Zale, A.V., T.M. Sutton, and D.L. Parrish. 2012. Conducting fisheries investigations. Pages 1-13 in A. V. Zale, D. L. Parrish, and T. M. Sutton, editors. Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland.
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January 2013
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Zale, A. V., D. L. Parrish, and T. M. Sutton, editors. 2012. Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland.
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January 2013
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Winter, M., J. A. Shaffer, D. H. Johnson, T. M. Donovan, W. D. Svedarsky, P. W. Jones, and B. R. Euliss. 2005. Habitat and nesting of Le Conte's Sparrows in the northern tallgrass prairie. Journal of Field Ornithology 76:61�71.
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April 2005
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Winter, M., D. H. Johnson, J. A. Shaffer, T. M. Donovan, and W. D. Svedarsky. 2006. How consistent are the effects of patch size and landscape composition on density and nest success of grassland birds? Journal of Wildlife Management 70:158-172.
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June 2006
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White, G., J. Claussen, C. Moffitt, B. Norcross, and D. Parrish. 2013. Dr. J Frances Allen: Pioneer of Women in Fisheries 38:103-111.
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Abstract
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March 2013
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no abstract for this
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Whalen, K. G., and D. L. Parrish. 1999. Nocturnal habitat use of Atlantic salmon parr in winter. Canadian Journal of Fisheries and Aquatic Sciences 56:1543-1550.
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September 1999
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Whalen, K. G., and D. L. Parrish. 1999. Effect of maturation on parr growth and smolt recruitment of Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences 56:79-86.
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January 1999
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Whalen, K. G., D. L. Parrish, and S. D. McCormick. 1999. Migration timing of Atlantic salmon smolts relative to environmental and physiological factors. Transactions of the American Fisheries Society 128:289-301.
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March 1999
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Whalen, K. G., D. L. Parrish, M. E. Mather. 1999. Effect of ice formation on selection of habitats and winter distribution of post-young-of-the-year Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences 56:87-96.
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January 1999
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Whalen, K. G., D. L. Parrish, M. E. Mather, J. R. McMenemy. 2000. Cross-tributary analysis of parr to smolt recruitment of Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences 57:1607-1616.
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January 2000
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Watrous, K. S., T. M. Donovan, R. Mickey, S. R. Darling, A. Hicks, and S. Von Oettengen. 2006. Predicting and mapping the minimum habitat requirements of the Indiana Bat in the Champlain Valley. Journal of Wildlife Management 70:1228-1237
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December 2006
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Van Vleet, N., Ward, D., Som, N., Barton, D., Anderson, C., and Henderson, M. It's about time: a multi-state 'continuous' time mark-recapture model to evaluate seasonal survival and movement rates of juvenile Coho Salmon in a small coastal watershed. Submitted to Transactions of the American Fisheries Society.
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Abstract
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August 2024
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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.
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Troy, A., A. M. Strong, S. C. Bosworth, T. M. Donovan, N. J. Buckley. 2005. Attitudes of dairy farmers regarding adoption of management practices for grassland songbirds. Wildlife Society Bulletin 33:528-538.
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Abstract
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October 2005
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In the northeastern United States, most populations of grassland songbirds occur on private lands. However, little information exists about the attitudes of farmers toward habitat management for this guild. To address this information gap, we surveyed 131 dairy farmers in Vermont’s Champlain Valley to assess current hayfield management practices and farmers’ willingness to adopt more “bird-friendly” practices. Our results showed a clear trend toward earlier and more frequent hayfield cuts. Farmers indicated they have little flexibility to alter the timing of their cuts on most of their land. However, many farmers (49%) indicated a willingness to adopt alternative management practices on at least a small portion of their land. Combined with the fact that many farmers characterized parts of their land as “wasteland,” or economically unproductive land, this result suggests that
some leeway exists for increasing songbird habitat quality on at least portions of dairy
farms. Although significant differences existed in the amount of land for which farmers were willing to adopt alternative management based on herd size, acreage, and experience, the directionality of these relationships could not be established except tentatively for herd size, in which case it appeared that farmers with smaller herds were more likely to dedicate a greater percentage of their land to alternative management. The results of this study likely have relevance to dairy farms throughout the northern-tier dairy states. Given the increasing trend for agricultural land to be converted into housing, we recommend
that extension and education efforts target farmers with large hayfield acreages,
encouraging the maintenance of high-quality habitat for grassland songbirds.
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Tierney, G., B. Mitchell;, A. Miller-Rushing, J. Katz, E. Denny, C. Brauer, T. Donovan, A. D. Richardson, M. Toomey, A. Kozlowski, J. Weltzin, K. Gerst, E. Sharron, O. Sonnentag, and F. Dieffenbach. 2013. Phenology monitoring protocol: Northeast Temperate Network. Natural Resource Report. NPS/NETN/NRR—2013/681. National Park Service. Fort Collins, Colorado. Published Report-2197242.
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Abstract
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Publisher Website
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July 2013
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Phenology is critical to many aspects of human life and nearly all ecological relationships and processes. As global climate continues to warm and change, widespread shifts in phenological patterns are occurring across the globe, and more change is inevitable. This protocol has been developed to provide standardized methods for monitoring phenology within the National Park Service (NPS) Northeast Temperate Network (NETN), as part of the NPS Inventory and Monitoring Program (I&M). NETN encompasses the Appalachian National Scenic Trail (APPA), Acadia National Park (ACAD), the Boston Harbor Islands National Recreation Area (BOHA), and 10 national historical parks and national historic sites in the Northeastern United States.
This protocol was developed in collaboration with and relies upon the procedures and infrastructure of the USA National Phenology Network (USA-NPN), including Nature’s Notebook, USA-NPN’s online plant and animal phenology observation program (www.nn.usanpn.org). Organized in 2007, USA-NPN is a nation-wide partnership among federal agencies, schools and universities, citizen volunteers, and others to monitor and understand the influence of seasonal cycles on the nation’s biological resources.
The overall goal of NETN’s phenology monitoring program is to determine trends in the phenology of key species in order to assist park managers with the detection and mitigation of the effects of climate change on park resources. An additional programmatic goal is to interest and educate park visitors and staff, as well as a cadre of volunteer monitors.
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Thompson, F. R. III, T. M. Donovan, R. DeGraaf, J. Faaborg, and S. K. Robinson. 2002. A multi-scale perspective of the effects of forest fragmentation on birds in eastern forests. Studies in Avian Biology 25:8-19.
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December 2002
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Thompson, F. R. III, S. K. Robinson, T. M. Donovan, J. Faaborg, and D. Whitehead. 2000. Biogeographic, landscape, and local factors affecting cowbird abundance and host parasitism levels. Pages 271-279 In Ecology and management of cowbirds (T. Cooke, S. K. Robinson, S. I. Rothstein, S. G. Sealy, J. N. M. Smith, eds. ). University of Texas Press, Austin, TX.
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January 2001
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Stritzel Thomson, J.L., D.L. Parrish, S.L. Parker-Stetter, L.G. Rudstam, and P.J. Sullivan. 2011. Growth rates of rainbow smelt in Lake Champlain: effects of density and diet. Ecology of Freshwater Fish 20: 503-512.
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December 2011
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Smith, K. W., W. S. Keeton, T. M. Donovan, and B. Mitchell. 2008. Stand-level forest structure in avian habitat: scale dependencies in predicting occurrences in a heterogeneous forest. Forest Science 54:36-46.
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Abstract
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February 2008
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We explored the role of stand-level forest structure and spatial extent of forest sampling in models of avian occurrence in northern hardwood-conifer forests for two species: black-throated blue warbler (Dendroica caerulescens) and ovenbird (Seiurus aurocapillus). We estimated site occupancy from point counts at 20 sites and characterized the forest structure at these sites at three spatial extents (0.2, 3.0, and 12.0 ha). Weight of evidence was greatest for habitat models using forest stand structure at the 12.0-ha extent and diminished only slightly at the 3.0-ha extent, a scale that was slightly larger than the average territory size of both species. Habitat models characterized at the 0.2-ha extent had low support, yet are the closest in design to those used in many of the habitat studies we reviewed. These results suggest that the role of stand-level vegetation may have been underestimated in the past, which will be of interest to land managers who use habitat models to assess the suitability of habitat for species of concern.
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Simonin, P.W., L.G. Rudstam, P.J. Sullivan, D.L. Parrish, and B. Pientka. 2019. Early mortality and freshwater forage fish recruitment: nonnative alewife and native rainbow smelt interactions in Lake Champlain. Canadian Journal of Fisheries and Aquatic Sciences 76(5): 806-814. doi: 10.1139/cjfas-2017-0571.
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July 2018
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Simonin, P.W., L.G. Rudstam, D.L. Parrish, B. Pientka, and P.J. Sullivan. 2018. Piscivore diet shifts and trophic level change after Alewife establishment in Lake Champlain. Transactions of the American Fisheries Society 147: 937-947. doi: 10.1002/tafs.10080.
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Abstract
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May 2018
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Invasions and deliberate introductions of new prey species are likely to affect prey choice and trophic level of resident predators. Rainbow Smelt (Osmerus mordax) and Alewife (Alosa pseudoharengus) are common prey fish species in lakes throughout North America either as native or non-native species. The establishment of Alewife in the 2000s in a lake with a native Rainbow Smelt population (Lake Champlain) presented an opportunity to study changes in the diet and trophic level of fish already established in the system. Using stable isotope analysis, we found that Alewife became a major component of predator diets, in particular of the diets of Atlantic Salmon (Salmo salar) and Walleye (Sander vitreus). Lake Trout (Salvelinus namaycush) consumed relatively few Alewives. For Walleye (the predator with both pre- and post-Alewife isotope ratios available), the δ15N values decreased significantly from the pre-Alewife period of the late 1990s, indicating that Walleye feed at lower trophic levels when Alewife are present. Predation on Alewife was correlated with the amount of spatial overlap of predators and prey. Our results show that the introduction of Alewife has altered the predator-prey linkages in Lake Champlain; alterations that can have major effects on food web structure and trophic cascades.
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Simonin, P.W., D.L. Parrish, L.G. Rudstam, P.J. Sullivan, B. Pientka. 2012. Native rainbow smelt and nonnative alewife distribution related to temperature and light gradients in Lake Champlain. Journal of Great Lakes Research 38 (Supplement 1): 115-122.
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March 2012
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Simonin, P.W., D. L. Parrish, L. G. Rudstam, P. J. Sullivan, and B. Pientka. 2016. Interactions between hatch dates, growth rates, and mortality of age-0 native Rainbow Smelt and nonnative Alewife in Lake Champlain. Transactions of the American Fisheries Society 145: 649-656. doi: 10.1080/00028487.2016.1143401
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Abstract
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April 2016
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Timing of hatch in fish populations can be critical for first-year survival and, therefore, year-class strength and subsequent species interactions. We compared hatch timing, growth rates and subsequent mortality of age-0 Rainbow Smelt Osmerus mordax and Alewife Alosa pseudoharengus, two common open-water fish of northern North America. In our study site, Lake Champlain, Rainbow Smelt hatched almost a month earlier than Alewife (hatching began on 26 May for Rainbow Smelt and 20 June for Alewife). Abundance in the sampling area was highest in July for age-0 Rainbow Smelt and August for age-0 Alewife. Later-hatching individuals of both species grew faster than those hatching earlier (0.6 mm/d vs. 0.4 for Rainbow Smelt; 0.7 mm/d vs. 0.6 for Alewife). Mean mortality rate for age-0 Rainbow Smelt was 3.4%/d and for age-0 Alewife was 5.5%/d during the first 45 days of life. Alewife mortality rates did not differ with hatch timing but daily mortality rates of Rainbow Smelt were highest for earlier-hatching fish. Cannibalism is likely the primary mortality source for age-0 Rainbow Smelt in this lake. Therefore, hatching earlier may not be advantageous as the overlap of adult and age-0 Rainbow Smelt is highest earlier in the season. However, Alewife, first documented in Lake Champlain in 2003, may increase the mortality of age-0 Rainbow Smelt in the summer, which should favor selection for earlier hatching.
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Shustack, D. P., A. M. Strong, and T. M. Donovan. 2010. Habitat use patterns of Bobolinks and Savannah Sparrows in the northeastern United States. Avian Conservation and Ecology 5(2): 11. [online] URL: http://www.ace-eco.org/vol5/iss2/art11/
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Abstract
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Publisher Website
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December 2010
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In the northeastern United States, grassland birds regularly use agricultural fields as nesting habitat. However, birds that nest in these fields regularly experience nest failure as a result of agricultural practices, such as mowing and grazing. Therefore, information on both spatial and temporal patterns of habitat use is needed to effectively manage these species. We addressed these complex habitat use patterns by conducting point counts during three time intervals between May 21, 2002 and July 2, 2002 in agricultural fields across the Champlain Valley in Vermont and New York. Early in the breeding season, Bobolinks (Dolichonyx oryzivorus) used fields in which the landscape within 2500 m was dominated by open habitats. As mowing began, suitable habitat within 500 m became more important. Savannah Sparrows (Passerculus sandwichensis) initially used fields that contained a high proportion of suitable habitat within 500 m. After mowing, features of the field (i.e., size and amount of woody edge) became more important. Each species responded differently to mowing: Savannah Sparrows were equally abundant in mowed and uncut fields, whereas Bobolinks were more abundant in uncut fields. In agricultural areas in the Northeast, large areas (2000 ha) that are mostly nonforested and undeveloped should be targeted for conservation. Within large open areas, smaller patches (80 ha) should be maintained as high-quality, late-cut grassland habitat.
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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.
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Abstract
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May 2023
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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.
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Schwenk, W. S., and T. M. Donovan. 2011. A multi-species framework for landscape conservation planning. Conservation Biology 25:1010-1021.
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Abstract
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October 2011
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Rapidly changing landscapes have spurred the need for quantitative methods for conservation
assessment and planning that encompass large spatial extents. We devised and tested a multispecies framework for conservation planning to complement single-species assessments and ecosystem-level approaches. Our framework consisted of 4 elements: sampling to effectively estimate population parameters, measuring
how human activity affects landscapes at multiple scales, analyzing the relation between landscape characteristics and individual species occurrences, and evaluating and comparing the responses of multiple species
to landscape modification. We applied the approach to a community of terrestrial birds across 25,000 km2 with a range of intensities of human development. Human modification of land cover, road density, and other elements of the landscape, measured at multiple spatial extents, had large effects on occupancy of the 67 species studied. Forest composition within 1 km of points had a strong effect on occupancy of many species and a range of negative, intermediate, and positive associations. Road density within 1 km of points, percent evergreen forest within 300 m, and distance from patch edge were also strongly associated with occupancy for many species. We used the occupancy results to group species into 11 guilds that shared patterns of association with landscape characteristics. Our multispecies approach to conservation planning allowed us to quantify the trade-offs of different scenarios of land-cover change in terms of species occupancy.
