T. Donovan, J. Murdoch, T. Smith, M. Heaton, T. Kalbfleisch, B. Murdoch, S. Bhattarai, E. Pacht, E. Verbist, V. Basnayake, and S. McKay. 2023. Genetic diversity and connectivity of moose (Alces alces americana) in eastern North America. Conservation Genetics 24:235-248. \| Download \| Publisher Website	January 2023
Rosenblatt, E., J. DeBow, J. Blouin, T. Donovan, J. Murdoch, S. Creel, W. Rogers, K. Gieder, N. Forti, and C. Alexander. Juvenile moose (Alces alces) stress and nutrition dynamics relate to landscape characteristics, climate-mediated factors, and survival. Conservation Physiology 9:coab048. \| Abstract \| Download	July 2021	Moose populations in the northeastern United States have declined over the past 15 years, primarily due to the impacts of winter ticks. Research efforts have focused on the effects of winter tick infestation on moose survival and reproduction, but stress and nutritional responses to ticks and other stressors remain understudied. We examined the influence of several environmental factors on moose calf stress hormone metabolite concentrations and nutritional restriction in Vermont, USA. We collected 407 fecal and 461 snow urine samples from 84 radio-collared moose calves in the winters of 2017–2019 (January–April) to measure fecal glucocorticoid metabolites (fGCM) concentrations and urea nitrogen:creatinine (UN:C) ratios. We used generalized mixed-effects models to evaluate the influence of individual condition, winter ticks, habitat, climate and human development on stress and nutrition in calf moose. We then used these physiological data to build generalized linear models to predict calf winter survival. Calf fGCM concentrations increased with nutritional restriction and snow depth during adult winter tick engorgement. Calf UN:C ratios increased in calves with lighter weights and higher tick loads in early winter. Calf UN:C ratios also increased in individuals with home ranges composed of little deciduous forests during adult winter tick engorgement. Our predictive models estimated that winter survival was negatively related to UN:C ratios and positively related to fGCM concentrations, particularly in early winter. By late March, as winter ticks are having their greatest toll and endogenous resources become depleted, we estimated a curvilinear relationship between fGCM concentrations and survival. Our results provide novel evidence linking moose calf stress and nutrition, a problematic parasite and challenging environment and winter survival. Our findings provide a baseline to support the development of non-invasive physiological monitoring for assessing environmental impacts on moose populations.
Rosenblatt, E, Cook, J. D., DiRenzo, G.V., Grant, E.H.C., Arce, F., Pepin, K. M., Rudolph, J.F., Runge, M.C., Shriner, S., Walsh, D., and Mosher, B.A. 2023. Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission. biorxiv.	September 2023
Rosenblatt, C.J. Ashley A Dayer, Jennifer N Duberstein, Tina B Phillips, Howard W Harshaw, David C Fulton, Nicholas W Cole, Andrew H Raedeke, Jonathan D Rutter, Christopher L Wood, Highly specialized recreationists contribute the most to the citizen science project eBird, Ornithological Applications, 2022;, duac008, https://doi.org/10.1093/ornithapp/duac008 \| Abstract	February 2022	Contributory citizen science projects (hereafter “contributory projects”) are a powerful tool for avian conservation science. Large-scale projects such as eBird have produced data that have advanced science and contributed to many conservation applications. These projects also provide a means to engage the public in scientific data collection. A common challenge across contributory projects like eBird is to maintain participation, as some volunteers contribute just a few times before disengaging. To maximize contributions and manage an effective program that has broad appeal, it is useful to better understand factors that influence contribution rates. For projects capitalizing on recreation activities (e.g., birding), differences in contribution levels might be explained by the recreation specialization framework, which describes how recreationists vary in skill, behavior, and motives. We paired data from a survey of birders across the United States and Canada with data on their eBird contributions (<i>n</i> = 28,926) to test whether those who contributed most are more specialized birders. We assigned participants to 4 contribution groups based on eBird checklist submissions and compared groups’ specialization levels and motivations. More active contribution groups had higher specialization, yet some specialized birders were not active participants. The most distinguishing feature among groups was the behavioral dimension of specialization, with active eBird participants owning specialized equipment and taking frequent trips away from home to bird. Active participants had the strongest achievement motivations for birding (e.g., keeping a life list), whereas all groups had strong appreciation motivations (e.g., enjoying the sights and sounds of birding). Using recreation specialization to characterize eBird participants can help explain why some do not regularly contribute data. Project managers may be able to promote participation, particularly by those who are specialized but not contributing, by appealing to a broader suite of motivations that includes both appreciation and achievement motivations, and thereby increase data for conservation.
Rosenberger, A.E. and G.A. Lindner. 2022. Use of a riverscape-scale model of fundamental physical habitat requirements for freshwater mussels to quantify mussel declines in a mining-contaminated stream: the Big River, Old Lead Belt, Southeast Missouri. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-147-2022, Washington, D. C. https://doi.org/10.3996/css78904468 \| Abstract \| Download	November 2022	The research described in this report was conducted as part of the Natural Resource Damage Assessment and Restoration process in the Big River. Our purpose was to refine understanding of the habitat features and landscape factors that are crucial for the establishment of mussel concentrations in the Big River by using the adjacent and relatively healthy Bourbeuse and Meramec rivers as reference streams. The study will help to establish expected baseline conditions related to mussel habitat in the Big River, which will assist.injury determination in the Southeast Missouri Lead Mining District Natural Resource Damage Assessment case.
Rosen, MR, SEW De La Cruz, KD Groover, I Woo, SA Roberts, MJ Davis, and CY Antonino. 2023. Selenium hazards in the Salton Sea environment—summary of current knowledge to inform future wetland management. USGS Scientific Investigations Report 2023-5042. https://doi.org/10.3133/sir20235042	July 2023
Roop, H. J., N. C. Poudyal, and C. A. Jennings. FSP initiated. Fishing preferences, angling behavior, and attitudes towards management: a comparison between White and Non-white Anglers. Human Dimensions of Wildlife. https://doi.org/10.1080/10871209.2020.1794082 \| Abstract	July 2020	Recent trends in outdoor recreation in the United States show declining participation in consumptive outdoor activities such as hunting and fishing, primarily because of a decline in per capita participation among certain ethnic groups, largely due to structural change in demography. In Georgia, the proportion of Whites, which have comprised the largest segment of the recreation resource user base, is declining while the share of other racial groups (i.e., Non-whites) is increasing. Fishery managers benefit by knowing if White anglers differ from Non-white anglers in attributes such as demographic characteristics and fishing behavior and preferences. In this study, we compared the racial differences on angling metrics and other attitudinal variables from an intensively managed fishery. There significant differences between user groups in many of the attributes measured. Differences in demographics, sportfish preference, and harvest-orientated behavior confirm that the White and Non-white anglers constitute two distinct segments of this fishery, and these findings, albeit from one study area, may be applicable to other similar fisheries.
Rolls, R.J., J.S. Rogosch, and L.M. Kuehne. 2022. How Shall We Meet? Embracing the Opportunities of Virtual Conferencing. Fisheries. https://doi.org/10.1002/fsh.10765	July 2022
Rolek, B.W., D.J. Harrison, D.W. Linden, C.S. Loftin, P.B. Wood. 2021. Habitat associations of breeding conifer-associated birds in managed and regenerating forested stands. Forest Ecology and Management.	October 2021
Rogosch, J.S., and J.D. Olden. 2020. Invaders induce coordinated isotopic niche shifts in native fish species. Canadian Journal of Fisheries and Aquatic Sciences. 77(8): 1348–1358. doi:10.1139/cjfas-2019-0346.	April 2020
Rogosch, J.S., H.I.A. Boehm, R.W. Tingley, K.D. Wright, E.B. Webb, C.P. Paukert. 2024. Evaluating effectiveness of restoration to address current stressors to riverine fish. Freshwater Biology, 69, 607-622. https://doi.org/10.1111/fwb.14232 \| Abstract	May 2024	1. River restoration programmes with the goal of conserving and rehabilitating inland fishes have a multi-decadal history, but evaluation and synthesis of past restora-tion actions have been limited by a lack of monitoring and reporting. Given that calls for both monitoring and systematic reviews of restoration have increased, we were interested in the influence that restoration has had on improving condi-tions for riverine fishes resulting from long-standing and increasingly prominent stressors. Our objectives were to (1) identify which stressors were targeted in river restoration efforts, (2) determine the proportion of published studies that articulate restoration goals and develop comparative monitoring designs for as-sessing the effects of restoration on fishes, and (3) conduct a meta-analysis to synthesise fish responses to restoration projects.<br>2. We assessed restoration effectiveness for increasing fish density and richness from peer- reviewed papers published over the past decade using a global system-atic review and meta-analysis.<br>3. We found that restoration actions addressed major stressors primarily by improv-ing in- stream habitat (37%), increasing in-stream longitudinal connectivity (26%) and increasing lateral floodplain connections (9%). Although 81% of studies had comparative monitoring designs (i.e., before/after and control/impact) and stated restoration goals, only 40% of those studies reported sufficient data to be in-cluded in the meta-analysis. Projects which increased in-stream connectivity had the largest positive effect size on fish density and richness compared to in-stream habitat improvements and increasing floodplain connections. Time since restora-tion and restoration size (i.e., geographical footprint) were not strong predictors of fish response effect sizes.<br>4. Restoration effectiveness was highly variable among project types. Authors of studies included in the meta-analysis often identified spatial or temporal scale of monitoring, overriding catchment conditions, and recolonisation potential as sources of variability and effectiveness in restoration outcomes. Systematic re-porting of these and other covariates may help guide processes in restoration evaluation and provide valuable research insights. Despite increased emphasis on monitoring, incomplete data reporting limited the number of studies that could be included for quantitative meta-analysis. Persistent emphasis on setting specific criteria (e.g., measurable outcomes of fish response) for restoration goals, project monitoring, data reporting, information sharing and collaborative projects is likely to continue to improve understanding of restoration effectiveness transferable to future endeavours.<br>5. Our results can be used to support river restoration practitioners with evidence- based information to evaluate the cost–benefit ratio of competing restoration priorities, and inform restoration planning and implementation for riverine fish.
Rogosch, J.S. and J.D. Olden. 2021. Comparing opportunistic and strategic removal efforts to manage invasive fish species using a dynamic multi‐state occupancy model. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.14012	September 2021
Rogan, J.E., M.R. Parker, Z.B. Hancock, A.D. Earl, E.K. Buchholtz, K. Chyn, J. Martina, & L.A. Fitzgerald (2023). Genetic and demographic consequences of range contraction patterns during biological annihilation. Scientific Reports 13, 1691. doi.org/10.1038/s41598-023-28927-z. \| Abstract	January 2023	Species range contractions both contribute to, and result from, biological annihilation, yet do not receive the same attention as extinctions. Range contractions can lead to marked impacts on populations but are usually characterized only by reduction in extent of range. For effective conservation, it is critical to recognize that not all range contractions are the same. We propose three distinct patterns of range contraction: shrinkage, amputation, and fragmentation. We tested the impact of these patterns on populations of a generalist species using forward-time simulations. All three patterns caused 86–88% reduction in population abundance and significantly increased average relatedness, with differing patterns in declines of nucleotide diversity relative to the contraction pattern. The fragmentation pattern resulted in the strongest effects on post-contraction genetic diversity and structure. Defining and quantifying range contraction patterns and their consequences for Earth’s biodiversity would provide useful and necessary information to combat biological annihilation.
Rodgers, P.A. et al. Rifle hunting alters habitat use but does not trigger migration in mule deer. for Journal of Wildlife Management	December 2021
Rodgers et al. Sex-specific migratory behaviors in a temperate ungulate. for Ecosphere	December 2021
Rodger, A. W., , S. L. Wolf, T. A. Starks, J. P. Burroughs, and S. K. Brewer. 2021. Seasonal diet and habitat use of large, introduced Rainbow Trout in an Ozark Highland stream, North American Journal of Fisheries Management 41:1764-1780. https://doi.org/10.1002/najfm.10694	December 2021
Rockweit, JT, KM Dugger, DB Lesmeister, RJ Davis, AB Franklin, and JM Highley. 2024. Changing Fire Regimes and Nuanced Impacts on a Critically Imperiled Species. Biological Conservation 296 (2024) 110701, DOI:10.1016/j.biocon.2024.110701. \| Download	July 2024
Rockweit, JT, JM Jenkins, JE Hines, JD Nichols, KM Dugger, AB Franklin, PC Carlson, WL Kendall, DB Lesmeister, C McCafferty, SH Ackers, LS Andrews, LL Bailey, JB, KP Burnham, T Chestnut, MM Conner, KE Dilione, RJ Davis, ED Forsman, EM Glenn, SA Gremel, KA Hamm, DR Herter, JM Higley, RB Horn, DW Lamphear, TL McDonald, JA Reid, CJ Schwarz, DC Simon, SG Sovern, JK Swingle, JD Wiens, H Wise, and CB Yackulic. 2022. Range-wide Sources of Variation in Reproductive Rates of Northern Spotted Owls. Ecological Applications 000:000-000, doi:10.1002/eap.2726.	August 2022
Roche, M.D., D.J. Saher, E.K. Buchholtz, M.R. Crist, D.J. Shinneman, C.L. Aldridge, B.E. Brussee, P.S. Coates, C.L. Weise, J.A. Heinrichs. 2024. Ecological trade-offs associated with fuel breaks in the sagebrush ecosystem. Fire Ecology. 107. https://doi.org/10.1186/s42408-024-00334-3 \| Abstract	December 2024	Background: Unprecedented wildfire frequency, fueled by invasive annual grasses, threatens sagebrush ecosystems. To suppress wildfire and conserve sagebrush, land management agencies have installed fuel breaks across the sagebrush biome. However, despite the potential reduction in wildfire, fuel breaks may have ecological costs. Determining an acceptable balance between risks and benefits of fuel breaks is needed to avoid accelerating sagebrush loss, annual grass invasion, and habitat degradation. To evaluate the potential for ecological trade-offs to occur, we characterized the contexts in which known fuel breaks currently exist. We synthesized spatial data on all known fuel breaks and a suite of variables that may contribute to fuel break risks and benefits, including burn probabilities, predicted fuel break effectiveness, linear infrastructure, invasive annual grass cover, soil moisture conditions that confer resistance to invasion and resilience to disturbance, and priority wildlife habitats across the sagebrush biome. Results: We found that within the sagebrush biome, fuel breaks are generally located in areas with high burn probability and are thus positioned well to intercept potential wildfires. However, fuel breaks are also frequently positioned in areas with lower predicted fuel break effectiveness relative to the sagebrush biome overall. Fuel breaks also are spatially associated with high invasive grass cover, indicating the need to better understand the causal relationship between fuel breaks and annual invasive grasses. We also show that the fuel break network is dense within priority wildlife habitats. Dense fuel breaks within wildlife habitats may trade off wildfire protection for decreased integrity of such habitats. Conclusions: Our analyses describe the potential for fuel breaks to invoke ecological trade-offs and show that the balance of risks and benefits differs across sagebrush ecosystems. Strategic research and actions are needed to evaluate which factors tip the balance towards maximizing wildfire suppression while minimizing risk to sensitive ecological resources.
Robison, V., Jones, M., Erickson, B., & Biedenweg, K. (2024). Communication Approaches and Specialists that Can Improve Fisheries Management. Fisheries, 49(7), 319-326. https://doi.org/10.1002/fsh.11090 \| Abstract	April 2024	This paper aims to expand fisheries managers’ and scientists’ understanding of how the science of communication can facilitate effective fisheries management. To do this, in this paper we define and create distinctions around common but often conflated fisheries communication approaches: Outreach, Education, Social Marketing, and Engagement. Further, we explain key scientific principles that support each communication approach and offer practical examples of their application. Finally, we highlight different communication research fields that can produce science that practitioners can use in their fisheries communication. These explanations support our claim that communication is required to meet the professional needs of fisheries managers but must also meet the needs of their audiences.
Robinson, K.F., S.M. Miehls, M.J. Siefkes. 2021. Understanding sea lamprey populations in the Great Lakes prior to broad implementation of sea lamprey control. Journal of Great Lakes Research, Special Issue on Sea Lamprey International Symposium III (SLIS III) 47 (Supplement 1):S328-334. DOI: 10.1016/j.jglr.2021.04.002 \| Download	December 2021
Robinson, K.F., P.J. Alsip. D.A.R. Drake, Y.-C. Kao, M.A. Koops, D.M. Mason, E.S. Rutherford, H. Zhang. 2021. Reviewing uncertainty in bioenergetics and food web models to project invasion consequences: four major Chinese carps in the Great Lakes. Journal of Great Lakes Research, Special Issue: Research and management efforts on invasive Asian carps in the Laurentian Great Lakes 47:83-95. DOI: 10.1016/j.jglr.2020.11.003	February 2021
Robinson, K.F., M.R. DuFour, J.L. Fischer, S.J. Herbst, M.L. Jones, L.R. Nathan, T.J. Newcomb. 2023. Lessons Learned in Applying Decision Analysis to Natural Resources Management for High Stakes Issues Surrounded by Uncertainty. Decision Analysis 20: 326-342. https://doi.org/10.1287/deca.2023.0015. \| Abstract	December 2023	Management agencies are tasked with difficult decisions for conservation and management of natural resources. These decisions are difficult because of ecological and social uncertainties, the potential for multiple decision makers from multiple jurisdictions, and the need to account for the diverse values of stakeholders. Decision analysis provides a needed framework for accounting for these difficulties when making conservation and management decisions. We discuss the benefits of the application of decision analysis for these types of issues and provide insights from three case studies from the Laurentian Great Lakes. These case studies describe applications of decision analysis for decisions within an agency (management of double-crested cormorant), among agencies (response to invasive grass carp), and among agencies and stakeholders (sustainable fisheries harvest management). These case studies provide insight into the ways that decision analysis can be useful for conservation and management of natural resources, but we also highlight future needs for decision making for these resources. In particular, applications of decision analysis for conservation and management would benefit from enhanced integration of both ecological and social science, inclusion of a broader base of stakeholders, and partnering with Indigenous peoples to better include traditional knowledge in these important decisions.
Robinson, K.F., M.L. Jones, R. Clark, B. Roth, J. Jonas, I. Tsehaye, M. Kornis, B. Turschak, D. O'Keefe, B. Brenton. 2023. Updated decision analysis to inform multi-species salmonine management in Lake Michigan. NCTC Cooperator Science Series. \| Download	November 2023
Robinson, K.F., M. DuFour, M. Jones, S. Herbst, T. Newcomb, J. Boase, T. Brenden, D. Chapman, J. Dettmers, J. Francis, T. Hartman, P. Kocovksy, B. Locke, C. Mayer, J. Tyson. 2021. Using decision analysis to collaboratively respond to invasive species threats: a case study of Lake Erie grass carp (Ctenopharyngodon idella). Journal of Great Lakes Research, Special Issue: Research and management efforts on invasive Asian carps in the Laurentian Great Lakes 47:108-119. DOI: 10.1016/j.jglr.2020.03.018	February 2021
Robinson, K.F., E. Baker, E. Ewing, V. Hemming, M. Kenney, M. Runge. 2023. Decision analysis to advance environmental sustainability. Decision Analysis 20:243-251. https://doi.org/10.1287/deca.2023.intro.v20.n4.	December 2023
Robinson, K.F., C.R. Bronte, D.B. Bunnell, P. Euclide, D. Hondorp, J. Janssen, M. Kornis, S. Riley, M. Vinson, S. Volkel, B. Weidel. 2021. A synthesis of the biology and ecology of sculpin species in the Laurentian Great Lakes and implications for the adaptive capacity of the benthic ecosystem. Reviews in Fisheries Science and Aquaculture 29:96-121. DOI: 10.1080/23308249.2020.1782341	January 2021
Robinson, K.F., A.K. Fuller, and M.L. Jones. 2021. Using structured decision making to incorporate ecological and social values into harvest decisions: case studies of white-tailed deer and walleye In: Harvest of Fish and Wildlife: New Paradigms for Sustainable Management. CRC Press.	June 2021
Robinson, K.F. (2024) Review of the SFHA SDM Process: a Report to the Delta Science Program. Delta Stewardship Council. San Francisco, CA. \| Download \| Publisher Website	June 2024
Robinson, D.H., Henderson, M.J., H.E., Goodman, Perry, R.W., Som, N.A. From site to system: approaches for producing system-wide estimates of fish habitat in large rivers. To be submitted to River Research and Applications. \| Abstract	October 2021	Worldwide, many productive rivers are dam-regulated and rely on flow management strategies that must balance support of ecological processes with human water use. One component of evaluating this balance is to understand ecological consequences of alternative flow management strategies, which has often been accomplished by coupling population dynamics models with models that relate streamflow to habitat availability and quality. Numerous methods assign habitat availability to locations within a river basin: these include fine-scale field-measured values that are extrapolated to other locations within the basin having similar physical characteristics, or equation-driven values created by functions of model-predicted values of physical characteristics. The array of options for creating habitat models is evolving rapidly as high-resolution remote sensing data becomes more accessible and computational capacity improves. Our objective was to identify tradeoffs among approaches that assign habitat relationships to large rivers, and to create a decision support tool to supplement choices of extent and granularity. Using a selection of case studies that represent a breadth of scales and diverse tradeoffs, we demonstrate the need for a transparent process of data evaluation and assessment to determine the appropriate fit for model scope or context that best supports management needs and recognize sources of uncertainty. The structured approach proposed here aims to improve future model development and refine population dynamics models that inform management of rivers.
