Colorado Research: Projects, Research Publications, Presentations, Thesis and Dissertations, Technical Publications

Colorado Research Activities

Electrofishing crew removing brown trout for a study evaluating the stocking of whirling disease resistant rainbow trout.

The Unit works toward three basic objectives: research, education, and technical assistance. The Unit emphasizes research related to specific management problems where results have a high probability of being applied. The program remains flexible to reflect changing cooperators' needs. The long-term fishery effort emphasizes a diversity of applied management projects having broad statewide and regional applicability. The wildlife component of the Unit emphasizes sampling and analysis of quantitative methodologies for management. The fisheries and wildlife activities are diverse and integrated with Unit cooperators. The results of research are transferred through formal graduate teaching and technical extension.

Overall Unit direction is provided by a Coordinating Committee with representatives from the cooperators (USGS, Colorado Parks and Wildlife, Colorado State University, USFWS and the Wildlife Management Institute.) Day to day operation of the Unit is provided by Dana Winkelman, Unit Leader and two Assistant Unit Leaders: William Kendall and Mevin Hooten. These individuals are employees of USGS and have faculty appointments, teach formal graduate courses, and advise and direct graduate students and their research. Research programs are the result of efforts by Unit people in obtaining contracts or grants from federal, state, or private organizations. Most frequently, the research is done by graduate students while earning advanced degrees. Their degrees, Master of Science or Doctor of Philosophy, are granted through the Department of Fish,Wildlife and Conservation Biology (formerly Fishery and Wildlife Biology).

Projects

Project	Completion Date
Estimation of Wind Farm Mortality: Development of Super Population Approach to Estimate Cumulative Mortality from Carcass Surveys Accounting for Carcass Removal and Non-Detection	September 2016	This project will have two phases and will lead to publications on the design and analysis of studies to estimated wind turbine mortality of avian species, and a guidelines document for the wind power community on conducting this post-construction monitoring. 1) Development of statistical methodology for providing robust estimates of wind turbine mortality, as well as designs for properly collecting mortality data. Expected results: Publications on the statistical methodology and study designs we develop 2) Test the developed methodology and study design in the field. Expected results: i) A guidelines document for conducting and analyzing data from studies of avian mortality at wind farms. ii) Possible publications on the number or pattern of avian mortality at existing wind farms.	TBA
Evaluation of PIT tag antennae array & analysis of Humpback Chub PIT tag antennae data from the Little Colorado River	September 2014	A key strategic science question (SSQ 1-8, Grand Canyon Monitoring and Research Center, 2007) is how can native and nonnative fishes best be monitored while minimizing repeated handling of fish. Managers wish to obtain population information in the least intrusive manner possible, especially when sampling the endangered HBC. Remote PIT-tag antennae have been shown to be very effective at continuous monitoring in other, generally smaller rivers and streams, alleviating the need for additional field sampling trips and multiple fish handling events. We propose to evaluate the efficiency of hoop-netting used for current monitoring compared to that of the new remote PIT tag antenna array, that does not require repeated handling of fishes, or additional field sampling in the Little Colorado River (LCR). PIT tags are already implanted in a large fraction of the adult population and to a lesser degree in the smaller life history stages of HBC in Grand Canyon. Antennae provide the opportunity to evaluate gear efficiency of hoop nets (e.g. what proportions of the fish present are captured), to increase precision of population estimates, direction and timing of movement within the LCR, and presence of fish in the LCR year round.	TBA
Mountain Lion Population Modeling	December 2014	: In order to set harvest quotas, evaluate management practices and understand the dynamics of predator-prey systems, it is desirable to have reliable estimates of population size. Unfortunately, as with many predators, it can be very difficult and expensive to obtain these estimates. This is especially true with mountain lions because of their low densities, secretive nature, and unpredictable response to lures, baits and/or calls. Most reliable estimates of population size for mountain lions have come from intensive capture and monitoring studies, The ability to estimate population size or track population changes is critical to the management of a species, especially when harvest quotas are being set for that species. This study is designed to develop tools that can be implemented in areas where mountain lions are not actively being studied and marked that will allow biologists/managers to gain a better idea of population size and population response to management prescriptions. Such estimates, in conjunction with harvest data, will allow managers to better understand the mountain lion populations they manage, set appropriate harvest quotas and defend our management actions to the public.	None
Design & Analysis of Demographic Studies of Sea Turtles	December 2014	Most species of sea turtle are endangered (Baillie and Groombridge 1996), and are therefore of great conservation concern. Conservation of these species is complicated by their complex life history, the broad spatial distribution of various life stages, and their migratory nature. Informed conservation of a species requires monitoring, not only to track general status but to evaluate the effect of management actions that might be taken to conserve the species. As articulated by a recent report by the National Research Council (2010), monitoring of sea turtles should take two forms. Monitoring of change in population size is important to assess whether a population is increasing or decreasing. However, in order to begin to evaluate the cause of that change, monitoring vital rates such as stage-specific survival and reproduction is important. With such estimates the relationship between vital rates and anthropogenic and other environmental variables can be evaluated. Monitoring vital rates is conducted through tagging studies, some combination of conventional tags (e.g., PIT tags, flipper tags, genetic fingerprinting) and telemetry devices. Such studies are expensive, and in some cases impractical, but strategic use of such studies facilitates informed sea turtle conservation.The overall goal of our work is to develop the protocols and statistical tools necessary to estimate and model the demographic parameters listed above (for both nesting and in water studies), to articulate the usefulness of (and how to use) these tools to the sea turtle community through publications and reports, and to train sea turtle biologists in these tools through hands-on short courses.	TBA
Predicting Migratory Bird Responses to Climate Change:	December 2017	Current adaptive management frameworks inform migratory bird habitat conservation and harvest decisions while accounting for a wide range of uncertainties (Nichols et al. 1995, Johnson et al. 1996, Williams et al. 1996). The wildlife management community has recently committed itself to a regional approach aimed at integrating habitat, harvest, and conservation management (Joint Ventures, Strategic Habitat Conservation, Landscape Conservation Cooperatives) and successful integration requires development of regional models for population and habitat dynamics that account for coordinated actions directed by habitat, conservation, and harvest management programs. Adaption of current models to meet the needs of an integrated approach are complicated by climate changes that will likely leading to shifts in system dynamics and introduce greater uncertainty into management decisions. In light of rapidly changing environmental conditions, adjustments of all elements of habitat and harvest management decision frameworks need consideration, including management objectives and actions, system models, and monitoring programs. This project focuses on redevelopment of system models for population dynamics to account for habitat conditions and environmental change, and the consequent monitoring needs. Top priorities include updating population databases for climate change analyses, developing habitat and environmental data scaled to population observations, and determining monitoring and estimation methods that are sensitive to changes in both population distributions and critical habitat features. The primary objectives of this study are: 1) to explore long-term data sets for waterfowl and breeding landbirds to understand and explain factors driving spatial and temporal variability; 2) to develop models relating breeding population sizes to environmental drivers that are linked to system changes predicted by climate models; 3) to predict population responses and implications for long-term monitoring programs and adaptive habitat and harvest management strategies, and 4) to provide recommendations for incorporating these new models into existing decision-making frameworks.	Current adaptive management frameworks inform migratory bird habitat conservation and harvest decisions while accounting for a wide range of. The wildlife management community has recently committed itself to a regional approach aimed at integrating habitat, harvest, and conservation management and successful integration requires development of regional models for population and habitat dynamics that account for coordinated actions directed by habitat, conservation, and harvest management programs. Adaption of current models to meet the needs of an integrated approach are complicated by climate changes that will likely leading to shifts in system dynamics and introduce greater uncertainty into management decisions. This project is a collaboration between the COCFWRU and the USFWS Division of Migratory Birds, Branch of Assessment and Decision Support. The primary objectives of this study are: 1) to explore long-term data sets for waterfowl and breeding landbirds to understand and explain factors driving spatial and temporal variability; 2) to develop models relating breeding population sizes to environmental drivers that are linked to system changes predicted by climate models; 3) to predict population responses and implications for long-term monitoring programs and adaptive habitat and harvest management strategies, and 4) to provide recommendations for incorporating these new models into existing decision-making frameworks.
Cougar Movement Modeling	June 2012	Problem statement: Western carnivore species navigate a complex matrix of land types as they undergo their life history. In Colorado, several species are tracked with a variety of telemetry devices to understand vital rates and demographics, but relatively little was known the movement of these carnivores. So What? Why this research matters: The ability to formally make inferences about large-scale spatial and temporal movement of wild carnivores in Colorado helps us understand the natural history of the species and rigorously quantifies their space use and behavior. Collaboration/Partners: This project is in collaboration with scientists at the Colorado Parks and Wildlife . Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in telemetry data help us make dependable inference about movement of large carnivores in Colorado that can help influence management decisions about landscape connectivity, development, and land use.	Problem statement: Western carnivore species navigate a complex matrix of land types as they undergo their life history. In Colorado, several species are tracked with a variety of telemetry devices to understand vital rates and demographics, but relatively little was known the movement of these carnivores. So What? Why this research matters: The ability to formally make inferences about large-scale spatial and temporal movement of wild carnivores in Colorado helps us understand the natural history of the species and rigorously quantifies their space use and behavior. Collaboration/Partners: This project is in collaboration with scientists at the Colorado Parks and Wildlife. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in telemetry data help us make dependable inference about movement of large carnivores in Colorado that can help influence management decisions about landscape connectivity, development, and land use.