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Schwenk, W. S., T. M. Donovan, W. S. Keeton, and J. S. Nunery. 2012. Carbon storage, timber production, and biodiversity: comparing ecosystem services with multi-criteria decision analysis. Ecological Applications 22:1612-1627.
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Abstract
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July 2012
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Increasingly, land managers seek ways to manage forests for multiple ecosystem services and functions, yet considerable challenges exist in comparing disparate services and balancing trade-offs among them. We applied multi-criteria decision analysis (MCDA) and forest simulation models to simultaneously consider three objectives: (1) storing carbon, (2)producing timber and wood products, and (3) sustaining biodiversity. We used the Forest Vegetation Simulator (FVS) applied to 42 northern hardwood sites to simulate forest development over 100 years and to estimate carbon storage and timber production. We estimated biodiversity implications with occupancy models for 51 terrestrial bird species that were linked to FVS outputs. We simulated four alternative management prescriptions that spanned a range of harvesting intensities and forest structure retention. We found that silvicultural approaches emphasizing less frequent harvesting and greater structural retention could be expected to achieve the greatest net carbon storage but also produce less timber. More intensive prescriptions would enhance biodiversity because positive responses of early successional species exceeded negative responses of late successional species within the heavily forested study area. The combinations of weights assigned to objectives had a large influence on which prescriptions were scored as optimal. Overall, we found that a diversity of silvicultural approaches is likely to be preferable to any single approach, emphasizing the need for landscape-scale management to provide a full range of ecosystem goods and services. Our analytical framework that combined MCDA with forest simulation modeling was a powerful tool in understanding trade-offs among management objectives and how they can be simultaneously accommodated.
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Rudstam, L. G., S. L. Parker, Einhouse, D. W., L. D. Witzel, D. M. Warner, J. L. Stritzel, D. L. Parrish, P. J. Sullivan. 2003. Application of in situ target strength estimations in lakes--examples from rainbow smelt surveys in Lakes Erie and Champlain. ICES Journal of Marine Science 60: 500-507.
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June 2003
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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.
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Abstract
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Publisher Website
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October 2023
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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.
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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.
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January 2023
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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.
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Abstract
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July 2021
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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.
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Rinehart, K., T. Donovan, B. Mitchell, R. Long. 2009. Factors influencing occupancy patterns of Eastern Newts across Vermont. Journal of Herpetology 43(3):521-531.
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Abstract
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September 2009
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Of the threats facing amphibian populations today, habitat transformation due to land-use is among the most pressing. Although conservation of pond-breeding salamanders clearly requires protection of breeding ponds and their surrounding habitat, little is known about the effects of land use and other factors on the occurrence of salamanders in the dispersal/terrestrial phase of their life cycle. To determine these effects, we surveyed populations of Eastern Newts (Notophthalmus viridescens) at 551 stations across Vermont, and modeled salamander distribution as a function of environmental variables hypothesized to influence site occupancy. We developed a set of 12 models based on seven a priori hypotheses of site occupancy. We hypothesized that occupancy was influenced by 1) amounts of available habitat types, 2) arrangement of these habitat types, 3) geographic position, 4) housing density, 5) road density, 6) short term changes in habitat distribution, or 7) habitat structure at the stand-level. We used a single-season occupancy model to rank and compare the 12 models. 232 Eastern Newts were detected at 82 of 551 stations. Of the 12 models, amount of habitat within 0.5 km of the survey station best represented the field data. Strong effects were indicated for developed land (-), open water (+), and forest (+) cover. Given a survey station with average forest and open water characteristics, stations with > 5% developed land classes within a 0.5 km buffer had a very low probability of occupancy. Further research is needed to determine the direct role of development on occupancy patterns.
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Raffenberg, M. J., and D. L. Parrish. 2003. Interactions of Atlantic salmon (Salmo salar) and trout (Salvelinus fontinalis and Oncorhynchus mykiss) in Vermont tributaries of the Connecticut River. Canadian Journal of Fisheries and Aquatic Sciences 60: 279-285.
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March 2003
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Puchala, E.A., D.L. Parrish, and T.M. Donovan. 2016. Predicting the stability of endangered Stonecats (Noturus flavus) in the LaPlatte River, Vermont. Transactions of the American Fisheries Society 145: 903-912.
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Abstract
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June 2016
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Stonecats (Noturus flavus, Rafinesque 1818) in Vermont fit into a rare distribution pattern, as designated by Rabinowitz, because their known distribution is limited to two systems, the LaPlatte and Missisquoi rivers. Here we focus on Stonecats in the LaPlatte River to predict the stability of the population. In 2012, 2013, and 2014 we captured, PIT tagged (> 90 mm total length), and VIE marked all Stonecats collected using backpack electrofishing. A total of 1671 Stonecats was captured, and of those, 1252 were PIT tagged. Only 12% (N=156) of the PIT tagged fish were recaptured and only 22 were recaptured more than one time. We used the Pradel model in Program MARK to estimate the survival and seniority of Stonecats and these values were used to derive lambda (λ), the population rate of change. We ran a total of 64 models in our candidate set with the following covariates: total length, maximum temperature, season, maximum discharge, and area sampled. Model results estimated that survival was highest in the spring, and increased with increasing total length of individuals. We also estimated increases in capture probability with increasing area sampled. We derived an annual λ of 0.9826, which indicates a slightly decreasing population. With only three years of data and a low recapture rate, our estimate has some uncertainty. Although the population could be declining at a slow rate, we have provided insight into population parameters that were otherwise unknown.
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Puchala, E.A., D. L. Parrish, and D. H. Ogle. 2018. Size and age of Lake Champlain Stonecats; estimating growth at the margin of their range. North American Journal of Fisheries Management 38:1316–1323. DOI:10.1002/nafm.10230
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Abstract
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October 2018
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Little is known about Stonecat (Noturus flavus) populations, especially in the Northeastern United States, where these madtoms are at the edge of their range. In Lake Champlain tributaries, Stonecats are listed as endangered in Vermont, but not in New York. Here we describe the growth of Stonecats in two tributaries to Lake Champlain, one in Vermont and one in New York. We also compared the growth of Stonecats in these waters to results from other locations near the middle of their distribution. Stonecats in the Great Chazy River, NY were larger at ages 1-3, but smaller at age 5, than Stonecats from the LaPlatte River, VT. Stonecats in Lake Champlain tributaries were generally larger at age than those from the middle of their range, except for those from Lake Erie. Lake Champlain Stonecats appear to reach maturity by age 3, though future research that directly estimates age at maturity would be more informative. These results expand the literature that lacks information about growth of this species while also providing specific information needed to manage this and other fishes in Lake Champlain tributaries.
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Pientka, B., and D. L. Parrish. 2002. Habitat selection of predator and prey: Atlantic salmon and rainbow smelt overlap, based on temperature and dissolved oxygen. Transactions of the American Fisheries Society 131: 1180-1193.
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November 2002
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Perlut, N., C. Freeman-Gallant, A. M. Strong, T. M. Donovan, C. W. Kilpatrick, and N. J. Zalik. 2008. Agricultural management affects evolutionary processes in a migratory songbird. Molecular Ecology 17:1248-1255.
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Abstract
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February 2008
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Hay harvests have detrimental ecological effects on breeding songbirds, as harvesting results in nest failure. Importantly, whether harvesting also affects evolutionary processes is not known. We explored how hay harvest affected social and genetic mating patterns, and thus, the overall opportunity for sexual selection and evolutionary processes for a ground-nesting songbird, the Savannah sparrow (Passerculus sandwichensis). On an unharvested field, 55% of females were in polygynous associations, and social polygyny was associated with greater rates of extra-pair paternity (EPP). In this treatment, synchrony explained variation in EPP rates, as broods by more synchronous females had more EPP than broods by asynchronous females. In contrast, on a harvested field, simultaneous nest failure caused by haying dramatically decreased the overall incidence of EPP by increasing the occurrence of social monogamy and, apparently, the ability of polygynous males to maintain paternity in their own nests. Despite increased social and genetic monogamy, these haying-mediated changes in mating systems resulted in greater than twofold increase in the opportunity for sexual selection. This effect arose, in part, from a 30% increase in the variance associated with within-pair fertilization success, relative to the unharvested field. This effect was caused by a notable increase (+110%) in variance associated with the quality of social mates following simultaneous nest failure. Because up to 40% of regional habitat is harvested by early June, these data may demonstrate a strong population-level effect on mating systems, sexual selection, and consequently, evolutionary processes.
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Perlut, N., A. Strong, T. M. Donovan, and N. Buckley. 2006. Grassland songbirds in a dynamic management landscape: behavioral responses and management strategies. Ecological Applications 16:2235-2247.
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December 2006
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Perlut, N. G., A. M. Strong, T. M. Donovan, and N. J. Buckley. 2008. Regional population viability of grassland songbirds: effects of agricultural management. Biological Conservation 141:3139-3151.
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December 2008
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Although population declines of grassland songbirds in North America and Europe are well-documented, the effect of local processes on regional population persistence is unclear. To assess population viability of grassland songbirds at a regional scale (not, vert, similar150,000 ha), we quantified Savannah Sparrow Passerculus sandwichensis and Bobolink Dolichonyx oryzivorus annual productivity, adult apparent survival, habitat selection, and density in the four most (regionally) common grassland treatments. We applied these data to a female-based, stochastic, pre-breeding population model to examine whether current grassland management practices can sustain viable populations of breeding songbirds. Additionally, we evaluated six conservation strategies to determine which would most effectively increase population trends. Given baseline conditions, over 10 years, simulations showed a slightly declining or stable Savannah Sparrow population (mean bootstrap λ = 0.99; 95% CI = 1.00–0.989) and severely declining Bobolink population (mean bootstrap λ = 0.75; 95% CI = 0.753–0.747). Savannah Sparrow populations were sensitive to increases in all demographic parameters, particularly adult survival. However for Bobolinks, increasing adult apparent survival, juvenile apparent survival, or preference by changing habitat selection cues for late-hayed fields (highest quality) only slightly decreased the rate of decline. For both species, increasing the amount of high-quality habitat (late- and middle-hayed) marginally slowed population declines; increasing the amount of low-quality habitat (early-hayed and grazed) marginally increased population declines. Both species were most sensitive to low productivity and survival on early-hayed fields, despite the fact that this habitat comprised only 18% of the landscape. Management plans for all agricultural regions should increase quality on both low- and high-quality fields by balancing habitat needs, nesting phenology, and species’ response to management.
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Perlut, N. G., A. M. Strong, T. M. Donovan, and N. J. Buckley. 2008. Grassland songbird survival and recruitment in heterogeneous agricultural landscapes: implications for source-sink demography. Ecology 89:1941-1952.
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July 2008
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Population growth and decline are particularly sensitive to changes in three key life-history parameters: annual productivity, juvenile survival, and adult survival. However, for many species these parameters remain unknown. For example, although grassland songbirds are imperiled throughout North America, for this guild, only a small number of studies have assessed these parameters. From 2002 to 2006, in the agricultural landscape of the Champlain Valley of Vermont and New York, USA, we studied Savannah Sparrow (Passerculus sandwichensis) and Bobolink (Dolichonyx oryzivorus) demography on four grassland treatments: (1) early-hayed fields cut before 11 June and again in early- to mid-July; (2) middle-hayed fields cut once between 21 June and 10 July; (3) late-hayed fields cut after 1 August; and (4) rotationally grazed pastures. We assessed whether these treatments affected adult apparent survival (phi) and recruitment (f), how sensitive these parameters were to the presence of nonbreeders and local dispersal, and the populations' ability to persist in these four habitats. On average, birds using late-hayed fields had >25% higher apparent survival than those on the more intensively managed early-hayed, middle-hayed, and grazed fields. Overall male phi was 35% higher than female phi, and Savannah Sparrow phi was 44% higher than Bobolink phi. Across all analyses and treatments, apparent survival estimates were 0.58–0.85 for male and 0.48–0.71 for female Savannah Sparrows, and 0.52–0.70 for male and 0.19–0.55 for female Bobolinks. For males of both species, potential nonbreeders decreased the precision of and lowered apparent survival estimates by 25%; female estimates showed little variation with the inclusion of nonbreeders. Inclusion of local dispersal observations increased apparent survival estimates and, in many cases, increased precision, though the effect was stronger for Savannah Sparrows than for Bobolinks, and also stronger for males than for females. High Savannah Sparrow apparent survival rates resulted in stable or near stable populations (λ ≈ 1), particularly in late-hayed and grazed fields, while low Bobolink apparent survival rates resulted in strongly declining populations (λ < 1) in all treatments.
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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.
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June 2020
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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.
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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
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September 2020
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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.
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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.
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March 2020
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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.
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Parrish, D. L., and F. J. Margraf. 1994. Spatial and temporal patterns of food use by white perch and yellow perch in Lake Erie. Journal of Freshwater Ecology 9(1):29-35.
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September 1994
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Parrish, D. L., R. J. Behnke, S. R. Gephard, S. D. McCormick, and G. H. Reeves. 1998. Why aren't there more Atlantic salmon (Salmo salar)? Canadian Journal of Fisheries and Aquatic Sciences 55 (Supple. 1):281-287.
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December 1998
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Parrish, D. L., M. E. Mather, and R. A. Stein. 1995. Problem-solving research for management: a perspective. Fisheries 20(10):6-12.
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October 1995
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Parrish, D. L., E. J. Hawes, and K. G. Whalen. 2004. Winter growth and survival of juvenile Atlantic salmon in experimental raceways. Canadian Journal of Fisheries and Aquatic Sciences 61: 2350-2357.
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February 2005
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Parrish, D. L., B. Vondracek, and W. J. Eckmayer. 1994. Accuracy and precision of daily age estimates of walleye from Ohio hatcheries and Lake Erie. Transactions of the American Fisheries Society 123:601-605.
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July 1994
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Parker Stetter, S. L., L. G. Rudstam, J. L. Stritzel Thomson, D. L. Parrish, and P. J. Sullivan. 2006. Hydroacoustic separation of rainbow smelt (Osmerus mordax) age groups in Lake Champlain. Fisheries Research 82:176-185.
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December 2006
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Parker Stetter, S. L., J. L. Stritzel Thomson, L. G. Rudstam, D. L. Parrish, and P. J. Sullivan. 2007. Analysis of cannibalism in Lake Champlain. Transactions of the American Fisheries Society 136:227-237.
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February 2007
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Overman, N. C., and D. L. Parrish. 2001. Stable isotope composition of walleye: 15N accumulation with age and area-specific differences in 13C. Canadian Journal of Fisheries and Aquatic Sciences 58: 1253-1260.
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June 2001
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Noa, L., D. H. Hirth, T. M. Donovan, and D. Cimprich. 2007. Demographic differences of black-capped vireos in two habitat types in central Texas. Journal of Wildlife Management 71:1042-1049.