Robertson, M. D., S. R. Midway, H. S. Embke, A. L. Kaz, M. Lang, C. P. Paukert, N. A. Sievert, L. Wszola, A. J. Lynch. 2024. Estimating Lentic Recreational Fisheries Catch and Effort Throughout the United States. Fisheries Management and Ecology. https://doi.org/10.1111/fme.12650.	July 2024
Robertson, E. P., D. P. Walsh, J. Martin, T. M. Work, C. A. Kellogg, J. S. Evans, V. Barker, A. Hawthorn, G. Aeby, V. J. Paul, B. K. Walker, Y. Kiryu, C. M. Woodley, J. L. Meyer, S. M. Rosales, M. Studivan, J. F. Moore, M. E. Brandt, and A. Bruckner. 2023. Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases. Journal of Environmental Management 337: 117668. https://doi.org/10.1016/j.jenvman.2023.117668. \| Abstract	July 2023	Emerging diseases can have devastating consequences for wildlife and require a rapid response. A critical first step towards developing appropriate management is identifying the etiology of the disease, which can be difficult to determine, particularly early in emergence. Gathering and synthesizing existing information about potential disease causes, by leveraging expert knowledge or relevant existing studies, provides a principled approach to quickly inform decision-making and management efforts. Additionally, updating the current state of knowledge as more information becomes available over time can reduce scientific uncertainty and lead to substantial improvement in the decision-making process and the application of management actions that incorporate and adapt to newly acquired scientific understanding. Here we present a rapid prototyping method for quantifying belief weights for competing hypotheses about the etiology of disease using a combination of formal expert elicitation and Bayesian hierarchical modeling. We illustrate the application of this approach for investigating the etiology of stony coral tissue loss disease (SCTLD) and discuss the opportunities and challenges of this approach for addressing emergent diseases. Lastly, we detail how our work may apply to other pressing management or conservation problems that require quick responses. We found the rapid prototyping methods to be an efficient and rapid means to narrow down the number of potential hypotheses, synthesize current understanding, and help prioritize future studies and experiments. This approach is rapid by providing a snapshot assessment of the current state of knowledge. It can also be updated periodically (e.g., annually) to assess changes in belief weights over time as scientific understanding increases. <i>Synthesis and applications</i>: The rapid prototyping approaches demonstrated here can be used to combine knowledge from multiple experts and/or studies to help with fast decision-making needed for urgent conservation issues including emerging diseases and other management problems that require rapid responses. These approaches can also be used to adjust belief weights over time as studies and expert knowledge accumulate and can be a helpful tool for adapting management decisions.
Roberts, N.M., M.J. Lovallo, and S.M. Crimmins. 2020. River otter (Lontra canadensis) status, management, and distribution in the United States: Evidence of large-scale population increase and range expansion. Journal of Fish and Wildlife Management 11:279-286.	December 2020
Roberts, C.P., Naugle, D., Allred, B.W., Donovan, V.M., Fogarty, D.T., Jones, M.O., Maestas, J.D., Olsen, A.C., Twidwell, D. New possibilities to track rangeland productivity at multiple scales and quantify conservation outcomes. Journal of Environmental Management. https://doi.org/10.1016/j.jenvman.2022.116359. \| Abstract	December 2022	Historically, relying on plot-level inventories impeded our ability to quantify large-scale change in plant biomass, a key indicator of conservation interventions in rangeland systems. Recent technological advances enable assessment at scales appropriate to inform management by providing spatially comprehensive estimates of productivity that are partitioned by plant functional group across all contiguous US rangelands. We partnered with the Sage Grouse and Lesser Prairie-Chicken Initiatives and the Nebraska Natural Legacy Project to demonstrate the ability of these new datasets to quantify multi-scale changes and heterogeneity in plant biomass following mechanical tree removal, prescribed fire, and prescribed grazing. In Oregon’s sagebrush steppe, for example, juniper tree removal resulted in a 21% increase in one pasture’s productivity and an 18% decline in another. In Nebraska’s Loess Canyons, perennial grass productivity initially declined 80% at sites invaded by trees that were prescriptively burned, but then fully recovered post-fire, representing a 492% increase from nadir. In Kansas’ Shortgrass Prairie, plant biomass increased 4-fold (966,809 kg/ha) in pastures that were prescriptively grazed, with gains highly dependent upon precipitation as evidenced by sensitivity of remotely sensed estimates (SD ±951,308 kg/ha). Our results emphasize that next-generation remote sensing datasets empower land managers to move beyond simplistic control versus treatment study designs to explore nuances in plant biomass in unprecedented ways. New remotely-sensed products also accelerate adaptive management and communicate wildlife and livestock forage benefits from management to diverse stakeholders.
Roberts, C. P., Scholtz, R., Fogarty, D. T., Twidwell, D., & Walker Jr, T. L. (2022). Large‐scale fire management restores grassland bird richness for a private lands ecoregion. Ecological Solutions and Evidence, 3(1), e12119. \| Abstract \| Download	January 2022	Of all terrestrial biomes, grasslands are losing the most biodiversity the most rapidly, so there is a critical need to document and learn from large-scale restoration successes. In the Loess Canyons ecoregion of the Great Plains, USA, an association of private ranchers and natural resource agencies has led a multi-decadal, ecoregion-scale initiative to combat the continued loss of grasslands to woody plant encroachment by restoring large-scale fire regimes. Here, we use 14 years of fire treatment history with 6 years of grassland bird monitoring and remotely-sensed tree cover data across 136,767 hectares of privately-owned grassland to quantify outcomes of large-scale grassland restoration efforts. Grassland bird richness increased across 65% (90,032 ha) of the Loess Canyons, and woody plant cover decreased up to 55% across 25% (7,408 ha) of all fire-treated areas. This was accomplished with extreme fire treatments that killed mature trees, were large (mean annual area burned was 3,100 ha), spatially clustered, and straddled boundaries between invasive woodlands and remaining grasslands—not heavily-infested woodlands. Findings from this study provide the first evidence of human management reversing the impacts of woody encroachment on grassland birds at an ecoregion scale.
Roberts, A.D., J. Besser, J. Hundley, D. Mosby, A. Rosenberger, K. L. Bouska, B. Simmons, L. Lueckenhoff, S. E. McMurray, S. Faiman, and L. Lueckenhoff. 2023. An assessment of the relation between metal contaminated sediment and freshwater mussel populations in the Big River, Missouri. Science of the Total Environment. 876: https://doi.org/10.1016/j.scitotenv.2023.162743. \| Abstract \| Download	June 2023	The Big River in east-central Missouri drains the largest lead mining area in the United States. Releases of heavy metal contaminated sediments into this river is well documented and suspected to be suppressing freshwater mussel populations. During this study, we characterized the spatial extent of metal contaminated sediments and evaluated its relationship with mussel populations in the Big River. Mussels and sediments were collected at 34 sites in the Big River and 3 reference sites in the Big, Bourbeuse, and Meramec rivers in 2008 and 2013. Analysis of sediment samples with X-ray fluorescence showed that lead (Pb) and zinc (Zn) exceeded background concentrations by between 1.5 and 65 times for 168 km downstream of Pb mining releases. Mussel abundance decreased acutely downstream of releases of large volumes of heavy metal mine waste and showed consistent increases with distance downstream. We compared Big River species richness with historical surveys and with all data from 3 similar nearby rivers with similar physical habitat characteristics and threats to mussels, minus Pb mining impacts. Big River species richness predicted by these regressions was only about one-half that expected on average and 70-75% lower in reaches with high median Pb concentrations. Sediment Pb, Zn, and cadmium had significant negative correlations with species richness and abundance. The association of sediment metal concentrations with mussel community metrics in otherwise high quality habitat indicates that Pb and Zn toxicity are responsible for the observed mussel population declines within the Big River. We used concentration-response regressions of mussel density vs sediment Pb to determine that Big River mussel community was adversely affected when sediment Pb concentrations were above 160 ppm, the concentration associated with 20% decreases in mussel density. Thus, based on this sediment metal and mussel fauna assessment, our findings indicate that approximately 140 km of the Big River has a toxic effect to mussels from Pb and other heavy metals.
Roberts CP, Uden DR, Allen CR, Angeler DG, Powell LA, Allred BW, Jones MO, Maestas JD, Twidwell D. 2022. Tracking spatial regimes in animal communities: implications for resilience-based management. Ecological Indicators. doi.org/10.1016/j.ecolind.2022.108567 \| Abstract \| Download	January 2022	Spatial regimes (the spatial extents of ecological states) exhibit strong spatiotemporal order as they expand or contract in response to retreating or encroaching adjacent spatial regimes (e.g., woody plant invasion of grasslands) and human management (e.g., fire treatments). New methods enable tracking spatial regime boundaries via vegetation landcover data, and this approach is being used for strategic management across biomes. A clear advancement would be incorporating animal community data to track spatial regime boundaries alongside vegetation data. In a 41,170-hectare grassland experiencing woody plant encroachment, we test the utility of using animal community data to track spatial regimes via two hypotheses. (H1) Spatial regime boundaries identified via independent vegetation and animal datasets will exhibit spatial synchrony; specifically, grassland:woodland bird community boundaries will synchronize with grass:woody vegetation boundaries. (H2) Negative feedbacks will stabilize spatial regimes identified via animal data; specifically, frequent fire treatments will stabilize grassland bird community boundaries. We used 26 years of bird community and vegetation data alongside 32 years of fire history data. We identified spatial regime boundaries with bird community data via a wombling approach. We identified spatial regime boundaries with vegetation data by calculating spatial covariance between remotely-sensed grass and woody plant cover per pixel. For fire history data, we calculated the cumulative number of fires per pixel. Setting bird boundary strength (wombling <i>R<sup>2</sup></i> values) as the response variable, we tested our hypotheses with a hierarchical generalized additive model (HGAM). Both hypotheses were supported: animal boundaries synchronized with vegetation boundaries in space and time, and grassland bird communities stabilized as fire frequency increased (HGAM explained 38% of deviance). We can now track spatial regimes via animal community data pixel-by-pixel and year-by-year. Alongside vegetation boundary tracking, tracking animal community boundaries can inform the scale of management necessary to maintain animal communities endemic to desirable ecological states. Our approach will be especially useful for conserving animal communities requiring large-scale, unfragmented landscapes—like grasslands and steppes.
Roberts CP, Ludwig A, Fogarty DT, Stuber E, Uden DR, Walker TJ, Twidwell D. *Population increases of the threatened American burying beetle (Nicrophorus americanus) linked to large-scale conservation strategies in a private lands ecoregion*. Biological Conservation. 301: https://doi.org/10.1016/j.biocon.2024.110865 \| Abstract	November 2024	Woody plant encroachment and row-crop agricultural land conversion are existential threats to species that rely on grassland ecosystems. The American burying beetle (<i>Nicrophorus americanus</i>) is a threatened species whose largest remnant populations are predominantly located in grassland ecoregions comprised of privately-owned ranching lands. Here, we seek to determine functional scaling patterns and population trends of the American burying beetle in the face of conservation threats and grassland restoration. We used 13 years (2007 – 2019) of American burying beetle abundance data collected from permanent sampling locations across the Loess Canyons ecoregion (Nebraska, USA), where a network of ranchers have been restoring large-scale grasslands. To estimate beetle abundance relative to land cover variables, we developed a Bayesian N-mixture model, incorporating the Bayesian latent indicator scale selection (BLISS) method to probabilistically determine at which scales land cover variables best explained beetle abundance. American burying beetle abundance significantly increased across the ecoregion, despite high interannual variation in abundance. Increases in beetle abundance were associated with large-scale (1,149 ha extent) grassland cover. Decreases in abundance were associated with large-scale crop conversion (590 ha extent) and large-scale increases in woody cover (1,149 ha extent). This study provides the first evidence of ecoregion-scale population increases of the American burying beetle. These increases are tied to landscape variables that are managed in a large-scale, coordinated private lands grassland restoration effort. Our results suggest that successful grassland restoration will depend on coordinating across property boundaries to implement conservation at scales necessary to conserve species that require large-scale, unfragmented grasslands.
Roberts CP, Grant WE, Horton ML, LaBrie LAP, Peterson MR, Rogosch JS, Wang H. 2024. Balancing ecology and practicality to rank waterbodies for preventative invasive species management. Ecological Solutions and Evidence. \| Abstract	August 2024	1. Early detection and rapid response (EDRR) is the most successful framework for preventative invasive species management, but prioritizing localized EDRR actions with limited resources is challenging. An approach that ranks individual locations, such as waterbodies, for EDRR by combining an invasive species’ establishment risk with the practicality of managing it could help set reasonable priorities.<br>2. Here, we worked with regional practitioners in Arkansas, USA and the broader Southeastern USA to co-produce a workflow for preventative aquatic invasive species management that 1) estimates establishment risk under current and future climates with a species distribution model, 2) scores waterbodies according to difficulty of eradicating an aquatic invasive species if it were introduced, and 3) combines establishment risk and eradication difficulty scores to rank waterbodies according to preventative management priority. As our focal species, we used giant salvinia (<i>Salvinia molesta</i>), a floating aquatic fern ranked among the worst weeds in the world due to its negative socioecological impacts and difficulty to eradicate once established.<br>3. Current establishment risk is low for much of our study area, but under future climate scenarios (RCP 8.5), areas with > 60% giant salvinia establishment risk increased from 546 km<sup>2</sup> to 30,219 km<sup>2</sup> between 2023 and 2040 in Arkansas.<br>4. We found giant salvinia establishment risk and eradication difficulty are independent of each other (<i>r</i> = 0.28), and it follows that, alone, early detection tools such as species distribution models are insufficient for managers to prioritize sites for EDRR.<br>5. We envision our approach fitting into a potential EDRR workflow that cascades from broad- to local-scale. To illustrate, 1) horizon scanning and/or climate matching generates lists of high-risk invasive species; 2) species lists are narrowed according to eradication feasibility scores; 3) for all remaining species, all waterbodies across a geography of interest receive prioritization rankings based on establishment risk and eradication difficulty scores. Given that climate change makes predicting invasive species’ distributions a moving target, combining co-produced eradication difficulty scoring with species distribution modeling will balance rigor with practicality when prioritizing locations for EDRR.<br><br>
Roberts CP, Grant WE, Horton ML, LaBrie LAP, Peterson MR, Rogosch JS, Wang H. 2024. Balancing ecology and practicality to rank waterbodies for preventative invasive species management. Ecological Solutions and Evidence. \| Abstract	August 2024	1. Early detection and rapid response (EDRR) is the most successful framework for preventative invasive species management, but prioritizing localized EDRR actions with limited resources is challenging. An approach that ranks individual locations, such as waterbodies, for EDRR by combining an invasive species’ establishment risk with the practicality of managing it could help set reasonable priorities.<br>2. Here, we worked with regional practitioners in Arkansas, USA and the broader Southeastern USA to co-produce a workflow for preventative aquatic invasive species management that 1) estimates establishment risk under current and future climates with a species distribution model, 2) scores waterbodies according to difficulty of eradicating an aquatic invasive species if it were introduced, and 3) combines establishment risk and eradication difficulty scores to rank waterbodies according to preventative management priority. As our focal species, we used giant salvinia (<i>Salvinia molesta</i>), a floating aquatic fern ranked among the worst weeds in the world due to its negative socioecological impacts and difficulty to eradicate once established.<br>3. Current establishment risk is low for much of our study area, but under future climate scenarios (RCP 8.5), areas with > 60% giant salvinia establishment risk increased from 546 km<sup>2</sup> to 30,219 km<sup>2</sup> between 2023 and 2040 in Arkansas.<br>4. We found giant salvinia establishment risk and eradication difficulty are independent of each other (<i>r</i> = 0.28), and it follows that, alone, early detection tools such as species distribution models are insufficient for managers to prioritize sites for EDRR.<br>5. We envision our approach fitting into a potential EDRR workflow that cascades from broad- to local-scale. To illustrate, 1) horizon scanning and/or climate matching generates lists of high-risk invasive species; 2) species lists are narrowed according to eradication feasibility scores; 3) for all remaining species, all waterbodies across a geography of interest receive prioritization rankings based on establishment risk and eradication difficulty scores. Given that climate change makes predicting invasive species’ distributions a moving target, combining co-produced eradication difficulty scoring with species distribution modeling will balance rigor with practicality when prioritizing locations for EDRR.
Roberts CP, Doser JW, Berry LL, Fowler A, Marshall PM, Middaugh C, Rowe K, Schmit JM, Shaw M, Wilson K. Scenario planning and multi-species occupancy models reveal positive avian responses to restoration of afforested woodlands. Restoration Ecology. 32(1), e13998. \| Abstract	April 2023	Scenario planning is a powerful approach for assessing restoration outcomes under alternative futures. However, developing plausible scenarios remains daunting in complex systems like ecological communities. Here, we used Bayesian multi-species occupancy modeling to develop scenarios to assess woodland restoration outcomes in afforested communities in seven wildlife management areas in Arkansas, USA. Our objectives were (1) define plausible woodland restoration and afforestation scenarios by quantifying historic ranges of variation in mean tree cover and tree cover heterogeneity from 1986 - 2021, and (2) predict changes in bird species richness and occupancy patterns for six species of greatest conservation need under two future scenarios: complete afforestation (100% tree cover) and woodland restoration (based on remotely-sensed historic tree cover). Using 35 years of remotely-sensed tree cover data and six years of bird monitoring data, we developed multi-species occupancy models to predict future bird species richness and occupancy under the complete afforestation and woodland restoration scenarios. Between 1986 and 2021, tree cover increased in all study areas–with one increasing 70%. Under the woodland restoration scenario, avian species richness increased up to 20%, and four of six species of greatest conservation need exhibited gains in occupancy probability. The complete afforestation scenario had negligible effects on richness and occupancy. Overall, we found decreasing tree cover to historic levels prior to widespread afforestation would provide community-level benefits and would do little harm even to forest-dependent species of conservation concern. Applying multi-species occupancy modeling within a scenario planning framework allows for comparing multi-scale tradeoffs between plausible futures.
Robb, B. et al. Nowhere to run: pronghorn space use impacted by semi-permeability of barriers	April 2022
Rivera-Burgos, A. C., J. A. Collazo, A. J. Terando, and K. Pacifici. 2021. Linking demographic rates to local environmental conditions in support of Climate Adaptation Strategies for Eleutherodactylus frogs. Global Ecology and Conservation 28 (2021) e01624. \| Abstract	May 2021	Conducting managed species translocations and establishing climate change refugia are adaptation strategies to cope with projected consequences of global warming, but successful implementation requires on-the-ground validation of demographic responses to transient climate conditions. Here we estimated the effect of nine abiotic and biotic factors on local occupancy and an index of abundance (few or chorus) for four amphibian species (<i>Eleutherodactylus wightmanae</i>, <i>E. brittoni</i>, <i>E. antillensis,</i> and <i>E. coqui</i>) in Puerto Rico, USA. We also assessed how the same factors influenced reproductive activity of <i>E. coqui</i> and how species responded to hurricane María (20 September 2017). As predicted, occupancy and abundance of <i>E. wightmanae</i>, <i>E. brittoni</i> and <i>E. coqui</i> were positively and strongly influenced by abiotic covariates (e.g., relative humidity) that characterize high elevation, mesic habitats. <i>E. antillensis</i> exhibited the opposite pattern, with highest probabilities (≥0.6) recorded at ≤300 m and with average relative humidity <75%. Biotic covariates (e.g., canopy cover) had a weak influence on both parameters, regardless of species. High probabilities (≥0.9) of detecting an <i>E. coqui</i> chorus and active nests occurred at sites experiencing average relative humidity of >80% and temperature of ≤26° C. Moderate to high probabilities of detecting a chorus (0.4 - 0.7) were recorded at sites with average temperatures >26°C, but no reproductive activity was detected, implying that monitoring abundance alone could misrepresent the capacity of a local population to sustain itself. The possibility underscores the importance of understanding the interplay between local demographic and environmental parameters in the advent of global warming to help guide monitoring and management decisions, especially for high elevation specialists. Hurricanes can inflict marked reductions in population numbers, but impacts vary by location and species. We found that the abundance (chorus) of <i>E. antillensis</i> and <i>E. brittoni</i> increased after the hurricane, but the abundance of the other two species did not differ between years. Lack of impacts was probably mediated by low structural damage to forest tracts (e.g., 9% canopy loss). Our findings help assess habitat suitability in terms of parameters that foster local population growth, which provides a basis for testing spatio-temporal predictions about demographic rates in potential climate refugia and for designing criteria to help guide managed translocations.