Movement Patterns, reproduction, and potential impacts of climate change on three native fishes in the upper White River drainage, Colorado	June 2015	Habitat alterations and introduction of non-native fishes have reduced the distributions of Flannelmouth Sucker Catostomus latipinnis, Bluehead Sucker Catostomus discobolus, and Roundtail Chub Gila robusta to less than 50% of their historic ranges in the Colorado River basin. Main-stem Colorado River habitat has been widely altered by construction of dams and is a main driver in the decline of native fishes. Tributaries are sometimes less altered than main-stem habitat, and may be important areas for life history processes such as spawning, but their role in population maintenance of Flannelmouth and Bluehead Sucker populations is poorly understood. Using mark-recapture techniques, I evaluated the use of tributaries as spawning areas for Flannelmouth and Bluehead suckers. Suckers were captured with fyke nets as they migrated upstream into Coal Creek, a tributary of the White River, presumably to spawn, and were PIT tagged and released. The PIT tagged fish were subsequently detected using two remote PIT tag antenna arrays placed in Coal Creek, one near the mouth and the other 2 km upstream. Suckers began to migrate into Coal Creek, in late May of 2012 and 2013 when water temperatures reached 9–12°C. Water temperature likely cued spawning movements because fish captures and PIT tag detections in Coal Creek occurred at similar temperatures in both years, despite different flow patterns. However, within 24 hours of capture and handling, the majority of suckers abandoned Coal Creek, and returned to the main-stem White River. Suckers not handled and detected only by PIT tag detector arrays remained resident in Coal Creek for an average of 10–12 days (1–32 days) depending on year and species. Handling-induced movement rendered abundance estimation of the Coal Creek population difficult and such post-handling movements should be considered when designing mark-recapture studies for these species. Tagged Flannelmouth and Bluehead suckers returned to Coal Creek in subsequent years, demonstrating >40% spawning site fidelity. High levels of site fidelity indicated that small tributaries may be important spawning habitat for these species. Finally, remote PIT tag detections also showed that 81% of tagged fish returning to Coal Creek were not also captured in fyke nets. Hence, remote PIT tag antenna arrays allowed stronger inference regarding movement and tributary use by these species than could be achieved using just fyke nets. This research shows that tributaries are an important part of Flannelmouth and Bluehead suckers life history and should be considered when developing management strategies for these species. Climate change may also alter flow and water temperature regimes in the upper Colorado River basin and impact native fish communities. Climate change models generally predict decreased stream flow and increased water temperatures. A better understanding of the impacts of flow and water temperature on the life histories of these species should lead to more informed management and allow assessments of how climate change will impact extant populations. Fish community sampling showed that the upper White River was pristine, as native fishes were > 90% of those captured. Timing of reproduction for Flannelmouth Sucker, Bluehead Sucker, and Roundtail Chub along a 150 river kilometer longitudinal gradient of a main-stem White River reach and two tributaries revealed that water temperature was the dominant environmental factor cueing reproduction for all three species. Flannelmouth Sucker, Bluehead Sucker, and Roundtail Chub reproduction began earlier in spring at warmer, lower-elevation, downstream locations and progressed longitudinally upriver in later spring or early summer as water temperatures increased. In tributaries, warmer water temperatures initiated reproduction by suckers earlier than in the adjacent main-stem White River. Timing of reproduction (based on detection of larvae) was 20-29 days earlier in 2012 than 2013 at the same locations due to earlier warming in the low flow year 2012. Daily growth microincrements in otoliths of larvae showed hatching dates were also earlier in 2012 due to warmer water temperatures and first hatching dates were progressively later in the year upstream. Presence of larvae and otolith-derived hatching dates demonstrated a distinct and predictable progression of first reproduction in an upstream direction associated with warming water. There was also a clear upstream limit to reproduction for all three species. The upstream limit for Roundtail Chub was at a lower elevation than for either sucker species. A regression model was used to predict water temperature during fish spawning seasons as a function of covariates air temperature, date, elevation, and flow. Using published climate change projections for water temperature and flow, the regression model showed that both years of this study were warmer than average and 2012 conditions approximated those for potential climate change scenarios modeled. Lower flows and warmer air temperatures as a result of climate change will result in earlier reproduction and may expand the upstream limits of thermally suitable habitat for reproduction by these three fishes, while reducing habitat size. Expansion of habitat for reproduction upstream does not ensure population persistence, as most juvenile recruitment for Flannelmouth Sucker and Bluehead Sucker occurred only in downstream reaches of the White River study area, and recruitment for Roundtail Chub was limited everywhere. Thus, populations of these species may require a network of suitable riverine habitat, including tributaries, along a relatively extensive longitudinal continuum, to promote survival of life stages needed for population persistence. The long-term implications of climate change are unknown and managers should strive to perpetuate this valuable and relatively pristine native fish community in the upper White River drainage as a vestige of the native fish communities that formerly existed throughout the Colorado River basin.	Habitat alterations and introduction of non-native fishes have reduced the distributions of Flannelmouth Sucker Catostomus latipinnis, Bluehead Sucker Catostomus discobolus, and Roundtail Chub Gila robusta to less than 50% of their historic ranges in the Colorado River basin. Main-stem Colorado River habitat has been widely altered by construction of dams and is a main driver in the decline of native fishes. Tributaries are sometimes less altered than main-stem habitat, and may be important areas for life history processes such as spawning, but their role in population maintenance of Flannelmouth and Bluehead Sucker populations is poorly understood. This research was done in collaboration with Colorado Parks and Wildlife and the USGS Southwest Biological Science Center. Populations of these species may require a network of suitable riverine habitat, including tributaries, along a relatively extensive longitudinal continuum, to promote survival of life stages needed for population persistence. The long-term implications of climate change are unknown and managers should strive to perpetuate this valuable and relatively pristine native fish community in the upper White River drainage as a vestige of the native fish communities that formerly existed throughout the Colorado River basin.
Identifying areas of abundance and species richness overlap to prioritize renewable energy exclusion zones.	June 2027	The Colorado state legislature has set a goal to transition to 100% renewable electricity generation by 2040, with an intermediate goal of 50% by 2030. This project will provide information and a spatial planning tool of renewable energy that minimizes impacts on avian species throughout the state.	None
Effects of temperature on fisheries across Colorado	June 2026	In the face of climate change, water demand, and extensive urbanization, water temperature is becoming an increasingly challenging pollutant in Colorado. Current temperature standards governing thermally-altering effluent are based on laboratory studies from a few select species that have adequate laboratory-based thermal data and most of laboratory data is focused on maximum thermal tolerances. More field data are needed to adequately address regulatory standards. Many agencies are collecting temperature data, but none specifically place their monitoring loggers where fisheries data are present. Thus, many sites have temperature data or fisheries data, but it is rare to have both at the same location. This project will fill that data-gap by placing temperature loggers at sites with good fisheries data, but inadequate temperature data. In addition, data will be collected on temperature tolerances of fish species of concern in Colorado.	None
Sea Turtle Demography	January 2027	The loggerhead sea turtle is a threatened species, including the Northwest Atlantic population. They face many threats, including fishery bycatch, and loss of foraging and nesting habitat. Monitoring sea turtles is difficult with much of it based on nest counts and tagging of nesting females. An evaluation of loggerhead monitoring and models to estimate nesting numbers and vital rates are needed to track the dynamics of nesting loggerheads. This project is a collaboration with the USGS Wetland and Aquatic Research Center, the University of Georgia, and state of Louisiana. nsights into monitoring design and effort needed to produce reasonable inference to loggerhead populations will inform USFWS and state agencies on the residual uncertainty about loggerhead dynamics that must be faced in making conservation decisions.	None
Effects of Variation in Survival, Lek Attendance, Inter-lek Movement, and Detectability of Male Greater Sage-Grouse, Count Effort, and Male Age Ratio on Lek Count Monitoring Data	June 2026	Conservation of Greater Sage-Grouse (<i>Centrocercus urophasianus</i>) is a major focus of state and federal land and wildlife management agencies in the western U.S. Greater sage-grouse populations are typically monitored and managed using data obtained from lek counts, but the reliability of lek counts as an index to abundance is uncertain. An examination of the factors that partially drive lek counts, such as survival, lek attendance rates, and interlek movements is needed to help interpret changes in lek counts. The project is a collaboration with the sage grouse research program of Colorado Parks and Wildlife, based on their information needs. From the evaluation of factors affecting lek counts simulations of conducting lek counts will assist resource managers in interpreting lek count changes and thus inform their conservation decisions.	None
META-ANALYSIS OF LEATHERBACK SEA TURTLE TAGGING DATA TO MODEL SURVIVAL, REMIGRATION, AND CLUTCH FREQUENCIES FOR THE NORTHWEST ATLANTIC POPULATION	May 2024	The Northwest Atlantic Population of the leatherback sea turtle, an endangered species, was increasing at the end of the 20th Century. However, nest count analyses indicate a declining trend over at least the last 25 years. It is not clear what demographic process(es) are causing this decline. A meta-analysis of tagging data across countries is needed to assess whether this decline is due to changes in survival, breeding probability, or reproductive effort. The project is a collaboration of researchers and biologists across multiple organizations, including WIDECAST, Ecolibrium, Inc., USGS Fort Collins Science Center, and many partners throughout Florida and the Caribbean, including the USFWS and NOAA in the USVI, Puerto Rico, and 12 other countries. The outcome of this analysis will inform conservation decisions such as mitigating bycatch in artisanal or commercial fisheries, or protecting nesting beaches.	None
Enhancing the population genetics capabilities of CPW's aquatic research section	December 2024	The project will address the growing need to understand and use population genetics concerning the regulation and conservation of native and sport aquatic species. Enhanced data capabilities will allow CPW to better ensure that national and state regulations consider Colorado-specific fish and amphibian species and ecosystem concerns. The primary goal of the project is to provide support for data curation, data analysis, and manuscript/report writing related to population genetics projects within CPW’s Aquatic Research Section. Data will be used for the management of amphibian and fish populations in Colorado	None
Using a whole-genome approach to distinguish native vs introduced genetic diversity in Colorado River Cutthroat Trout	June 2025	TBA	None
Development of protective temperature criteria for Bluehead Sucker, Flannelmouth Sucker and Roundtail Chub Larvae	June 2026	Water temperature is a critical abiotic factor that contributes to larval fish survival. Many fish species are poorly adapted to survive water temperatures that lie outside historic annual or seasonal variability. To properly manage the three species it is essential to understand their thermal tolerances. Bluehead Sucker, Flannelmouth Sucker, and Roundtail Chub, hereinafter referred to as the three species, intermittent and ephemeral streams for refugia from high main-stem flows, foraging, and for spawning and larval rearing. A review of these three species in the Colorado River basin suggest that they occupy 50% or less of their historic ranges, and current populations are still declining. The declines are thought to be in part caused by changing stream water temperatures. These data will be used to address management concerns regarding the three species and stream water temperature.	TBA
Assessing virulence and distribution of Renibacterium salmoninarum found in Colorado	January 2025	TBA	TBA
Application of Artificial Learning Technology to Colorado Parks and Wildlife Camera Data	June 2025	Remote cameras, which can take photos on sequential or time-lapse schedules, or via activation of an infrared trigger, are now used in a wide array of research and monitoring programs and they generate vast volumes of data. In order to use animal data from these photos to estimate occupancy or abundance, an efficient process is needed that uses machine learning (ML) techniques to extract species identification and accounts for classification error. The project is a collaboration with mammal researchers of Colorado Parks and Wildlife. The ML model and workflow developed will be used to build models to assess species distribution and population dynamics, by researchers as well as managers for different species.	Remote cameras, which can take photos on sequential or time-lapse schedules, or via activation of an infrared trigger, are now used in a wide array of research and monitoring programs and they generate vast volumes of data. In order to use animal data from these photos to estimate occupancy or abundance, an efficient process is needed that uses machine learning (ML) techniques to extract species identification and accounts for classification error. The project is a collaboration with mammal researchers of Colorado Parks and Wildlife. The ML model and workflow developed will be used to build models to assess species distribution and population dynamics, by researchers as well as managers for different species.