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June 2007
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To understand the effects of habitat selection, we analyzed differences in abundance, age structure, and nesting success of black-capped vireos (Vireo atricapilla) in 2 early successional habitat types found on Fort Hood, a 87,890-ha Military Reservation in central Texas, USA. These habitats were 1) large areas of continuously shrubby vegetation (both natural and mechanically made), referred to as shrubland habitat, and 2) anthropogenically created small patches of shrubby vegetation centered on one or several large trees, known locally as donut habitat. The objectives of our study were to determine whether there were differences in abundance, age structure, and daily nest survival in these 2 habitat types and to determine whether donut habitat is high- or low-quality habitat. Donut habitat had a lower abundance of vireos (half as many as shrubland/point count) and a higher percentage of second-year males, suggesting donut habitat was lower-quality habitat than shrubland. Analyses of daily nest survival indicated that habitat, nest height, and year were all important variables. Nests initiated in 2004, located in shrubland habitats, and higher from the ground were more likely to succeed. Our study provided evidence that habitat is a limiting factor for this federally endangered species. Because habitat is limiting, wildlife biologists at Fort Hood should focus on managing higher quality, contiguous shrubland habitat. Wildlife biologists should also continue to monitor areas of donut habitat to determine whether they represent potential population sinks.
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Nislow, K. H., C. L. Folt, and D. L. Parrish. 2000. A spatially-explicit bioenergetic analysis of habitat quality for age-0 Atlantic salmon. Transactions of the American Fisheries Society 129:1067-1081.
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January 2000
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Nislow, K. H., C. L. Folt, and D. L. Parrish. 1999. Favorable foraging locations for young Atlantic salmon: application to the restoration of populations and habitats. Ecological Applications 9:1085-1099.
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August 1999
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Murdoch, J., H. Davie, M. Galbadrah, T. Donovan, and R. Reading. 2013. Do Siberian marmots influence toad-headed agama occupancy? Examining the influence of marmot colonies and three steppe habitats in Mongolia. Journal of Arid Environments 92:76-80.
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January 2013
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Mitro, M. G., and D. L. Parrish. 1997. Temporal and spatial abundances of larval walleyes in two tributaries of Lake Champlain. Transactions of the American Fisheries Society 126:273-287.
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March 1997
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Mitchell, B. R., and T. M. Donovan. Mob mentality: the effect of a mobbing tape on detections during point count surveys. Open Ornithology Journal 1:8-19.
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Abstract
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July 2008
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The probability of detecting an individual or species is an important parameter in studies using mark-recapture and occupancy models to estimate population sizes and occurrence. Because low detection probabilities result in biased estimators and decreased precision, biologists seek methods that maximize detection probability. We evaluated whether we could increase detections of bird species by playing a tape of Black-capped Chickadee (Poecile atricapillus) mobbing calls during point counts. We conducted trios of 10-minute counts (two pre-playback and a playback) at 684 stations throughout Vermont, in forested, agricultural/grassland, and developed habitats. For each of 73 species detected during the surveys, we used occupancy modeling and information-theoretic model selection and averaging methods to evaluate whether detection probabilities varied due to playback or habitat type. Models containing a playback effect accounted for over 90% of the Akaike weights for 41 species. With 15 of these species, habitat effects also accounted for over 90% of the Akaike weights. The playback increased estimated detection probability in all habitats for 14 species, decreased estimated detection probability for 20 species, and had an estimated effect that varied by habitat for 7 species (many species with habitat effects simply had differing magnitudes of the effect dependent on habitat). Smaller resident species were detected more often during tape playbacks, but responses were highly variable for most species and the responses did not appear to follow a taxonomic pattern. We encourage researchers to evaluate their list of target species carefully before deciding to use mobbing playbacks to enhance response rates; in many situations mobbing tapes will not enhance detections and may complicate the interpretation of model parameters.
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McKenny, H., W. S. Keeton, and T. M. Donovan. 2006. The effects of structure-based forestry on red-backed salamander (Plethodon cinereus) populations in northern hardwood forests. Forest Ecology and Management 230:186-196.
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April 2006
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Mather, M. E., D. L. Parrish. C. A. Campbell, J. R. McMenemy, and J. M. Smith. 2008. Summer temperature variation and implications for juvenile Atlantic salmon. Hydrobiologia 603:183-196
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March 2008
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Mather, M. E., D. L. Parrish, and J. M. Dettmers. 2012. Now That You Have Great Results, Where Should You Submit Your Manuscript? In Scientific Communication for Natural Resources Professionals. Editors C. Jennings,T. Lauer, B. Vondracek. PAGES 121-133. American Fisheries Society, Bethesda, MD.
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August 2012
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Mather, M. E., D. L. Parrish, and J. M. Dettmers. 2009. The extensive and complex landscape of fish-related journals authors’ response. Fisheries 34:144-145.
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March 2009
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Mather, M. E., D. L. Parrish, R. A. Stein, and R. M. Muth. 1995. Management issues and their relative priority with state fisheries agencies. Fisheries 20(10):14-21.
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October 1997
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Mather, M. E., D. L. Parrish, J. M. Dettmers. 2008. Mapping the changing landscape of fish-related journals: setting a course for successful communication of scientific information. Fisheries 33(9): 444-453.
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September 2008
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Mather, M. E., D. L. Parrish, C. L. Folt, and R. M. DeGraaf. 1998. Integrating across scales: effectively applying science for the successful conservation of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 55 (Supple. 1):1-8.
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December 1998
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Marschall, E.A., M.E. Mather, D.L. Parrish, G. Allison, and J. McMenemy. Migration delays caused by anthropogenic barriers: modeling dams, temperature, and success of migrating salmon smolts. Ecological Applications 21: 3014-3031.
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December 2011
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Marschall, E.A., D.C. Glover, M.E. Mather, and D.L. Parrish. 2021. Modeling larval American Shad recruitment in a large river. North American Journal of Fisheries Management 41: 939-954. https://doi.org/10.1002/nafm.10460
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Abstract
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May 2020
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We used an bioenergetics-based modeling approach to track American Shad Alosa sapidissima offspring within a template of spatial and temporal habitat conditions defined by a combination of abiotic conditions and prey availability models. We simulated spawning at each river kilometer (RKM 138-280) on each day (1 April-31 August) to understand how spawning date and location drive larval recruitment differentially across years and decades. For both temperature and flow, inter-annual variation was large in comparison to interdecadal differences. Variation in simulated recruitment was best explained by a combination of season-specific temperature and location in along the course of the river. Greatest potential recruitment occurred in years in which June temperatures were relatively high. In years when June and July were warmer than average, maximum recruitment resulted from spawning taking place at the upstream portion of the modeled reach. Model scenarios (stationary or passive-drift larvae and dams or no dams) had predictable effects. When dams were present, but offspring were stationary, the area directly above the dams resulted in poor recruitment, due to the habitat being inappropriate for eggs. When offspring exhibited passive drift, they traveled far downstream. If dams were present, they frequently ended their movement at the dams. When larvae moved downstream but their movement was not limited by dams, spatial differences in expected recruitment relative to spawning sites were reduced. Our results demonstrate the importance of spatiotemporal environmental heterogeneity for producing positive recruitment over the longterm. In addition, our results suggest the importance of successful passage of spawners to historical spawning sites upstream of Vernon Dam in the Connecticut River, especially as conditions shift with climate change.
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M. McClure, M.A. Haltuch, E. Willis-Norton, D.D. Huff, E.L. Hazen, L.G. Crozier, M.G. Jacox, M.W. Nelson, K.S. Andrews, L.A.K. Barnett, A.M. Berger, S. Beyer, J. Bizzarro, D. Boughton, J.M. Cope, M. Carr, H. Dewar, E. Dick, E. Dorval, J. Dunham, V. Gertseva, C. Greene, R.G. Gustafson, O.S. Hamel, C.J. Harvey, M.J. Henderson, C.E. Jordan, I.C. Kaplan, S.T. Lindley, N.J. Mantua, S.E. Matson, M.H. Monk, P. Moyle, C. Nicol, J. Pohl, R.R. Rykaczewski, J.F. Samhouri, S. Sogard, N. Tolimieri, J. Wallace, C. Wetzel, S.J. Bograd. 2023. Vulnerability to climate change of managed stocks in the California Curret large marine ecosystem. Frontiers in Marine Science. 10, 1103767.
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Abstract
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February 2023
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Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. This study applies the NOAA Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information will inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially important to protect or restore.
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Long, R. A., T. M. Donovan, P. MacKay, W. J. Zielinski, and J. S. Buzas. 2007. Effectiveness of scat detection dogs for detecting forest carnivores. Journal of Wildlife Management 71:2007-2017.
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Abstract
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August 2007
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We assessed the detection and accuracy rates of detection dogs trained to locate scats from free-ranging black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus). During the summers of 2003–2004, 5 detection teams located 1,565 scats (747 putative black bear, 665 putative fisher, and 153 putative bobcat) at 168 survey sites throughout Vermont, USA. Of 347 scats genetically analyzed for species identification, 179 (51.6%) yielded a positive identification, 131 (37.8%) failed to yield DNA information, and 37 (10.7%) yielded DNA but provided no species confirmation. For 70 survey sites where confirmation of a putative target species' scat was not possible, we assessed the probability that ≥1 of the scats collected at the site was deposited by the target species (probability of correct identification; PID). Based on species confirmations or PID values, we detected bears at 57.1% (96) of sites, fishers at 61.3% (103) of sites, and bobcats at 12.5% (21) of sites. We estimated that the mean probability of detecting the target species (when present) during a single visit to a site was 0.86 for black bears, 0.95 for fishers, and 0.40 for bobcats. The probability of detecting black bears was largely unaffected by site- or visit-specific covariates, but the probability of detecting fishers varied by detection team. We found little or no effect of topographic ruggedness, vegetation density, or local weather (e.g., temp, humidity) on detection probability for fishers or black bears (data were insufficient for bobcat analyses). Detection dogs were highly effective at locating scats from forest carnivores and provided an efficient and accurate method for collecting detection–nondetection data on multiple species.
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Long, R. A., T. M. Donovan, P. MacKay, W. J. Zielinski, and J. S. Buzas. 2007. Comparing scat detection dogs, cameras, and hair snares for surveying carnivores. Journal of Wildlife Management 71:2018-2025.
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Abstract
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August 2007
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Carnivores typically require large areas of habitat, exist at low natural densities, and exhibit elusive behavior—characteristics that render them difficult to study. Noninvasive survey methods increasingly provide means to collect extensive data on carnivore occupancy, distribution, and abundance. During the summers of 2003–2004, we compared the abilities of scat detection dogs, remote cameras, and hair snares to detect black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus) at 168 sites throughout Vermont. All 3 methods detected black bears; neither fishers nor bobcats were detected by hair snares. Scat detection dogs yielded the highest raw detection rate and probability of detection (given presence) for each of the target species, as well as the greatest number of unique detections (i.e., occasions when only one method detected the target species). We estimated that the mean probability of detecting the target species during a single visit to a site with a detection dog was 0.87 for black bears, 0.84 for fishers, and 0.27 for bobcats. Although the cost of surveying with detection dogs was higher than that of remote cameras or hair snares, the efficiency of this method rendered it the most cost-effective survey method.
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Long, R. A., T. M. Donovan, P. MacKay, J. S. Buzas, and W. J. Zielinski. Predicting carnivore occurrence using data collected with multiple, noninvasive methods.Landscape Ecology 26:327-340.
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Abstract
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October 2010
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Terrestrial carnivores typically require large areas of habitat and exist at low densities. As “top level” consumers, carnivores affect the biological structure and composition of ecosystems. We employed multiple, noninvasive survey methods—scat detection dogs, remote cameras, and hair snares—to collect detection-nondetection data for American black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus) throughout Vermont. We analyzed these data using an occupancy modeling approach that explicitly incorporated detectability as well as habitat and landscape variables. Model results were then used to predict occurrence for each species across the study area. Receiver operating characteristic (ROC) analyses of our models for species with high detectability suggest that the results of such surveys and modeling efforts may be useful for those striving to conserve or manage species at the regional or landscape scale. The noninvasive methods used for this project enabled us to collect important detection-nondetection information from low density, secretive, and wide-ranging species, without the need to capture or interact with the study subjects directly.
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Katz, J., S. Hafner, and T. Donovan. 2016. Tools for automated acoustic monitoring within the R package monitoR. Bioacoustics. DOI:10.1080/09524622.2016.1138415
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January 2016
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The R package monitoR contains tools for managing an acoustic-monitoring program including survey metadata, template creation and manipulation, automated detection and results management. These tools are scalable for use with small projects as well as larger long-term projects and those with expansive spatial extents. Here, we describe typical workflow when using the tools in monitoR. Typical workflow utilizes a generic sequence of functions, with the option for either binary point matching or spectrogram cross-correlation detectors.
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Katz, J., S. Hafner, and T. Donovan. 2016. Assessment of Error Rates in Acoustic Monitoring with the R package monitoR. Bioacoustics. DOI:10.1080/09524622.2015.1133320
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Abstract
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January 2016
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Detecting population-scale reactions to climate change and land-use change may require monitoring many sites for many years, a process that is suited for an automated system. We developed and tested monitoR, an R package for long-term, multi-taxa acoustic monitoring programs. We tested monitoR with two northeastern songbird species: black-throated green warbler (Setophaga virens) and ovenbird (Seiurus aurocapilla). We compared detection results from monitoR in 52 10-minute surveys recorded at 10 sites in Vermont and New York, USA to a subset of songs identified by a human that were of a single song type and had visually identifiable spectrograms (e.g. a signal:noise ratio of at least 10 dB: 166 out of 439 total songs for black-throated green warbler, 502 out of 990 total songs for ovenbird). monitoR’s automated detection process uses a ‘score cutoff’, which is the minimum match needed for an unknown event to be considered a detection and results in a true positive, true negative, false positive or false negative detection. At the chosen score cut-offs, monitoR correctly identified presence for black-throated green warbler and ovenbird in 64% and 72% of the 52 surveys using binary point matching, respectively, and 73% and 72% of the 52 surveys using spectrogram cross-correlation, respectively. Of individual songs, 72% of black-throated green warbler songs and 62% of ovenbird songs were identified by binary point matching. Spectrogram cross-correlation identified 83% of black-throated green warbler songs and 66% of ovenbird songs. False positive rates were for song event detection.
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Katz, J. and T. M. Donovan. 2017. AMModels: Adaptive Management Model Manager. R package version 0.1.2.
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February 2016
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Jackson, J. R., T. J. Kwak, and D. L. Parrish. 2009. Members of the AFS Education Section response. Fisheries 34:85-86.