Rivera, S.J., K.M. Alpi, J. A. Collazo, M. K. Stoskopf. 2022. Statistical Methods Used In Research Concerning Endangered and Threatened Animal Species of Puerto Rico: A Meta-study. Caribbean Journal of Science. \| Abstract	January 2022	A concern about statistics in wildlife studies, particularly of endangered and threatened species, is whether the data collected meet the assumptions necessary for the use of parametric statistics. This study identified published papers on the nine endangered and six threatened species found only on Puerto Rico using 5 different databases. The results from the database Zoological Record identified the most articles, including all identified by the other databases. Of the 220 articles identified, 113 included some form of statistics, 28 used only descriptive statistics, 42 included parametric statistics, 24 used only nonparametric statistics, and 19 reported both parametric and nonparametric statistical analyses. This meta-study showed that the percentage of articles with no statistical treatment decreased in the most recent 20 years and that although parametric statistics continue to be most commonly used in published wildlife studies of Puerto Rican wildlife, there has been a distinct increase in the use of nonparametric statistics over time.
Rivera, S.J., K.M. Alpi, J. A. Collazo, M. K. Stoskopf. 2022. Statistical Methods Used In Research Concerning Endangered and Threatened Animal Species of Puerto Rico: A Meta-study. Caribbean Journal of Science. \| Abstract	January 2022	A concern about statistics in wildlife studies, particularly of endangered and threatened species, is whether the data collected meet the assumptions necessary for the use of parametric statistics. This study identified published papers on the nine endangered and six threatened species found only on Puerto Rico using 5 different databases. The results from the database Zoological Record identified the most articles, including all identified by the other databases. Of the 220 articles identified, 113 included some form of statistics, 28 used only descriptive statistics, 42 included parametric statistics, 24 used only nonparametric statistics, and 19 reported both parametric and nonparametric statistical analyses. This meta-study showed that the percentage of articles with no statistical treatment decreased in the most recent 20 years and that although parametric statistics continue to be most commonly used in published wildlife studies of Puerto Rican wildlife, there has been a distinct increase in the use of nonparametric statistics over time.
Rivera, K., Garcia-Quijano, C., Sonnet, V., & Gerber, B. D. (2024). Applying a hierarchical Bayesian framework to reveal how fear and animal ownership drive human's valuation of and interactions with coyotes. Conservation Science and Practice, e13177. https://doi.org/10.1111/csp2.13177 \| Download	August 2024
Rivera, K, Fidino, M, Farris, ZJ, Murphy, A, Magle, S, and Gerber, BD. 2022. Rethinking habitat occupancy modeling and the role of diel activity in an anthropogenic world. American Naturalist, 200, 4, 556-570. https://doi.org/10.1086/720714	August 2022
Rivera, D., JP Zegarra, CE Figuerola-Hernández, JL Herrera-Giraldo, N Arocho-Hernández, NJ Hostetter, J Collazo, RC Bell. 2023. Contemporary record and photographs of the rarely seen and poorly known Mona Blind Snake, Antillotyphlops monensis (Serpentes: Typhlopidae), with comments on ecology and conservation. Herpetology Notes 16:915-918. \| Abstract	November 2023	NA
Rivera, D., JP Zegarra, AR Puente-Rolon, N Arocho-Hernández, NJ Hostetter, JA Collazo, RC Bell. 2024. Multiple Records of the Introduced Parthenogenetic Smooth-scaled Tegulet (Gymnophthalmus underwoodi Grant 1958) in Puerto Rico. Reptiles & Amphibians 31:e21466–e21466. doi.org/10.17161/randa.v31i1.21466. \| Abstract	March 2024	NA
Rivera, D, JB Henderson, AW Lam, NJ Hostetter, JA Collazo, RC Bell. 2024. High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae. Genome Biology and Evolution evae079. doi.org/10.1093/gbe/evae079.	April 2024
Ritter, T. D., A. V. Zale, G. Grisak, and M. J. Lance. 2020. Groundwater upwelling regulates thermal hydrodynamics and salmonid movements during high temperature events at a montane tributary confluence. Transactions of the American Fisheries Society doi.org/10.1002/tafs.10259 \| Abstract	August 2020	The Smith River is a popular recreational sport fishery in western Montana, but salmonid abundances there are thought to be limited by riparian land-use alterations, irrigation water withdrawals, and high summer water temperatures. We used integrated networks of temperature loggers, PIT-tag antenna stations, and in-situ temperature mapping to investigate thermal hydrodynamics and associated movements of PIT-tagged salmonids at the confluence of Tenderfoot Creek, a major, unaltered coldwater tributary of the Smith River. Contrary to expectations, Tenderfoot Creek itself was not used as a thermal refuge by salmonids during periods of high main-stem water temperatures; rather, its cool outflow into the Smith River was used instead. Mean outflow water temperatures were 2.9 °C lower than those of the Smith River during summer and ranged from 0.5 °C to 6.1 °C less. Moreover, measured and estimated temperatures in the outflow were cooler (by up to 2.8 °C) than in Tenderfoot Creek itself at times as a result of groundwater upwelling at the confluence. Detections of PIT-tagged fish in the thermal plume increased, especially at night, when daily mean water temperatures exceeded 20°C in the main stem Smith River; 4 times as many PIT-tagged fish were detected in the plume (<i>N = </i>52) than along the opposite bank (<i>N = </i>12), which ostensibly afforded better cover. Coldwater tributary confluences may provide superior thermal refuges for salmonids—cooler and more secure than the tributaries themselves—when water temperatures in river main stems are stressful.
Ritenour, K., S.L.King, S. Collins, and M. D. Kaller. 2022. FACTORS AFFECTING NEST SUCCESS OF COLONIAL NESTING WATERBIRDS IN SOUTHWEST LOUISIANA. Estuaries and Coasts. 45:897-912. \| Publisher Website	August 2021
Riley, Shawn. J., and Angela K. Fuller. 2023. “Integrating social and environmental science in decision making for endangered species management.” In The codex of the Endangered Species Act: the next fifty years (Volume II). L. E. Baier, and J. F. Organ, Editors. Lanham, Maryland: Rowman and Littlefield): Chapter 14.	November 2023
Riley, I. P., and C. J. Conway. 2020. Methods for estimating vital rates of greater sage-grouse broods: A review. Wildlife Biology 2020:wlb.00700.	September 2020
Riley, I. P., C. J. Conway, B. S. Stevens, and S. Roberts. 2021. Survival of greater sage-grouse broods: survey method affects disturbance, detection probability, and ability to detect age-specific mortality. Journal of Field Ornithology 92:88-102. doi: 10.1111/jofo.12356	April 2021
Riley, I. P., C. J. Conway, B. S. Stevens, and S. Roberts. 2021. Aural and visual detection of greater sage-grouse leks: implications for population trend estimates. Journal of Wildlife Management 85:508-519. DOI: 10.1002/jwmg.21991	January 2021
Riepe, T.B., V. Vincent, Vicki Milano, E.R. Fetherman, and D.L. Winkelman. Evidence for the use of mucus swabs to detect Renibacterium salmoninarum in Brook Trout. Pathogens 10, 460. https://doi.org/10.3390/ pathogens10040460 \| Download	April 2021
Riepe, T.B., E.R. Fetherman, B. Neuschwanger, T. Davis, A. Perkins, and D.L. Winkelman. 2023. Vertical Transmission of Renibacterium salmoninarum in Cutthroat Trout (Oncorhynchus clarkii). Journal of Fish Diseases DOI:10.1111/jfd13745 \| Download	December 2022
Riepe, T.B., B.W. Avila, and D.L. Winkelman. 2022. Effects of 17a-ethinylestradiol and Density on Juvenile Fathead Minnow Growth and Survival. Journal of Aquatic Pollution and Toxicology 6:60 DOI:10.21767/2581-804X.22.6.60 \| Download	October 2022
Rieber, C.J., T.J. Hefley, and D.A. Haukos. 2024. Treed Gaussian processes for animal movement modelling. Ecology and Evolution 14:e11447.	June 2024
Richardson, E.T. and Patiño, R. 2021, Growth of the harmful alga, Prymnesium parvum (Prymnesiophyceae), after gradual and abrupt increases in salinity. Journal of Phycology 57, 1335–1344. https://doi.org/10.1111/jpy.13172. \| Abstract \| Publisher Website	August 2021	<i>Prymnesium parvum</i> is a euryhaline, toxin‐producing microalga. Although its abundance in inland waters and growth potential in the laboratory are reduced at high salinity (>20), the ability of inland strains to adjust their growth after long‐term residence in high salinity is uncertain. An inland strain of <i>P. parvum</i> maintained at salinity of 5 in modified artificial seawater medium (ASM‐5) was subjected to the following treatments over five sequential batch‐culture rounds: ASM‐5 (control); modified ASM at salinity of 30, raised with NaCl; modified ASM at salinity incrementally increased to 30 with NaCl; and Instant Ocean® at salinity of 30 (IO‐30). Exponential growth rate (<i>r</i>) was reduced when salinity was increased from 5 to 30 in ASM but returned to control values during the second round. When salinity was incrementally increased, a reduction in <i>r</i> still occurred when salinity reached 25‐30. Maximum density was reduced at salinity of 30 in ASM upon abrupt transfer or incremental increase, and compensation did not occur. Growth performance in IO‐30 was comparable to control values. In conclusion, (1) long‐term compensation for acute inhibitory effects of high salinity occurred for <i>r</i> but not maximum density, (2) incremental increases in salinity did not prevent growth inhibition, suggesting the existence of a salinity threshold of 25‐30 for onset of salinity stress, and (3) the presence of a seawater‐like salt mixture prevented growth inhibition by high salinity. These findings provide new insights on <i>P. parvum</i>’s long‐term ability to adjust its growth in environments of different salinity and ionic composition.
Richardson, E.T. and Patiño, R. 2021, Growth of the harmful alga, Prymnesium parvum (Prymnesiophyceae), after gradual and abrupt increases in salinity. Journal of Phycology 57, 1335–1344. https://doi.org/10.1111/jpy.13172. \| Abstract \| Publisher Website	August 2021	<i>Prymnesium parvum</i> is a euryhaline, toxin‐producing microalga. Although its abundance in inland waters and growth potential in the laboratory are reduced at high salinity (>20), the ability of inland strains to adjust their growth after long‐term residence in high salinity is uncertain. An inland strain of <i>P. parvum</i> maintained at salinity of 5 in modified artificial seawater medium (ASM‐5) was subjected to the following treatments over five sequential batch‐culture rounds: ASM‐5 (control); modified ASM at salinity of 30, raised with NaCl; modified ASM at salinity incrementally increased to 30 with NaCl; and Instant Ocean® at salinity of 30 (IO‐30). Exponential growth rate (<i>r</i>) was reduced when salinity was increased from 5 to 30 in ASM but returned to control values during the second round. When salinity was incrementally increased, a reduction in <i>r</i> still occurred when salinity reached 25‐30. Maximum density was reduced at salinity of 30 in ASM upon abrupt transfer or incremental increase, and compensation did not occur. Growth performance in IO‐30 was comparable to control values. In conclusion, (1) long‐term compensation for acute inhibitory effects of high salinity occurred for <i>r</i> but not maximum density, (2) incremental increases in salinity did not prevent growth inhibition, suggesting the existence of a salinity threshold of 25‐30 for onset of salinity stress, and (3) the presence of a seawater‐like salt mixture prevented growth inhibition by high salinity. These findings provide new insights on <i>P. parvum</i>’s long‐term ability to adjust its growth in environments of different salinity and ionic composition.
Ribic, C.A., D.J. Rugg, K. E. Ellison, N. Koper, and P.J. Pietz. 2021. Diel patterns of predation and fledging at nests of four species of grassland songbirds. Ecology and Evolution 11:6913–6926, DOI: 10.1002/ece3.7541.	June 2021
Ribeiro J. W., Siqueira, T., DiRenzo, G. V., Lambertini, C., Lyra, M. L., Toledo, L. F., Haddad, C. F. B., Becker, C. G. 2020. Assessing infection risk in tropical amphibians while accounting for imperfect detection of Batrachochytrium dendrobatidis. Oecologia 193: 237-248. \| Abstract \| Download \| Publisher Website	December 2020	Ecologists studying emerging wildlife diseases need to confront the realism of imperfect pathogen detection across heterogeneous habitats to aid in conservation decisions. For example, spatial risk assessments of amphibian disease caused by Batrachochytrium dendrobatidis (Bd) has largely ignored imperfect pathogen detection across sampling sites. Because changes in pathogenicity and host susceptibility could trigger recurrent population declines, it is imperative to understand how pathogen prevalence and occupancy vary across environmental gradients. Here, we assessed how Bd occurrence, prevalence, and infection intensity in a diverse Neotropical landscape vary across streams in relation to abiotic and biotic predictors using a hierarchical Bayesian model that accounts for imperfect Bd detection caused by qPCR error. Our model indicated that the number of streams harboring Bd-infected frogs is higher than observed, with Bd likely being present at ~ 43% more streams than it was detected. We found that terrestrial-breeders captured along streams had higher Bd prevalence, but lower infection intensity, than aquatic-breeding species. We found a positive relationship between Bd occupancy probability and stream density, and a negative relationship between Bd occupancy probability and amphibian local richness. Forest cover was a weak predictor of Bd occurrence and infection intensity. Finally, we provide estimates for the minimum number of amphibian captures needed to determine the presence of Bd at a given site where Bd occurs, thus, providing guidence for cost-effective disease risk monitoring programs.
Rhynd, Kamara J. R., Walsh, Daniel P., Arthur-Banfield, Linnell C. M. 2021. Efficacy of fenbendazole and ivermectin against Trichuris spp. in African green monkeys (Chlorocebus sabaeus) in Barbados West Indies. Journal of the American Association for Laboratory Animal Science 60: 475-483. https://doi.org/10.30802/AALAS-JAALAS-20-000103	January 2021
Rhea, A. M., and A. D. Chalfoun. 2023. Experimental reduction of a primary nest predator fails to decrease nest predation rates of sagebrush songbirds. Ornithological Applications 1:10 - 23. \| Abstract	September 2023	The use of predator removal to increase the reproductive success of a prey species of concern is relatively common in wildlife management. The efficacy of such an approach, however, depends partly on the extent to which predation risk is additive or compensatory, which remains unknown for many systems. We experimentally reduced the local abundance of deer mice (<i>Peromyscus maniculatus</i>), a primary nest predator of three sagebrush-obligate songbirds (Brewer’s Sparrow [<i>Spizella breweri</i>], Sagebrush Sparrow [<i>Artemisiospiza nevadensis</i>], and Sage Thrasher [<i>Oreoscoptus montanus</i>]) in western Wyoming, USA to assess whether nest predation risk was additive or compensatory, and whether nest predator removal could comprise a potentially effective management tool. Deer mouse removal did not affect the daily nest survival of songbirds, despite a reduction of 68 ̶ 85% in the deer mouse population within treatment areas. Nest mortality in this system therefore likely operates in a compensatory way, in which new immigrants or other species of nest predator can maintain similar levels of nest predation risk regardless of the prevalence of a dominant predator. We caution that predator removal may not be an effective management tool in open systems with many potential predator species, even when a single species typically is responsible for the majority of predation events.
Rhea, A. M., J. D. Carlisle, and A. D. Chalfoun. Intrabrood variation in nestling size among three sagebrush-associated songbirds. Wilson Journal of Ornithology. \| Abstract	June 2022	The young of some altricial bird species hatch asynchronously, sometimes leading to considerable size differences among siblings. Asynchronous hatching may comprise a bet-hedging strategy whereby adults can maximize the probability of successfully fledging at least one young from the nest even when resources are limited. Despite the potential importance of intrabrood variation in nestling size to the breeding strategy of altricial birds, the extent of this phenomenon remains largely unclear for many species. We weighed 453 nestlings from 148 nests of three sympatric, sagebrush-associated songbird species in Wyoming, USA to describe the magnitude of intrabrood size differences for these species. Intrabrood differences in nestling mass were greatest for the largest species, the Sage Thrasher (<i>Oreoscoptes montanus</i>), for which the smallest nestling in a brood was on-average 26.2% smaller than the largest. The smaller Vesper Sparrow (<i>Pooecetes gramineus</i>) and Brewer’s Sparrow (<i>Spizella breweri</i>) exhibited similar intrabrood size ratios, with the smallest nestling being 17.4% and 18.4% smaller on average than the largest for the two species, respectively. For each additional nestling within a brood, the smallest nestling was an additional 6.6 ̶ 13.6% smaller than the largest nestling, depending on species. Understanding the extent of intrabrood variation in nestling traits has important implications for the productivity of sensitive species facing increasingly unpredictable environments.
Remiszewski,T.T., P. Budy, and W. W. Macfarlane. In review. Examining the Impacts of Extreme Geomorphic Change on Habitat Diversity in a Historically Degraded Desert River. Submitted to River Research and Applications. DOI: 10.1002/rra.4213. USGS FSP IP: 147695. \| Abstract \| Download	September 2023	Widespread hydrologic alterations have simplified in-stream habitats in rivers globally, driving population declines and local extirpations of many native fishes. Here, we examine how extreme geomorphic change in a historically degraded desert river has impacted habitat diversity and persistence. Due to the introduction of a sediment plug from a tributary wash in 2010, a large reach of the degraded and simplified San Rafael River, Utah, began to actively change from a single-thread channel to a complex, multi-threaded riverscape. We combined field measurements and drone-collected imagery to document habitat changes due to this new habitat feature and monitored habitat use by native and endemic fishes. Our results demonstrate the habitat feature is more diverse than any other stream reach along the lower SRR, with reaches located at the edge of the expanding wash feature containing 17% more complex habitat (e.g., pools, riffles, backwaters) on average than reference reaches, and containing 641% more diverse habitat overall than 5 years prior to the start of our study. The wash feature is also retaining water for periods beyond what is expected during seasonal drying, with the total extent of inundation within the riverscape increasing by over 2,800%. Since the formation of the 2010 sediment plug, riparian habitat has increased by 230% since 2009, and channel networks have expanded from a single thread channel to more than 50 distinct channels throughout the sediment plug’s zone of influence. These results will inform management and conservation of habitat for imperiled desert fishes and encourage the use of process-based restoration tools such as “low-tech” habitat restoration in order to mitigate the impacts of simplification and increase habitat persistence in the face of increasing aridity in the desert Southwest.
Reitsma, L. R., M. T. Hallworth, M. McMahon, and C. J. Conway. 2020. Canada Warbler (Cardellina canadensis), version 2.0. In Birds of the World (P. G. Rodewald and B. K. Keeney, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.canwar.02	May 2020
Reid, A. J., A. K. Carlson, D. E. L. Hanna, J. D. Olden, S. J. Ormerod, and S. J. Cooke. 2020. Conservation challenges to freshwater ecosystems. In: Goldstein, M.I., DellaSala, D.A. (Eds.), Encyclopedia of the World's Biomes, vol. 4. Elsevier, pp. 270–278. https://doi.org/10.1016/b978-0-12-409548-9.11937-2	January 2020
Rehm, T.R., S.R. Chipps, and J.L. Davis. 2020. Effects of density reduction on age-specific growth of stream-dwelling Brown Trout Salmo trutta. North American Journal of Fisheries Management 40:1355-1366.	December 2020
Regehr EV, MC Runge, A Von Duyke, RR Wilson, L Polasek, KD Rode, NJ Hostetter, and SJ Converse. 2021. Demographic risk assessment for a harvested species threatened by climate change: polar bears in the Chukchi Sea. Ecological Applications: e02461.	September 2021
Reed, K., L. Izzo, T. Binder, T. Hayden, D. Dembkowski, S. Hansen, D. Caroffino, C. Vandergoot, C. Krueger, and D. Isermann. 2023. Initial insights on the thermal ecology of Lake Whitefish in northwestern Lake Michigan. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2023.03.002	June 2023
Reddell, C.D., G.W. Roemer, D.K. Delaney, T. Karish, and J.W. Cain III. 2023. Anthropogenic subsidies influence resource use during a mange epizootic in a desert coyote population. Oecologia 201:435–447. https://doi.org/10.1007/s00442-023-05328-7 \| Download	February 2023
Reddell, C.D., F. Abadi, D.K. Delaney, J.W. Cain III, and G.W. Roemer. 2021. Urbanization’s influence on the distribution of mange in a carnivore revealed with multistate occupancy models. Oecologia 195:105-116. \| Download	February 2021
Rebholz, P.F., L.P. Waits, and D.E. Ausband. 2024. Gray wolf breeders are more vulnerable to harvest during the breeding season. Wildlife Society Bulletin. \| Abstract	November 2024	In cooperatively breeding carnivores, the composition (i.e., the number of different sex and age classes) and size of a group influence recruitment and group survival. For group living canids like gray wolves (<i>Canis lupus</i>), breeders are vital to perpetuating the group, and the death or removal of an individual breeder can greatly affect a group’s composition, genetic content, and short-term population growth (Ausband et al. 2015; Ausband et al. 2017). Monitoring these parameters in remote populations through traditional approaches such as radio-telemetry and direct observation is difficult and costly due to geographic obstacles, large home ranges, and reduced sampling opportunities for cryptic and elusive species. Understanding how many breeders are harvested from a population may better our understanding of how mortality can affect groups of cooperative breeders like gray wolves that are exposed to annual harvest; and may be useful for altering management and conservation actions. We estimated the frequency of breeders in harvest and whether breeders were more vulnerable to harvest during the breeding season. We demonstrate a novel approach for using genetic data collected opportunistically from harvested wolves to determine if/when breeders are more vulnerable to harvest and to estimate the minimum number of breeders harvested annually in Idaho, USA, using pedigree analyses. We genotyped and aged 229 adult wolves and 203 pups using tissue and tooth samples, respectively, from wolves harvested between 2014 and 2016. We identified a minimum count of 36 breeders (n = 18 in 2014 and 18 in 2015) and found that breeders were disproportionately harvested (<i>P</i> = 0.08) during the breeding season (January; 25% of all breeders harvested during 2014 and 2015 harvest seasons). We estimate that a minimum of 16% of adult wolves harvested annually are breeders, or roughly 1 in 6. Our estimate of the number of breeders harvested annually is conservative because the pedigree analysis is dependent on both a pup and breeder from the same group having been harvested in the same year, and samples were excluded from the analysis if they were missing age and harvest month data or had <16 confirmed loci. Our results demonstrate that breeders are routinely harvested and that their behavior during breeding season may increase their vulnerability to harvest.