Windy Gap	December 2006	Windy Gap Reservoir (WGR), a 38 hectare impoundment on the Colorado River in Middle Park, Colorado, has been a major point source of production of triactinomyxon (TAM) actinospores of Myxobolus cerebralis (Mc) since the 1990s. Beginning in 2001, TAM production in WGR declined dramatically and remained low through June 2006. The decline was correlated with a change in oligochaete dominance from parasite susceptible strains of Tubifex tubifex (lineage III) to resistant strains (lineages I, V, VI). These results support the hypothesis that resistant T. tubifex lineage worms (I, V and VI) are acting as biofilters in WGR and may deactivate myxospores of M. cerebralis, thereby reducing ambient levels of TAM production.	Windy Gap Reservoir (WGR), a 38 hectare impoundment on the Colorado River in Middle Park, Colorado, has been a major point source of production of triactinomyxon (TAM) actinospores of Myxobolus cerebralis (Mc) since the 1990s. Total numbers of TAMs observed in water discharged annually from WGR from April 1997 through March 1998 and April 1998 through March 1999 were conservatively estimated at 960 billion and 1.8 trillion, respectively. Two separate studies in 1998 identified the area of the lake receiving the inflow of water from the Colorado River as the zone where Mc infection was highest among Tubifex tubifex worms and also the area where TAM production was highest. Beginning in 2001, TAM production in WGR declined dramatically and remained low through June 2006. Between 2001 and 2004 several hypotheses were tested to determine whether or not they explained the decline in ambient levels of TAM production that began in 2001. These hypotheses included differences in water level in WGR between years, changes in the thermal regime of the lake, severe drought and concomitant low levels of inflow, changes in the fish population structure in WGR, and changes in the prevalence and severity of Mc infection in brown and rainbow trout in the Colorado and Fraser rivers upstream of WGR. All were discarded as plausible explanations for the decline in TAM production. In 2005, a new study was conducted to replicate studies completed in 1998. Results of the 2005 study suggest that compared to 1998, the density of aquatic oligochaetes and T. tubifex may have increased, TAM production was greatly reduced, and that decline was congruent with the dominance of the lineage I, V and VI T. tubifex in the oligochaete population. These three lineages in WGR are refractory or highly resistant to infection by M. cerebralis. These results support the hypothesis that the non-susceptible T. tubifex lineage worms (I, V and VI) are acting as biofilters in WGR that deactivate myxospores of M. cerebralis and thereby reduce ambient levels of TAM production.
William's Fork	December 2005	The physical variables influencing the distribution and abundance of Tubifex tubifex in stream habitats are not well understood and could have implications for the success of using resistant T. tubifex lineages to manage whirling disease. Our primary objective was to evaluate if sediment size distribution and other physical microhabitat factors were associated with lineage composition of T. tubifex. Our second objective was to randomly sample stream habitats to gain a more complete understanding of T. tubifex distribution across a wide variety of stream habitat types.	The physical variables influencing the distribution and abundance of Tubifex tubifex in stream habitats are not well understood and could have implications for the success of using resistant T. tubifex lineages to manage whirling disease. Our primary objective was to evaluate if sediment size distribution and other physical microhabitat factors were associated with lineage composition of T. tubifex. Our second objective was to randomly sample stream habitats to gain a more complete understanding of T. tubifex distribution across a wide variety of stream habitat types. Canonical Correspondence Analysis showed that lineage III, V, and VI differed in their relative abundances among sites and that depth and sediment characteristics were the physical habitat variables that best explained the differences in lineage composition among the sites. Lineage V worms were associated with higher levels of coarse sand and gravel, as well as somewhat deeper habitats than lineage III worms. Lineage VI worms appear to be associated with somewhat deeper habitats than either lineage III or V. The spatial distribution of lineages did not follow a predictable longitudinal pattern. Lineage V was the dominant lineage at all stream reaches with interspersed samples being dominated by lineage III. The T. tubifex composition at 23 of 29 targeted sampling sites was dominated by lineage V and 3 of 29 samples were dominated by lineage III. Two samples had about equal proportions of lineage III and V. Lineage VI was represented at 27 of the sites but was dominant in only one sample. T. tubifex CPUE was not significantly related to either depth or flow velocity; however, flow velocity was more strongly related to CPUE than depth. A MANOVA indicated that the overall difference in depth and flow between sites with and without T. tubifex was not significantly different.
Reproductive Consequences of Exposure to Exogenous Estrogens	June 2008	Endocrine disrupting chemicals (EDCs) have been detected in surface waters worldwide and can lead to developmental and reproductive disruption in exposed fishes. In the Great Plains, EDCs are impacting streams and rivers and may be causing adverse reproductive effects. To examine how estrogenic EDCs might affect reproductive success of plains fishes, we experimentally exposed male red shiners (Cyprinella lutrensis) to exogenous 17β-estradiol. We characterized the effects of estradiol on male gonadal histology and secondary sexual characteristics, determined whether exposure reduced reproductive success, and examined the effects of depuration. Adults were exposed to a mean concentration of 70 ngL-1 estradiol, a solvent control, or a water control for at least 83 d. Male exposure to estradiol resulted in elevated plasma vitellogenin concentrations, changes in spermatogenesis, reduced mating coloration and tubercles, altered mating behaviors, and reduced reproductive success with no viable progeny produced. Reproductive endpoints improved upon depuration (28 d). Exposure to estradiol had significant adverse effects on red shiners, indicating that wild populations may face developmental and reproductive difficulties if they are chronically exposed to estradiol.	tba
Use of Otolith Elemental Signatures in Estimating Sources of Northern Pike Recruitment	September 2008	We used otolith microchemistry to develop elemental signatures that could be used to identify sources of northern pike recruitment throughout the Yampa River basin in Colorado	Predation from nonnative northern pike, Esox lucius, has caused extensive problems for native fish assemblages in the Yampa River and evaluating potential control options for northern pike requires a clearer understanding of recruitment. If recruitment sources can be identified, then management efforts can focus on these areas to reduce reinvasion. We used otolith microchemistry to identify trace elemental signatures that could be used to identify sources of northern pike recruitment throughout the Yampa basin. We found that 2-3 elements (Sr, Ba, and Mn) were useful in discriminating among sites on the Yampa River. Due to annual variation in the trace elemental signatures, age 0 northern pike would need to be collected and analyzed each year to use these signatures to classify unknown fish. Our analyses indicate that classifying northern pike is variable, particularly among small off-channel ponds. When all sampling sites were included in the analysis the percentage of fish correctly classified to their natal area, averaged 64% in 2005 and 58% in 2006. However, classifying fish from larger reservoirs was more successful. Classification rates between Stagecoach Reservoir and Lake Catamount ranged from 73-100% from 2004 to 2007, with an overall average of 90%. Classification rates were higher in low runoff years than in high runoff years. Despite challenges associated with the technique, we believe that otolith microchemistry is a useful tool for explaining northern pike recruitment and can help managers focus control efforts. We recommend that managers; 1) continue collections of age-0 northern pike in the Yampa River and develop a database of annual signatures. 2) We recommend that managers of Lake Catamount continue to monitor pike elemental signatures to address rates of immigration from Stagecoach Reservoir to Lake Catamount to address the efficacy of pike removal. We recommend that future research; 1) examine other potential markers such as strontium isotopes. 2) Otolith trace elemental analyses should continue to allow examination of interannual variability and determine if this challenge can be overcome.