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February 2009
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Izzo, L.K., D.L. Parrish, and G.B. Zydlewski. 2021. Multi-run migratory behavior of adult male lake sturgeon in a short river. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2021.06.012
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Abstract
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July 2021
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Lake sturgeon (<i>Acipenser fulvescens</i>) can migrate long distances to spawn, but many populations currently spawn in systems where the length of accessible riverine migratory habitat has been greatly reduced by dam construction. With the increased prevalence of shortened rivers, focusing on migratory dynamics in short rivers (<30 km) is beneficial to understanding the migratory needs of lake sturgeon populations. Here we document male lake sturgeon movements during the spawning period in the Winooski River, Vermont, USA; a river with only 17 km to the first natural upstream barrier. Male lake sturgeon were acoustically tagged (n = 25, 1215–1470 mm TL) and tracked using five to nine stationary receivers from 2017 to 2019. River discharge, temperature, the lagged effect of temperature (3-day), and time of day were significant factors describing upstream movements of tagged fish. Migrating male lake sturgeon (n = 10 in 2017, n = 18 in 2018, and n = 17 in 2019) displayed general movement patterns during the spawning period that included a single run upstream to the spawning site (60%), upstream and downstream movements throughout the river during the season (20%), or multiple runs made up the entire length of the spawning tributary to the spawning site (20%). No multi-run males were observed during 2018 when discharge was less flashy (i.e., fewer steep increases and declines in discharge) than in 2017 and 2019. These results suggest that the prevalence of multi-run spawning behavior of male lake sturgeon is related to flow conditions.
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Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and R. Koenigs. 2021. Second fin ray shows promise for estimating ages of juvenile but not adult Lake Sturgeon. North American Journal of Fisheries Management 41: 217-228. doi: 10.1002/nafm.10561.
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Abstract
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February 2021
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The first marginal pectoral fin ray (fin spine) is the most common structure used for estimating the age of sturgeons, including listed Lake Sturgeon <i>Acipenser fulvescens </i>populations. However, conflicting results on the effects of fin spine removal have made some managers hesitant about the practice. We investigate if the second pectoral fin ray, which can be removed in a less invasive procedure, could be used for estimating ages of Lake Sturgeon. Ages estimated from fin spine and second fin ray samples were compared for 53 wild (470 to 1981 mm total length, TL) and 16 stocked, known-age (ages 8 – 18) Lake Sturgeon. Mean coefficient of variation (CV) for all samples was 12.4% for the fin spine and 17.5% for the second fin ray. In known-age fish, 17% of estimated ages for the fin spine and the second fin ray matched true age. For the remaining estimates, the difference between the second fin ray and true age was greater than the difference between the fin spine and true age (<i>P </i>< 0.05, Wilcoxon signed rank test). In juvenile fish (n = 24), 75% of ages estimated from fin spines and second fin rays were within ± 4 annuli, which was similar to differences in reader agreement for the same fin spine. Age estimates for adult Lake Sturgeon (n = 45) were less when using the second fin ray relative to the fin spine (up to -34 years). Additionally, poor annulus clarity was observed in > 70% of the second fin rays sampled from adult fish. Our results suggest that the second fin ray does not provide reliable age estimates for adult Lake Sturgeon but may have some utility for estimating age of juvenile Lake Sturgeon. Additional research with a larger sample size would be required to provide more conclusive results.
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Irwin, E. R., F. J. Rahel, D. L. Parrish, D. H. Wahl. 1998. Enhancing professionalism: awards and grants for student members of the American Fisheries Society. Fisheries 23(8):20-23.
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January 1998
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Hyrcik, A.E., P.W. Simonin, L.G. Rudstam, D.L. Parrish, B. Pientka, and T.B. Michuc. 2015. Mysis zooplanktivory in Lake Champlain: a bioenergetics analysis. Journal of Great Lakes Research 41: 492-501. doi:10.1016/j.jglr.2015.03.011
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Abstract
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Publisher Website
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April 2015
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Mysid shrimp are important as both predators on zooplankton and as prey for a variety of fish species across most of the Laurentian Great Lakes. In Lake Champlain, where little is known about mysids, this may also be true. We evaluated the role of Mysis diluviana as a planktivore in Lake Champlain using hydroacoustics, gut content analysis, stable isotopes, cohort analysis, and bioenergetics models to estimate Mysis density, diets, growth rates, and prey consumption rates. Density of Mysis in the water column of the deeper Main Lake was lower in July-August of 2008-2011 (38, 38, 21, and 74 Mysis /m2, respectively) than historical values from the 1970s. Mysis selectively foraged for cladocerans, but also consumed cyclopoid and calanoid copepods in 2011. Stable isotope data suggest a mostly carnivorous diet, although agreement between isotope mixing models and observed diets varied. Cohort analyses revealed growth rates ranging from 2.7 mm/month in late spring to 1.3 mm/month in late summer. In contrast to the offshore areas of Lake Ontario and Lake Huron, zooplankton consumption by the Mysis population was low relative to zooplankton density and production indicating that Mysis are not currently a major zooplanktivore in Lake Champlain.
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Howell, C. A., S. C. Latta, T. M. Donovan, P. A. Porneluzi, and J. Faaborg. 2000. Landscape effects mediate breeding bird abundance in midwestern forests. Landscape Ecology 15:547-563.
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January 2001
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Howe, E., J. E. Marsden, T. M. Donovan, and R. Lamberson. 2012. A life cycle approach to modeling sea lamprey population dynamics in the Lake Champlain basin to evaluate alternative control strategies. Journal of Great Lakes Research 38:101-114.
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Abstract
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Publisher Website
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December 2011
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Sea lamprey (Petromyzon marinus) is a nuisance species in the Laurentian Great Lakes and Lake Champlain that has devastated native fi sh populations and hampered sport fi sheries development. We developed a modified stage-based life history matrix for sea lamprey to analyze the effects of various management efforts to suppress sea lamprey population growth in Lake Champlain. These efforts targeted different life stages of the sea lamprey life cycle. A beta distribution was used to distribute stochastic larval populations among
twenty sea lamprey-bearing tributaries and five deltas to Lake Champlain, from which sea lamprey that survive through larval metamorphosis were then pooled into a lake-wide parasitic-phase population. Parasitic-phase survival to the spawning stage was evaluated based on proximity to the natal tributary and on the size of the resident larval population in each tributary. Potential control strategies were modeled at egg to emergence, larval, and spawning stages to reduce vital rates at each stage, with the goal of suppressing parasitic-phase production. Simulations indicate that control of the larval stage was essential to achieving this goal,
and with supplemental effort to reduce the vital rates at early life stages and at the spawning stage, the parasitic-phase population can be further suppressed. Sensitivity simulations indicate that the life history model was sensitive to egg deposition rate, abundance of parasitic-phase sea lamprey from unknown, uncontrolled sources, and the method in which parasitic-phase sea lamprey select tributaries for spawning. Results from this model can guide management agencies to optimize future management programs.
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Henderson, M.J., Loomis, C., Michel, C., Smith, J., Iglesias, I., Lehman, B., Huff, D. Estimates of predator densities using mobile DIDSON surveys: implications for survival of Central Valley Chinook salmon. North American Journal of Fisheries Management 43: 628-645.
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Abstract
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June 2023
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The Sacramento-San Joaquin Delta (the Delta) is one of the most invaded estuaries in the world, and non-native predators may be a major factor in the observed decline of Central Valley Chinook salmon over recent decades. In order for managers to take actions that might reduce predation related mortality for these ecologically, culturally, and economically valuable salmon, it’s important to understand the factors influencing the distribution and abundance of piscivores in the Delta. In this study, we use a multibeam imaging sonar (i.e., DIDSON) to conduct mobile surveys and quantify the abundances of piscivores in the Delta. We then used these data to identify the habitat features that are correlated with the abundance of piscivores. Prior to conducting the surveys, we used DIDSON data from captured fish to develop an algorithm to distinguish piscivores from non-piscivores with high confidence (98% accuracy). Results from the surveys indicated that predator abundances were most associated with areas of increased submerged aquatic vegetation (SAV) patches, sites that are straighter, and sites with increased bathymetric complexity. When applied to the entire survey area, this model was successfully able to predict known areas of high predator densities. These results indicate that one approach to reduce predator densities along these migration corridors, and improve juvenile salmon outmigration survival, is to reduce the extent of invasive SAV. Because experimental predator removals have been largely ineffective in the Delta, efforts to manipulate habitat to discourage non-native predator recruitment and favor native species recruitment may be more effective.
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Hawes, E. J., and D. L. Parrish. 2003. Factors affecting the expansion of white perch in Lake Champlain. Journal of Great Lakes Research 29:268-279.
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April 2003
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Hartman, K. J., B. Vondracek, D. L. Parrish, and K. M. Muth. 1992. Diets of emerald and spottail shiner and potential interactions with other western Lake Erie prey fishes. Journal of Great Lakes Research 18:43-50.
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January 1992
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Hall, C. A. S., P. W. Jones, T. M. Donovan, and J. P. Gibbs. 2000. Neoclassical economics and its effects on wildlife and wildlife management. The Wildlife Society Bulletin 28:16-25.
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January 2001
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Gries, G., K. G. Whalen, F. Juanes, and D. L. Parrish. 1997. Nocturnal activity of juvenile Atlantic salmon in late summer: evidence of diel activity partitioning. Canadian Journal of Fisheries and Aquatic Sciences 54:1408-1413.
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July 1997
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Greenwald, K., A. Stedman, D. Mifsud, M. Stapleton, K. Larson, I. Chellman, D. L. Parrish, and C. W. Kilpatrick. 2020. Phylogeographic analysis of Mudpuppies (Necturus maculosus). Journal of Herpetology 54: 78-86. doi: 10.1670/19-070
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Abstract
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March 2020
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The geology of the Pleistocene, and particularly the Last Glacial Maximum approximately 26.5 ka, is a critical driver of species’ present-day distributions and levels of genetic diversity in northern regions. Using mitochondrial DNA sequence data, we tested several predictions relating to the postglacial recolonization of the northern United States and southern Canada by Mudpuppies (Necturus maculosus). Our analyses revealed a significant split between western and eastern lineages, with the divide corresponding to the location of the Mississippi River. Our data support the presence of one or more Mississippian glacial refugia, with subsequent expansion and diversification of a western clade into the upper Midwest, and an eastern cluster into the eastern Great Lakes and New England. As predicted in cases of postglacial colonization, each of these clades contains a single widespread and common haplotype, along with numerous low-frequency, closely related haplotypes. Given recent conservation concerns about amphibians in general, and Mudpuppies specifically, we discuss our results in light of species conservation. Knowledge of a species’ genetic diversity allows for informed management and facilitates decisions that preserve local adaptation and evolutionary potential.
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Futia, M.H., Binder, T.R., Henderson, M.J., J.E. Marsden. Modelling broad-scale occupancy of fishes using acoustic telemetry: a model comparison framework applied to lake trout. Submitted to Animal Biotelemetry.
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Abstract
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September 2024
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Acoustic telemetry is a common tool used in fisheries management to estimate fish space use (i.e., occupancy) from a local habitat scale to entire systems. Numerous analytical models have been developed to estimate different aspects of fish movement from telemetry datasets, yet evaluations of model performance and comparisons among models are limited. Here, we develop a framework to evaluate model estimates of regional occupancy in large and fragmented systems using an acoustic receiver array in Lake Champlain. We simulated the tracks of 100 acoustically tagged fish using a random walk function and created detection events based on receiver positions and distance-based detection probability. Regional occupancy for the simulated data was estimated by six movement models that ranged in analytical complexity, and results were compared to the true distributions for each simulated track to evaluate model error. The six movement models included (1) a basic residency index using detections alone, (2) a residency index using last-observation-carried-forward, (3) a centers of activity model, (4) linear and non-linear interpolations (i.e., least-cost paths), and (5 and 6) two dynamic Brownian bridge movement models generated using separate packages in R. We developed a model selection process to compare model performance and select the optimal analysis based on simulation error. This process showed significant differences in model performance among the six movement models based on model error. Overall, the model generating least-cost paths using linear and non-linear interpolations consistently provided the most accurate regional occupancy estimates. Based on these simulation results, we applied this model to a case study that evaluated patterns in the regional distribution of stocked lake trout (<i>Salvelinus namaycush</i>) in Lake Champlain, which demonstrated distinct regional occupancy of two stocked lake trout groups. These results demonstrate potential for substantial variability in interpretation of acoustic telemetry data for describing regional fish distribution dependent on the analytical method used.
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Farrell, L. E. D M. Levy, T. Donovan, R. Mickey, A. Howard, J. Vashon, M. Freeman, K. Royar, and C. W. Kilpatrick. 2018. Landscape connectivity for bobcat (Lynx rufus) and lynx (Lynx canadensis) in the northeastern Northeastern United States. PLoS ONE 13(3): e0194243. https://doi.org/10.1371/journal.pone.0194243
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Abstract
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Publisher Website
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March 2018
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Landscape connectivity is integral to the persistence of metapopulations of wide ranging carnivores and other terrestrial species. The objectives of this research were to investigate the landscape characteristics essential to use of areas by lynx and bobcats in northern New England, map a habitat availability model for each species, and explore onnectivity across areas of the region likely to experience future development pressure. A Mahalanobis distance
analysis was conducted on location data collected between 2005 and 2010 from 16 bobcats in western Vermont and 31 lynx in northern Maine to determine which variables were most consistent across all locations for each species using three scales based on average 1) local (15 minute) movement, 2) linear distance between daily locations, and 3) female home range size. The bobcat model providing the widest separation between used locations and random study area locations suggests that they cue into landscape features such as edge, availability of cover, and evelopment density at different scales. The lynx model with the widest separation between random and used locations contained five variables including natural habitat, cover, and levation—all at different scales. Shrub scrub habitat—where lynx’s preferred prey is most abundant—was represented at the daily distance moved scale. Cross validation indicated that outliers had little effect on models for either species. A habitat suitability value was calculated for each 30 m2 pixel across Vermont, New Hampshire, and Maine for each species and used to map connectivity between conserved lands within selected areas across the region. Projections of future landscape change illustrated potential impacts of anthropogenic development on areas lynx and bobcat
may use, and indicated where connectivity for bobcats and lynx may be lost. These projections provided a guide for conservation of landscape permeability for lynx, bobcat,
and species relying on similar habitats in the region.
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Fabrizio, M.C., Henderson, M.J., Rose, K., Petitgas, P. Editorial: Habitat and Distribution Models of Marine and Estuarine Species: Advances for a Sustainable Future. Submitted to Frontiers in Marine Science.