Ray, Andrew M., Blake R. Hossack, William R. Gould, Debra A. Patla, Stephen F. Spear, Robert W. Klaver, Paul E. Bartelt, David P. Thoma, Kristin L. Legg, Rob Daley, P. Stephen Corn, Charles R. Peterson. 2022. Multi-species amphibian monitoring across a protected landscape: Critical reflections on 15 years of wetland monitoring in Grand Teton and Yellowstone national parks. Ecological Indicators 135: 108519. https://doi.org/10.1016/j.ecolind.2021.108519 \| Abstract \| Download	February 2022	Widespread amphibian declines were well documented at the end of the 20th century, raising concerns about the need to identify individual and interactive contributors to this global trend. At the same time, there was growing interest in the use of amphibians as ecological indicators. In the United States, wetland and amphibian monitoring programs were launched in some national parks as a necessary first step to evaluating the status and trends of amphibian populations within some of North America’s most protected areas. In Grand Teton and Yellowstone national parks, a multi-species amphibian monitoring program was launched by many of the authors in 2006 and continues to this day. This Viewpoint Article serves as a self-evaluation of our journey from conception through implementation of an ongoing, long-term monitoring program. This self-evaluation should provide a framework and guidance for other monitoring programs. We address whether we are fulfilling the program’s main objective of describing status and trends of the four amphibian species, discuss how a one-size-fits-all monitoring approach does not serve all species equally, and describe opportunities to bolster our core work using emerging statistical approaches and thoughtful integration of remote sensing and molecular tools. We also describe how the data generated over the program’s first 15 years have been useful beyond our initial goal of characterizing status and trend. Notably, our integration of climate datasets has allowed us to describe wetland and species-specific amphibian responses to variations in climate drivers. Documenting climate links to amphibian occurrence and their primary habitats has allowed us to identify which species, habitat types, and subregions within this large, protected landscape are most vulnerable to anticipated climate change. Recognizing that tools and threatschange over time, it will be important to adapt our original monitoring design to maximize opportunities and use of resulting information. Maintaining engagement by multiple stakeholders and expanding our funding portfolio will also be necessary to sustain our program into the future. Finally, collaboration has become standard for longterm, cross-jurisdictional, landscape-scale monitoring. We argue that collaborative monitoring facilitates resource sharing, leveraging of limited funds, completion of work, and mutual learning. Such collaboration also increases the efficacy of conservation.
Ranney, SH, SR Chipps and DH Wahl. 2024. Effect of feeding history on routine metabolic rate of largemouth bass: implications for bioenergetics models. Can. J. Zool. 102: 207–216 dx.doi.org/10.1139/cjz-2023-0047 \| Abstract	December 2023	Metabolic rate is a key parameter in fish energy budgets that strongly influences the output of bioenergetics models. In this study, we tested the hypothesis that metabolic rate varies with growth history of age-1 largemouth bass. Two groups of fish were fed alternating maintenance or <i>ad libitum</i> rations of fathead minnow, so that<i> </i>over a 9-week period, initial and ending size of fish was similar. After 9 weeks, oxygen consumption was measured using static, closed respirometry. Although final body weight was similar between the two groups (means, 104 to 108 g), specific oxygen consumption for fish fed maintenance rations (0.094 mg O<sub>2</sub> g<sup>-2</sup> h<sup>-1</sup>) was 38% less than that measured for fish fed <i>ad libitum</i> (0.152 mg O<sub>2</sub> g<sup>-2</sup> h<sup>-1</sup>). Bioenergetic estimates of food consumption were similar to observed values for fish fed <i>ad</i> <i>libitum</i> (~7% error), but for fish fed maintenance rations, the model overestimated food consumption by 65%. By accounting for changes in metabolic rate owing to reduced feeding, error in model estimates of food consumption was reduced. These findings shed new insight on factors associated with consumption-dependent error in bioenergetic models and highlight the importance of feeding history on metabolic rate of fish. Incorporating growth-dependent metabolism into bioenergetics models can improve model accuracy and allow fisheries biologists to make more informed decisions regarding fish growth and energetics.
Ramsey, P.Q.,J. Dattilo, D. Devries, and S. K. Brewer. 2024. Context dependency in nursery habitants of juvenile in a large river. Rivers Research and Applications 40(5): 761–779. https://doi.org/10.1002/rra.4259	March 2024
Ramos, S. and M. Culver. 2024. Integrating the Seemingly Disparate in Molecular Ecology: Indigenous Research Methodologies, Traditional Ecological Knowledge and molecular scatology in a wildlife survey on Yurok Tribe Ancestral Lands. Molecular Ecology Respouces, May 2024 Molecular Ecology Resources DOI: 10.1111/1755-0998.13963	May 2024
Ramos, R., V.H. Paiva, Z. Zajkova, C. Precheur, A.I. Fagundes, P.G.R. Jodice, W. Mackin, V. Neves, F. Zino, V. Bretagnolle, J. Gonzalez-Solis. 2020. Spatial ecology of closely related taxa: the case of the little shearwater complex in the North Atlantic Ocean. Zoological Journal of the Linnean Society XX 1-21. https://doi.org/10.1093/zoolinnean/zlaa045 \| Download	May 2020
Ramirez-Reyes, C., M. Nazeri, G. Street, D. Todd Jones-Farrand, F.J. Vilella, and K.O. Evans. 2021. Embracing ensemble species distribution models to inform at-risk species status assessments. Journal of Fish and Wildlife Management 12(1):98-111. \| Abstract \| Publisher Website	May 2021	Effective conservation planning requires reliable information on the geographic distribution of species, which is often incomplete due to limited availability of presence data. Species distribution models (SDMs) and associated tools have proliferated in the past decades and have proven valuable in evaluating suitability of habitat for species. However, practitioners have yet to fully adopt the potential of SDMs to inform surveys and other conservation efforts for information-limited species. Instead, most efforts rely on expert knowledge and other traditional methods to locate extant populations. In particular, the Species Status Assessment (SSA) framework of the United States Fish and Wildlife Service would benefit from incorporating SDM approaches to facilitate conservation decisions. Here, we describe an SDM approach for at-risk species that would benefit SSAs and similar species conservation efforts. We applied four modeling techniques (generalized additive, maximum entropy, generalized boosted, and weighted ensemble) to recent monitoring data for three at-risk species proposed for listing under the U.S. Endangered Species Act (<i>Papaipema eryngii, Scutellaria ocmulgee, Balduina atropurpurea</i>) in the Southeastern U.S. The ensemble models reduced uncertainty caused by differences among modeling techniques and improved the predictive accuracy of fitted models. Incorporating an ensemble modeling approach into the SSA framework would benefit monitoring efforts and provide more robust status assessments for at-risk species. We emphasize the importance of producing SDM in close collaboration among the stakeholders involved in use of model outputs.
Ramirez-Reyes, C., F.J. Vilella, K.O. Evans, G. Street, C. Pacheco, O. Monzon, and A.L. Morales Perez. 2023. Geographic distribution of the Puerto Rican Harlequin Butterfly (Atlantea tulita): an ensemble modeling approach. Caribbean Journal of Science 53(1):37-44. \| Abstract	May 2023	Species distribution models have become increasingly important tools for species conservation. This modeling approach can help guide conservation practitioners and inform decisions. Distribution models are particularly relevant for rare species, whose habitat associations are often not well understood. Using species occurrence data, and a variety of predictor variables, we developed three individual distribution models and a weighted ensemble model for the Puerto Rican harlequin butterfly (<i>Atlantea tulita</i>). The ensemble model had the greatest accuracy (AUC = 0.92). Further, the ensemble model indicated 7.1% of the main island of Puerto Rico encompassed suitable habitat for the harlequin butterfly. However, only 0.5% was classified as including the greatest suitability. Using an ensemble modeling approach to delineate areas of the island with suitable environmental conditions may improve habitat conservation efforts for the species.
Ramirez-Reyes C., G. Street, F.J. Vilella, D.T. Jones-Farrand, M.S. Wiggers, and K.O. Evans. 2021. Ensemble species distribution model identifies survey opportunities for at-risk bearded beaksedge (Rhynchospora crinipes) in the southeastern United States. Natural Areas Journal 41(1):55-63. \| Abstract \| Download \| Publisher Website	February 2021	Locating additional occurrences of at-risk species can inform assessments of their status and conservation needs (including potential legal protections). The perennial bearded beaksedge (<i>Rhynchospora crinipes</i>) has been found from Mississippi to North Carolina, but known occurrences are limited. Because of the species’ apparent rarity, a model to identify areas with a high likelihood of locating additional occurrences will allow conservationists to effectively prioritize and allocate scarce surveying resources. We used known occurrence records, a suite of environmental datasets, and four species distribution modeling techniques (generalized additive, GAM; maximum entropy, MaxEnt; generalized boosted, GBM; and weighted ensemble) to generate maps to inform surveys for <i>R. crinipes</i>. The ensemble approach improved predictive performance (AUC-PR = 0.95) compared to other techniques (individual model AUC-PR ranged from 0.7 to 0.8). We also obtained quantitative insights on the species’ habitat relationships, including the likelihood of <i>R. crinipes</i>’s presence near Atlantic white cedar (<i>Chamaecyparis thyoides</i>) habitat and floodplains, which is consistent with prior field observations. The ensemble model indicated that 3.6% of the study area could be suitable habitat, but only 0.38% had high suitability. Small stream riparian habitats and Atlantic swamp forests in Alabama, Florida, and Georgia had the highest proportion of suitable areas. Prioritizing surveys in areas with model-indicated high habitat suitability is expected to reveal additional <i>R. crinipes</i> occurrences. We suggest surveying efforts for other at-risk species may benefit from using an ensemble modeling approach to identify and prioritize survey areas and improve ecological knowledge of these species.
Ramberg-Pihl, N., Klemmer, A., Zydlewski, J., Coghlan, Jr.,S., and Greig, H. (2023) Unraveling the impacts of competition and warming on juvenile Atlantic salmon (Salmo salar) performance in Maine streams. Ecology of Freshwater Fish. 32:606–617. DOI: 10.1111/eff.12711 \| Download	April 2023
R Etzel, M Cornish, MS Kifer, L Nuñez, G Valladao, BFolt. 2020. Subterranean advertisement and duet calling behavior in Ptychohyla legleri (Legler’s Stream Frog). Alytes 37(3–4): 57–61.	March 2020
Quist, M. C., M. E. Ulaski, K. M. Manuell, Z. J. Jackson, and T. Gatewood. 2023. Precision of structures used to estimate age and growth of Apache Trout from Arizona. Journal of Fish and Wildlife Management 14:188-194.	August 2023
Quist, M. C., D. K. McCarrick, and L. M. Harris. 2022. Comparison of hard structures used to estimate age and growth of Yellowstone Cutthroat Trout. Journal of Fish and Wildlife Management 13:554-551.	January 2023
Quinn TP, Scheuerell MD, Losee JP, Hanada D. 2022. Multi-decadal trends in body size of Puget Sound Chinook salmon: Analysis of data from the Tengu Derby, a culturally unique fishery. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 14:e10205 https://doi.org/10.1002/mcf2.10205 \| Abstract \| Download	May 2022	In Pacific salmon, downward trends in size and abundance have been reported for species and stocks for over 40 years, but the patterns are inconsistent among regions and species. Interpretation of these trends is complicated by the many possible contributing factors, including short time series, data comprising a mix of stocks, and varying gear types. Here, we present data on the mass of individual Chinook salmon, <i>Oncorhynchus tshawytscha</i>, caught in the winter from 1946 to 2019 in central Puget Sound, Washington by participants in what may be the longest running salmon derby in North America, the Tengu Derby. In this annual recreational fishing competition, established by Japanese-Americans immediately after release from internment camps at the end of World War II, participants follow strict gear, area, and methods regulations, and catch almost exclusively salmon originating from and remaining in Puget Sound. Records revealed an overall decline in fish mass over the decades with a high degree of variability throughout the time series. Specifically, resident Chinook salmon exhibited several shifts, including an increase in size from a high in the 1950s to a low around 1980, followed by an increase to another high around 1990, and then a decline over the most recent 30 years. These salmon, displaying a form of differential migration by remaining in Puget Sound rather than migrating to the ocean coast, showed dissimilar trajectories compared with size trends of Puget Sound Chinook salmon as a whole reported previously. These distinct patterns in size for Chinook salmon from common origins associated with different migration patterns exemplify yet another important factor to be considered in the analysis and interpretation of such trends.
Quinlan, B.A., J.P. Rosenberger, D.M. Kalb, H.N. Abernathy, E.D. Thornes, W.M. Ford and M.J. Cherry. 2022. Drivers of habitat quality for a reintroduced elk herd. Scientific Reports Using home range composition and size as a proxy of habitat quality for female elk. Scientific Reports (2022) 12:20960 doi.org/10.1038/s41598-022-25058-9IP-142951.	December 2022
Quinlan, B.A., J.P. Rosenberger, D.M. Kalb, E.D. Thorne, W.M. Ford and M.J. Cherry. 2022. Estimating elk abundance in Buchanan County, Virginia using Lincoln-Petersen Indices. Journal of the Southeastern Association of Fish and Wildlife Agencies 10:135–141.	March 2023
Qui, Q., Y. Xu, S.S. Matsuzaki, K. Komatsu, Z. Liang, T. Wagner. 2021.A statistical framework to track temporal dependence of chlorophyll–nutrient relationships with implications for lake eutrophication management. Journal of Hydrology 603:127134. https://doi.org/10.1016/j.jhydrol.2021.127134	November 2021
Prude, C.H. and J.W. Cain III. 2021. Habitat diversity influences puma Puma concolor diet in the Chihuahuan Desert. Wildlife Biology wlb.00875. https://doi.org/10.2981/wlb.00875 \| Download	October 2021
Prosdocimi, L., N. Teryda, G. Navarro, and R. R. Carthy. 2020. Use of remote sensing tools to predict focal areas for sea turtle conservation in the Southwestern Atlantic. Aquatic Conservation: Marine and Freshwater Ecosystems, 2020:1–11. DOI: 10.1002/aqc.3478 \| Abstract	December 2020	1. Fisheries bycatch of non- target species in the commercial fleet is a major source of anthropogenic injury and mortality for sea turtles and marine megafauna. 2. The Río de la Plata, Maritime Front (RLPMF) and its adjacent international waters - comprising part of the Argentine and Uruguayan exclusive economic zones (EEZs), is a highly important fishing ground in the South-western Atlantic Ocean (SWAO) as well as feeding and development grounds for sea turtles. 3. This paper analyses the distribution of the bottom and pelagic trawling fishery within the RLPMF using information from Vessel Satellite Monitoring System (VMS). With this information, areas of highest trawling intensity were defined and further evaluated their overlap with sea turtle habitat-use areas from available sea turtle satellite tracking information.4. Results besides identifying high-susceptibility areas for sea turtle bycatch by the commercial trawler fleet along the RLPMF, provide predictive tools to identify vulnerable areas to interaction of sea turtles and the commercial fishing fleet.5. Implementation of bycatch mitigation measures, such as reduced fishing effort areas by the Argentine and Uruguayan fisheries management agencies has the potential to benefit the fisheries as well as marine megafauna. Furthermore, there is a need for additional research on the impact this fleet can have on sea turtles present in the area.
Pronkevich, V. V., P. N. Maleko, K. S. Maslovsky, and J. C. Slaght. 2022. Trapping shorebirds using bow-net tables: An example with Endangered Nordmann’s Greenshank. Wader Study 129(1): 56-60. doi:10.18194/ws.00262	March 2022
Proctor, M.F., D. Garshelis, P. Thatte, R. Steinmetz, B. Crudge, B. McLellan, W. McShea, D. Ngoprasert, M. Ali Nawaz, S.T. Wong, S. Sharma, A.K. Fuller, N. Dharaiya, K.E. Pigeon, M. Hwang, G. Fredriksson, D. Wang, and S. Li. 2022. Review of field methods for monitoring Asian bears. Global Ecology and Conservation. https://doi.org/10.1016/j.gecco.2022.e02080	January 2022
Price, N. B., C. J. Chizinski, J. J. Fontaine, K. L. Pope, M. Rahe, and J. Rawlinson. 2020. An open-sourced, web-based application to improve our ability to understand hunter and angler purchasing behavior from license data. PLoS ONE 15(10):e0226397. \| Download	October 2020
Price, A.N., M.A. Zimmer, A.J. Bergstrom, A.J. Burgin, E.C. Seybold, C.A. Krabbenhoft, S. Zipper, M.H. Busch, W.K. Dodds, A.W. Walters, J.S. Rogosch, R. Stubbington, R.H. Walker, J.C. Stegen, T. Datry, M.L. Messager, J.D. Olden, S. Godsey, M. Shanafield, D.A. Lytle, R.M. Burrows, K.E. Kaiser, G.H. Allen, M.C. Mims, J.D. Tonkin, M. Bogan, J. Hammond, K.S. Boersma, A.N. Myers-Pigg, A.G. DelVecchia, D.C. Allen, S. Yu, A. Ward, 2024. Biogeochemical and community ecology responses to the wetting of non-perennial streams. Nature Water 2: 815-826. https://www.nature.com/articles/s44221-024-00298-3	September 2024
Prentice, M.B., M.L.J. Gilbertson, D.J. Storm, W.C. Turner, D.P. Walsh, M.E. Pinkerton, P.L Kamath. 2024. Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus), Microbial Genomics, 10:001214. https://doi.org/10.1099/mgen.0.001214	March 2024
Pregler KC, Obedzinski M, Gilbert-Horvath EA, White B, Carlson SM, Garza JC. 2023. Assisted geneflow from outcrossing shows the potential for genetic rescue in an endangered salmon population. Conservation Letters. 16:e12934. doi: https://doi.org/10.1111/conl.12934 \| Download	April 2023
Pregler KC, Lu X, Valentine G, Kim S, Kanno Y. 2023. Temperature variation generates sympatric synchrony but spatial asynchrony in survival for freshwater fish communities. Ecology & Evolution. 13:e10700. doi: http://dx.doi.org/10.1002/ece3.10700	November 2023
Pregler KC, Clemento A, Grill M, Adelizi P, Carlson SM, Garza JC. 2024. Reintroduction of spring-run Chinook salmon in the San Joaquin River: evaluating genetic and phenotypic effects of captive breeding. Conservation Science & Practice. 6:e13176. doi: https://doi.org/10.1111/csp2.13176	September 2024
Prado, S. G., J. A. Collazo, M. H. Marand, R. E. Irwin. 2021. The influence of floral resources and microclimate on pollinator visitation in an agro-ecosystem. Agriculture, Ecosystems and Environment 307 (2021) 107196. \| Abstract	January 2021	As agriculture expands to meet the needs of a growing global population, natural ecosystems are threatened by deforestation and habitat fragmentation. Tropical agroforestry systems offer a sustainable alternative to traditional agriculture by providing food for production while also supporting biodiversity and ecosystem services. Previous studies have shown that these systems may even improve crop pollination, but the mechanisms of how these improvements occur are still poorly understood. Using coffee as a focal crop, we explored how microclimatic conditions affected nectar traits (sugar and caffeine concentration) important for pollinator visitation. We also studied how microclimate, floral traits, floral availability at the coffee plant level, availability of floral resources provided by other plant species in the agroecosystem (“neighborhood floral availability”), and the presence of other bees affected the amount of time bees spent foraging on coffee flowers and the proportion of coffee pollen carried on their bodies. We explored these factors using the two dominant coffee species farmed on Puerto Rico, <i>Coffea canephora</i> and <i>C. arabica</i>, under sun and shade management.<i> </i>We found that high nectar sugar concentration and temperature were important predictors of short floral visits (<15 seconds), while increased numbers of bees and open coffee flowers were important predictors of longer floral visits (16-180 seconds). High nectar caffeine concentration was an important predictor of longer visits on <i>C. arabica </i>flowers while the opposite was observed for <i>C. canephora </i>flowers. For both species, high coffee floral availability was the main predicting factor for the proportion of coffee pollen on the bees’ bodies. Surprisingly, neither neighborhood floral availability nor the type of coffee plantation (agroforest/shade or sun) were important predictors of bee visitation. These results suggest non-coffee flowering plants in coffee plantations were neither competitors nor facilitators of coffee plants for pollinators. Additionally, most of the bees surveyed were carrying ≥80% pollen from one species (<i>C. arabica </i>or <i>C. canephora</i>), likely resulting in little heterospecific pollen deposition between <i>Coffea</i> and non-<i>Coffea</i> flowers. Shade trees in coffee plantations do not detract from pollinator visitation to coffee flowers, suggesting that the provision of multiple ecological and wildlife conservation benefits by shade trees is not in conflict with a grower’s ability to maximize the benefits of insect pollination on fruit production.