Evaluation of Myxobolus Cerebralis Distribution and Infection Severity in Labarge Creek	June 2026	The overall goal of our project is to provide an evaluation of the current distribution and infection severity of MC in the LaBarge watershed above the fish migration barrier. Understanding the distribution of the parasite and disease severity will be essential to formulating future management options. <br>In year 1, we will address disease levels in wild fish and use eDNA sampling to identify the distribution of MC and the density of TAM production. These data are an essential first step in evaluating the spatial distribution and disease severity in LaBarge Creek and will help guide future sampling and research efforts. The use of eDNA could reduce sampling effort and cost in the future and reduce the need to sample rare or sensitive fish populations. They will also be immediately useful to managers for decisions relative to the stocking of CRC.<br>In year 2, we will evaluate the spatial distribution and relative disease risk, using caged sentinel CRC. We will collect data on the prevalence of infection, disease severity, and TAM production during the experiment. These data will compliment the field data from the first season and provide a more nuanced examination of MC disease severity and risk. The spatial component will be especially useful in future decisions about CRC reintroduction. <br>Finally, we propose to conduct a laboratory study to correlate disease severity to TAM exposure and compare these results to disease severity and TAM production estimates from LaBarge Creek. Laboratory exposures will allow a more controlled initial exposure and we can compare these data to the field observations and caging, allowing for more precise inferences on MC disease risk in LaBarge Creek. <br>Our proposed study will be useful in management decision making, especially in identifying areas that may be more suitable for reintroduction or mitigation to allow reintroduction.	Colorado River Cutthroat Trout (CRC) occupy about 550 miles of stream habitat in Wyoming, which entails about 13% of the historical distribution; however, only 3.7% of the current distribution is considered core conservation populations.<br><br>One major conservation effort is in LaBarge Creek and it is thought that the reintroduction effort may be threatened by the presence of <i>Myxobolus cerebralis</i> (MC), the parasite that causes whirling disease. We will assess the distribution of MC infection throughout the LaBarge watershed, which is necessary for understanding future management options to reestablish and increase recruitment for CRC.<br><br>The research is in collaboration and funded by Wyoming Game and Fish Department.<br><br><br> The overall goal of our project is to provide an evaluation of the current distribution and infection severity of MC in the LaBarge watershed above the fish migration barrier. Understanding the distribution of the parasite and disease severity will be essential to formulating future management options.
Assesing the role of Whirling Disease in Causing Trout Declines in the North Tongue River	June 2025	Identifying whether whirling disease is contributing to trout population declines is essential to formulating management strategies that will maintain viable trout populations on the North Tongue. Using the approaches outlined in the proposal, we will be able to better understand natural disease levels in wild fish and exposure risk to fish over the controlled caging study duration. The expected results will include MC infection prevalence and infection intensity information across species and life stages of the five trout species present. We will also have a clearer understanding of spatial variation in disease risk across the six stations. In general, this information will determine whether MC is contributing significantly to trout population declines or whether more studies are needed to evaluate other possible causal factors of population declines. These results will collectively be useful in management decision making, including possible adjustments to the number and strains of trout that are stocked to better sustain fish populations for angling in the presence of MC. For instance, it may be desirable to shift the fishery towards more resistant strains, but detailed information on MC status is needed beforehand.	Identifying whether whirling disease is contributing to trout population declines is essential to formulating management strategies that will maintain viable trout populations on the North Tongue River, Wyoming.<br><br>Using the approaches outlined in the proposal, we will be able to better understand natural disease levels in wild fish. The expected results will include <i>Myxobolus cerebralis</i> (the parasite that causes the disease) infection prevalence and infection intensity information across species and life stages in five trout species. We will also have a clearer understanding of spatial variation in disease risk.<br><br>The project is being done in collaboration with and funded by Wyoming Game and Fish Department.<br><br>These results will collectively be useful in management decision making, including possible adjustments to the number and strains of trout that are stocked to better sustain fish populations for angling in the presence of MC. For instance, it may be desirable to shift the fishery towards more resistant strains, but detailed information on MC status is needed beforehand.
Evaluation of Decision Structures and Monitoring Programs for Managing Sandhill Cranes	December 2014	Harvest management of sandhill cranes currently uses simple threshold approaches based on three-year average population objectives.The primary objective of this study is to develop stage-based models of the Rocky Mountain and Mid-Continent Populations, to address two general questions about crane management. First and foremost, what are the risks to these populations, in light of management objectives, of continuing the current decision rules for harvest decisions? If the risks are unacceptable, should the decision rules be altered, and is additional monitoring information needed to better inform decisions? In addition, for any specified level of monitoring effort, what can be expected in terms of performance measures identified in management objectives (e.g., crane harvest and crane numbers)? Second, given the limitations of our knowledge of crane populations and the best-case scenario with respect to the monitoring effort that could be devoted to cranes, what are the potential advantages and limitations for using models to directly inform management decisions? As part of this effort, hypotheses about other important and measurable limiting factors on a population or subpopulation can be evaluated (e.g., the effect of climatic variables on recruitment).<br>Results from an initial modeling effort using existing data will provide an assessment of these issues, as well as tools to build a decision-making framework that would be applicable to all hunted sandhill cranes populations, and ultimately would improve harvest management decisions that sustain sandhill cranes at identified abundance levels and distributions. Such sandhill crane models also could be informative for non-hunted populations of cranes, and could be further adapted to address their management needs.	None
Design and Analysis of Manatee Demographic Models	June 2014	The Manatee Population Status Working Group, convened by USFWS as part of its Florida Manatee Recovery Team, submitted a Biological Population Assessment of the Florida Manatee to the Service in 2005. The Group listed research priorities to improve future assessments and reduce uncertainty in models of population dynamics, which primarily are based on parameter estimates from photo-identification data in the Manatee Individual Photo-identification System (MIPS). Top priorities included: fill the gaps in regional estimates of calf and subadult survival rates and breeding rates, incorporate carcass recovery data into estimation of survival rates, and improve precision of population parameter estimates by joint analysis of multiple data sources. The primary objectives of this study are to: 1) develop manatee demographic models integrating photo-identification and genetic fingerprinting of live individuals and recovered carcasses; 2) develop and implement a model of adult manatee survival probabilities specific to migration patterns identified for manatees of the Atlantic Coast region; and 3) implement a model to estimate boat-strike scar acquisition probabilities for manatees in the Northwest region.	TBA
Building USGS Capacity in Modeling: a Collaboration among the Colorado Cooperative Research Unit, the Alaska Science Center, and the Patuxent Wildlife Research Center	August 2015	The overarching objective is to develop, in collaboration with stakeholders and USGS research scientists, an adaptive management framework for wildlife populations on the National Petroleum Reserve – Alaska (NPRA). Specific objectives related to this are: (1) to facilitate the development by various stakeholders of specific management objectives that balance the dual Department of Interior (DOI) mandates of facilitating responsible extraction of oil and gas reserves and sustaining wildlife populations, such as molting geese; (2) to work with these same stakeholders to identify practical and politically feasible management actions that could meet the specified objectives; (3) to work with research and management biologists to develop empirically or theoretically tenable models that predict the system response and consequences with respect to the objectives of each candidate management action identified in objective 3; (4) to review current monitoring programs for this system, to determine if they could be improved to inform the decision process more directly; and (5) depending on the agreed upon management objectives and constraints, to explore mathematical approaches to identification of an optimal or satisfactory management policy for this system. Finally, the outcome of developing an adaptive management framework for this particular system should provide at least a structure and perhaps a template for considering adaptive management of other arctic systems.	TBA
Evaluation & Control of Whirling Disease in the White River, CO	June 2011	Field observations and experiments are being conducted to estimate the impact of new artificial trout ponds on the prevalence and severity of whirling disease (Myxobolus cerebralis) in the White River, CO. We are monitoring triactinomyxon production, Tubifex tubifex lineage composition, as well as the prevalence of the parasite in fish populations in the White River. Manipulative experiments are also being conducted to evaluate the potential for using parasite resistant T. tubifex to control the severity of whirling disease in pond environments.	None
Whirling Disease-Resistant Trout Evaluation	June 2013	Myxobolus cerebralis, the parasite responsible for whirling disease, has caused widespread population collapses in wild rainbow trout (Oncorhynchus mykiss) populations throughout the intermountain west. Disease-resistant rainbow trout have been considered as a potential option for reintroducing rainbow trout populations in the presence of the disease and the German strain (GR) of rainbow trout is at least as resistant to whirling disease as the highly-resistant brown trout (Salmo trutta) under laboratory conditions. The GR strain has been crossed with the susceptible Colorado River rainbow (CRR) to produce rainbow trout that are resistant to whirling disease but retain traits necessary for survival in the wild. However, little is known about how these strains will survive and reproduce when stocked in streams and rivers. Our study has two objectives: one is to evaluate the success of ongoing resistant rainbow trout introductions in Colorado. We will assess survival, reproduction, and recruitment using mark-recapture and genetic methods. The second objective is to evaluate brown trout removal as a management option to promote the retention and survival of introduced whirling disease resistant rainbow trout. This study is designed to estimate the rate and magnitude of rainbow trout migration in areas with ambient levels of brown trout and in areas where brown trout numbers have been reduced. We are assessing rainbow and brown trout movement using Radio Frequency Identification (RFID) Passive Integrated Transponder (PIT) tags and 8 in-stream RFID antennas. We have marked 4000 rainbow trout which have been introduced into two areas of the Poudre River, CO. In one area brown trout were removed using electrofishing. We have about 1500 brown trout marked in each section. The study is designed to allow us to estimate the movement and survival of rainbow trout in each section.	TBA
Population Dynamics Modeling of Introduced Smallmouth Bass-Upper CO River	September 2014	Piscivores such as smallmouth bass Micropterus dolomieu and northern pike Esox lucius are established and common in the lower Yampa River, the upper and middle Green River basins, and the upper Colorado River. The threat of these introduced predators is substantial and smallmouth bass are problematic because of their high abundance, habitat use that overlaps with most native fishes, and capability to consume a wide variety of life stages of native fishes in the Colorado River Basin. Expanded populations of smallmouth bass are a major impediment to conservation actions aimed at recovery efforts for four endangered fishes in the Upper Colorado River Basin. In response to the predatory threat posed by non-native fishes such as smallmouth bass, the Upper Colorado River Recovery Implementation Program initiated efforts to control such species via mechanical removal in affected stream reaches. Substantial information has been collected on distribution, population abundance, size structure, and movements of smallmouth bass concurrent with removal actions throughout the Upper Colorado River Basin. The Upper Colorado Recovery Program has initiated population modeling to analyze some of these data and to gain insight into removal strategies for smallmouth bass. However, more detailed modeling and analyses are necessary to provide a clearer understanding of population level effects of removal, to help formulate a comprehensive control strategy to reduce populations of smallmouth bass, and to enhance recovery of native fish populations. We are expanding the scope of recent population dynamics models using data collected in the system, the summary database for removal, and our own unpublished information. Our goal is to develop a comprehensive age- or size-structured model to understand factors that affect smallmouth bass population dynamics in the Upper Colorado River Basin. Our model will include density dependent feedback and environmental inputs that can be manipulated independently of each other. The model will also address uncertainty and variability in the parameters and relationships in the model to evaluate its influence on the outcomes and predictions.	TBA
Integrating Population Modeling for Laysan and Black-Footed Albatross	July 2023	TBD	TBD
Evaluation of Cripple Creek (mule deer herd D16) and Wet Mountain (mule deer D34) Demographics (Auction and Raffle funded M.S. project)	March 2024	Colorado Parks and Wildlife (CPW) initiated a research project in 2017 to examine predator-prey dynamics between cougars and mule deer in the Upper Arkansas drainage within the South East region of Colorado. These data include GPS location data for deer (does and fawns) across all years of the study. Although a thorough examination of habitat use and movement patterns of mule deer has been conducted on migratory deer populations the western slope of Colorado, a similar evaluation of the mostly non-migratory population on the eastern slope is needed. The project is a collaboration with researchers and managers of CPW. Results will be used to inform population and habitat management of mule deer in Colorado.	Colorado Parks and Wildlife (CPW) initiated a research project in 2017 to examine predator-prey dynamics between cougars and mule deer in the Upper Arkansas drainage within the South East region of Colorado. These data include GPS location data for deer (does and fawns) across all years of the study. Although a thorough examination of habitat use and movement patterns of mule deer has been conducted on migratory deer populations the western slope of Colorado, a similar evaluation of the mostly non-migratory population on the eastern slope is needed. The project is a collaboration with researchers and managers of CPW. Results will be used to inform population and habitat management of mule deer in Colorado.