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Abstract
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October 2022
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The physical and biological characterization of suitable habitats and species-specific models to estimate the extent of available suitable habitats are valuable for conservation and fisheries management. As exploited species and habitats face challenges from anthropogenic influences, such as fishing and climate change, the identification and protection of habitats becomes increasingly important. Most of the papers within this special topic issue used some form of species distribution model (SDM) to identify habitats used by fishes (Asch et al. 2022, Crear et al. 2020, Fabrizio et al. 2021, Freidland et al. 2021, Zydlewski et al. 2021), marine mammals (Astarloa et al. 2021), nearshore invertebrates (Cristiani et al. 2021, Behan et al. 2021), or deep-sea communities (Bowden et al. 2021, Saunders et al. 2021). A few papers focused on developing methods to better describe habitats (Griffin et al. 2021, Henderson et al. 2020, Cecino et al. 2021), while others investigated model performance and incorporation of new statistical methods to improve model accuracy (Asch et al. 2022, Behan et al. 2021, Bowden et al. 2021). Below we provide a synthesis of these papers and examine data sources used for analyses, statistical methods, stationarity and model performance, connectivity, and management implications; we conclude with a consideration of opportunities for advancing this field of study.
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Espenshade, J., J. D. Murdoch, T. M. Donovan, R. E. Manning, and C. A. Bettigole. 2018. Public acceptability of development in the Northern Forest of Vermont, USA – the influence of wildlife information, recreation involvement, and demographic characteristics. PLoS ONE 13(12):e0203515.
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Abstract
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Publisher Website
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December 2018
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Increasing development such as roads and houses will alter future landscapes and result in biological, social, and economic trade-offs. Managing development requires information on the public’s acceptability of development and understanding which factors shape acceptability. In this study, we examined three questions: 1) What is the public’s acceptability of development? 2) Is acceptability of development influenced by wildlife information? and 3) Is the maximum amount of acceptable development influenced by views about wildlife, involvement in outdoor recreation, and demographic factors? We conducted a visual-preference survey of 9,000 households in Vermont, USA that asked about acceptable levels of development, acceptability of wildlife, involvement in recreation, and individual and town demographics. The survey response rate was 44%. Maximum acceptable condition (MAC) for development was 41 houses/km2 and not meaningfully influenced by broader consequences of development on seven common wildlife species. MAC was influenced by views on individual species, including bear and coyote, but not by other species such as deer, fox, and bobcat. Respondents with a positive attitude toward bear favored less development, whereas the opposite relationship existed for coyote. Similarly, MAC was negatively influenced by involvement in birding and hunting, but not by other common recreational activities. Among demographic factors, respondents that were younger and not born in Vermont were more accepting of development. Population density also positively influenced development acceptability. Results provide measures of the public’s acceptability of development that can help guide decision-making about development, wildlife, and recreation management.
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Eisenhower, M. D., and D. L. Parrish. 2009. Double-crested cormorant and fish interactions in a shallow basin of Lake Champlain. Waterbirds 32:388-399.
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September 2009
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Duerr, A., D. E. Capen, and T. M. Donovan. 2007. Wildlife management increases breeding dispersal in double-crested cormorants. Journal of Wildlife Management 71:2565-2574.
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Abstract
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Publisher Website
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November 2007
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We studied breeding dispersal of double-crested cormorants {Phalacrocorax auritus) associated with management practices that suppressed their reproduction on Lake Champlain in the northeastern United States. We implemented an experiment on one colony by spraying corn oil on cormorant eggs in portions of the colony and leaving other portions untreated. Gulls (Larus spp.) consumed cormorant eggs during the oiling process, but we reduced and then eliminated predation levels after the first year of the study. We used mark-recapture techniques within the experimental framework to measure rates of breeding dispersal for cormorants from the experimental colony and an unmanaged colony in Lake Champlain. Egg oiling increased the movement rate to the unmanaged colony by 3% during the year with no egg predation by gulls. When gulls depredated cormorant eggs at high rates during egg oiling, movement to the unmanaged colony increased by 20%. When cormorants are managed to reduce population sizes, methods that limit dispersal away from the managed colony may be most effective. Such methods would mitigate effects to nontarget populations and allow for a greater portion of the metapopulation to be managed.
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Duerr, A., D. E. Capen, and T. M. Donovan. 2012. Energetic considerations for managing double-crested cormorants on Lake Champlain. Journal of Great Lakes Research 38:131-140.
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Abstract
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Publisher Website
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December 2011
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We studied foraging distribution, activity budgets, fi sh consumption, and energetics of double-crested cormorants (Phalacrocorax auritus) at two breeding colonies on Lake Champlain. Our objective was to determine
if fi sh consumption and distribution of predation changed with movements of cormorants associated with efforts to reduce numbers of cormorants on one of the colonies. Wildlife managers reduced populations of cormorants on Young Island, Vermont by oiling their eggs, which resulted in dispersal of breeding cormorants
35 km south to Four Brothers Islands, New York. We found that as cormorants shifted from Young Island to the colony on Four Brothers Islands, energy demands, foraging distribution, and total fi sh consumption increased. Birds on Four Brothers Islands foraged a greater distance from the colony compared to birds on Young Island. Additionally, consumption of yellow perch (Perca flavescens) shifted to rainbow smelt (Osmerus
mordax) when more birds bred on Four Brothers Islands. The dispersal of cormorants from Young Island to Four Brothers Islands reduced predation on yellow perch but increased overall fish consumption. Our estimates of fish consumption ranged from 322,000–425,000 kg of fi sh per year at Young Island to 899,000–1,086,000 kg of
fish per year at Four Brothers Islands. Results from this study demonstrate secondary impacts of management on Young Island to unmanaged areas.
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Driscoll, M. L., and T. M. Donovan. 2004. Landscape context moderates edge effects: Nesting success of Wood Thrushes in central New York. Conservation Biology 18:1330-1338.
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October 2004
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Driscoll, M. L., T. M. Donovan, R. Mickey, A. Howard, and K. Fleming. 2005. Determinants of Wood Thrush nesting success: a multi-scale, model selection approach. Journal of Wildlife Management 69:699-708.
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May 2004
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Donovan. T. M., C. Balantic, J. Katz, M. Massar, R. Knutson, K. Duh, P. W. Jones, K. Epstein, J. Lacasse-Roger, and J. Dias. 2021. Remote Ecological Monitoring with Smartphones and Tasker. Journal of Fish and Wildlife Management 12:163–173.
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Abstract
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Publisher Website
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June 2021
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Researchers have increasingly used autonomous monitoring units to record animal sounds, track phenology with timed photographs, and snap images when triggered by motion. We piloted the use of smartphones to monitor wildlife in the Riverside East Solar Energy Zone (California) and at Indiana Dunes National Park (Indiana). For both efforts, we established remote autonomous monitoring stations in which we housed an Android smartphone in a weather-proof box mounted to a pole and powered by solar panels. We connected each smartphone to a Google account, and the smartphone received its recording/photo schedule daily via a Google Calendar connection when in data transmission mode. Phones were automated by Tasker, an Android application for automating cell phone tasks. We describe a simple approach that could be adopted by others who wish to use nonproprietary methods of data collection and analysis.
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Donovan, T.M., and R. M. Mickey. 2019. Bayesian Statistics for Beginners. Oxford University Press, Oxford, UK.
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May 2019
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Donovan, T.M., M.D. Freeman, A. Howard, K. Royar, H. Abouelezz, and R. Mickey. 2011. Quantifying home range habitat requirements for bobcats (Lynx rufus) in Vermont. Biological Conservation 144:2799-2809.
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Abstract
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Publisher Website
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October 2011
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We demonstrate how home range and habitat use analysis can inform landscape-scale conservation planning for the bobcat, Lynx rufus, in Vermont USA. From 2005 to 2008, we outfitted fourteen bobcats with GPS collars that collected spatially explicit locations from individuals every 4 h for 3–4 months. Kernel home range techniques were used to estimate home range size and boundaries, and to quantify the utilization distribution (UD), which is a spatially explicit, topographic mapping of how different areas within the home range are used. We then used GIS methods to quantify both biotic (e.g. habitat types, stream density) and abiotic (e.g. slope) resources within each bobcat’s home range. Across bobcats, upper 20th UD percentiles (core areas) had 18% less agriculture, 42% less development, 26% more bobcat habitat (shrub, deciduous, coniferous forest, and wetland cover types), and 33% lower road density than lower UD percentiles (UD valleys). For each bobcat, we used Akaike’s Information Criterion (AIC) to evaluate and compare 24 alternative Resource Utilization Functions (hypotheses) that could explain the topology of the individual’s UD. A model-averaged population-level Resource Utilization Function suggested positive responses to shrub, deciduous, coniferous forest, and wetland cover types within 1 km of a location, and negative responses to roads and mixed forest cover types within 1 km of a location. Applying this model-averaged function to each pixel in the study area revealed habitat suitability for bobcats across the entire study area, with suitability scores ranging between −1.69 and 1.44, where higher values were assumed to represent higher quality habitat. The southern Champlain Valley, which contained ample wetland and shrub habitat, was a concentrated area of highly suitable habitat, while areas at higher elevation areas were less suitable. Female bobcat home ranges, on average, had an average habitat suitability score of near 0, indicating that home ranges consisted of both beneficial and detrimental habitat types. We discuss the application of habitat suitability mapping and home range requirements for bobcat conservation and landscape scale management.
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Donovan, T.M. and J. E Katz. 2018. AMModels: An R package for storing models, data, and metadata to facilitate adaptive management. PLoS ONE 13(2): e0188966. https://doi.org/10.1371/journal.pone.0188966
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Abstract
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Publisher Website
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January 2018
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Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an. RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and using knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date.
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Donovan, T., and J. Hines. 2007. Exercises in occupancy modeling and estimation. Electronic book.
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Publisher Website
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December 2007
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Donovan, T., J. Hines, and D. MacKenzie. 2024. occupancyTuts: Occupancy Modeling Tutorials with RPresence. Methods in Ecology and Evolution. 10.1111/2041-210X.14285
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Abstract
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Publisher Website
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January 2024
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Abstract<br><br>1. The occupancy modelling framework offers tremendous flexibility in estimating species abundance and distribution patterns while accounting for imperfect detection, and has seen rapid growth and adoption since its introduction at the beginning of the century.<br><br>2. At the same time, in an era of big data, there are increasing demands on developing quantitative skills and proficiency in young ecologists, many of whom lack the quantitative training needed to conduct research professionally.<br><br>3. We introduce <i>occupancyTuts</i>, an R package that features 28 <i>learnr </i>tutorials that teach the statistical underpinnings of several occupancy models. The tutorials include written content, instructional videos, R exercises, and quiz elements, covering a range of topics including statistical underpinnings, single- and dynamic-occupancy models, study design and several of the ‘spin-off’ models that extend the basic framework.<br><br>4. We plan for development of new tutorials that use <i>RPresence</i> as the analysis engine, and welcome new tutorial contributions that use other R packages as the analysis engine as well.
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Donovan, T., Brown, M., & Katz, J. 2015. Vermont Cooperative Fish and Wildlife Research Unit R Projects: R for Fledglings. Retrieved from https://www.uvm.edu/rsenr/vtcfwru/R/?Page=fledglings/fledglings.htm
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January 2015
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Donovan, T. M., and C. Welden. 2002. Spreadsheet exercises in ecology and evolution. Sinauer Associates, Inc. Sunderland, MA. 556 pages.
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Publisher Website
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January 2002
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Donovan, T. M., and C. Welden. 2002. Spreadsheet exercises in conservation biology and landscape ecology. Sinauer Associates, Inc. Sunderland, MA. 464 pages.
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Publisher Website
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January 2002
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Donovan, T. M., and C. Flather. 2002. Relationships among North American songbird trends, habitat fragmentation, and landscape occupancy. Ecological Applications. 12:364-374.
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September 2001
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Donovan, T. M., and A. M. Strong. 2002. Linkages between landscape theory and population dynamics: a review of empirical evidence. Pages 35-54 In: J. Bissonnette and I. Storch, editors. Landscape ecology and resource management: linking theory with practice. Island Press.
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December 2002
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Donovan, T. M., J. Buzas, P. W. Jones, H. L. Gibbs. 2006. Tracking dispersal in birds: assessing the potential of elemental markers. Auk 123:1-12.
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April 2006
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Donovan, T. M., G. S. Warrington, W. S. Schwenk, and J. H. Dinitz. 2012. Estimating landscape carrying capacity through maximum clique analysis. Ecological Applications 22:2265-2276.
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December 2012
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Habitat suitability (HS) maps are widely used tools in wildlife science and establish a link between wildlife populations and landscape pattern. Although HS maps spatially depict the distribution of optimal resources for a species, they do not reveal the population size a landscape is capable of supporting – information that is often crucial for decision makers and managers. We used a new approach, maximum clique analysis, to demonstrate how HS maps for territorial species can be used to estimate the carrying capacity, Nk, of a given landscape. We estimated Nk of ovenbirds (Seiurus aurocapillus) and bobcats (Lynx rufus) in an 1,153 km2 study area in Vermont, USA. These two species were selected to highlight different approaches in building an HS map as well as computational challenges that can arise in a maximum clique analysis. We derived 30 m2 HS maps for each species via occupancy modeling (ovenbird) and by resource utilization modeling (bobcats). For each species, we then identified all pixel locations on the map (points) that had sufficient resources in the surrounding area to maintain a home range (termed a pseudo home range). These locations were converted to a mathematical graph, where any two points were linked if two pseudo home ranges could exist on the landscape without violating territory boundaries. We used the program, Cliquer, to find the maximum clique of each graph. The resulting estimates of Nk = 236 ovenbirds and Nk = 42 female bobcats were sensitive to different assumptions and model inputs. Estimates of Nk via alternative, ad-hoc methods were 1.4 to > 30 times greater than the maximum clique estimate, suggesting that the alternative results may be upwardly biased. The maximum clique analysis was computationally intensive but could handle problems with <1,500 total pseudo home ranges (points). Given present computational constraints, it is best suited for species that occur in clustered distributions (where the problem can be broken into several, smaller problems), or for species with large home ranges relative to grid scale where resampling the points to a coarser resolution can reduce the problem to manageable proportions.
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Donovan, T. M., F. R. Thompson III, and J. Faaborg. 2000. Cowbird distribution at different scales of fragmentation: Tradeoffs between breeding and feeding opportunities. Pages 255-264 In Ecology and management of cowbirds (T. Cooke, S. K. Robinson, S. I. Rothstein, S. G. Sealy, J. N. M. Smith, eds. ). University of Texas Press, Austin, TX.
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January 2001
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Donovan, T. M., C. Danforth, D. Shustack. 2008. Predicting annual fecundity from nest success. Open Ornithology Journal 1:20-28.