Pracheil, B. M., P. J. Braaten, E. B. Macias, C. S. Guy, D. P. Herzog, M. J. Hamel, J. C. Justice, A. R. Loeppky, J. M. Mollish, J. W. Simmons, S. J. Tripp. 2024. Warmwater fish in rivers. Pages 85 – 110 in S. A. Bonar, N. Mercado-Silva, and K. L. Pope, editors. Standard methods for sampling North American freshwater fishes, 2nd edition. American Fisheries Society, Bethesda, Maryland.	September 2024
Powers, K.E., W.M. Ford, R.J. Reynolds, W.D. Orndorff, D.E. Yates, and T.E. Malabad. 2024. Reproductive Trends in Little Brown Bats Before and After the Onset of White-nose Syndrome in Virginia. Journal of North American Bat Research 6:1-12.	September 2024
Powers, K.E., M.T. Mengak, R.R. Sherry, W.M. Ford and R.J. Reynolds. 2020. Bot Fly Parasitism of Allegheny Woodrats (Neotoma magister) in Virginia. American Midland Naturalist 184:62-72.	August 2020
Powers, K.E., E.D. Thorne, L.R. Platt, K.M. Nelson, L. Van MEter, C.M. Wozniak, R.J. Reynolds and W.M. Ford. 2023. Activity patterns of Allegheny woodrats (Neotoma magister) and two potential competitors in Virginia. Northeastern Naturalist 30(1):41-58	February 2023
Poutanen, J., A.K. Fuller, J. Pusenius, J.A. Royle, M. Wikström, and J.E. Brommer. 2023. Density-habitat relationships of white-tailed deer (Odocoileus virginianus) in Finland. Ecology and Evolution. http://dx.doi.org/10.1002/ece3.9711	January 2023
Poulet, C., Lassalle, G., Jordaan, A., Limburg, K., Nack, C., Nye, J., O’Malley, A., O’Malley-Barber, B., Stich,D., Waldman, J., Zydlewski, J. and Lambert, P. (2023) Effect of dispersal capacities and reproductive strategies/tactics on the structure of American shad populations across the species native range: an exploration based on a mechanistic species distribution model. Ecosphere 14(12): 1-21. DOI: 10.1002/ecs2.4712	October 2023
Post van der Burg, M., Smith, D.R., Cupp, A.R., Rogers, M.W., and Chapman, D.C., 2021, Decision analysis of barrier placement and targeted removal to control invasive carp in the Tennessee River Basin: U.S. Geological Survey Open-File Report 2021–1068, 18 p., https://doi.org/10.3133/ofr20211068.	June 2021
Portillo-Quintero, C., B. Grisham, D. Haukos, C. Boal, C. Hagen, Z. Wan, and N. Menkiti. 2022. Trends in lesser prairie-chicken habitat extent and distribution on the Southern High Plains. Remote Sensing (Special Issue Wildlife Ecology for a Dynamic Future). Remote Sens. 2022, 14, 3780. https://doi.org/10.3390/rs14153780	August 2022
Porath, M.T., T.J. Kwak, B.C. Neely, and D.E. Shoup. 2021. Catfish 2020, A clear vision of the future. Invited, special issue on Catfish Conservation and Management. North American Journal of Fisheries Management 41(Special Issue 1): S1-S10. DOI: 10.1002/nafm.10688	October 2021
Pope, K. L., and L. A. Powell. 2021. Preface. Pages xi–xv in K. L. Pope and L. A. Powell, editors. Harvest of fish and wildlife: new paradigms for sustainable management. CRC Press, Boca Raton, Florida, USA.	June 2021
Pope, A.C., Kock, T.J., Perry, R.W., Cogliati, K.M., O'Malley, K.G., Murphy, C.A., Hance, D.J., Fielding, S.D. Using parentage based tagging to estimate survival of Chinook salmon fry in a large storage reservoir. Environmental Biology of Fishes.	July 2024
Popa, D., Waterhouse, L., Duchnick, J., Neuman, T., and P. Witucki. 2021. Performance of the Uni-Vent Eagle(TM) Model 754 ventilator under hyperbaric conditions. Undersea & Hyperbaric Medical Society, Inc. 48(4):409-416. PMID: 34847304. \| Abstract \| Publisher Website	October 2021	Critically ill patients needing mechanical ventilation may require hyperbaric oxygen therapy. Some institutions still use ventilators that were available prior to the advent of hyperbaric-specific units, such as the Uni-Vent Eagle™ Model model 754. Here we examine the performance of the Uni-Vent model 754 under hyperbaric conditions and investigate concerns of an oxygen leak in the ventilator housing, which poses a fire risk. We studied the ventilator at 1.0, 2.4 and 2.8 ATA in assist control mode using a Michigan test lung and a variety of tidal volumes and respiratory rates. We recorded the delivered volumes, peak pressures, and oxygen percentages within the hyperbaric chamber at 2.4 and 2.8 ATA and within the ventilator housing. At those pressures the ventilator delivered approximately 25% less volume than at 1.0 ATA. We observed breath stacking at high respiratory rates, but this was blunted at both 2.4 and 2.8 ATA. Oxygen levels did not rise in the housing during our investigation. In addition, we fit a linear regression to the data comparing set tidal volumes and delivered tidal volumes in order to model the changes observed. Hyperbaric conditions caused decreased delivered tidal volumes in a depth-dependent fashion, and oxygen levels within the housing did not rise. The Uni-Vent Eagle model 754 performed safely and effectively at depth but requires spirometry to correctly program desired ventilator settings.
Poole, A. S., T. M. Koel, N. A. Thomas, and A. V. Zale. 2020. Benthic suffocation of invasive Lake Trout embryos by fish carcasses and sedimentation in Yellowstone Lake. North American Journal of Fisheries Management. doi.org/10.1002/nafm.10492 \| Abstract	July 2020	Introduced Lake Trout <i>Salvelinus namaycush</i> threaten native Yellowstone Cutthroat Trout <i>Oncorhynchus clarkii bouvieri</i> in Yellowstone Lake, Yellowstone National Park, where gill nets have been used to suppress subadult and adult Lake Trout since 1995. However, survival of embryonic and larval life history stages can have profound effects on population dynamics of Lake Trout. Inducing additional mortality at those stages, especially if used in concert with intensive gillnetting of older fish, could enhance overall suppression efforts. Therefore, we conducted controlled field experiments at Yellowstone Lake to systematically evaluate the effects of sediment deposition and ground Lake Trout carcass deposition on Lake Trout embryos in prepositioned incubators. Sediment deposition caused dissolved oxygen concentrations to decline below lethal levels for a prolonged period (92 d) overwinter. Embryo mortality among overwintering incubators varied from 97 ± 5.3% at the substrate surface to 100 ± 0.0% 20 cm below the substrate surface. Decomposition of ground carcass material on spawning sites caused dissolved oxygen concentrations to decline to lethal levels (<3.4 mg/L) for about 9 days following biomass application rates of 14 and 28 kg/m2 in treatment plots. Exposure to ground carcass material resulted in 100 ± 0.0% (mean ± SE) embryo mortality at the substrate surface and within interstices 20 cm below the surface in 14 and 28 kg/m2 biomass treatments. Embryo mortality was probably caused by hypoxic conditions within substrates in both experiments. The deposition of sediment and ground Lake Trout carcass material on Lake Trout spawning sites in Yellowstone Lake could provide an additional source of mortality in ongoing Lake Trout suppression efforts. These methods may also be beneficial in other systems when incorporated in an integrated pest management approach (IPM) targeting multiple life history stages of invasive freshwater fish.
Poole, A. S., T. M. Koel, A. V. Zale, and M. A. H. Webb. 2023. Rotenone induces mortality of invasive Lake Trout and Rainbow Trout embryos. Transactions of the American Fisheries Society 152:3-14. https://doi.org/10.1002/tafs.10394	January 2023
Poli, C., E. P. Robertson, J. Martin, A. N. Powell, and R. J. Fletcher Jr. 2022. An invasive prey provides long-lasting silver spoon effects for an endangered predator. Proc. R. Soc. B 289: 20220820. https://doi.org/10.1098/rspb.2022.0820	May 2022
Plymesser, K., M. Blank, M. Conley, K. Kappenman, J. Cahoon, D. Dockery, and A. V. Zale. 2022. A scaled Denil fishway for upstream passage of Arctic Grayling. Journal of Ecohydraulics https://doi.org/10.1080/24705357.2022.2105756	August 2022
Plumpton, H.M., S.G. Gilliland, and B.E. Ross. 2020. Geographic differences in the winter movements of the Atlantic population of Black Scoters. Submitted to Avian Conservation and Ecology. https://doi.org/10.5751/ACE-01654-150206	August 2020
Pitman, J.W., J.W. Cain III, W.R. Gould, N.T. Tatman, and S.G. Liley. 2024. Habitat selection and survival of elk neonates. Southwestern Naturalist 67:205–215. \| Download	September 2023
Piel III, R. B., S. E. Veneziano, E. Nicholson, D. P. Walsh, A. D. Lomax, T. A. Nichols, C. M. Seabury, and D. A. Schneider. 2024. Validation of a Real-Time Quaking-Induced Conversion (RT-QuIC) Assay Protocol to Detect Chronic Wasting Disease using Rectal Mucosa of Naturally Infected, Pre-Clinical White-Tailed Deer (Odocoileus Virginianus). PLoS ONE 19(6): e0303037. https://doi.org/10.1371/journal.pone.0303037 \| Abstract	June 2024	Chronic wasting disease (CWD) is a fatal prion disease of cervids spreading across North America. More effective mitigation efforts may require expansion of the available toolkit to include new methods that provide earlier antemortem detection, higher throughput, and less expense than current immunohistochemistry (IHC) methods. The rectal mucosa near the rectoanal junction is a site of early accumulation of CWD prions and is safely sampled in living animals by pinch biopsy. A fluorescence-based, 96-well format, protein-aggregation assay—the real-time quaking-induced conversion (RT-QuIC) assay—is capable of ultra-sensitive detection of CWD prions. Notably, the recombinant protein substrate is crucial to the assay's performance and is now commercially available. In this blinded independent study, the preclinical diagnostic performance of a standardized RT-QuIC protocol using a commercially sourced substrate (MNPROtein) and a laboratory-produced substrate was studied using mock biopsy samples of the rectal mucosa from 284 white-tailed deer (<i>Odocoileus virginianus)</i>. The samples were from a frozen archive of intact rectoanal junctions collected at depopulations of farmed herds positive for CWD in the United States. All deer were pre-clinical at the time of depopulation and infection status was established from the regulatory record, which evaluated the medial retropharyngeal lymph nodes (MRPLNs) and obex by CWD-IHC. A pre-analytic sample precipitation step was found to enhance the protocol’s detection limit. Performance metrics were influenced by the choice of RT-QuIC diagnostic cut points (minimum number of positive wells and assay time) and by deer attributes (preclinical infection stage and prion protein genotype). The peak overall diagnostic sensitivities of the protocol were similar for both substrates (MNPROtein, 76.8%; laboratory-produced, 73.2%), though each was achieved at different cut points. Preclinical infection stage and prion protein genotype at codon 96 (G = glycine, S = serine) were primary predictors of sensitivity. The diagnostic sensitivities in late preclinical infections (CWD-IHC positive MPRLNs and obex) were similar, ranging from 96% in GG96 deer to 80% in xS96 deer (x = G or S). In early preclinical infections (CWD-IHC positive MRPLNs only), the diagnostic sensitivity was 64-71% in GG96 deer but only 25% in xS96 deer. These results demonstrate that this standardized RT-QuIC protocol for rectal biopsy samples using a commercial source of substrate produced stratified diagnostic sensitivities similar to or greater than those reported for CWD-IHC but in less than 30 hours of assay time and in a 96-well format. Notably, the RT-QuIC protocol used herein represents a standardization of protocols from several previous studies. Alignment of the sensitivities across these studies suggests the diagnostic performance of the assay is robust given quality reagents, optimized diagnostic criteria, and experienced staff.
Pickzak, M.L., J.A. Robichaud, P. Morrison, A.M. Rous, I.M. Mulder, C.J. Hill, T.S. Prystay, H. Rosner-Katz, K.F. Robinson, J.R. Bennett, S.J. Cooke. 2024. Structured decision making remains underused in ecological restoration despite opportunities. Environmental Systems and Decisions. https://doi.org/10.1007/s10669-023-09940-z	September 2023
Pfab, F., DiRenzo, G. V., Gershman, A., Briggs, C. J., & R. Nisbet. 2020. Energy budget for tadpoles approaching metamorphosis. Ecological Modeling 436: 109261. https://doi.org/10.1016/j.ecolmodel.2020.109261 \| Abstract \| Download \| Publisher Website	December 2020	We describe a dynamic energy budget (DEB) model for tadpoles over the course of metamorphosis. The model accounts for details in the tadpoles feeding behavior, as feeding and indirectly respiration are reduced in the late developmental stages preceding metamorphosis to an immature froglet.<br>We propose two versions of our DEB model, one where the energy reserves of the organism are accounted for explicitly (a variant on Kooijman’s ”standard” DEB model), and one where reserves and structural biomass are lumped together so that only the size of the organism is tracked (a variant on DEBkiss). Both models are parameterized using a time series of measurements on a cohort of tadpoles of the Pacific tree frog, <i>Pseudacris regilla</i>. The models describe tadpoles from the middle of their development as tadpoles until they emerge as froglets. Visually, both models fit the growth and respiration empirical data reasonably well; statistically the fit to the full DEB model is slightly better.<br>The models highlight the metabolic changes during the life of a tadpole and demonstrate how morphological changes in developing organisms can be accomodated in the DEB framework.
Petracca LS, B Gardner, BT Maletzke, and SJ Converse. 2024. Merging integrated population models and individual-based models to project population dynamics of a recolonizing species. Biological Conservation 289:110340. \| Abstract	January 2024	Recolonizing species exhibit unique population dynamics, namely dispersal to and colonization of new areas, that have important implications for their management. One challenge is how to simultaneously model demographic and movement processes so that recolonizing species can be accurately projected over both time and space. Integrated population models (IPMs) have proven useful for making inference about population dynamics by integrating multiple data streams related to population states and demographic rates. However, traditional IPMs are not capable of representing complex dispersal and colonization processes, and the data requirements for building spatially explicit IPMs to do so are often prohibitive. Contrastingly, individual-based models (IBMs) have been developed to describe dispersal and colonization processes but do not traditionally integrate an estimation component, which is a major strength of IPMs. We introduce a framework for spatially explicit projection modeling that answers the challenge of how to project an expanding population using IPM-based parameter estimation while harnessing the individual-based movement modeling made possible by an IBM. Our model has two main components: [1] a Bayesian IPM-driven age- and state-structured population model that governs the population state process and estimation of demographic rates, and [2] an IBM-driven spatial model describing the dispersal of individuals and colonization of new territories. We applied this model to estimate current and project future dynamics of gray wolves (<i>Canis lupus</i>) in Washington State, USA. We used data from 74 telemetered wolves and yearly pup and pack size counts to parameterize the model, and then projected statewide dynamics over the next 50 years. Mean population growth was 1.29 (95% CRI 1.26-1.33) during initial recolonization from 2009 - 2020 and decreased to 1.03 (95% Prediction Interval 1.00-1.05) in the projection period (2021-2070). Our results suggest that gray wolves have a very high (>99%) probability of colonizing the last of Washington State’s three specified recovery regions by 2030, depending on alternative assumptions about how dispersing wolves select new territories. The spatially explicit modelling framework developed here can be used to project the dynamics of any species for which spatial spread is an important driver of population dynamics.
Peterson, S.M., H.M. Streby, G.R. Kramer, J.M Feura, and D.E. Andersen. 2022. Patterns of parental care and movement in divided broods of golden-winged warblers. Journal of Avian Biology 2022:e02938. https://doi.org/10.1111/jav.02938	March 2022
Peterson, J.T., J.A. Pease, L. Whitman, J. White, L. Stratton Garvin, S. Rounds, and R. Wallick. 2022. Integrated tools for identifying optimal flow regimes and evaluating alternative minimum flows for recovering at risk salmonids in a highly managed system. River Research and Applications 38: 293-308. https://doi.org/10.1002/rra.3903 \| Abstract \| Publisher Website	December 2021	Water resource managers are faced with difficult decisions on how to satisfy human water needs while maintaining or restoring riverine ecosystems. Decision sciences have developed approaches and tools that can be used to break down difficult water management decisions into their composite parts. An essential aspect of these approaches is the use of quantitative models to evaluate alternative management strategies. Here, we describe four integrated decision support models for evaluating the effect of flows on two life history stages of Chinook salmon (<i>Oncorhynchus tshawytscha</i>) and Steelhead trout (<i>O. mykiss</i>). We then use constrained nonlinear optimization to identify optimal flow regimes for the water year type with the least available water. These flow regimes were then used by managers to develop candidate minimum flow strategies that were evaluated using forward simulation and sensitivity analyses. We found that optimal flow regimes differed markedly from existing regulations and varied among species and life history stages. However, evaluation of tradeoffs among the four competing objectives indicated relatively minimal losses for most objectives when the optimal flows were based on equally weighting the objectives. Sensitivity analysis indicated that water temperature was the primary driver of estimated outcomes and suggested that managers consider alternative means of managing temperatures. Decision sciences have created multiple analytical tools and approaches that simplify complex problems, such as water resource management and we believe that water resource management would benefit from their increased use.
Peterson, J.T., E. McCreless, A. Duarte, P. Wohner, S. Hamilton, J. Medellin-Azuara, and A. Escriva-Bou. Structured Decision Making for Scientific Management in the San Francisco Bay-Delta. Environmental Science and Policy. 157, p.103775. https://doi.org/10.1016/j.envsci.2024.103775 \| Abstract \| Publisher Website	May 2024	A structured decision making (SDM) approach can help evaluate tradeoffs between conservation and human-benefit objectives by fostering communication and knowledge transfer among stakeholders, decision makers, and the public. However, the process is iterative and completing the full process may take years to accomplish. Thus, it can be difficult to initiate an SDM effort when problems seem insurmountable. In many instances, SDM may not even be the best or correct approach for addressing the conservation problem at hand. We describe the implementation of an SDM process to help inform difficult decisions related to competing objectives. We convened a diverse stakeholder group from the largest estuary in the western United States; the San Francisco Bay and Sacramento-San Joaquin Delta (Bay-Delta). The stakeholder group consisted of representatives from local, state, and federal agencies, non-profit organizations, and recreational fishermen. The stakeholder group agreed on a problem statement and identified four priority objectives related to Chinook salmon, delta smelt, water availability and reliability, and agricultural water use. Furthermore, they proposed 14 candidate management actions to achieve their objectives. The group then used existing quantitative models and data to evaluate trade-offs in proposed management actions to identify areas of agreement of proposed candidate actions. The clear communication of the problem statement and objectives among the stakeholder group, along with evaluation of tradeoffs and uncertainty via decision-support models suggest that SDM may work in the Bay-Delta. We further communicate lessons learned during our implementation of SDM to help guide future SDM efforts in the region and elsewhere.