Burrowing Owl population assessment on Colorado's black tailed prairie dog colonies	December 2024	Burrowing owls (<i>Athene cunicularia, </i>hereafter BUOW) are classified as a Tier 1 species of greatest conservation need in Colorado’s State Wildlife Action Plan, and are associated with prairie dog colonies. However, there is little information on population status or trends for this species, with the last previous assessment conducted 18 years ago. A current assessment of BUOW distribution, reproductive success, and abundance, and how these relate to prairie dog colony attributes is needed. The project is a collaboration with Colorado Parks and Wildlife, with the cooperation of numerous private landowners. The models for species distribution, abundance, and reproductive success, and their relationship with prairie dog colony attributes, will be useful to managers for assessing the status of BUOW in Colorado, and will inform their interactions with landowners in managing prairie dogs.	Burrowing owls (<i>Athene cunicularia, </i>hereafter BUOW) are classified as a Tier 1 species of greatest conservation need in Colorado’s State Wildlife Action Plan, and are associated with prairie dog colonies. However, there is little information on population status or trends for this species, with the last previous assessment conducted 18 years ago. A current assessment of BUOW distribution, reproductive success, and abundance, and how these relate to prairie dog colony attributes is needed. The project is a collaboration with Colorado Parks and Wildlife, with the cooperation of numerous private landowners. The models for species distribution, abundance, and reproductive success, and their relationship with prairie dog colony attributes, will be useful to managers for assessing the status of BUOW in Colorado, and will inform their interactions with landowners in managing prairie dogs.
Whirling Disease	June 2012	None	None
Endocrine Disruption Survey	February 2013	The presence of endocrine-disrupting compounds (EDCs) in aquatic ecosystems is widespread and these compounds have been shown to cause developmental and reproductive disruption in wild freshwater fishes worldwide. Although the effects of endocrine disrupting compounds (EDCs) on the individual physiology of animals are well known, less is known about the ultimate population-level consequences, and it is important to begin to understand how exposure to EDCs influences animal population dynamics. We are particularly interested in effects of EDCs on resident Great Plains fish populations and communities that are downstream of large urban centers along the front range of the Colorado Rocky Mountains, such as Boulder, Denver, Fort Collins, and Colorado. We have completed one study investigating the effects of a known endocrine disruptor, 17-β estradiol (E2), on reproductive behavior and success of red shiner (Cyprinella lutrensis), a fish native to the plains region of Colorado. Male exposure to estradiol resulted in elevated plasma vitellogenin concentrations, changes in spermatogenesis, reduced mating coloration and tubercles, altered mating behaviors, and reduced reproductive success with no viable progeny produced. Our results indicate that wild populations of red shiners may face developmental and reproductive difficulties if they are chronically exposed to estradiol. Additional field, laboratory, and mesocosm experiments are currently in progress. Field experiments consist of caging fathead minnows above and below waste water effluents to estimate the effects of exposure on several physiological endpoints. These physiological metrics will be compared to results from more controlled exposures in the lab. Field collections of fish and water chemistry will be made to estimate correlations between water quality and population and community composition. Mesocosm experiments are currently underway to estimate the effects of exposure to 17α-ethynylestradiol (EE2) on survival, reproduction, and recruitment of fathead minnows.	None
Evaluating tiger muskellunge as a multi-purpose management tool: protecting native fish species from multiple conservation threats	June 2026	Under the supervision of Colorado Parks and Wildlife’s (CPW) Aquatic Research Section, and with specialized equipment and expertise provided by CPW, the Research Associate will implement an evaluation of stocking tiger muskellunge (sterile northern pike and muskellunge hybrids) as a means to disadvantage introduced species (northern pike, smallmouth bass, white sucker), while simultaneously diminishing motivation to illicitly transplant non-native predators that negatively impact native fish species and whole ecosystems. This approach compliments native fish protection efforts in the Yampa and Colorado river basins.One of the biggest threats to the protection and conservation of native fishes in Colorado is the spread of invasive species. The information gained from this project will provide an indication of the efficacy of tiger muskellunge stocking as a management tool in Shadow Mountain and Elkhead reservoirs to combat factors threatening native fishes in Colorado. Tiger muskellunge have the potential to provide several benefits to fisheries and native species (i.e., cutthroat trout, native three-species, mountain whitefish) including:<br><br>• Improving conditions for native fish by disadvantaging non-native predators (northern pike and smallmouth bass) that have been illegally introduced, and undesirable species that are spreading in Colorado like white suckers<br><br>• A controllable method for disadvantaging nuisance species that is compatible (sterile hybrid) with native fish conservation goals, and discouraging further spread/introduction of non-native predators	One of the biggest threats to the protection and conservation of native fishes in Colorado is the spread of invasive species. <br><br>The information gained from this project will provide an indication of the efficacy of tiger muskellunge stocking as a management tool in Shadow Mountain and Elkhead reservoirs to combat factors threatening native fishes in Colorado.<br><br>The project is being done in collaboration with Colorado Parks and is funded by CPW.<br><br>Improving conditions for native fish by disadvantaging non-native predators (northern pike and smallmouth bass) that have been illegally introduced, and undesirable species that are spreading in Colorado like white suckers
Coop Unit Administrative Support from CPW	June 2027	The Colorado Cooperative Fish and Wildlife Research Unit receives annual contributions from Colorado Parks and Wildlife to aid in the administrative functions of the Unit and to enhance ongoing graduate student research projects.	The Colorado Cooperative Fish and Wildlife Research Unit receives annual contributions from Colorado Parks and Wildlife to aid in the administrative functions of the Unit.<br><br>These funds are critical to the ongoing research, graduate education and technical assistance mission of the unit. <br><br>The funds are part of the cooperative agreement with Colorado Parks and Wildlife.<br><br>These funds help support all aspects of the Unit mission.
Heavy Metals in Cape Krusenstren National Monument	June 2024	N/A	N/A
Burrowing Owl population assessment on Colorado's black tailed prairie dog colonies	June 2022	N/A	N/A
Modeling and Decision Analysis for Plague in Prairie Dog Colonies	February 2023	N/A	N/A
Integrated Ecosystem Modeling Fish In the Grand Canyon	September 2024	Several fish species of interest to federal and state managers occupy the Colorado River within the Grand Canyon, including humpback chub (<i>Gila cypha</i>), flannel mouth suckers (<i>Catostomus latipinnis</i>), and rainbow trout (<i>Oncorhynchus mykiss</i>). A better understanding of how environmental variation and various management actions affect population and ecosystem dynamics requires development of new models that integrate disparate data informing both population and food web processes. Therefore an integrated ecosystem model for the Grand Canyon that includes the dynamics of humpback chub, flannelmouth sucker, and rainbow trout, combined with the dynamics of invertebrates and primary productivity, and assesses the transfer energy efficiency among trophic levels, is needed. This project is a collaboration with USGS Grand Canyon Monitoring and Research Center. The model and its results can be used by federal and state managers to better understand the ecosystem and fish populations, to evaluate which flows are best for meeting multiple management goals.	Several fish species of interest to federal and state managers occupy the Colorado River within the Grand Canyon, including humpback chub (<i>Gila cypha</i>), flannel mouth suckers (<i>Catostomus latipinnis</i>), and rainbow trout (<i>Oncorhynchus mykiss</i>). A better understanding of how environmental variation and various management actions affect population and ecosystem dynamics requires development of new models that integrate disparate data informing both population and food web processes. Therefore an integrated ecosystem model for the Grand Canyon that includes the dynamics of humpback chub, flannelmouth sucker, and rainbow trout, combined with the dynamics of invertebrates and primary productivity, and assesses the transfer energy efficiency among trophic levels, is needed. This project is a collaboration with USGS Grand Canyon Monitoring and Research Center. The model and its results can be used by federal and state managers to better understand the ecosystem and fish populations, to evaluate which flows are best for meeting multiple management goals.