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Abstract
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July 2008
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Nest success, the probability that a nest will fledge offspring, is a widely measured parameter in ornithological studies, and is usually estimated by monitoring the fates of nests throughout a breeding season. Because nest success estimates are commonly reported in the avian literature, a key question in population studies is how to derive annual fecundity rates, F (a vital parameter in population biology), from nest success data when breeding individuals are not marked. In this manuscript, we describe a simple, recursive model that generates an estimate of the frequency distribution of annual fecundity rates that can be achieved for a species, given precise and unbiased estimates of nest success, the average number of young that fledge per successful nest, and three life history parameters: the maximum number of possible successful broods per breeding season (J), the maximum number of possible nesting attempts per breeding season (K), and the maximum brood size (B). We illustrate the model for 3 hypothetical species in which the average young that fledge per successful nest is 2 offspring: (1) a single-brooded species in which J =1, K = 3, B = 3; (2) a double-brooded species in which J = 2, K = 3, B = 3, and (3) a triple-brooded species in which J =3, K = 3, B = 3. In general, the frequency distributions of acceptable fecundity solutions for single-, double-, and triple-brooded species are all approximately symmetric, and are defined by Fave (the average acceptable solution), Fmin (the minimum acceptable solution), and Fmax (the maximum acceptable solution). The “breadth” of these distributions, or the difference between Fmin and Fmax, appears to be controlled largely by solutions where an unequal number of young fledge across attempts. However, when examining relationships between annual fecundity and nest success across the full spectrum of nest success values, we find that, more often than not, non-linear relationships characterized the association between nest success, Fmax, Fmin, and Fave. The only case where nest success predicts annual fecundity in a linear fashion occurred when J = K. Thus, the assumption that nest success is an adequate indicator of annual fecundity should be viewed with caution.
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Donovan, T. M., C. Beardmore, D. Bonter, J. Brawn, J. A. Fitzgerald, R. Ford, S. Geautreax, L. George, C. Hunter, T. E. Martin, J. Price, K. Rosenberg, P. Vickery, and T. Bentley Wigley. (The Partners in Flight Research Working Group). 2002. Priority research needs for conservation of Neotropical migrants. Journal of Field Ornithology 73:329-338.
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September 2001
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Dick, C., Larson, W.A., Karpan, K., Baetscher, D.S., Shi, Y., Sethi, S., Fangue, N.A., Henderson, M.J. Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding. Submitted to Molecular Ecology Resources.
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Abstract
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August 2023
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Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two different rations of Chinook salmon (<i>Oncorhynchus tshawytscha</i>) to two piscivorous fish species (striped bass [<i>Morone saxatilis</i>] and channel catfish [<i>Ictalurus punctatus</i>]) held at two different temperatures (15.5°C and 18.5°C) and sacrificed at regular intervals up to 120 hours from the time of ingestion to quantify digestive tract contents. We found that ration size had the largest influence on digestion rate followed by prey species and temperature. DNA based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~6 hours for visual analysis versus ~72 hours for molecular analyses). Notably, metabarcoding results had substantially less variance than qPCR results and produced better quantitative estimates of evacuation rates that could be more confidently integrated into modeling efforts. Our study provides evidence that modeling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.
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DeBow, J., J. Blouin, E. Rosenblatt, K. Gieder, W. Cottrell, J. Murdoch, and T. Donovan. 2021. Effects of winter ticks and internal parasites on moose survival in Vermont, USA. Journal of Wildlife Management. DOI: 10.1002/jwmg.22101
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August 2021
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Moose (<i>Alces alces</i>) have experienced considerable declines along the periphery of their range in the northeastern United States. In Vermont, the population declined 45% from 2010 to 2017 despite minimal hunter harvest and adequate habitat. Similarly, nearby populations recently experienced epizootics characterized by >50% mortality. Declines have largely been associated with the effects of winter ticks (<i>Dermacentor albipictus</i>), but uncertainty exists about the effects of environmental and other parasite-related conditions on moose survival. We examined patterns of moose survival among a radio-collared population (<i>n</i> = 127) in Vermont from 2017 to 2019. Our objectives were to estimate causes of mortality and model survival probability as a function of individual and landscape variables for calves (<1 yr) and adults (≥1 yr). Observed adult survival was 90% in 2017, 84% in 2018, and 86% in 2019, and winter calf survival was 60% in 2017, 50% in 2018, and 37% in 2019. Winter tick infestation was the primary cause of mortality (91% of calves, 25% of adults), and 32% of all mortalities had evidence of meningeal worm (<i>Parelaphostrongylus tenuis</i>). Other sources of mortality such as vehicles, harvest, predation, deep snow, and other parasitic infections were negligible. The best supported calf model included sex differences and negative effects of tick engorgement (%/week) and parasite level (roundworm and lungworm). The best supported adult model included the effect of cumulative tick engorgement (cumulative %/week), which negatively affected survival. Our results indicate that winter tick engorgement strongly affects survival, and is probably compounded by the presence of meningeal worm and other parasites. Reduced tick effects may be achieved by decreasing moose density through harvest and managing late winter habitat to minimize tick density. Management of white-tailed deer (<i>Odocoileus virginianus</i>) density may also affect the transmission of meningeal worm.
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DeBow, J., J. Blouin, E. Rosenblatt, K. Gieder, J. Murdoch, and T. Donovan. 2023. Birth Rates and Calf Survival in a Parasite Rich Moose Herd in Vermont, USA. Alces 58: 51–73.
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February 2023
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Moose (<i>Alces alces</i>) populations have recently declined across the southern portion of their geographic range in North America. In Vermont and other northeastern U.S. states, declines have been attributed to low survival rates driven primarily by winter tick (<i>Dermacentor albipictus</i>), which may also affect birth rate and survival of new calves. We radio-collared and monitored 75 female moose (38 calves and 37 adults) in Vermont from 2017 to 2020 and examined the effects of physiological conditions and spatial and temporal factors on adult birth rates. Physiological measures included fecal glucocorticoid metabolites concentrations (fGCM), which reflect stress, and urine urea nitrogen:creatinine ratio (UN:C), which proxies nutritional state. The pregnancy rate at capture across years was 0.67 (95% CI = 0.50 – 0.80), and negatively influenced by the presence of lungworm (<i>Dictyocaulus </i>spp.). Birth rates, calculated as the average number of offspring delivered per adult female, were < 1.0 overall, did not differ among years (2017-2020, LCI = 0.22, UCI = 0.86), but differed by adult age class, where rates increased with age. We further evaluated daily calf survival rates to age 60 days, the point at which calves become independent of direct care. Logistic exposure models indicated that daily calf survival increased as Julian birth date and days since birth increased (log odds = 0.0819, SE = 0.0215). The per capita independence rate (the rate at which adult females add independent calves to the population) was negatively influenced by average UN:C ratios and positively influenced by fGCM levels. Further, this rate was related to the habitat conditions in home ranges of adult females during the fall, when ticks attach to moose. Specifically, female adults whose fall home ranges were characterized by high levels of mature (canopy) evergreen forests and wetland habitats, and low levels of mixed forests and elevation, had a higher, average binomial success rate in adding an independent calf into the population than those whose home ranges consisted of high levels of mixed forest at high elevation. Our results suggest that winter ticks negatively affect fecundity, and that efforts to reduce parasite loads on individual moose (e.g., directly by reducing moose density or indirectly through habitat alteration) may improve productivity and recruitment.
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Cunjak, R. A., T. D. Prowse, and D. L. Parrish. 1998. Atlantic salmon (Salmo salar) in winter: the season of parr discontent. Canadian Journal of Fisheries and Aquatic Sciences 55(Supple. 1):161-180.
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December 1998
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Cornell, K., and T. Donovan. 2010. Effects of spatial habitat heterogeneity on habitat selection and annual fecundity for a forest songbird. Landscape Ecology 25:109-122.
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January 2010
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Understanding how spatial habitat patterns influence abundance and dynamics of animal populations is a primary goal in landscape ecology. We used an information-theoretic approach to investigate the association between habitat patterns at multiple spatial scales and demographic patterns for black-throated blue warblers (Dendroica caerulescens) at 20 study sites in west-central Vermont, USA from 2002 to 2005. Sites were characterized by: (1) territory-scale shrub density, (2) patch-scale shrub density occurring within 25 ha of territories, and (3) landscape-scale habitat patterns occurring within 5 km radius extents of territories. We considered multiple population parameters including abundance, age ratios, and annual fecundity. Territory-scale shrub density was most important for determining abundance and age ratios, but landscape-scale habitat structure strongly influenced reproductive output. Sites with higher territory-scale shrub density had higher abundance, and were more likely to be occupied by older, more experienced individuals compared to sites with lower shrub density. However, annual fecundity was higher on sites located in contiguously forested landscapes where shrub density was lower than the fragmented sites. Further, effects of habitat pattern at one spatial scale depended on habitat conditions at different scales. For example, abundance increased with increasing territory-scale shrub density, but this effect was much stronger in fragmented landscapes than in contiguously forested landscapes. These results suggest that habitat pattern at different spatial scales affect demographic parameters in different ways, and that effects of habitat patterns at one spatial scale depends on habitat conditions at other scales.
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Cornell, K. L, and T. M. Donovan. 2010. Scale-dependent mechanisms of habitat selection for a migratory passerine: An experimental approach. Auk 127:899-908.
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Abstract
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November 2010
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Habitat selection theory predicts that individuals choose breeding habitats that maximize fitness returns on the
basis of indirect environmental cues at multiple spatial scales. We performed a 3-year field experiment to evaluate five alternative
hypotheses regarding whether individuals choose breeding territories in heterogeneous landscapes on the basis of (1) shrub cover
within a site, (2) forest land-cover pattern surrounding a site, (3) conspecific song cues during prebreeding settlement periods, (4) a
combination of these factors, and (5) interactions among these factors. We tested hypotheses with playbacks of conspecific song across
a gradient of landscape pattern and shrub density and evaluated changes in territory occupancy patterns in a forest-nesting passerine,
the Black-throated Blue Warbler (Dendroica caerulescens). Our results support the hypothesis that vegetation structure plays a primary
role during presettlement periods in determining occupancy patterns in this species. Further, both occupancy rates and territory
turnover were affected by an interaction between local shrub density and amount of forest in the surrounding landscape, but not by
interactions between habitat cues and social cues. Although previous studies of this species in unfragmented landscapes found that
social postbreeding song cues played a key role in determining territory settlement, our prebreeding playbacks were not associated with
territory occupancy or turnover. Our results suggest that in heterogeneous landscapes during spring settlement, vegetation structure
may be a more reliable signal of reproductive performance than the physical location of other individuals.
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Clarfeld, L., A. Sirén, B. Mulhall, T. Wilson, E. Bernier, J. Farrell, G. Lunde, N. Hardy, K. Gieder, R. Abrams, S. Staats, S. McLellan, and T. Donovan. 2023. Evaluating a tandem human-machine approach to labelling of wildlife in remote camera monitoring. Ecological Informatics 77:e102257 https://doi.org/10.1016/j.ecoinf.2023.102257.
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August 2023
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Remote cameras (“trail cameras”) are a popular tool for non-invasive, continuous wildlife monitoring, and as they become more prevalent in wildlife research, machine learning (ML) is increasingly used to automate or accelerate the labor-intensive process of labelling (i.e., tagging) photos. Human-machine hybrid tagging approaches have been shown to greatly increase tagging efficiency (i.e., time to tag a single image). However, those potential increases hinge on the extent to which an ML model makes correct vs. incorrect predictions. We performed an experiment using a ML model that produces bounding boxes around animals, people, and vehicles in remote camera imagery (MegaDetector) to consider the impact of a ML model's performance on its ability to accelerate human labeling. Six participants tagged trail camera images collected from 12 sites in Vermont and Maine, USA (January–September 2022) using three tagging methods (one with ML bounding box assistance and two without assistance). We used a generalized linear mixed model to examine the influence of ML model performance and tagging method on tagging efficiency. We found that ML bounding boxes offer significant improvement in tagging efficiency when labelling data compared to unassisted tagging. Additionally, the time taken to label with bounding boxes was not statistically different from an unassisted tagging approach. However, we found that gains in efficiency are contingent on the ML algorithm's performance and that incorrect ML predictions, particularly the 4.2% false positive and 3.6% false negative predictions, can slow the tagging process compared to a non-hybrid approach. These findings indicate that although practitioners usually forgo the production of bounding boxes when selecting a data labelling process due to the increased effort, ML bounding box-assisted tagging can offer an efficient method for labeling. More broadly, ML-assisted data labelling offers an opportunity to accelerate the analysis of trail camera imagery, but an assessment of the ML model's performance can illuminate whether the hybrid-tagging approach is ultimately a help or hinderance.
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Cherukuri, A, A. Strong, and T. M. Donovan. 2018. Developing a monitoring protocol for least bitterns (Ixobrychis exilis) in New England: Detection probability and occupancy modeling. Northeastern Naturalist 25:56-71. https://doi.org/10.1656/045.025.0104
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January 2018
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Ixobrychus exillis (Least Bittern) is listed as a species of high concern in the North American Waterbird Conservation Plan and is a US Fish and Wildlife Service migratory bird species of conservation concern in the Northeast. Little is known about the population of Least Bitterns in the Northeast because of their low population density, tendency to nest in dense wetland vegetation, and secretive behavior. Urban and agricultural development is expected to encroach on and degrade suitable wetland habitat; however, we cannot predict the effects on Least Bittern populations without more accurate information on their abundance and distribution. We conducted surveys of wetlands in Vermont to assess the efficacy of a monitoring protocol and to establish baseline Least Bittern abundance and distribution data at a sample of 29 wetland sites. Surveys yielded detections of 31 individuals at 15 of 29 sites across 3 biophysical regions and at 5 sites where occupancy had not been previously reported. Probability of occupancy was positively related to wetland size and number of patches, though the relationships were not strong enough to conclude if these were true determinants of occupancy. Call—response broadcast surveys yielded 30 detections, while passive surveys yielded 13. Call—response broadcasts (P = 0.897) increased the rate of detection by 55% compared to passive surveys (P = 0.577). Our results suggest that call—response broadcast surveys are an effective means of assessing Least Bittern occupancy and may reduce bias in long-term monitoring programs.
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Chellman, I.C., D.L. Parrish, and T.M. Donovan. 2017. Estimating population demographic parameters for the mudpuppy (Necturus maculosus) in Vermont. Herpetological Conservation and Biology 12(2):422-434.
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Abstract
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August 2017
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The Mudpuppy (Necturus maculosus) is classified as a Species of Greatest Conservation Need by the state of Vermont. There is concern regarding status of populations in the Lake Champlain basin because of habitat alteration and potential effects of 3-trifluromethyl-4-nitrophenol (TFM), a chemical used to control Sea Lamprey (Petromyzon marinus). The purpose of our research was to assess Mudpuppy capture methods and abundance in the Lamoille River, Vermont, USA. We sampled Mudpuppies under a mark-recapture framework, using modified, baited minnow traps set during two winter-spring periods. We marked each Mudpuppy with a passive integrated transponder (PIT) tag and released individuals after collecting morphological measurements. We collected 80 individuals during 2,581 trap days in 2008–2009 (year 1), and 81 individuals during 3,072 trap days in 2009–2010 (year 2). We estimated abundance from spring trapping periods in 2009 and 2010, during which capture rates were sufficient for analysis. Capture probability was low (< 0.04), but highest following precipitation events in spring, during periods of higher river flow, when water temperatures were approximately 3 to 6° C. During October 2009, management agencies treated the Lamoille River with TFM. Surveyors recovered more than 500 dead Mudpuppies during the post-treatment assessment. Overall, Mudpuppy captures did not change between sampling periods; however, we captured fewer females during year 1 compared to year 2, and the sex ratio changed from 0.79:1 (M:F) during year 1 to 3:1 (M:F) during year 2. Our data may help wildlife managers assess population status of Mudpuppies in conjunction with fisheries management techniques.