Peterson, J.T. and A. Duarte. 2024. An evaluation of tradeoffs in restoring ephemeral vs. perennial habitats to conserve animal populations. Frontiers in Conservation Science, 5, p.1428697. https://doi.org/10.3389/fcosc.2024.1428697 \| Abstract \| Publisher Website	July 2024	Habitat loss and degradation pose significant threats to global fish and wildlife populations, prompting substantial investments in habitat creation and restoration efforts. Not all habitats provide equal benefits, leading to challenges in prioritizing restoration actions. For example, juvenile anadromous salmonids require high quality rearing aquatic habitats to achieve the physiological requirements needed to successfully migrate to the ocean. However, there are profound disagreements among anadromous salmon restoration managers whether it is best to focus efforts restoring in-channel habitats that are available for the entire rearing period or floodplain habitats that, while facilitating greater growth and survival than in-channel habitats, are available for a few weeks at a time. To address this uncertainty, we used a fall-run Chinook Salmon decision model to evaluate under what conditions floodplain restoration would provide greater benefits than in-channel habitat restoration. The simulations results indicated that in-channel habitat restoration was always the best habitat restoration action when there was no existing in-channel despite simulating a wide range of flood frequency, duration, and growth and survival benefits. Floodplain restoration was generally best when there was sufficient in-channel habitat available to successfully rear most of the juveniles produced by the returning adult salmon. We hypothesize that in-channel and floodplain habitats have different roles in salmon population maintenance with in-channel habitats regulating the overall population size and floodplains acting as recurrent resource pulses. Our study provides a quantitative framework to evaluate the benefit of these two habitat types and provides generalizable rulesets that can be used by managers when implementing habitat restoration strategies for species that inhabit both in-channel and floodplain habitats.
Peterson, J.T. and A. Duarte. 2020. Decision analysis to develop and evaluate restoration strategies for Chinook salmon in California’s Central Valley. Restoration Ecology https://doi.org/10.1111/rec.13244 \| Abstract \| Publisher Website	November 2020	A considerable amount of resources have been invested in ecological restoration projects across the globe to restore ecosystem integrity. These restoration strategies are often diverse and have been met with mixed success. In this paper, we describe the Chinook salmon (<i>Oncorhynchus tshawytscha</i>) decision-support models developed by the Central Valley Project Improvement Act Science Integration Team as part of a larger structured decision making effort aimed at maximizing natural adult production of Chinook salmon in California’s Central Valley, USA. We then describe the decision analytic tools the stakeholder group used to solve the models and explore model results, including stochastic dynamic programming, forward simulation, proportional scoring, relative loss, expected value of perfect information, response profile analyses, and indifference curves. Using these tools, the stakeholder group was able to develop and quantitatively evaluate restoration strategies for multiple Chinook salmon runs simultaneously, a first for the restoration program. Furthermore, information uncovered during this process was then used to direct efforts towards targeted research/monitoring to reduce critical uncertainties and make better restoration decisions moving forward. The decision sciences have established a wide range of analytical tools and approaches to simplify complex problems into key components, and we believe the concepts described in this paper are of great interest to many restoration practitioners that undoubtedly face similar difficulties when implementing restoration strategies for complex systems.
Peterson, J.M., J.E. Earl, S.D. Fuhlendorf, D. Elmore, D.A. Haukos, A.M. Tanner, and S.A. Carleton. 2020. Estimating response distances of lesser prairie-chickens to anthropogenic features during long-distance movements. Ecosphere 11(9):e03202. 10.1002/ecs2.3202	September 2020
Peterson, E., Thors, R., Frechette, D. and Zydlewski, J.D. (2023). Adult Sea Lamprey approach and passage at the Milford Dam fishway, Penobscot River, Maine, United States. North American Journal of Fisheries Management, 43(4), pp.1052–1065. doi:https://doi.org/10.1002/nafm.10919 \| Download	May 2023
Peterson, E., Sheehan, T., and Zydlewski, J. (2021) Verification of circulus deposition rates in Atlantic Salmon, Salmo salar, smolts from three Maine rivers. Journal of Northwest Atlantic Fishery Science, Vol. 52: 19–27. DOI: 10.2960/J.v52.m733 \| Download	September 2021
Pershyn, N.A., Gese, E.M., Stuber, E.F. and Kluever, B.M., 2024. Kit foxes demonstrate adaptive compromise characteristics under intraguild predation pressure by coyotes in the Great Basin desert. Scientific Reports, 14(1), p.14446.	June 2024
Perry, G., C.W. Boal, R. Verble, and M.C. Wallace. 2020. “Good’ and ‘bad’ urban wildlife. Pages 141-170 in Problematic Wildlife Vol. 2: New conservation and management challenges in the human-wildlife interactions (F.M. Angelici and L. Rossi, editors). Springer International Publishing, Switzerland.	June 2020
Perkin, J. S., Brewer, S. K., Echelle, A. A., & Kočovský, P. M. (2023). Avoiding a macabre future for Macrhybopsis—A special section on improving management and conservation of chubs. North American Journal of Fisheries Management, 43, 1145–1150. https://doi.org/10.1002/nafm.10950	October 2023
Pepin, K. M., T. J. Smyser, A. J. Davis, R. S. Miller, K. C. VerCauteren, W. L. Kendall, and C Slootmaker. 2020. Optimal spatial prioritization of control resources for elimination of invasive species under demographic uncertainty. Ecological Applications, in review.	March 2020
Pepin, K. M., A. J. Davis, R. S. Epanchin-Niell, A. M. Gormley, J. L. Moore, T. J. Smyser, B. Shaffer, W. L. Kendall, K. Shea, M. C. Runge, and S. McKee. 2022. Optimizing management of invasions in an uncertain world using dyamic spatial models. Ecological Applications 32:e2628. https://doi.org/10.1002/eap.2628.	April 2022
Pennock, C.A., W.C. Saunders, and P. Budy. 2022. High densities of conspecifics buffer native fish from negative interactions with an ecologically similar invasive. Biological Invasions https://doi.org/10.1007/s10530-021-02725-y. USGS FSP IP-130496. \| Download	January 2022
Pennock, C.A., P. Budy, and N. Barrett. 2021. Effects of increased temperature on arctic fish is mediated by food availability: Implications for climate change. Freshwater Biology 66:549-561. DOI: 10.1111/fwb.13659. USGS FSP ID-121940. \| Download	March 2021
Pennock, C.A., P. Budy, and N. Barrett. 2021. Effects of increased temperature on arctic fish is mediated by food availability: Implications for climate change. Freshwater Biology 66:549-561. DOI: 10.1111/fwb.13659. USGS FSP ID-121940. \| Download	March 2021
Pennock, C.A., Budy P, Macfarlane, WW. 2022. Effective conservation and restoration of desert riverscapes requires conservation and restoration of in-stream flows with rehabilitation approaches tailored to water availability. Invited: Frontiers in Environmental Science 10:870488. doi: 10.3389/fenvs.2022.870488. USGS FSP IP- 138466. \| Abstract	May 2022	Desert riverscape restoration practitioners must contend with compounding effects of increasing human water demand, persistent drought, nonnative species establishment, and climate change, which further stress desert riverine ecosystems such as rivers in the Colorado River basin, USA. Herein, we provide our perspective on the importance of natural flows, large floods in particular, for successful conservation and restoration of riverscapes. We present ideas developed from our experience with restoration projects across multiple desert tributary rivers with varying levels of habitat degradation and water abstraction. We propose broad-scale measures such as protection of in-stream flows, tailoring restoration efforts to available annual water availability, and working with nature using low-tech process-based techniques to more completely address the mechanisms of habitat degradation, such as flow reduction and vegetation-induced channel narrowing. Traditionally, restoration efforts in the Colorado River basin take place at relatively fine-scales, at convenient locations and, largely focus on reducing nonnative plant and fish species. We suggest that we need to think more broadly and creatively, and that conservation or restoration of natural flow regimes is crucial to long-term success of almost all management efforts for both in-stream and riparian communities.
Pennock, C.A. and Bruckerhoff, L.A., 2020. Qualitative observations of successful spawning by two species of small-bodied minnows following PIT tagging. Western North American Naturalist, 80(2), pp.253-256. https://doi.org/10.3398/064.080.0213	April 2020
Pennock, C.A, L. Bruckerhoff, K.B. Gido, A.L. Barkalow, M.J. Breen, P. Budy, W.W. Macfarlane, and D.L. Propst. 2022. Failure to achieve recommended environmental flows coincides with declining fish populations: Long-term trends in regulated and unregulated rivers. Freshwater Biology https://doi.org/10.1111/fwb.13966. USGS FSP IP- 134441 (LB). \| Abstract	July 2022	Dams can be operated to mimic components of the natural flow regime to minimize impacts on downstream ecosystems. However, infrastructure, societal needs, and watershed runoff constrain which and when flow regime attributes can be mimicked. We compared fish assemblage responses, including native and nonnative species, over two decades of managed environmental flows to those in a river retaining a relatively natural flow regime. Both of these arid-land rivers are within the Colorado River basin and have experienced declines in watershed runoff over the past twenty years. We predicted fish-flow relationships would be conserved across time and between managed and unmanaged rivers. Declines in flow in both rivers coincided with declines in some native fishes, and more native and nonnative fish species exhibited declines in the managed river than in the unmanaged river. Our ability to detect previously documented native fish-flow relationships diminished in the managed river system because established environmental flow targets were not met due to water management, but we detected these fish-flow relationships in the unmanaged river. Our results suggest declining watershed runoff and increased consumptive water use could reduce the effectiveness of environmental flows that have lower priority in most years.
Pennock, C., P. Budy, W.W. Macfarlane, M.J. Breen, J. Jimenez, and J.C. Schmidt. 2021. Native fish need a natural flow regime, not more water development. Fisheries, ‘Perspectives’ Article 47:118-123. DOI: 10.1002/fsh.10703. USGS FSP IP-130996.	November 2021
Pennock, C. A., and K. B. Gido. 2021. Spatial and temporal dynamics of fish assemblages in a desert reservoir over 38 years. Hyrdrobiologia 848:1231-1248. https://doi.org/10.1007/s10750-021-04514-z	March 2021
Pennock, C. A., P. Budy, S. A. Bonar, T. E. Dowling, K. B. Gido, E. I. Gilbert, B. R. Kesner, C. P. Paukert, M. C. Quist, J. Stahli, T. F. Turner, and D. L. Ward. 2022. Assessment of potential augmentation and management strategies for Razorback Sucker Xyrauchen texanus in Lake Mead and Grand Canyon: A Science Panel Summary. UTCFWRU 2022 (3):1-3	September 2022
Pennock, C. A., P. Budy, S. A. Bonar, T. E. Dowling, K. B. Gido, E. I. Gilbert, B. R. Kesner, C. P. Paukert, M. C. Quist, J. Stahli, T. F. Turner, and D. L. Ward. 2022. Assessment of potential augmentation and management strategies for Razorback Sucker Xyrauchen texanus in Lake Mead and Grand Canyon: A Science Panel Summary. (No FSP possible).	April 2022
Pennock CA, Ahrens ZT, McKinstry MC, Budy P, Gido KB. 2021. Trophic niches of native and nonnative fishes along a river-reservoir continuum. Scientific Reports 11:12140 (2021). https://doi.org/10.1038/s41598-021-91730-1 \| Download	June 2021
Penland, T.N., W.G. Cope, T.J. Kwak, M.J. Strynar, C.A. Grieshaber, R.J. Heise, and F.W. Sessions. 2020. Trophodynamics of per- and polyfluoroalkyl substances in the food web of a large Atlantic Slope river. Environmental Science and Technology 54: 6800-6811. DOI:10.1021/acs.est.9b05007	June 2020
Pell, C.J., S.L. King, T. Hawkins, and M. Symmank. 2025. Determining the effects of reduced water availability on seed germination of five bottomland hardwood tree species. Forest Ecology and Management 577, 122410. https://doi.org/10.1016/j.foreco.2024.122410	February 2025
Pease, B., K. Pacifici, and J. A. Collazo. 2021. Survey design optimization for monitoring wildlife communities in areas managed for federally endangered species. Animal Conservation 24:756–769.	March 2021
Pease AA, JE Pease, PT Bean, & TB Grabowski. 2022. Endemic Guadalupe Bass (Micropterus treculii) are supported by isotopically distinct resources in tributary versus mainstem river food webs. River Research and Applications. doi: 10.1002/rra.4015 \| Abstract	June 2022	We used stable isotope analysis to investigate differences in Guadalupe bass<i> Micropterus treculii</i> resource use that might be associated with population-level variation in main-stem river versus tributary stream habitats. <i>Micropterus treculii</i> from main-stem sites had more enriched δ<sup>13</sup>C and δ<sup>15</sup>N signatures compared to those collected in tributaries, likely reflecting greater importance of algae as a basal resource and influences of urban wastewater in main-stem habitats. Documenting ecological variation across ecosystem types is important to inform fish conservation efforts, especially for species that occupy a range of stream sizes.
Pearse, A.T., M.L. Szymanski, C.A. Anchor, M.J. Anteau, R.M. Murano, D.A. Brandt, and J.D. Stafford. 2023. Factors influencing autumn-winter movements of midcontinent Mallards and consequences for harvest and habitat management. Ecology and Evolution DOI: 10.1002/ece3.10605.	October 2023
Pearman-Gillman, S., M. Duveneck, J. Murdoch, and T. M. Donovan. 2020. Species distribution changes under alternative landscape futures: Using a scenario framework to identify drivers and consequences of landscape change on wildlife in New England. Frontiers in Ecology and Evolution 8:164. doi: 10.3389/fevo.2020.00164. \| Abstract \| Download \| Publisher Website	June 2020	In an era of rapid climate and land transformation, it is increasingly important to understand how future changes impact natural systems. Scenario studies can offer the structure and perspective needed to understand the impacts of change and help inform management and conservation decisions. We implemented a scenario-based approach to assess how two high impact drivers of landscape change influence the distributions of managed wildlife species (<i>n</i> = 10) in the New England region of the northeastern United States. We used expert derived species distribution models (SDMs) and scenarios developed by the New England Landscape Futures Project (NELFP) to estimate how species distributions change under various trajectories (<i>n</i> = 5) of landscape change. The NELFP scenarios were built around two primary drivers – Socio-Economic Connectedness (SEC) and Natural Resource Planning and Innovation (NRPI) – and provide plausible alternatives for how the New England region may change over 50 years (2010–2060). Our models generally resulted in species occurrence and richness declines by 2060. The majority of species (7 of 10) experienced declines in regional occurrence for all NELFP scenarios, and one species experienced a projected increase in mean regional occurrence for all scenarios. Our results indicate that the NRPI and SEC drivers strongly influenced projected distribution changes compared to baseline projections. NRPI had a greater impact on distribution change for five species (coyote, moose, striped skunk, white-tailed deer, and wild turkey), while SEC had a greater impact on four species (American black bear, bobcat, raccoon, and red fox); one species (gray fox) was equally influenced by both NRPI and SEC. These results emphasize the importance of integrating both natural resource planning and socio-economic factors when addressing issues of distribution change and offer insights that can inform proactive management and conservation planning.
Pearman-Gillman, S., M. Duveneck, J. Murdoch, and T. Donovan. 2020. Wildlife resistence and protection in a changing New England landscape. PLOS ONE 15(9): e0239525. https://doi.org/10.1371/journal.pone.0239525 \| Abstract \| Publisher Website	September 2020	Rapid changes in climate and land use threaten the persistence of wildlife species. Understanding where species are likely to occur now and in the future can help identify areas that are resistant to change over time and guide conservation planning. We estimated changes in species distribution patterns and spatial resistance in five future scenarios for the New England region of the northeastern United States. We present scenario-specific distribution change maps for nine harvested wildlife species, identifying regions of increasing, decreasing, or stable habitat suitability within each scenario. Next, we isolated areas where species occurrence probability is high (p > 0.7) and resistant to change across all future scenarios. Resistance was also evaluated relative to current land protection to identify patterns in and out of Protected Areas (PAs). Generally, species distributions declined in area over the 50-year assessment period (2010–2060), with the greatest average declines occurring for moose (-40.9%) and wild turkey (-22.1%). Species resistance varied considerably across the region, with coyote demonstrating the highest average regional resistance (91.81% of the region) and moose demonstrating the lowest (0.76% of the region). At the state level, average focal species resistance was highest in Maine (the largest state) and lowest in Massachusetts. Many of the focal species showed high overlap in resistance and land protection. Coyote, white-tailed deer, and black bear had the highest probability of resistance, given protection, while moose and wild turkey had the highest probability of protection, given resistance. Overall, relatively small portions of New England—ranging between 0.25% and 21.12%–were both protected and resistant for the focal species. Our results provide estimates of resistance that can inform conservation planning for commonly harvested species that are important ecologically, economically, and culturally to the region. Expanding protected area coverage to include resistant areas may provide longer term benefits to these species.
Pearman-Gillman, S, J. E. Katz, R. Mickey, J. Murdoch, and T. Donovan. 2020. Predicting wildlife distribution patterns in New England USA with expert elicitation techniques. Global Ecology and Conservation 21:e00853. \| Abstract \| Download \| Publisher Website	March 2020	Understanding the impacts of landscape change on species distributions can help inform decision-making and conservation planning. Unfortunately, empirical data that span large spatial extents across multiple taxa are limited. In this study, we used expert elicitation techniques to develop species distribution models (SDMs) for harvested wildlife species (n = 10) in the New England region of the northeastern United States. We administered an online survey that elicited opinions from wildlife experts on the probability of species occurrence throughout the study region. We collected 3396 probability of occurrence estimates from 46 experts, and used linear mixed-effects methods and landcover variables at multiple spatial extents to develop SDMs. The models were in general agreement with the literature and provided effect sizes for variables that shape species occurrence. With the exception of gray fox, models performed well when validated against crowdsourced empirical data. We applied models to rasters (30 × 30 m cells) of the New England region to map each species’ distribution. Average regional occurrence probability was highest for coyote (0.92) and white-tailed deer (0.89) and lowest for gray fox (0.42) and moose (0.52). We then stacked distribution maps of each species to estimate and map focal species richness. Species richness (<i>s</i>) varied across New England, with highest average richness in the least developed states of Vermont (<i>s</i> = 7.47) and Maine (s = 7.32), and lowest average richness in the most developed states of Rhode Island (s = 6.13) and Massachusetts (s = 6.61). Our expert-based approach provided relatively inexpensive, comprehensive information that would have otherwise been difficult to obtain given the spatial extent and range of species being assessed. The results provide valuable information about the current distribution of wildlife species and offer a means of exploring how climate and land-use change may impact wildlife in the future.
Pearce, D.L., J.E. Edson, C.S. Jennelle, and W.D. Walter. 2024. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Scientific Reports 14, 11340. https://doi.org/10.1038/s41598-024-56128-9 \| Abstract	May 2024	Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method, however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the DNA requirements between microsatellites and SNPs being different, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We found four sample categories that met the DNA requirements for use in all three panels, three sample categories that only met the DNA requirements for two panels, and one sample category that did not meet any of the three panels requirements. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates, tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction could influence DNA yield.
Payton Q, AF Evans, NJ Hostetter, DD Roby, BM Cramer, and K Collis. 2020. Measuring the additive effects of predation on prey survival across multiple spatial scales. Ecological Applications. 30:e02193. https://doi.org/10.1002/eap.2193	June 2020
Payne, N., Combrink, L., Kraberger, S., Fontenele, R.S., Schmidlin, K., Cassaigne, I., Culver, M., Varsani, A., and Van Doorslaer, K. 2023. DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico. Frontiers in Ecology and Evolution, October 14:esad057. doi: 10.1093/jhered/esad057. \| Abstract	April 2023	With viruses often having devastating effects on wildlife population fitness and with wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat (<i>Lynx rufus</i>, n = 9) and puma (<i>Puma concolor</i> , n = 13) scat samples non-invasively collected from Sonora, Mexico, to identify viruses in fecal viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research should aim to clarify host associations and determine the pathogenicity of detected viruses.
Payne N, Kraberger S, Fontenele RS, Schmidlin K, Bergeman MH, Cassaigne I, Culver M, Varsani A and K Van Doorslaer. 2020, Novel circoviruses detected in feces of Sonoran felids. Viruses, 12(9), 1027; https://doi.org/10.3390/v12091027 \| Abstract \| Publisher Website	September 2020	Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids
Payne N, JA Erwin, J Morrison, J Dwyer and M Culver. 2023. Genomic Insights into Isolation of the Threatened Florida Crested Caracara (Caracara plancus). J Heredity, 14:esad057. doi: 10.1093/jhered/esad057. \| Abstract	October 2023	We conducted a population genomic study of the crested caracara (<i>Caracara</i> <i>plancus</i>) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, USA. Crested caracaras are non-migratory raptors ranging from the southern tip of South America up to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since the last ice age. Our objectives were to evaluate genetic diversity and population structure of Florida’s apparently isolated population and to evaluate taxonomic relationships of caracaras at the northern edge of their range. Using DNA purified from blood samples, we conducted double-digest restriction site associated DNA sequencing and sequenced the mitochondrial <i>ND2</i> gene.<b> </b>Analyses of population structure using over 9000 SNPs suggest two major clusters are best supported, one cluster including only Florida individuals and the other cluster including Arizona and Texas individuals.<b> </b>Both SNPs and mitochondrial haplotypes reveal the Florida population to be highly differentiated genetically from Arizona and Texas populations, whereas Arizona and Texas populations are moderately differentiated from each other.<b> </b>The Florida population’s mitochondrial haplotypes form a separate monophyletic group, while Arizona and Texas populations share mitochondrial haplotypes.<b> </b>Results of this study provide substantial genetic evidence that Florida’s crested caracaras have experienced long-term isolation from caracaras in Arizona and Texas, representing a distinct evolutionary lineage possibly warranting distinction as an Evolutionarily Significant Unit (ESU) or subspecies. Inclusion of these results will aid development of conservation strategies focused on long-term survival of Florida’s distinct, panmictic population.