Enhancing Capabilities of CPW's Statewide Aquatic Toxicology Program	June 2023	NA	NA
Field examination of thermal pollution on stream temperature and reproductive development of Johnny Darter, Etheostoma nigrum (Percidae)	April 2022	<b><u>Project Description</u></b><b>: </b><br><b> </b><br><u>Objective 1. Characterizing Wastewater Effluent Water Temperatures</u><br><u> </u><br><i>Goal:</i> To characterize WWTP effluent and its effect on stream thermal characteristics. <br> <br><i>Background:</i> Wastewater effluents (WWE) will have varying influences on stream temperature depending on the temperature of the effluent and the discharge and temperature of the receiving stream. The effects of WWE will also vary seasonally based on water temperature and discharge. We propose to monitor temperature from sites that characterize various effluent scenarios as a baseline for interpreting biological data (See Objective 2 below). These data will also serve as a temperature baseline for future monitoring and management of eastern Colorado transitional and warm water streams. <br> <br> <i>Approach:</i> <br> <br><b><i><u>Task 1</u></i></b>. We propose to meet with managers and scientists from Colorado Parks and Wildlife, other interested agencies, and WWTPs to determine appropriate field sites for monitoring temperature. Once sites are identified, we will deploy temperature-monitoring equipment. We will also and monitor stream discharge and basic water quality seasonally at the same sites. Stream discharge will be measured using standard USGS methods. Basic water quality data will include specific conductance, pH, water temperature, turbidity, and dissolved oxygen. We also propose to gather, collate, and summarize existing historical records for temperature from WWTP’s and other groups that monitor temperature on eastern Colorado transitional and warm water streams. <br> <br><b><i><u>Task2.</u></i></b> To understand the influence of WWTP effluent on stream temperature it is important to consider the longitudinal aspects of water temperature (Figure 1). VerHoef and Peterson’s (2010) spatial statistical network models are a well-recognized tool for analyzing stream attributes like temperature. The GIS tools and R script for implementing these models are available and have been used extensively in temperature modeling (Issak et al. 2014 and http://www.fs.fed.us/rm/boise/AWAE/projects/SpatialStreamNetworks.shtml). We propose to analyze data collected in Task 1 using these models. <br> <br>Figure 1. Conceptual model of stream temperature measurement and modeling. The x-axis represents distance to and from a WWTP. The hashes on the x-axis represent locations of temperature monitors. The dashed line represents a temperature threshold and this could represent an important temperature for any biological activity (i.e. reproduction). The WWTP effluent raises the base stream temperature. In this example, the temperature decreases exponentially back to the base stream temperature. However, the relationship of stream temperature to distance downstream could be any function. In this example, the stream temperature returns to the threshold between two temperature monitors. If the function is known, then the spatial location of the event can be identified, as well as the uncertainty of that location. The same modeling can be done with other events, such as return to base temperature. Covariates that effect the shape of the function can also be included (i.e. air temperature, discharge, land cover). <br> <br> <br><u>Objective 2. Evaluating Johnny Darter reproduction in the field</u><br><u> </u><br><i>Goal: </i>To evaluate reproductive condition of Johnny Darter in the wild.<br><i> </i><br><i>Background: </i>Gonad weight changes seasonally and can indicate reproductive status in fishes. However, inferences that are more detailed can be made using histology and histology is an effective tool to study the reproductive cycle in fishes (Blazer 2002). It is routinely used for sex verification and assessing reproductive development (Blazer 2002). It can also be used to document abnormalities, such as intersex, and diseases, such as tumors and parasites (Blazer 2002). Gonadal histology can provide insights into reproductive timing as well as the effects of various environmental stressors on reproductive health (Blazer 2002). <br><i> </i><br><i>Approach:</i> We will evaluate reproductive condition using gonad weights and histology. The general strategy will be to collect Johnny Darter seasonally from above and below WWTP’s at the sites identified in Goal 1-Task 1. We will compare fish reproductive status among sites and correlate those observations with water temperature.	Wastewater effluents (WWE) influence stream temperature and may have effects on the timing and magnitude of fish reproduction. Understanding the effects of WWE on fish reproduction is critical to developing stream temperature standards. This project is a collaboration of USGS, Colorado Parks and Wildlife, Colorado Department of Public Health and Environment, and several municipalities and Waste Water Treatment Plants. The data will be used to evaluate the current warm-water stream temperature standard.
Evaluation of Cripple Creek (mule deer herd D16) and Wet Mountain (mule deer D34) Demographics (Auction and Raffle funded M.S. project)	June 2022	Colorado Parks and Wildlife (CPW) initiated a research project in 2017 to examine predator-prey dynamics between cougars and mule deer in the Upper Arkansas drainage within the South East region of Colorado. This is a 9 year study that is generating a tremendous amount of data on both deer and cougars. These data include GPS location data for deer (does and fawns) across all years of the study. While these data are important to the original study objectives it will not be used to its fullest potential, including a thorough examination of habitat use and movement patterns of mule deer in this area. While such research has been conducted on the western slope of Colorado, where mule deer are largely migratory, very little research has been conducted on the eastern slope. Therefore, there is a great opportunity to leverage these data to learn more about mule deer in this area and on a predominantly non-migratory population.	Very little is known about non-migratory mule deer populations and how they utilize these landscapes. While these populations are not migratory, they are still moving across the landscape in response to many factors.<br><br>Understanding seasonal movements of non-migratory mule deer with various landscape and climate factors will provide useful information to wildlife managers as this is not well understood.<br>
A genetic assessment of cutthroat trout movement across the Continental Divide	December 2021	TBA pending	TBA pending
Moss Tissue Concentrations	July 2021	Pndg	Pndg
Brook Trout Population	June 2024	Pndg	Pndg
Modeling the Effect of White-nose Syndrome Mitigation Decisions on Cave Hibernating Myotis Species	September 2022	Pndg	Pndg
Lesser Prairie-Chicken	September 2022	Pndg	pndg
Quantitative Assessment of Pelagic Fishes in Colorado Reservoirs	June 2027	<b>The goals of this project are to implement a statewide pelagic fish </b><b>assessment, involving paired gill-netting and nocturnal hydroacoustics surveys. We wish to quantify the density</b><br><b>and distribution of key sport and forage fish in Colorado's large standing waters. </b>	<b><b>Kokanee salmon and other pelagic sportfish are worth millions of dollars annually to Colorado's economy and it is critically important to collect date to guide management decisions. A</b>nnual </b><b>hydroacoustics surveys are particularly important for monitoring and managing Colorado's pelagic f</b><b>isheries. They provide population assessments as well as estimates of forage and environmental conditions.</b><b> The assessment is being done in collaboration with Colorado Parks and Wildlife</b><b>. </b>
Field Examination of Wastewater Treatment Effluent Thermal Regimes and Effects on Reproduction of Johnny Darter Etheostoma Nigrum	June 2022	The ultimate goal of our study is to provide Colorado Parks and Wildlife guidance as to appropriate thermal regimes to conserve transition zone native fishes. The results will be implemented into management strategies for the conservation and recovery of native transition zone fishes.<br><br>We will characterize wastewater treatment effluent thermal effects on transition zone streams by placing temperature loggers above and below wastewater treatment facilities along the Front Range to determine potential thermal alterations. Wastewater treatment facilities will be included based on input from previous research and CPW staff—especially the Water Quality Coordinator. Critical time periods include winter and shoulder seasons (transition seasons between fall–winter and winter–spring).<br> <br>We will also evaluate how altered thermal regimes are affecting reproduction of Johnny darter, <i>Etheostoma nigrum</i>. Field collections of Johnny darter will take place above and below wastewater treatment facilities to examine if there are differences in reproductive output. To examine seasonality of egg production, Johnny darter will be collected every month. Once collected, fish will be preserved and examined for egg production. Egg production includes number of eggs produced, size of eggs, developmental stage of eggs, and timing of egg production.<br>	Historically, the South Platte River Basin naturally experienced a wide range of seasonal temperatures. However, urbanization and development of WWTPs have contributed to warmer and more consistent water temperatures throughout the year that may effect fish reproduction. We are collaborating with Colorado Parks and Wildlife on this project. Assessing the thermal requirements of warm water fishes will provide valuable information towards establishing protective winter water temperature standards in effluent-dominated streams.
Control of sucker spawning migrations in a major tributary of the Gunnison River to increase the production of native sucker larvae	September 2021	Non-native suckers in the Upper Colorado River are a major threat to the persistence of native suckers. Our project seeks to manage that threat by removing non-native suckers during the spawning migration. The project consists of 2 goals. First, we will preclude entry of non-native and hybrid suckers to the native spawning run, thus increasing the proportion of native sucker larvae produced in Roubideau Creek. Second, we will PIT tag some of the expected 10,000s of fishes to study the spawning tributary fidelity of Bluehead Sucker, Flannelmouth Sucker and Roundtail Chub. If these fishes exhibit spawning system fidelity the odds of long-term success via exclusion of non-native is possible.	Non-native suckers in the Upper Colorado River are a major threat to the persistence of native suckers. Our project seeks to manage that threat by removing non-native suckers during the spawning migration. The project consists of 2 goals. First, we will preclude entry of non-native and hybrid suckers to the native spawning run, thus increasing the proportion of native sucker larvae produced in Roubideau Creek. Second, we will PIT tag some of the expected 10,000s of fishes to study the spawning tributary fidelity of Bluehead Sucker, Flannelmouth Sucker and Roundtail Chub. If these fishes exhibit spawning system fidelity the odds of long-term success via exclusion of non-native is possible.<br><br>The research is being conducted in collaboration with Colorado Parks and Wildlife. <br><br>Data from our study will be used to inform management decisions regarding native suckers in the Upper Colorado River Basin.
Genomic & Phenotypic Links	December 2023	Improving our understanding of the interplay between genetics and population dynamics in invasive cheatgrass throughout the intermountain west.	Problem Statement: <br><br>Intermountain west ecosystems involve sensitive plant and animal communities that are adapted to specialized and often harsh conditions. Invasive species such as cheatgrass can dramatically affect these natural systems.<br><br>Why this Research Matters:<br><br>We are developing a large-scale western regional experiment to learn about the connections between genetics, traits, and population dynamics in cheatgrass under a variety of environmental conditions. This research will help us understand how and why cheatgrass has been such a successful invader.<br><br>Collaboration/Partners:<br><br>This project involves a variety of institutions and agencies, including main collaborators at CSU, USU, Penn State, UNR, and USDA.<br><br>Research that Informs Decisions:<br><br>Sagebrush occupies a large portion of the western region and is a keystone species in these ecosystems. Several important species depend on sagebrush in their lifecycle and cheatgrass can alter the way these ecosystems function. Our research will help provide guidance about how the mechanisms in this invasive species biology lead to varying levels of success depending on environmental conditions and other biotic interactions.