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Butryn, R.S., D.L. Parrish, and D.M. Rizzo. 2013. Summer stream temperature metrics for predicting brook trout (Salvelinus fontinalis) distribution in streams. Hydrobiologia 703:47-57.
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January 2013
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Brown, M., C. D. Canham, L. Murphy, and T. M. Donovan. 2018. Timber harvest as the predominant disturbance regime in northeastern U.S. forests: effects of harvest intensification. Ecosphere 9:1-19. DOI:10.1002/ecs2.2062
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April 2018
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Harvesting is the leading cause of adult tree mortality in forests of the northeastern United States. While current rates of timber harvest are generally sustainable, there is considerable pressure to increase the contribution of forest biomass to meet renewable energy goals. We estimated current harvest regimes for different forest types and regions across the U.S. states of New York, Vermont, New Hampshire, and Maine using data from the U.S. Forest Inventory and Analysis Program. We implemented the harvest regimes in SORTIE-ND, an individual-based model of forest dynamics, and simulated the effects of current harvest regimes and five additional harvest scenarios that varied by harvest frequency and intensity over 150 yr. The best statistical model for the harvest regime described the annual probability of harvest as a function of forest type/region, total plot basal area, and distance to the nearest improved road.Forests were predicted to increase in adult above ground biomass in all harvest scenarios in all forest type and region combinations. The magnitude of the increase, however, varied dramatically—increasing from 3% to 120% above current landscape averages as harvest frequency and intensity decreased. The variation can be largely explained by the disproportionately high harvest rates estimated for Maine as compared with the rest of the region. Despite steady biomass accumulation across the landscape, stands that exhibited old-growth characteristics (defined as≥300 metric tons of biomass/hectare) were rare (8% or less of stands). Intensified harvest regimes had little effect on species composition due to widespread partial harvesting in all scenarios, resulting in dominance by late-successional species over time. Our analyses indicate that forest biomass can represent a sustainable, if small, component of renewable energy portfolios in the region, although there are tradeoffs between carbon sequestration in forest biomass and sustainable feedstock supply. Integrating harvest regimes into a disturbance theory framework is critical to understanding the dynamics of forested landscapes, especially given the predominance of logging as a disturbance agent and the increasing pressure to meet renewable energy needs.
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Brown, M., C. Canham, T. Buchholz, J. Gunn, and T. Donovan. 2024. Net carbon sequestration implications of intensified timber harvest in northeastern U.S. forests. Ecosphere 15(2): e4758. https://doi.org/10.1002/ecs2.4758
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Abstract
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February 2024
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U.S. forests, particularly in the eastern states, provide an important offset to greenhouse gas (GHG) emissions. Some have proposed that forest-based natural climate solutions can be strengthened via a number of strategies, including increases in the production of forest biomass energy. We used output from a forest dynamics model (SORTIE-ND) in combination with a GHG accounting tool (ForGATE) to estimate the carbon consequences of current and intensified timber harvest regimes in the Northeastern United States. We considered a range of carbon pools including forest ecosystem pools, forest product pools, and waste pools, along with different scenarios of feedstock production for biomass energy. The business-as-usual (BAU) scenario, which represents current harvest practices derived from the analysis of U.S. Forest Service Forest Inventory and Analysis data, sequestered more net CO<sub>2</sub> equivalents than any of the intensified harvest and feedstock utilization scenarios over the next decade, the most important time period for combatting climate change. Increasing the intensity of timber harvest increased total emissions and reduced landscape average forest carbon stocks, resulting in reduced net carbon sequestration relative to current harvest regimes. Net carbon sequestration “parity points,” where the regional cumulative net carbon sequestration from alternate intensified harvest scenarios converge with and then exceed the BAU baseline, ranged from 12 to 40 years. A “no harvest” scenario provides an estimate of an upper bound on forest carbon sequestration in the region given the expected successional dynamics of the region's forests but ignores leakage. Regional net carbon sequestration is primarily influenced by (1) the harvest regime and amount of forest biomass removal, (2) the degree to which bioenergy displaces fossil fuel use, and (3) the proportion of biomass diverted to energy feedstocks versus wood products.
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Brown, M. L., T. M. Donovan, W. S. Schwenk, and D. M. Theobald. 2013. Predicting impacts of future human population growth and development on occupancy rates of forest-dependent birds . Biological Conservation. Available online 31 October 2013, ISSN 0006-3207, http://dx.doi.org/10.1016/j.biocon.2013.07.039
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October 2013
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Forest loss and fragmentation are among the largest threats to forest-dwelling wildlife species today, and projected increases in human population growth are expected to increase these threats in the next century. We combined spatially-explicit growth models with wildlife distribution models to predict the effects of human development on 5 forest-dependent bird species in Vermont, New Hampshire, and Massachusetts, USA. We used single-species occupancy models to derive the probability of occupancy for each species across the study area in the years 2000 and 2050. Over half a million new housing units were predicted to be added to the landscape. The maximum change in housing density was nearly 30 houses per hectare; however, 30% of the towns in the study area were projected to add less than 1 housing unit per hectare. In the face of predicted human growth, the overall occupancy of each species decreased by as much as 38% (ranging from 19% to 38% declines in the worst-case scenario) in the year 2050. These declines were greater outside of protected areas than within protected lands. Ninety-seven percent of towns experienced some decline in species occupancy within their borders, highlighting the value of spatially-explicit models. The mean decrease in occupancy probability within towns ranged from 3% for hairy woodpecker to 8% for ovenbird and hermit thrush. Reductions in occupancy probability occurred on the perimeters of cities and towns where exurban development is predicted to increase in the study area. This spatial approach to wildlife planning provides data to evaluate trade-offs between development scenarios and forest-dependent wildlife species.
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Brown, M. L., T. M. Donovan, R. M. Mickey, G. S. Warrington, W. S. Schwenk, and D. S. Theobald. 2017. Predicting effects of future development on a territorial forest songbird: methodology matters. Landscape Ecology 33:93-108. DOI 10.1007/s10980-017-0586-8
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Abstract
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October 2017
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Context
Projected increases in human population size are expected to increase forest loss and fragmentation in the next century at the expense of forest-dwelling species.
Objectives
We estimated landscape carrying capacity (Nk) for Ovenbirds in urban, suburban, exurban, and rural areas for the years 2000 and 2050, and compared changes in Nk with changes in occupancy probability.
Methods
Maximum clique analysis, a branch of mathematical graph theory, was used to estimate landscape carrying capacity, the maximum potential number of territories a given landscape is capable of supporting (Nk). We used occupancy probability maps as inputs for calculating Ovenbird Nk in the northeastern USA and a spatially explicit growth model to forecast future development patterns in 2050. We compared occupancy probability with estimates of
Nk for urban, suburban, exurban, and rural areas for the
years 2000 and 2050.
Results
In response to human population growth and development, Ovenbird Nk was predicted to decrease23% in urban landscapes, 28% in suburban landscapes, 43% in exurban landscapes, and 20% in rural landscapes. These decreases far exceeded decreases in mean occupancy probabilities that ranged between 2 and 5% across the same development categories. Thus, small decreases in occupancy probability between 2000 and 2050 translated to much larger decreases in Nk.
Conclusions
For the first time, our study compares occupancy probability with a species population metric, Nk, to assess the impact of future development. Maximum clique analysis is a tool that can be used to estimate Nk and inform landscape management and communication with stakeholders.
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Brauer, C., T. Donovan, R. Mickey, J. Katz, and B. Mitchell. 2016. A comparison of acoustic montoring methods for common anurans of the northeastern United States. Wildlife Society Bulletin 40:140-149.
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Publisher Website
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February 2016
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Bonter, D. N., T. M. Donovan, and E. W. Brooks. 2007. Daily changes in energetic condition in landbirds during migration stopover on the south shore of Lake Ontario. Auk 124:122-133
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January 2007
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Assigning conservation priorities to areas used by birds during migration requires information on the relative quality of areas and habitats. The rate at which migratory birds replenish energy reserves during stopover may be used as an indicator of stopover-site quality. We estimated the rate of mass gain of 34 landbird species during stopover at a near-shore terrestrial site on the south shore of Lake Ontario in New York during 12 migration seasons from 1999 to 2004. The average rate of mass gain was estimated by relating a measure of condition to time of capture (hour after sunrise) with linear regression. Data from 25,385 captures were analyzed. Significantly positive rates of mass change were detected for 20 of 30 species during spring migration and 19 of 21 species during autumn migration. No significantly negative trends were detected in either season. Daily rates of mass gain across all species averaged 9.84% of average lean body weight during spring migration and 9.77% during autumn migration. Our regression estimates were significantly greater than estimates from traditional analyses that examine mass changes in recaptured birds. Analyses of mass changes in recaptured birds revealed a mean daily change of -0.68% of average lean mass in spring and 0.13% in autumn. Because of sampling biases inherent in recapture analyses, the regression approach is likely more accurate when the assumptions of the method are met. Similar studies in various habitats, landscapes, and regions are required to prioritize conservation efforts targeting migratory stages of the annual cycle.
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Bonter, D. N., T. M. Donovan, E. Brooks. 2008. What are we missing with ground-level mist nets? Using elevated nets at a migration stopover site. Journal of Field Ornithology 79:314-320.
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Abstract
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September 2008
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Mist nets deployed in a standard ground-level fashion capture birds approximately 0.5–2.6 m above the ground. In habitats where the vegetation extends above this height, standard mist net deployment may inadequately sample the targeted avian community and age- and sex-classes within species. Such sampling biases may raise questions regarding studies based on data from mist-net captures. To determine if birds were equally likely to be captured by mist nets at different heights, we constructed a series of paired ground-level and elevated mist nets (hereafter "net rigs") at a research station in western New York State. Net rigs were operated during 14 migration seasons from 2000 to 2006 (spring and fall each year), and 19,735 birds of 118 species were captured. Capture rates were significantly higher in ground-level nets, but 12 species were only captured in elevated nets. Of 44 species with at least 50 captures, 25 species were more likely to be captured in the ground-level nets and two species in the elevated nets. For four of 18 species, more birds were captured in the elevated nets during fall migration than during spring migration. We conclude that standard ground-level net placement was more efficient in capturing birds in the secondary growth habitats that we sampled. However, ground-level nets may not adequately sample the entire targeted community or all age- or sex-classes within species.
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Bonter, D. N., S. A. Gauthreaux, Jr., and T. M. Donovan. 2009. Characteristics of important stopover locations for migrating birds: Remote sensing with radar in the Great Lakes Basin. Conservation Biology 23:440-448.
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April 2009
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A preliminary stage in developing comprehensive conservation plans involves identifying areas used by the organisms of interest. The areas used by migratory land birds during temporal breaks in migration (stopover periods) have received relatively little research and conservation attention. Methodologies for identifying stopover sites across large geographic areas have been, until recently, unavailable. Advances in weather-radar technology now allow for evaluation of bird migration patterns at large spatial scales. We analyzed radar data (WSR-88D) recorded during spring migration in 2000 and 2001 at 6 sites in the Great Lakes basin (U.S.A.). Our goal was to link areas of high migrant activity with the land-cover types and landscape contexts corresponding to those areas. To characterize the landscapes surrounding stopover locations, we integrated radar and land-cover data within a geographic information system. We compared landscape metrics within 5 km of areas that consistently hosted large numbers of migrants with landscapes surrounding randomly selected areas that were used by relatively few birds during migration. Concentration areas were characterized by 1.2 times more forest cover and 9.3 times more water cover than areas with little migrant activity. We detected a strong negative relationship between activity of migratory birds and agricultural land uses. Examination of individual migration events confirmed the importance of fragments of forested habitat in highly altered landscapes and highlighted large concentrations of birds departing from near-shore terrestrial areas in the Great Lakes basin. We conclude that conservation efforts can be more effectively targeted through intensive analysis of radar imagery.
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Blouin, J., J. DeBow, E. Rosenblatt, J. Hines, C. Alexander, K. Gieder, N. Fortin, J. Murdoch, and T. Donovan. 2021. Moose habitat selection and fitness consequences during two critical winter tick life stages in Vermont, USA. Frontiers in Ecology and Evolution 9:642276.
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May 2021
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Moose (<i>Alces Alces</i>) are a charismatic species that has been in decline across much of their southern range.<b> </b>In New England, USA, the reduction has been attributed, in part, to winter tick (<i>Dermacentor albipictus</i>) infestations. Winter ticks tend to be fairly immobile throughout all life stages, and therefore their distribution patterns at any given time are shaped largely by the occurrence of moose across the landscape during the peak of two critical time periods; fall questing (when ticks latch onto a moose, which coincides with the rut) and spring drop-off (when engorged female ticks detach from moose and lay their eggs in leaf litter). We used recent land cover and lidar data within a dynamic occupancy modeling framework to estimate first-order habitat selection (use vs non-use) of female moose (n = 74) during the questing and drop-off periods. Patch (1 km<sup>2</sup>) extinction and colonization rates during spring drop-off periods were strongly influenced by habitat and elevation, but these effects were diminished during the questing period when moose were more active across the landscape. In the spring drop-off period, patches where colonization was high and extinction low (highest probability of female moose occupancy) had higher proportions of young (shrub/forage) mixed forest at greater elevations. We evaluated the fitness consequences of individual-based habitat selection (second-order habitat selection) by comparing Resource Selection Functions (RSF) for 5 females that successfully reared a calf with 5 females whose calf perished. Second-order habitat selection analyses showed adult female moose whose offspring perished selected patches during the questing period that matched the first-order selection during the spring drop-off period. In contrast, adult female moose whose offspring survived selected areas with proportions of young deciduous habitats, as well as higher proportions of mature (canopy) evergreen forests and wetlands at lower elevations, i.e., their second-order habitat selection patterns deviated from the overall patterns illuminated by the multi-season occupancy analysis. Our model coefficients and mapped results define “hotspots” that are likely encouraging the deleterious effects of the tick-moose cycle. Knowledge about the composition and structure of these hotspots may influence more direct (i.e. hunter harvest) and indirect (i.e. conservation, modification, or formation of habitats) management decisions.
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Blouin, J., J. DeBow, E. Rosenblatt, C. Alexander, K. Gieder, J. Murdoch, and T. Donovan. Modeling moose habitat use by age, sex, and season in Vermont, USA using high-resolution lidar and National Land Cover data. Alces 57:71-98.