Paukert, C., E. Webb, D. Fowler, and C. Hilling. 2021. Harvest as a Tool to Manage Populations of Undesirable or Overabundant Fish and Wildlife Species. Pages 249 to 262 in: L. Powell and K. Pope, editors. Harvest of Fish and Wildlife: New Paradigms for Sustainable Management. CRC Press.	June 2021
Paukert, C. P., J. D. Olden, A. J. Lynch, D. Brashears, R. C. Chambers, C. Chu, M. Daly, K. L. Dibble, J. Falke, D. Issak, P. Jacobson, O. P. Jensen, and D. Munroe. 2021. Climate change effects on North American fish and fisheries to inform adaptation strategies. Fisheries 46: 449-464. https://doi.org/10.1002/fsh.10668	September 2021
Paukert, C. P. 2020. Don’t Worry, Be Happy: Learning to Let Go. in: Lessons in Leadership: Integrating Courage, Vision, and Innovation for the Future of Sustainable Fisheries. American Fisheries Society	August 2020
Paufve MR, Sethi SA, Weidel BC, Lantry BF, Yule DL, Rudstam LG, Jonas JJ, Berglund E, Connerton MJ, Gorsky D, Herbert M, Smith J. (2022) Diversity in spawning habitat use among Great Lakes Cisco populations. Ecology of Freshwater Fish 31: 379-388. \| Abstract	April 2022	Cisco (<i>Coregonus artedi</i>) once dominated fish communities in the Laurentian Great Lakes. Restoring the abundance and distribution of this species has emerged as a management priority, yet our understanding of Cisco spawning habitat use is insufficient to characterize habitat needs for these populations and assess whether availability of suitable spawning habitat could be a constraint to recovery. We characterized the distribution of incubating Cisco eggs <i>in situ</i> across gradients of depth and substrate types to describe the spawning habitat used by three Great Lakes populations. In Chaumont Bay, Lake Ontario, eggs were concentrated on shallow bedrock shoals and not found on deeper silt or sand substrate. In contrast, eggs in Thunder Bay, Lake Superior, and Elk Rapids, Lake Michigan, were found on deeper fine grain sediments with low utilization of shallow rocky and cobble habitats. These patterns of egg incubation habitat use suggest a broad spawning habitat niche at the species level but distinct spawning habitat preferences at the population level. While our results indicate some historical diversity in spawning habitat use has been maintained across the species’ range in the Great Lakes, comparisons of contemporary spawning habitat utilization against historical accounts raise questions as to whether some spawning habitat use behaviors may no longer be prevalent within specific lakes. Thus, characterizing the portfolio of spawning strategies remaining within lakes may improve our understanding of habitat needs and identify opportunities to maintain population diversity while supporting Cisco rehabilitation.
Paufve MP, Sethi SA, Rudstam L, Weidel BC, Lantry BF, Chalupnicki M. (2020) Differentiation between Lake Whitefish and Cisco eggs based on diameter. Journal of Great Lakes Research. 46:1058-1062. \| Abstract	July 2020	Cisco (Coregonus artedi) and lake whitefish (Coregonus clupeaformis) are native fish species of management concern in the Laurentian Great Lakes that often overlap in spawning locations and timing. Thus, species-level inference from in situ sampling requires methods to differentiate their eggs. Genetic barcoding and rearing of live eggs to visually identify larvae are used but can be time and cost intensive. Observations in published literature indicate that in the Great Lakes, lake whitefish eggs may be larger than those of cisco, but this has not yet been substantiated. Samples from shared spawning grounds are unlikely to contain similarly sized or colored eggs from other species. Thus, we assessed whether their eggs could be separated based on size alone. Fertilized, hardened eggs were collected in situ during spawning at Elk Rapids, Lake Michigan and Chaumont Bay, Lake Ontario and preserved in ethanol. Individual eggs were measured and genetically identified. Mean diameter for cisco (2.45 mm, SD = 0.22, n = 444) was smaller than for lake whitefish (3.21 mm, SD = 0.20, n = 99). We used classification trees to identify a species-separating size threshold of 2.88 mm (95% bootstrap CI = [2.88, 2.95]), which classified eggs with an accuracy rate of 96%. Differences between species across other samples from the same locations were mostly consistent with the threshold size, but we suggest validation if applying this method to other populations. Separation of cisco and lake whitefish eggs by diameter can be accurate, efficient, and especially suitable for large sample sizes.
Patton, P. T., K. Pacifici, and Jaime A. Collazo. 2022. Modeling and Estimating Co-occurrence between generalist brood parasites and host communities. Biological Invasions.	March 2022
Patton, BA, Nyman JA, La Peyre MK. 2020. Living on the edge: Multi-scale analyses of waterbird habitat use in coastal wetlands of Barataria Basin, Louisiana, USA. Wetlands doi: 10.1007/s13157-020-01324-2,	July 2020
Patiño, R., Christensen, V.G., Graham, J.L., Rogosch, J.S, and Rosen, B.H. 2023. Toxic algae in inland waters of the conterminous United States—A review and synthesis.Water, 15(15), 2808. https://doi.org/10.3390/w15152808. \| Abstract \| Publisher Website	August 2023	Cyanobacteria are the most common toxigenic algae in inland waters. Their toxins can affect the health of aquatic and terrestrial organisms, including humans. Other algal groups, such as haptophytes (e.g., Prymnesium parvum) and euglenoids (e.g., Euglena sanguinea), can also form harmful algal blooms (HABs) whose toxins cause injury to aquatic biota but currently have no known effects on human health. Prymnesium parvum, however, is responsible for some of the worst HAB-related ecological disasters recorded in inland waters. Here, we provide an overview of the primary toxigenic algae found in U.S. inland waters: cyanobacteria (planktonic forms), P. parvum, and E. sanguinea with the objective of describing their similarities and differences in the areas of HAB ecology, algal toxins, and the potential for future range expansion of HABs. A detailed account of bloom habitats and their known associations with land cover and use is provided from the perspective of water quality. This review revealed that salinity may have an influence on inland cyanobacterial blooms and cyanotoxins that had not been fully recognized previously.
Pasternak, G., C.A. Ribic, E. Spanier, and D. Zviely. Stormwater systems as a source of marine debris: a case study from the Mediterranean coast of Israel. Journal of Coastal Conservation 25: article 27 (Online). https://doi.org/10.1007/s11852-021-00818-3	February 2021
Parker, S. W., T. S. Coleman, A. K. Carlson, and J. R. Fischer. 2023. Characterization of fish assemblages in eleven multi-use reservoirs from North Carolina, USA. Journal of Freshwater Ecology 38(1):2241494.	August 2023
Parker, N.J., D.S. Sullins, D.A. Haukos, K.A. Fricke, and C.A. Hagen. 2022. Recovery of working grasslands following a megafire in the southern mixed-grass prairie Global Ecology and Conservation 36 (2022) e02142. https://doi.org/10.1016/j.gecco.2022.e02142	May 2022
Parker, N.J., D.S. Sullins, D.A. Haukos, K.A. Fricke, and C.A. Hagen. 2022. Demographic effects of a megafire on a declining prairie grouse in the mixed-grass prairie. Ecology and Evolution 12:e9544.	November 2022
Parker, N. J.*, D. S. Sullins, D. A. Haukos, K. A. Fricke, and C. A. Hagen. 2022. Recovery of working grasslands following a megafire in the southern mixed-grass prairie. Global Ecology and Conservation 36: e02142. DOI: 10.1016/j.gecco.2022.e02142.	October 2022
Parker, N. J.*, D. S. Sullins, D. A. Haukos, K. A. Fricke, and C. A. Hagen, A. A. Ahlers. 2022. Demographic effects of a megafire on a declining prairie grouse in the mixed-grass prairie. Ecology and Evolution 12: e9544. DOI: 10.1002/ece3.9544	November 2022
Parikh, G.L., R.C. Karsch, J.W. Cain III, E.M Rominger, and E.J. Goldstein. 2024. Neonate morphometrics and lambing season characteristics of desert bighorn sheep. Mammalia 2024-0074. https://doi.org/10.1515/mammalia-2024-0074 \| Download	December 2024
Paprocki, N., and C. J. Conway. 2025. The underlying causes of differential migration: assumptions, hypotheses, and predictions. Biological Reviews 100:in press.	November 2024
Paprocki, N., S. Blair, C. J. Conway, J. Adams, S. Nerkowski, J. Kidd, and L. P. Waits. 2024. Comparison of seven DNA metabarcoding sampling methods to assess diet in a large avian predator. Environmental DNA 6:e70000.	August 2024
Paine, R.T.R., Rogers, M.W., and Rosenberger, A.E. 2024. Environmental DNA reveals invasion of Puerto Rican waterways by non-native Clarias catfish. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-164-2024, Washington, D.C. https://doi.org/10.3996/css20629765 \| Abstract \| Download \| Publisher Website	December 2024	The Sharptooth walking catfish (Clarias gariepinus) is native to parts of the Middle East, Asia, and Africa but is one of the world's most invasive freshwater fish species. The species’ ability to invade is partly due to its ability to breathe atmospheric oxygen, thereby avoiding hypoxia or poor water quality in receiving waterbodies; further, it can crawl over moist land to disperse to new systems. In 2018, two individuals purported to be Sharptooth walking catfish were collected and identified within the Canal de Patillas, a canal in the Guayama municipality in southeastern Puerto Rico. Several other specimens were also collected the following year. Given that this invasion was in its infancy, environmental DNA (eDNA) surveillance was employed as a rapid and efficient surveillance tool to help delineate the extent of this invasion. Water samples were collected and analyzed for Clarias eDNA from 63 sites encompassing a wide range of habitats in canals, lakes, and a river surrounding the area where they were first reported. Using eDNA-metabarcoding, we detected Clarias eDNA at 40 of the 63 sites throughout the sampled waterbodies. Furthermore, our molecular analysis indicated that the Whitespotted Clarias (C. fuscus) is the likely invader, and the original specimens, classified as C. gariepinus, were misidentified based on the use of morphological rather than genetic features for species classification. Environmental DNA surveillance indicated that the distribution of Clarias catfish in this system is substantially more extensive than previously documented. These findings suggest that additional survey efforts could help determine the invasion's full spatial extent and leading edge to inform the scope and scale of any potential management responses.
Paine, R.T.R., M.W. Rogers, and A. E. Rosenberger. 2024. Environmental DNA (eDNA) surveillance of the federally threatened Slender Chub (Erimystax cahni) in the Clinch River and Powell River. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-156-2024, Washington, D.C. https://doi.org/ 10.3996/css55463605 (IP-156546) \| Abstract	July 2024	The slender chub (<i>Erimystax cahni</i>) is a federally threatened fish native to and geographically restricted to eastern North America. More specifically, the Powell, Clinch, and lower Holston Rivers in Tennessee were historical collection areas. Habitat degradation from multiple sources, including surface mining, agriculture, dams, and urbanization, is associated with the decline of this species - an obligate inhabitant of gravel shoals in large rivers. As of 1964, only 15 voucher specimens were known and no living specimens were documented for decades. A federal recovery plan and Species Status Assessment were developed to determine if slender chub still exists and could be restored. Given the lack of recent observations using conventional sampling to search for its presence, we used environmental DNA sampling to determine their potential presence. Our specific objectives were to (1) develop a quantitative polymerase chain reaction (qPCR) assay aimed at species-specific detection and (2) sample historically known areas of collection. We sampled 43 sites in the Clinch and Powell Rivers. For the first time in almost two decades, we provide the first evidence for the continued existence of a putatively extinct species. We detected evidence of <i>E. cahni</i> in both the Powell and Clinch Rivers, but only at a few sites. We cannot confirm the presence of <i>E. cahni</i>, and positive eDNA matches could be attributed to amplification from a hybrid. Our results do indicate presence of slender chub DNA perseveres in the system and can inform resource agencies of localities to pursue on-the-ground searches for the slender chub with conventional methods (e.g., snorkeling) and potential restoration and recovery sites.
Paine, R. T. R., Hurt, C. R., & Mattingly, H. T. (2021). Monitoring a minuscule madtom: Environmental DNA surveillance of the endangered pygmy madtom (Noturus stanauli Etnier & Jenkins 1980) in the Duck and Clinch rivers, Tennessee. Environmental DNA, 3(4), 745-759. DOI: 10.1002/edn3.179 \| Abstract \| Download \| Publisher Website	February 2021	Environmental DNA (eDNA) detection has been shown to be an effective biosurveillance tool for freshwater fishes, but further research is needed to apply eDNA detection tools to small and rare fishes in large rivers. We developed an eDNA surveillance assay and protocol for monitoring the presence of the pygmy madtom (<i>Noturus stanauli</i>), a federally protected freshwater fish endemic to the Clinch and Duck rivers in Tennessee (United States, North America). <i>Noturus stanauli</i> is a diminutive fish that is exceedingly rare throughout its range; it is currently known only from a 115-river-km section of the Duck River and a 5-river-km section of the Clinch River. The aim of this research was to develop an eDNA assay to detect the presence of <i>N. stanauli</i> in both the Duck and Clinch rivers. We used this newly developed eDNA protocol to assess detection as a function of water depth and to further delineate the distribution of <i>N. stanauli</i> in both the Duck and Clinch rivers. Field sampling was performed to delineate the extent of <i>N. stanauli</i>'s range in both rivers. Our results indicated that samples collected from three areas within the water column, as well as a sediment core samples, yielded equal detection rates. Our assay detected the presence of <i>N. stanauli</i> at a previously unknown site outside the current distribution in the Clinch River, located approximately 2.5-river-km downstream from the Tennessee-Virginia state line. We demonstrated that eDNA detection is a promising tool for delineating the distribution of <i>N. stanauli</i>; however, further research is needed to assess environmental and life history variables that influence eDNA detection probability of small fish in large rivers.
Paige E. Howell, Blake R. Hossack, Erin Muths, Brent H. Sigafus, Richard B. Chandler "Informing Amphibian Conservation Efforts with Abundance-Based Metapopulation Models," Herpetologica, 76(2), 240-250, (23 June 2020) \| Abstract \| Publisher Website	June 2020	Science-based management strategies are needed to halt or reverse the global decline of amphibians. In many cases, sound management requires reliable models built using monitoring data. Historically, monitoring and statistical modeling efforts have focused on estimating occupancy using detection–nondetection data. Spatial occupancy models are useful for studying colonization–extinction dynamics, but richer insights can be gained from estimating abundance and density-dependent demographic rates. We developed an integrated abundance-based metapopulation model of the processes contributing to spatiotemporal variation in patch population density. We fit our model to a combination of detection–nondetection and count data from a 14-yr study of a reintroduced metapopulation of federally threatened Chiricahua Leopard Frogs (Lithobates chiricahuensis). Pond-specific population growth rate was influenced by pond hydroperiod and frog density, such that permanent and semipermanent ponds with low densities of adult frogs experienced the highest annual population growth rates. Immigration rate declined as the distance among ponds increased. After reintroduction in 2003, metapopulation-level abundance increased and appeared to stabilize around 1300 adult frogs (95% CI = 1192–1471) by year 2015. Further, changes in metapopulation abundance were driven mostly by changes in abundance at a few ponds. These high-density populations, which would not have been identifiable with traditional occupancy-based metapopulation models, are likely especially important for species recovery in the area. Abundance-based metapopulation models can be widely applied to inform conservation efforts, by providing higher quality information needed to prioritize habitat patches for management and can be used to make more accurate predictions of metapopulation extinction risk.
Padilla, C.J., J.T. Martin, J.W. Cain III, and M.E Gompper. 2024. Abiotic and demographic drivers of flea parasitism on deer mice in a recovering mixed-conifer forest a decade post-fire. Journal of Parasitology 110:375-385. \| Download	August 2024
Padilla, C.J., C.Q. Ruhl, J.W. Cain III, and M.E Gompper. 2024. Effects of Mycoplasma ovipneumoniae, abundance, and environmental conditions on bighorn sheep lamb:ewe ratios and adult survival in New Mexico. Ecosphere 15:e70095. DOI: 10.1002/ecs2.70095 \| Download	December 2024
Oyler-McCance, S.J., Ryan, M.J., Sullivan, B.K. et al. Genetic connectivity in the Arizona toad (Anaxyrus microscaphus): implications for conservation of a stream dwelling amphibian in the arid Southwestern United States. Conserv Genet (2024). https://doi.org/10.1007/s10592-024-01606-w \| Abstract \| Download \| Publisher Website	March 2024	The Arizona Toad (Anaxyrus microscaphus) is restricted to riverine corridors and adjacent uplands in the arid southwesternUnited States. As with numerous amphibians worldwide, populations are declining and face various known or suspectedthreats, from disease to habitat modification resulting from climate change. The Arizona Toad has been petitioned to belisted under the U.S. Endangered Species Act and was considered “warranted but precluded” citing the need for additionalinformation – particularly regarding natural history (e.g., connectivity and dispersal ability). The objectives of this studywere to characterize population structure and genetic diversity across the species’ range. We used reduced-representationgenomic sequencing to genotype 3,601 single nucleotide polymorphisms in 99 Arizona Toads from ten drainages across itsrange. Multiple analytical methods revealed two distinct genetic groups bisected by the Colorado River; one in the northwesternportion of the range in southwestern Utah and eastern Nevada and the other in the southeastern portion of the range incentral and eastern Arizona and New Mexico. We also found subtle substructure within both groups, particularly in centralArizona where toads at lower elevations were less connected than those at higher elevations. The northern and southernparts of the Arizona Toad range are not well connected genetically and could be managed as separate units. Further, thesedata could be used to identify source populations for assisted migration or translocations to support small or potentiallydeclining populations.
Owen, R.K., E.B. Webb, D.A. Haukos, and K.W. Goyne. 2020. Projected climate and land use changes drive plant community composition in agricultural wetlands. Environmental and Experimental Botany 175 (2020) 104039.	April 2020
Owen, R.K., E.B. Webb, D.A. Haukos, F.B. Fritschi and K.W. Goyne. 2020. Barnyardgrass (Echinochloa crusgalli) emergence and growth in a changing climate in Great Plains wetlands. Wetlands Ecology and Management https://doi.org/10.1007/s11273-019-09693-0	January 2020
Overpeck, J. T., and S. A. Bonar. 2021. Southwestern fish and aquatic systems: the climate challenge. In D.L. Propst, J.E. Williams, K.R. Bestgen, and C.W. Hoagstrom, eds. Standing between life and extinction: ethics and ecology of conserving aquatic species in the American Southwest. Chicago, IL: University of Chicago Press. IP-088747	March 2021
Overduijn, K. S., C. M. Handel, and A. N. Powell. 2020. Does habitat partitioning by sympatric plovers affect nest survival? The Auk 137:1-16. DOI: 10.1093/auk/ukaa018	May 2020
Ottinger, M.A., T. Maness, J.K. Grace, R. Wilson, P.G.R. Jodice. 2019. Strategic Avian Monitoring Plan for the Gulf of Mexico: Avian Health Assessments. In Wilson et al. (eds.). Strategic Bird Monitoring Guidelines for the Northern Gulf of Mexico, Mississippi Agricultural and Forestry Extension Research Bulletin 1228, Mississippi State University. \| Download	January 2020
Oteyza, J. C., J. C. Mouton, and T. E. Martin. 2021. Adult survival probability and body size affect parental risk-taking across latitudes. Ecology Letters 24:20-26.	January 2021
Ortega, A.C., Dwinnell, S.P.H., LaSharr, T.N., Jakopak, R.P., Denryter, K., Huggler, K., Hayes, M., Aikens, E.O., Verzuh, T., May, A., Kauffman, M.J., and Monteith, K.L. (2020). Effectiveness of Partial Sedation to Reduce Stress in Captured Mule Deer. Journal of Wildlife Management, 84: 1445–1456. https://doi.org/10.1002/jwmg.21929. \| Abstract	July 2020	Information garnered from the capture and handling of free-ranging animals helps advance understanding of wildlife ecology and can aid in decisions on wildlife management. Unfortunately, animals may experience increased levels of stress, injuries, and death resulting from captures (e.g., exertional myopathy, trauma). Partial sedation is a technique proposed to alleviate stress in animals during capture, yet efficacy of partial sedation for reducing stress and promoting survival post-capture remains unclear. We evaluated the effects of partial sedation on physiological, biochemical, and behavioral indicators of acute stress and probability of survival post-capture for mule deer (<i>Odocoileus hemionus</i>) that were captured via helicopter net-gunning in the eastern Greater Yellowstone Ecosystem, Wyoming, USA. We administered 10–30 mg of midazolam and 15 mg of azaperone intramuscularly (IM) to 32 mule deer in 2016 and 53 mule deer in 2017, and maintained a control group (captured but not sedated) of 38 mule deer in 2016 and 54 mule deer in 2017. To evaluate indicators of acute stress, we measured heart rate, blood-oxygen saturation, body temperature, respiration rate, and levels of serum cortisol. We recorded number of kicks and vocalizations of deer during handling and evaluated behavior during release. We also measured levels of fecal glucocorticoids as an indicator of baseline stress. Midazolam and azaperone did not reduce physiological, biochemical, or behavioral indicators of acute stress or influence probability of survival post-capture. Mule deer that were administered midazolam and azaperone, however, were more likely to hesitate, stumble or fall, and walk during release compared with individuals in the control group, which were more likely to trot, stot, or run without stumbling or falling. Our findings suggest that midazolam (10–30 mg IM) and azaperone (15 mg IM) may not yield physiological or demographic benefits for captured mule deer as previously assumed and may pose adverse effects that can complicate safety for captured animals, including drug-induced lethargy. Although we failed to find efficacy of midazolam and azaperone as a method for reducing stress in captured mule deer, the efficacy of midazolam and azaperone or other combinations of partial sedatives in reducing stress may depend on the dose of tranquilizer, study animal, capture setting, and how stress is defined.