Modeling Tree Growth	September 2021	Coupling ecosystem models that can simulate forests and how they change over time with field data collected in the Alaska network of National Parks.	Problem Statement: <br><br>Alaskan ecosystems are undergoing rapid environmental change, yet the extent to which this change affects ecological communities is not well understood. In particular, for tree species that depend on certain environmental conditions, we seek to better understand how growth and volume may have changed over the past several decades. <br><br>Why this Research Matters:<br><br>Substantial progress has been made in developing ecosystem models that simulate vegetation communities and nutrient cycling over decades. However, formal statistical implementations of these models that assimilate field data are still evolving and have not been applied in many systems throughout Alaska. We are developing ways to fit ecosystem models to tree ring data collected in the Alaska network of National Parks to better understand changes in growth and volume of tree species over time.<br><br>Collaboration/Partners:<br><br>This project involves a collaboration with the National Park Service and Colorado State University.<br><br>Research that Informs Decisions:<br><br> Understanding how forests have changed over decades is a long studied subject throughout the world. However, combing computational ecosystem models and field data can shed new light on best ways to manage and conserve important protected ecosystems in our National Parks.
Evaluating the status and distributions of bats in WNS-free areas using data from the North American Bat Monitoring Program: acoustic data processing and analysis (RWO122)	December 2022	The North American Bat Monitoring Program (NABat) was established to provide standardized monitoring protocols and a continental-scale collaborative framework to evaluate the status and distributions of bat species in areas unaffected by white-nose syndrome. This survey is multi-species, and based on detections by stationary and mobile acoustic receivers. An integration of data from each type of receiver is needed, including statistical methods for species occupancy under this integration which account for species identification error, in order to extract maximum information from this monitoring program. This project is a collaboration of USGS-FORT, USGS-NOROCK, NPA, and the Colorado Natural Heritage Program. Result from the analysis will be used to refine NABat monitoring in the future, and species distributions from the analysis will be used as a baseline for assessing WNS impacts.	The North American Bat Monitoring Program (NABat) was established to provide standardized monitoring protocols and a continental-scale collaborative framework to evaluate the status and distributions of bat species in areas unaffected by white-nose syndrome. This survey is multi-species, and based on detections by stationary and mobile acoustic receivers. An integration of data from each type of receiver is needed, including statistical methods for species occupancy under this integration which account for species identification error, in order to extract maximum information from this monitoring program. This project is a collaboration of USGS, National Park Serivce, and the Colorado Natural Heritage Program. Result from the analysis will be used to define NABat monitoring in the future, and species distributions from the analysis will be used as a baseline for assessing WNS impacts.
Spring and fall stopover food resources and land use patterns for Rocky Mountain Population Sandhill Cranes in the San Luis Valley, Colorado (RWO121)	September 2023	The Rocky Mountain population (RMP) of greater sandhill cranes (<i>Antigone canadensis tabida</i>) and a portion of the Mid-Continent Population (MCP) of cranes use the San Luis Valley (SLV) of Colorado as an important migrational stopover area each spring and fall. Declines in water availability for roosts, and in important food sources such as barley, could have negative impacts on these populations. An assessment of available roost habitat and grain, the use of these habitats by cranes, and the carrying capacity of the SLV for cranes is needed to assess the future of these populations and inform refuge management decisions. This project is a collaboration with USFWS Regions 6 and 2, the Intermountain West Joint Venture, Colorado Parks and Wildlife, and Colorado Open Lands. Results from the analyses will be used to build a decision model to assist Monte Vista NWR in making water and grain management decisions.	The Rocky Mountain population (RMP) of greater sandhill cranes (<i>Antigone canadensis tabida</i>) and a portion of the Mid-Continent Population (MCP) of cranes use the San Luis Valley (SLV) of Colorado as an important migrational stopover area each spring and fall. Declines in water availability for roosts, and in important food sources such as barley, could have negative impacts on these populations. An assessment of available roost habitat and grain, the use of these habitats by cranes, and the carrying capacity of the SLV for cranes is needed to assess the future of these populations and inform refuge management decisions. This project is a collaboration with USFWS Regions 6 and 2, the Intermountain West Joint Venture, Colorado Parks and Wildlife, and Colorado Open Lands. Results from the analyses will be used to build a decision model to assist Monte Vista NWR in making water and grain management decisions.
Nearshore Ecosystem Glacier Bay	December 2024	Synthesizing many different sources of information and data that have been collected in Glacier Bay National Park and connect to our ongoing sea otter spatio-temporal population models to identify knowledge gaps in our understanding of the nearshore food web.	Problem Statement: <br><br>Glacier Bay National Park contains one of the world's largest protected tidewater glacier ecosystems. A variety of complex and dynamic relationships among species in Glacier Bay exist and are critical to conservation and management. <br><br>Why this Research Matters: <br><br>We are combing multiple sources of data that have been collected in Glacier Bay for decades to better understand the ecological processes in near shore communities of the park. <br><br>Collaboration/Partners:<br><br>This project involves a collaboration among partners at the National Park Service, U.S. Geological Survey, and Colorado State University. <br><br>Research that Informs Decisions: <br><br>A strong theme of our research is combine existing scientific information about the near shore food web in Glacier Bay with various disparate data sources to identify knowledge gaps that will help guide future monitoring and protocol in the park.
Western Gulf Coast Population of Mottled Ducks Banding Needs Assessment	September 2023	The mottled duck (<i>Anas fulvigula</i>) is a relatively sedentary hunted waterfowl species dependent on coastal marsh and other habitats along the Gulf Coast for its entire life cycle, and therefore especially subject to development and habitat loss along the Gulf Coast. Various monitoring programs are in place to assess the status of this species, and inform harvest and habitat management decisions. A banding needs assessment is needed to evaluate the experimental banding done since the 1990’s, to design an operational banding program that accounts for harvest rates, survival rates, and movements among states, and integrates with the other monitoring programs for this population. This project is a collaboration with USFWS Regions 2 and 9, Division of Migratory Birds and Refuges; Texas Parks and Wildlife; and the Louisiana Department of Fisheries and Wildlife. The banding data, along with abundance surveys and harvest surveys, will be integrated in a population model to inform future monitoring and mottled duck management decisions.	The mottled duck (<i>Anas fulvigula</i>) is a relatively sedentary hunted waterfowl species dependent on coastal marsh and other habitats along the Gulf Coast for its entire life cycle, and therefore especially subject to development and habitat loss along the Gulf Coast. Various monitoring programs are in place to assess the status of this species, and inform harvest and habitat management decisions. A banding needs assessment is needed to evaluate the experimental banding done since the 1990’s, to design an operational banding program that accounts for harvest rates, survival rates, and movements among states, and integrates with the other monitoring programs for this population. This project is a collaboration with USFWS Regions 2 and 9, Division of Migratory Birds and Refuges; Texas Parks and Wildlife; and the Louisiana Department of Fisheries and Wildlife. The banding data, along with abundance surveys and harvest surveys, will be integrated in a population model to inform future monitoring and mottled duck management decisions.
Estimating population size and demographic parameters for Rio Grande Sucker and Rio Grande Chub at Baca National Wildlife Refuge	July 2024	The Baca National Wildlife Refuge is home to one of only two aboriginal populations of Rio Grande sucker (<i>Catostomus plebeius</i>) and Rio Grande chub (<i>Gila pandora</i>) in the state of Colorado, the conservation of which is part of their Comprehensive Conservation Plan. These fish have been PIT tagged and re-detected by capture and remote antennas for the last few years, as part of a program to improve fish passage on the refuge. An evaluation and analysis of these data for population size and vital rates is needed to assess the status of these native fish and their response to passage improvements. Training is also needed to increase capacity for demographic analyses within the USFWS. This project is a collaboration with USFWS Region 6, including the Colorado Fish and Wildlife Conservation Office, Refuge Inventory and Monitoring, and the Baca NWR. Results from the analysis will be used to inform future fish passage management decisions, and the design of future monitoring for these populations.	The Baca National Wildlife Refuge is home to one of only two aboriginal populations of Rio Grande sucker (<i>Catostomus plebeius</i>) and Rio Grande chub (<i>Gila pandora</i>) in the state of Colorado, the conservation of which is part of their Comprehensive Conservation Plan. These fish have been PIT tagged and re-detected by capture and remote antennas for the last few years, as part of a program to improve fish passage on the refuge. An evaluation and analysis of these data for population size and vital rates is needed to assess the status of these native fish and their response to passage improvements. Training is also needed to increase capacity for demographic analyses within the USFWS. This project is a collaboration with USFWS Region 6, including the Colorado Fish and Wildlife Conservation Office, Refuge Inventory and Monitoring, and the Baca NWR. Results from the analysis will be used to inform future fish passage management decisions, and the design of future monitoring for these populations.
Transmission of Bacterial Kidney Disease in CO Greenback Cutthroat Trout	June 2022	Since 2015, several state fish hatcheries in Colorado have had positive detections of <i>Renibacterium salmoninarum</i>, the causative agent for bacterial kidney disease (BKD) in salmonids. Since there is little known about the pathophysiology of inland trout, management efforts have been implemented at many hatcheries to reduce the transfer of this bacterium to offspring during spawning seasons. One management strategy is the removal of all fish once <i>R. salmoninarum</i> has been detected. However, it is unclear if depopulation of positive fish is necessary to eliminate the bacterium and, in many instances, critical and sometimes irreplaceable broodstocks are lost. The Colorado native greenback cutthroat trout (<i>Oncorhynchus clarkii stomias</i>)<i> </i>is one species of concern because depopulation may endanger populations of critical broodstocks. We are proposing to assess the bacterial load of <i>R. salmoninarum</i> within parents and evaluate the vertical transmission to progeny and to assist in developing non-lethal management strategies. We also propose to evaluate the consequences of keeping infected broodstock in a hatchery and the potential for horizontal transmission to other fish within the facility.	Since 2015, several state fish hatcheries in Colorado have had positive detections of <i>Renibacterium salmoninarum</i>, the causative agent for bacterial kidney disease (BKD) in salmonids. The Colorado native greenback cutthroat trout (<i>Oncorhynchus clarkii stomias</i>)<i> </i>is one species of concern because depopulation due to disease may endanger populations of critical broodstocks. We are assessing the bacterial load of <i>R. salmoninarum</i> within parents and evaluate the vertical transmission to progeny and to assist in developing non-lethal management strategies. We also propose to evaluate the consequences of keeping infected broodstock in a hatchery and the potential for horizontal transmission to other fish within the facility.<br><br>This research is being done in collaboration with Colorado Parks and Wildlife.<br><br>The results will directly inform management decisions at hatchery facilities in Colorado and can be used at a national scale if needed.