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September 2021
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Moose (<i>Alces alces</i>) populations have experienced unprecedented declines along the southern periphery of their range, including Vermont, USA. Habitat management may be used to improve the status of the population and health of individuals. To date, however, Vermont wildlife managers have been challenged to effectively use this important tool due to the lack of fine-scale information on moose space use and habitat characteristics. To assess habitat use, we combined more than 40,000 moose locations collected from radio-collared individuals (n = 74), recent land cover data, and high resolution, 3-dimensional lidar (light detection and ranging) data to develop Resource Utilization Functions (RUF) by age (mature and young adult), season (dormant and growth), and sex. Each RUF linked home range use to average habitat conditions within 400 m or 1 km of each 30 m2pixel within the home range. Across analyses, the top RUF models included both composition (as measured through the National Land Cover Database) and structure (as measured through lidar) variables, and significantly outperformed models that excluded lidar variables. These findings support the notion that lidar is an effective tool for improving the ability of models to estimate patterns of habitat use, especially for larger bodied mammals. Generally speaking, female moose actively used areas with proportionally more regenerating forest (i.e., forage < 3.0 m) and more mature forest (i.e., canopy structure > 6.0 m), while males actively used more high elevation, mixed forest types. Further, moose exhibited important seasonal differences in habitat use that likely reflect temporal changes in energetic and nutritional requirements and behavior across the year. Moose used areas with proportionally more regenerating forest (i.e., forage < 3.0 m) during the growth period and female moose had strong positive associations with lidar-derived canopy structure during the growth (but not the dormant) period. Ultimately, the resultant maps of habitat use provide a means of informing management activities (e.g., the restoration or alteration of habitats to benefit moose) and policies around land use that may contribute to population recovery.
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Bettigole, C., T. M. Donovan, R. Manning, and J. Austin. 2013. Normative standards for land use in Vermont: Implications for biodiversity. Biological Conservation.
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August 2013
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The conversion of natural lands to developed uses poses a great threat to global terrestrial biodiversity. Natural resource managers, tasked with managing wildlife as a public trust, require techniques for predicting how much and where wildlife habitat is likely to be converted in the future. Here, we develop a methodology to estimate the “social carrying capacity for development” –SKd – for 251 towns across the state of Vermont, USA. SKd represents town residents’ minimum acceptable human population size and level of development within town boundaries. To estimate SKd across towns within the state of Vermont (USA), as well as the average state-wide SKd, we administered a visual preference survey (n = 1505 responses) to Vermont residents, and asked respondents to rate alternative landuse scenarios in a fictional Vermont town on a scale of +4 (highly acceptable) to −4 (highly unacceptable). We additionally collected demographic data such as age and income, as well as ancillary information such as participation in town-planning meetings and location of residence. We used model selection and AIC to fit a cubic function to the response data, allowing us to estimate SKd at a town scale based on town demographic characteristics. On average, Vermonters had a SKd of 9.1% development on the landscape; this estimate is 68% higher than year 2000 levels for development (5.4%). Respondents indicated that management action to curb development was appropriate at 9.4% development (roughly the statewide SKd average). Management by local, regional, and state levels were considered acceptable for curbing development while federal level management of development was considered unacceptable. Given a scenario where development levels were at SKd, we predicted a 16,753 km2 reduction in forested land (−11.16%) and a 1038 km2 reduction in farmland (−60.45%). Such changes would dramatically alter biodiversity patterns state-wide. In a companion paper, we estimate how these changes would affect the distribution of wildlife species.
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Bettigole, C., T. Donovan, R. Manning, J. Austin, and R. Long. 2013. Acceptability of residential development in a regional landscape: Potential effects on wildlife occupancy patterns. Biological Conservation.
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October 2013
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The conversion of natural lands to developed uses may pose the single greatest human threat to global terrestrial biodiversity. Continued human growth and development over the next century will further exacerbate these effects of habitat loss and fragmentation. Natural resource managers are tasked with managing wildlife as a public trust, yet often have little say in land use decisions. Generally speaking, decision makers could benefit from an understanding of what different regulations mean in terms of wildlife distribution. In a companion paper (Bettigole et al., 2013), we surveyed town residents throughout Vermont to measure how respondents feel about a range of development levels within their town boundaries. We estimated the “social carrying capacity for development” – or SKd – for 251 towns in Vermont. SKd provides an estimate of the level of developed land cover classes that town residents deem “acceptable” within their town boundaries. In this paper, we design a framework for linking the town-specific SKd estimates with the wildlife distribution patterns for three wide-ranging mammalian species: American black bear (Ursus americanus), fisher (Martes pennanti), and bobcat (Lynx rufus). We simulated landscape conditions at SKd for each town in Vermont, and then used existing occupancy models for the three target species to spatially map and compare occupancy rates in the baseline year 2000 with occupancy rates at SKd. With nearly 90% of Vermont towns willing to increase developed landcover classes within town boundaries compared to baseline levels, significant state-wide changes in occupancy rates were predicted for all three focal species. Average occupancy rates declined by −15.9% and −3.1% for black bear and bobcats, respectively. Average occupancy rates for fisher increased by 9.0%. This study provides a method for linking development standards within a town with wildlife occurrence. Across towns, the methodology spatially identifies areas that may be at risk of future development, as well as identifying areas where wildlife distribution patterns may face future change as a result of increased human population growth and development.
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Beauchamp, D. A., D. L. Parrish, and R. A. Whaley. 2009. Salmonids/coldwater species in large standing waters, Chapter 7, Pages 97-117 In S. Bonar, D. Willis, and W. Hubert, editors. Standard Sampling Methods for North American Freshwater Fishes. American Fisheries Society.
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August 2009
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Balantic, C., and T. M. Donovan. 2019. Temporally-adaptive acoustic sampling to maximize detection across a suite of focal wildlife species. Ecology and Evolution 9(18)10582-10600. DOI: 10.1002/ece3.5579
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August 2019
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1. Acoustic recordings of the environment can produce species presence–absence data for characterizing populations of sound‐producing wildlife over multiple spatial scales. If a species is present at a site but does not vocalize during a scheduled audio recording survey, researchers may incorrectly conclude that the species is absent (“false negative”). The risk of false negatives is compounded when audio devices have sampling constraints, do not record continuously, and must be manually scheduled to operate at pre‐selected times of day, particularly when research programs target multiple species with acoustic availability that varies across temporal conditions.<br><br>2. We developed a temporally adaptive acoustic sampling algorithm to maximize detection probabilities for a suite of focal species amid sampling constraints. The algorithm combines user‐supplied species vocalization models with site‐specific weather forecasts to set an optimized sampling schedule for the following day. To test our algorithm, we simulated hourly vocalization probabilities for a suite of focal species in a hypothetical monitoring area for the year 2016. We conducted a factorial experiment that sampled from the 2016 acoustic environment to com ‐pare the probability of acoustic detection by a fixed (stationary) schedule versus a temporally adaptive optimized schedule under several sampling efforts and monitoring durations.<br><br>3. We found that over the course of a study season, the probability of acoustically capturing a focal species (given presence) at least once via automated acoustic monitoring was greater (and acoustic capture occurred earlier in the season) when using the temporally adaptive optimized schedule as compared to a fixed schedule.<br><br>4. The advantages of a temporally adaptive optimized acoustic sampling schedule are magnified when a study duration is short, sampling effort is low, and/or species acoustic availability is minimal. This methodology presents the opportunity to maximize acoustic monitoring sampling efforts amid constraints.
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Balantic, C., and T. M. Donovan. 2019. Statistical learning mitigation of false positive detections in automated acoustic wildlife monitoring. Bioacoustics 29(3):296-321. DOI: 10.1080/09524622.2019.1605309
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May 2019
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Audio sampling of the environment can provide long-term, landscape-scale presence-absence data to model populations of sound-producing wildlife. Automated detection systems allow researchers to avoid manually searching through large volumes of recordings, but often produce unacceptable false positive rates. We developed methods that allow researchers to improve template-based automated detection using a suite of statistical learning algorithms when false positive rates are problematic. To test our method, we acquired 668 hours of recordings in the Sonoran Desert, California USA between March 2016 and May 2017, and created spectrogram cross-correlation templates for three target avian species. We trained and tested five classification algorithms and four performance-weighted ensemble classifier methods on target signals and false alarms from March 2016, and then selected high-performing ensemble classifiers from the train/test phase to predict the class of new detections thereafter. For three target species, our ensemble classifiers were able to identify 98%, 81%, and 100% of false alarms compared with the baseline template detection system, and comparative positive predictive values improved from 6% to 69%, 87% to 95%, and 2% to 77%. We show that statistical learning approaches can be implemented to mitigate false detections acquired via template-based automated detection in automated acoustic wildlife monitoring.
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Balantic, C., and T. M. Donovan. 2019. Dynamic wildlife occupancy models using automated acoustic monitoring data. Ecological Applications 29(3):e01854.
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April 2019
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Automated acoustic monitoring of wildlife has been used to characterize populations of sound‐producing species across large spatial scales. However, false negatives and false positives produced by automated detection systems can compromise the utility of these data for researchers and land managers, particularly for research programs endeavoring to describe colonization and extinction dynamics that inform land use decision‐making. To investigate the suitability of automated acoustic monitoring for dynamic occurrence models, we simulated underlying occurrence dynamics, calling patterns, and the automated acoustic detection process for a hypothetical species under a range of scenarios. We investigated an automated species detection aggregation method that considered a suite of options for creating encounter histories. From these encounter histories, we generated parameter estimates and computed bias for occurrence, colonization, and extinction rates using a dynamic occupancy modeling framework that accounts for false positives via small amounts of manual confirmation. We were able to achieve relatively unbiased estimates for all three state parameters under all scenarios, even when the automated detection system was simulated to be poor, given particular encounter history aggregation choices. However, some encounter history aggregation choices resulted in unreliable estimates; we provide caveats for avoiding these scenarios. Given specific choices during the detection aggregation process, automated acoustic monitoring data may provide an effective means for tracking species occurrence, colonization, and extinction patterns through time, with the potential to inform adaptive management at multiple spatial scales.
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Balantic, C., and T. Donovan. 2020. AMMonitor: Remote monitoring of biodiversity in an adaptive framework with R. Methods in Ecology and Evolution 11:869-877. DOI: 10.1111/2041-210X.13397
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April 2020
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1. Ecological research and management programs are increasingly using autonomous monitoring units (AMUs) to collect large volumes of acoustic and/or photo data to address pressing management objectives or research goals. The data management requirements of an AMU-based monitoring effort are often overwhelming, with a considerable amount of processing to translate raw data into models and analyses that have research and management utility.<br><br>2. We created the r package AMMonitor to simplify the process of moving from remotely collected data to analysis and results, using a comprehensive SQLite database for data management that tracks all components of a remote monitoring program. This framework enables the tracking of analyses and research/ management objectives through time.<br><br>3. We illustrate the AMMonitor approach with the example of evaluating an occurrence-based management objective for a target species. First, we provide an overview of the database and data management approach. Next, we illustrate a few available workflows: temporally adaptive sampling, automated detection of species sounds from acoustic recordings and aggregation of automated detections into an encounter history for use in an occupancy analysis, the outcome of which can be analysed with respect to the motivating management objective.<br><br>4. Without a comprehensive framework for efficiently moving from raw remote monitoring data collection to results and analysis, monitoring programs are limited in their capacity to systematically characterize ecological processes and inform management decisions through time. AMMonitor provides an option for such a framework. Code, comprehensive documentation and step-by-step examples are available online at https://code.usgs.gov/vtcfwru/AMMonitor
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Aylward, C. J. D. Murdoch, T. M. Donovan, C. W. Kilpatrick, C. Bernier, and J. Katz. 2018. Estimating distribution and connectivity of recolonizing American marten (Martes americana) in the northeastern United States using expert elicitation techniques. Animal Conservation. doi:10.1111/acv.12417
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June 2018
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The American marten, Martes americana, is a species of conservation concern in the northeastern United States due to widespread declines from over-harvesting and habitat loss. Little information exists on current marten distribution and how landscape characteristics shape patterns of occupancy across the region, which could help develop effective recovery strategies. The rarity of marten and lack of historical distribution records are also problematic for region-wide conservation planning. Expert opinion can provide a source of information for estimating species–landscape relationships and is especially useful when empirical data are sparse. We created a survey to elicit expert opinion and build a model that describes marten occupancy in the northeastern United States as a function of landscape conditions. We elicited opinions from 18 marten experts that included wildlife managers, trappers and researchers. Each expert estimated occupancy probability at 30 sites in their geographic region of expertise. We, then, fit the response data with a set of 58 models that incorporated the effects of covariates related to forest characteristics, climate, anthropogenic impacts and competition at two spatial scales (1.5 and 5 km radii), and used model selection techniques to determine the best model in the set. Three top models had strong empirical support, which we model averaged based on AIC weights. The final model included effects of five covariates at the 5-km scale: percent canopy cover (positive), percent spruce-fir land cover (positive), winter temperature (negative), elevation (positive) and road density (negative). A receiver operating characteristic curve indicated that the model performed well based on recent occurrence records. We mapped distribution across the region and used circuit theory to estimate movement corridors between isolated core populations. The results demonstrate the effectiveness of expert-opinion data at modeling occupancy for rare species and provide tools for planning marten recovery in the northeastern United States.
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Abouelezz, H. G, T. M. Donovan, J. Murdoch. R. M. Mickey, M. Freeman, and K. Royar. 2018. Landscape composition mediates movement and habitat selection in bobcats (Lynx rufus): Implications for conservation planning. Landscape Ecology 33:1301-1318. https://doi.org/10.1007/s10980-018-0654-8
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August 2018
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Context
The analysis of individual movement choices can be used to better understand population-level resource selection and inform management.
Objectives
We investigated movements and habitat selection of 13 bobcats in Vermont, USA, under the assumption individuals makes choices based upon their current location. Results were used to identify “movement-defined” corridors.
Methods
We used GPS-collars and GIS to estimate bobcat movement paths, and extracted statistics on land cover proportions, topography, fine-scale vegetation, roads, and streams within “used” and “available” space surrounding each movement path. Compositional analyses were used to determine habitat preferences with respect to landcover and topography; ratio tests were used to determine if used versus available ratios for vegetation, roads, and streams differed from 1. Results were used to create travel cost maps, a primary input for corridor analysis.
Results
Forested and scrub-rock land cover were most preferred for movement, while developed land cover was least preferred. Preference depended on the composition of the “available” landscape: Bobcats moved > 3 times more quickly through forest and scrub-rock habitat when these habitats were surrounded by agriculture or development than when the available buffer was similarly composed. Overall, forest edge, wetland edge and higher stream densities were selected, while deep forest core and high road densities were not selected. Landscape-scale connectivity maps differed depending on whether habitat suitability, preference, or selection informed the travel cost map.
Conclusions
Both local and landscape scale land cover characteristics affect habitat preferences and travel speed of bobcats, which in turn can inform management and conservation activities.
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