Ortega etal. Expenditure of energy in a large herbivore is non-linear over winter	April 2023
Ortega et al. Migrating mule deer compensate en route for phenological mismatches	April 2023
Ortega et al. A test of the frost wave hypothesis in a temperate ungulate	January 2024
Orning, EK, KM Dugger, and DG Clark. 2021. Gray wolf (Canis lupus) predation patterns following recent recolonization in a multi-predator, multi-prey system. Canadian Journal of Zoology 99: 902–911. doi.org/10.1139/cjz-2021-0027 .	July 2021
Oppel S, BL Clark, MM Risi, C Horswill, SJ Converse, CW Jones, AM Osborne, K Stevens, V Perold, AL Bond, RM Wanless, R Cuthbert, J Cooper, PG Ryan. 2022. Demographic consequences of invasive species predation and management on the population of a long-lived seabird species. Journal of Applied Ecology 59:2059-2070.	June 2021
Olson, L.O., T.R. Van Deelen, D.J. Storm, and S.M. Crimmins. 2021. Understanding environmental patterns of canid predation on white-tailed deer (Odocoileus virginianus). Canadian Journal of Zoology 99:912-920. https://doi.org/10.1139/cjz-2021-0024	September 2021
Olah, A. M., C. A. Ribic, K. Grveles, S. Warner, D. Lopez, and A. M. Pidgeon. 2022. Kirtland’s Warbler breeding productivity and habitat use in red pine-dominated habitat in Wisconsin, USA. Avian Conservation and Ecology 17(1):3. [online] https://doi.org/10.5751/ACE-02009-170103	February 2022
Okun, N., McGuire, J., Henderson, M., Gallagher, S., Lang, E. and Mackey, E. Large Wood Restoration Effectiveness Monitoring in a Coastal Northern California Stream: A Paired Watershed Before-After-Control-Impact Study. Final Report to California Department of Fish and Wildlife Fisheries Restoration Grant Program May 2021.	August 2021
Odom, R.H. and W.M. Ford. 2021. Developing species-age cohorts from forest inventory and analysis data to parameterize a forest landscape model. International Journal of Forestry Research 6650821(2021) doi.org/10.1155/2021/6650821 16 p	March 2021
Odom, R.H. and W.M. Ford. 2020. Assessing the vulnerability of military installations in the coterminous United States to potential biome shifts resulting from rapid climate change. Environmental Management doi.org/10.1007/s00267-020-01331-3. 27 p.	July 2020
Odom, R.H. and W.M. Ford. 2020. Assessing the vulnerability of military installations in the coterminous United States to potential biome shifts resulting from rapid climate change. Environmental Management doi.org/10.1007/s00267-020-01331-3. 27 p.	July 2020
Ochs, C., C. Johnston, P. Hartfield, A. Harrison, J. Baustian, B. Piazza, C. Justis, D. Larsen, A. Michelson, J. Spurgeon. Chapter 6 - Lower Mississippi River Tributaries. In: J. Delong, T. Jardine (eds) Rivers of North America (2nd edition).	April 2023
Ochoa, A; David P. Onorato, Melody E. Roelke-Parker, Melanie Culver, and Robert Fitak. 2022. Give and Take: Effects of Genetic Admixture in Endangered Florida Panther Mutation Load. Journal of Heredity, 113, 491-499 doi.org/10.1093/jhered/esac037 \| Abstract	February 2022	Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, little is known about the fine-scale costs of admixture at the molecular level. In this study, we analyzed nonsynonymous variation from conserved genes to quantify and compare mutation load levels (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers with different genetic backgrounds and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F<sub>1</sub> (canonical Florida x Texas) panthers dating from a genetic rescue program, including Florida panthers with Central American ancestry resulting from an earlier admixture event. We found genetic drift had no significant effect in reducing overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Furthermore, these deleterious alleles were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding and inefficient purifying selection in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results highlight concerns that introduced novel deleterious alleles (temporarily present in heterozygous state) could potentially be expressed in subsequent generations of rescued populations if their effective sizes remain small.
Ochai, S.O., L. Snyman, A.C. Dolfi, A. Ramoelo, B.K. Reilly, J.M. Botha, P.L. Kamath, E. Archer, W.C. Turner, H. van Heerden. 2024. The roles of host and environment in shift of primary anthrax host species in Kruger National Park, PLOS ONE, 19(12): e0314103. https://doi.org/10.1371/journal.pone.0314103 \| Abstract	December 2024	Environmental and climatic factors, as well as host demographics and behaviour significantly influence the exposure of herbivorous mammalian hosts to pathogens such as <i>Bacillus anthracis</i>, the causative agent of anthrax. Until the early 1990s in Kruger National Park (KNP), kudu (<i>Tragelaphus strepsiceros</i>) was the host species most affected by anthrax, with outbreaks occurring predominantly in the dry season, particularly during drought cycles. However, the most affected host species shifted to impala (<i>Aepyceros melampus</i>), with more frequent anthrax outbreaks during the wet season. This study investigates the roles of environmental variation and other host species in this shift in KNP. Temporal trends in environmental variables such as precipitation, soil moisture, temperature, and normalised difference vegetation index (NDVI) were analyzed in relation to anthrax occurrence (presence/ absence and counts). Additionally, correlations between host species’ densities and anthrax mortalities over time were examined. Anthrax cases in 1990 were concentrated in the central and northern regions of KNP(excluding Pafuri), primarily affected kudus; while subsequent mortalities affected mostly impala and were restricted to the far north, in Pafuri. Significant correlations were found between kudu anthrax mortality and a decrease in NDVI, average temperature, SPI-6 and SPI-12 (Standardised Precipitation Index in various time intervals. Conversely, anthrax occurrence in impalas was associated with a decline in SPI-3, and temperature rise, with increased mortality during the rainy season. Elephant density showed negatively correlation with kudu mortality, but a positively correlation with both impala mortality and impala density. The study concludes that environmental variables and species’ densities may alter the diversity and frequency of hosts exposed to <i>B. anthracis.</i> Climate extremes and alterations therein may exacerbate anthrax severity by modifying species susceptibility and their probability of exposure over time.
Ochai, S.O., J.E. Crafford, P.L. Kamath, W.C. Turner, H. van Heerden. 2023. Development of conjugated secondary antibodies for wildlife disease surveillance. Frontiers in Immunology, 14: 1221071. \| Abstract \| Publisher Website	July 2023	Disease monitoring in free-ranging wildlife is a challenge and often relies on passive surveillance. Alternatively, proactive surveillance that relies on the detection of specific antibodies could give more reliable and timely insight into disease presence and prevalence in a population, especially if it occurs below detection thresholds for passive surveillance. An example is the Bacillus anthracis protective antigen (PA)-ELISA (Enzyme-Linked Immunosorbent Assay) that was used for surveillance of anthrax exposure in impala (Aepyceros melampus) and kudu (Tragelaphus strepsiceros) in the Kruger National Park, South Africa. However, serological biosurveillance is hampered by a lack of species-specific conjugates that can be used in assays. In this study we developed anti-kudu and anti-impala immunoglobulin specific conjugates in chickens and examined their binding, compared to the binding of commercially available protein-G and -AG conjugates, to different herbivore species using an ELISA-based avidity index. The conjugates were evaluated for cross-reaction with other wild herbivores to assess future use in diagnostic ELISAs for other species. The developed conjugates had a high relative avidity of > 70% against kudu and impala sera. The commercial conjugates (protein -G and -AG) had significantly low relative avidity (<20%) against these species. Eighteen other wildlife species demonstrated cross-reactivity with a mean relative avidity of >50% with the impala and kudu conjugates and <40% with the commercial conjugates. These results demonstrate the need for species-specific conjugates to improve the quality of immunoassays currently in use in wildlife, thus providing better tools for the surveillance of zoonotic agents along the livestock-wildlife-human interface.
Ochai, S.O., J. Crafford, A. Hassim, C. Byaruhanga, Y.-H. Huang, A. Hartmann, E.H. Dekker, O.L. van Schalkwyk, P.L. Kamath, W.C. Turner, and H. van Heerden. 2022. Immunological evidence of variation in exposure and immune response to Bacillus anthracis in herbivores of Kruger and Etosha National Parks. Frontiers in Immunology, 13:814031. https://doi.org/10.3389/fimmu.2022.814031 \| Abstract \| Publisher Website	February 2022	Exposure and immunity to generalist pathogens differ among host species and vary across spatial scales. Anthrax, caused by a multi-host bacterial pathogen, <i>Bacillus anthracis,</i> is enzootic in Kruger National Park (KNP), South Africa and Etosha National Park (ENP), Namibia. These parks share many of the same potential host species, yet the main anthrax host in one (greater kudu (<i>Tragelaphus</i> <i>strepsiceros</i>) in KNP and plains zebra (<i>Equus</i> <i>quagga</i>) in ENP) is only a minor host in the other. We investigated species and spatial patterns in anthrax mortalities,<i> B. anthracis</i> exposure, and the ability to neutralise the anthrax lethal toxin to determine if observed host mortality differences between locations could be attributed to population-level variation in pathogen exposure and/or immune response. Using serum collected from 20 individuals per primary host species (zebra, kudu), except for kudu in KNP (low incidence = 18, high incidence = 19) in high and low incidence areas of each park, we estimated pathogen exposure from anti-protective antigen (PA) antibody response using enzyme-linked immunosorbent assay (ELISA) and lethal toxin neutralisation with a toxin neutralisation assay (TNA). Serological evidence of pathogen exposure followed mortality patterns within each system (kudus: 95% positive in KNP versus 40% in ENP; zebras: 83% positive in ENP versus 63% in KNP). Animals in the high-incidence area of KNP had higher anti-PA responses than those in the low-incidence area, but there were no significant differences in exposure by area within ENP. Toxin neutralizing ability was higher for host populations with lower exposure prevalence, i.e., higher in ENP kudus and KNP zebras than their conspecifics in the other park. These results indicate that host species differ in their exposure to and adaptive immunity against <i>B. anthracis</i> in the two parks. These patterns may be due to environmental differences such as vegetation, rainfall patterns, landscape or forage availability between these systems and their interplay with host behaviour (foraging or other risky behaviours), resulting in differences in exposure frequency and dose, and hence immune response.
Ochai, S.O., A. Hassim, E.H. Dekker, T. Magome, E. Lekota, S.M. Makgabo, L.-M. de Klerk-Loris, O.L. van Schalkwyk, P.L. Kamath, W.C. Turner, H. van Heerden. 2024. Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax. PLoS Neglected Tropical Diseases, 18(11): e0012122. https://doi.org/10.1371/journal.pntd.0012122	November 2024
Oates and others. Spatially explicit demography reveals disparate influences of resource limitation and predation on population growth of a large herbivore	December 2021
O. Robinson, J. Socolar, E. F. Stuber, T. Auer, A. Berryman, P. H. Boersch-Supan, D. Brightsmith, A. Burbidge, S. Butchart, C. L. Davis, A. M. Dokter, A. S. Di Giacomo, A. Farnsworth, D. Fink, W. M. Hochachka, P. E. Howell, F. A. La Sorte, A. C. Lees, S. Marsden, R. Martin, R. O. Martin, J. F. Masello, E. T. Miller, Y. Moodley, A. Musgrove, D. Noble, V. Ojeda, P. Quillfeldt, J. A. Royle, V. Ruiz-Gutierrez, J. L. Tella, P. Yorio, C. Youngflesh, A. Johnston. Extreme uncertainty and unquantifiable bias do not inform population sizes. Proceedings of the National Academy of Sciences 119 (10) e2113862119 https://doi.org/10.1073/pnas.2113862119	March 2022
Nunez, T. et al. A statistical framework for modeling migration corridors	September 2022
Nunes, L.A., C.A. Ribic, and B. Zuckerberg. 2021. Integration of citizen science and spatial simulations identifies mismatches between conservation area networks and hotspots of declining grassland birds. Ecology and Evolution 11:16006-16020. DOI: http://dx.doi.org/10.1002/ece3.8270	November 2021
Nowak, J. J., Hurley, M. A., Lukacs, P. M., Walsh, D., & White, C. L. (2023). Population Monitoring. In Ecology and Management of Black-tailed and Mule Deer of North America (pp. 291-306). CRC Press. https://doi.org/10.1201/9781003354628-19 \| Abstract	April 2023	This chapter describes the importance of population monitoring, a complex task with many interrelated parts. The theoretical foundation for monitoring lies in the random sample and the field of statistics. Effective survey design provides the building blocks for monitoring all relevant quantities in a general and reusable fashion. Population models help to formalize hypotheses, design monitoring programs, find efficient uses of resources, and make proactive assessments of management actions. By combining the guidance received from population models with strict sampling procedures, the state of the population can efficiently be established, which facilitates adoption of the scientific method and rigorous decision making.
Notch J.J., McHuron A.S., Michel C.J., Cordoleani F., Johnson M., Henderson M.J., and Ammann A.J. (in press) Outmigration survival of wild Chinook salmon smolts through the Sacramento River during historic drought and high water conditions. environmental biology of fishes. \| Abstract	May 2020	Populations of wild spring-run Chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley, once numbering in the millions, have dramatically declined to record low numbers in recent years. Dam construction, habitat degradation, and altered flow regimes have all contributed to depress populations of spring-run salmon, which currently persist in only a few tributaries to the Sacramento River. Mill Creek (Tehama County) continues to support these threatened fish, and contains some of the most pristine spawning and rearing habitat available in the Central Valley. Despite this pristine habitat, the number of spring-run salmon returning to spawn has declined to record low numbers, and is likely attributed to poor outmigration survival rates. Using miniature acoustic tags, it is now possible to track out-migrating juveniles throughout the freshwater migration corridor. From 2013-2017 we captured and acoustic tagged 334 smolts out-migrating from Mill Creek, tracking their movement and survival rates over 250 kilometers through the Sacramento River. During this study California experienced both an unprecedented drought and record rainfall, resulting in dramatic fluctuations in year-to-year river flows and water temperature. Cumulative survival of tagged smolts from Mill Creek through the Sacramento River was 9.5% (±1.6) during the study, with relatively low survival during historic drought conditions in 2015 (4.9% ± 1.6) followed by increased survival during high flows in 2017 (42.3% ± 9.1). From these data, we modeled survival in Mill Creek and the Sacramento River over a range of flow values, which indicated that higher flows in each region result in increased survival rates. Data gathered in this study can help focus management and restoration actions over a relatively long migration corridor to specific regions of low survival, and provide guidance for management actions in the Sacramento River aimed at restoring populations of threatened Central Valley spring-run Chinook salmon.
Northrup, J., Vander Wal. E, Bonar, M, Fieberg, J, Laforge, MP, Leclerc, M, Prokopenko,C., and Gerber, BD. 2021. Conceptual and methodological advances in habitat5selection modeling: guidelines for ecology and evolution. Ecological Applications,32:e02470. https://doi.org/10.1002/eap.2470 \| Download	October 2021
Northrup, J, Anderson, C, Gerber, BD, and Wittemeyer, G. 2021. Behavioral and demographic responses of mule deer to energy development on winter range. WildlifeMonograph, 208, 1-37. https://doi.org/10.1002/wmon.1060 \| Download	January 2021
North, J.S., E.M. Schliep, G.J.A. Hansen, J. Kundel, C.A. Custer, P. McLaughlin, and T. Wagner. 2024. Accounting for spatiotemporal sampling variation in joint species distribution models. Journal of Applied Ecology 61:186-201. http://doi.org/10.1111/1365-2664.14547	November 2023
Norris, D.M., M.E. Colvin, L.E. Miranda, and M.A. Lashley. 2021. Supplemental habitat is reservoir dependent: Identifying optimal planting decision using Bayesian Decision Networks. Journal of Environmental Management. doi.org/10.1016/j.jenvman.2021.114139 \| Abstract	December 2021	Environmental management often requires making decisions despite system uncertainty. One such example is mudflat mediation in flood control reservoirs. Reservoir mudflats limit development of diverse fish assemblages due to the lack of structural habitat provided by plants. Seeding mudflats with agricultural plants may mimic floodplain wetlands once inundated and provide fish habitat and achieve habitat management objectives. However, planting success is uncertain because of unpredictable water level fluctuations that affect plant survival and growth. Decision support tools can account for uncertainty that influences decision outcomes and reduce the risk in reservoir mudflat planting decisions. We used Bayesian decision networks and sensitivity analyses to quantify uncertainty surrounding mudflat plantings as supplemental fish habitat in four northwest Mississippi reservoirs. When averaged across all uncertainty, planting was the optimal decision only in Enid Lake. Response profiles identified planting decisions depended on elevation contours within Enid, Sardis, and Grenada reservoirs. No planting was optimal at all elevations for Arkabutla Lake. These results provide a quantified basis for establishing best management practices and identifying key system states that influence decision outcomes. The process used in this study to evaluate planting decisions can be applied to any reservoir by modifying reservoir dependent inputs to evaluate planting decisions to provide supplemental fish habitat.
Norris, D.M., Hatcher, H.R., Colvin, M.E., Coppola, G., Lashley, M.A., and Miranda, L.E. 2020. Assessing establishment and growth of agricultural plantings on reservoir mudflats. North American Journal of Fisheries Management 40:394-3405. doi.org/10.1002/nafm.10419 \| Abstract	April 2020	Winter drawdowns in flood control reservoirs create expansive mudflats that lack the vegetation typical of littoral zones, which reduces the amount of structure available for fish habitat. This study investigated the feasibility of establishing agricultural plantings as a management action to ameliorate mudflats by providing structural cover following reservoir refilling. We tested cool‐season annual grasses and clovers applied in several mixed and monoculture treatments that were sown on the mudflats of Enid Reservoir, Mississippi, during the winter drawdown in three consecutive years. Soil samples were taken for analysis of pH and macronutrients prior to planting. Plantings were monitored until the following spring to evaluate effectiveness of establishment through ground coverage, height, and stem density sampling. Plots were assigned a seeding treatment of either grasses (ryegrass <i>Lolium</i> spp. or triticale <i>x Triticosecale</i> sp.), clovers (balansa clover <i>Trifolium michelianum</i> or berseem clover <i>Trifolium alexandrinum</i>), or both (mixed plantings) or left as an unseeded control. Differences among plant treatments were assessed via repeated measures analysis of variance and differences among means evaluated with Tukey's honestly significant difference test. Soil productivity within the study area was poor all 3 years. Grasses germinated both when disked into the soil and when top sown, while clover only germinated when disked. Plots seeded with grasses performed better than control plots with respect to stem density, height, and ground coverage, while plots seeded with grass and clover mixtures performed better than control plots only with respect to height, and plots seeded with only clover did not perform significantly better than control plots. Results serve as an evaluation of the efficacy of agricultural plant establishment on the mudflats of a flood control reservoir, inform the direction of future research, and identify considerations regarding the application of agricultural plantings as a management tool to create fish habitat.
Noring, A.M., G.G. Sass, S.R. Midway, J.A. VanDeHey, J.K. Raabe, D.A. Isermann, J.M. Kampa, T.P. Parks, J. Lyons, and M.J. Jennings. 2021. Pelagic forage versus abiotic factors as drivers of walleye growth in northern Wisconsin lakes. In Jared Meyers (Ed), Biology and Management of Coregonid Fishes - 2017: 13th International Symposium on the Biology and Management of Coregonid Fishes, Bayfield, USA (p 207-223). Schweizerbart Science Publishers.	December 2021
Noonan et al. Body-size-dependent underestimation of mammalian area requirements.	May 2020
Nocera, T., W.M. Ford, A. Silvis and C.A. Dobony. 20

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