Rocky Mountain Elk Recruitment & Habitat	March 2022	The Rocky Mountain Elk (<i>Cervus elaphus</i>) is an iconic species, with a high recreational value to hunters, photographers, artists, and other wildlife enthusiasts. Although recruitment in elk is naturally variable, over the last 10 years recruitment has declined in some populations within Colorado, due to unknown causes. An assessment is needed on the timing of the loss of calves between parturition and the following winter, and identification of the cause(s), including predators, habitat quality, and anthropogenic factors. This project is a collaboration with Colorado Parks and Wildlife and the Rocky Mountain Elk Foundation. Results from this study will be used to inform Colorado Parks and Wildlife management decisions for mitigating this decline.	The Rocky Mountain Elk (<i>Cervus elaphus</i>) is an iconic species, with a high recreational value to hunters, photographers, artists, and other wildlife enthusiasts. Although recruitment in elk is naturally variable, over the last 10 years recruitment has declined in some populations within Colorado, due to unknown causes. An assessment is needed on the timing of the loss of calves between parturition and the following winter, and identification of the cause(s), including predators, habitat quality, and anthropogenic factors. This project is a collaboration with Colorado Parks and Wildlife and the Rocky Mountain Elk Foundation. Results from this study will be used to inform Colorado Parks and Wildlife management decisions for mitigating this decline.
Spring and fall stopover food resources and land use patterns for RMP Sandhill Cranes in the San Luis Valley, CO	December 2023	The Rocky Mountain population (RMP) of greater sandhill cranes (<i>Antigone canadensis tabida</i>) and a portion of the Mid-Continent Population (MCP) of cranes use the San Luis Valley (SLV) of Colorado as an important migrational stopover area each spring and fall. Declines in water availability for roosts, and in important food sources such as barley, could have negative impacts on these populations. An assessment of available roost habitat and grain, the use of these habitats by cranes, and the carrying capacity of the SLV for cranes is needed to assess the future of these populations and inform refuge management decisions. This project is a collaboration with USFWS Regions 6 and 2, the Intermountain West Joint Venture, Colorado Parks and Wildlife, and Colorado Open Lands. Results from the analyses will be used to build a decision model to assist Monte Vista NWR in making water and grain management decisions.	The Rocky Mountain population (RMP) of greater sandhill cranes (<i>Antigone canadensis tabida</i>) and a portion of the Mid-Continent Population (MCP) of cranes use the San Luis Valley (SLV) of Colorado as an important migrational stopover area each spring and fall. Declines in water availability for roosts, and in important food sources such as barley, could have negative impacts on these populations. An assessment of available roost habitat and grain, the use of these habitats by cranes, and the carrying capacity of the SLV for cranes is needed to assess the future of these populations and inform refuge management decisions. This project is a collaboration with USFWS Regions 6 and 2, the Intermountain West Joint Venture, Colorado Parks and Wildlife, and Colorado Open Lands. Results from the analyses will be used to build a decision model to assist Monte Vista NWR in making water and grain management decisions.
Evaluating the status and distributions of bats in WNS-free areas using standardized acoustic monitoring data from the North American Bat Monitoring Program (RWO118)	August 2023	White-nose syndrome has decimated hibernating bat populations across North America since it emerged 10 years ago in New York. The North American Bat Monitoring Program (NABat) was established to assess the true ecological impacts of these unprecedented declines, providing standardized monitoring protocols and a continental-scale collaborative framework to evaluate the status and distributions of bat species. After four years of conducting the survey an assessment to date of species distribution and changes therein, and distribution of results to partners, is needed. Furthermore, an assessment of the monitoring design and sampling methods is also needed, to inform the survey moving forward. The project is a collaboration among the USGS-COCFWRU, the USGS Fort Collins Science Center, the USGS Northern Rocky Mountain Science Center, the USGS Upper Midwest Environmental Science Center, the NPS Upper Columbia Basin Network, and numerous partners throughout the range of the NABat monitoring program. Maps of distribution and status of bat populations to date will provide a baseline for comparison with further encroachment by white-nose syndrome and other threats. Evaluation of the survey methods and data will inform refinement of the NABat monitoring program, to make it more efficient and robust, leading to publication of the State of North America’s Bats report in 2021.	White-nose syndrome has decimated hibernating bat populations across North America since it emerged 10 years ago in New York. The North American Bat Monitoring Program (NABat) was established to assess the true ecological impacts of these unprecedented declines, providing standardized monitoring protocols and a continental-scale collaborative framework to evaluate the status and distributions of bat species. After four years of conducting the survey an assessment to date of species distribution and changes therein, and distribution of results to partners, is needed. Furthermore, an assessment of the monitoring design and sampling methods is also needed, to inform the survey moving forward. The project is a collaboration among the USGS-COCFWRU, the USGS Fort Collins Science Center, the USGS Northern Rocky Mountain Science Center, the USGS Upper Midwest Environmental Science Center, the NPS Upper Columbia Basin Network, and numerous partners throughout the range of the NABat monitoring program. Maps of distribution and status of bat populations to date will provide a baseline for comparison with further encroachment by white-nose syndrome and other threats. Evaluation of the survey methods and data will inform refinement of the NABat monitoring program, to make it more efficient and robust, leading to publication of the State of North America’s Bats report in 2021.
Temperature and Winter Duration Requirements for Reproductive Success in Johnny Darter, Etheostoma nigrum (Percidae), in the South Platte River Basin, Colorado	June 2021	Water temperature is a critical ecological variable and changes in water temperature and its seasonal timing may influence biological processes in aquatic ectotherms. Historically, the South Platte River Basin naturally experienced a wide range of seasonal temperatures However, urbanization and development of Waste Water Treatment Plants have contributed to warmer and more consistent water temperatures throughout the year, particularly in winter months. Less variation in seasonal temperatures could have adverse effects on native fishes that previously relied on temperature fluctuations for important biological processes, such as reproduction. Assessing the thermal requirements of warm water fishes will provide valuable information towards establishing protective winter water temperature standards in effluent-dominated streams.	Historically, the South Platte River Basin naturally experienced a wide range of seasonal temperatures However, urbanization and development of Waste Water Treatment Plants have contributed to warmer and more consistent water temperatures throughout the year, particularly in winter months. Less variation in seasonal temperatures could have adverse effects on native fishes that previously relied on temperature fluctuations for important biological processes, such as reproduction. <br><br>The project is being conducted with Colorado Parks and Wildlife, Colorado Department of Public Health and the environment, and several municipal Waste Water Treatment Plants. <br><br>Assessing the thermal requirements of warm water fishes will provide valuable information towards establishing protective winter water temperature standards in effluent-dominated streams.
Demography of Black-footed and Laysan Albatross: Kilaua Point & Tern Island Populations	June 2022	The black-footed (Phoebastria nigripes; BFAL) and Laysan (Phoebastria immutabilis; LAAL) albatrosses are long-lived seabirds of conservation concern to the USFWS, and a petition to list the BFAL under the Endangered Species Act has recently been submitted to USFWS. Furthermore, over 65% of the world population of these albatross species nest on remote low island refuges in the Pacific, and in smaller numbers in the main Hawaiian Islands. Relatively little is known about the life history, survival, and breeding frequency of Northern Hemisphere albatross species, and in how this compares between the low islands of the Northwestern Hawaiian Islands and the main Hawaiian Islands. Such information is important, given the variety of threats that these species face (e.g., fishery bycatch, plastics ingestions, contaminants, loss of breeding habitat due to sea level rise). The project is a collaboration among the USGS-COCFWRU, the USFWS Region 1 Migratory Bird and Habitat and Inventory and Monitoring programs, the Marine National Monuments of the Pacific, and the USGS Bird Banding Laboratory. A model for annual survival and breeding probability for albatross will be developed for Kilauea Point NWR and Tern Island, allowing these processes to be connected with threats such as overlap with long-line fishing and other environmental factors. A vetted banding database will be provided for future analyses and recommendations for future monitoring intensity will also be provided to Refuge personnel.	The black-footed (Phoebastria nigripes; BFAL) and Laysan (Phoebastria immutabilis; LAAL) albatrosses are long-lived seabirds of conservation concern to the USFWS, and a petition to list the BFAL under the Endangered Species Act has recently been submitted to USFWS. Furthermore, over 65% of the world population of these albatross species nest on remote low island refuges in the Pacific, and in smaller numbers in the main Hawaiian Islands. Relatively little is known about the life history, survival, and breeding frequency of Northern Hemisphere albatross species, and in how this compares between the low islands of the Northwestern Hawaiian Islands and the main Hawaiian Islands. Such information is important, given the variety of threats that these species face (e.g., fishery bycatch, plastics ingestions, contaminants, loss of breeding habitat due to sea level rise). The project is a collaboration among the USGS-COCFWRU, the USFWS Region 1 Migratory Bird and Habitat and Inventory and Monitoring programs, the Marine National Monuments of the Pacific, and the USGS Bird Banding Laboratory. A model for annual survival and breeding probability for albatross will be developed for Kilauea Point NWR and Tern Island, allowing these processes to be connected with threats such as overlap with long-line fishing and other environmental factors. A vetted banding database will be provided for future analyses and recommendations for future monitoring intensity will also be provided to Refuge personnel.
Woody Plants on the Move	September 2021	Problem statement: Massive data sets have been collected over the past several decades on plant communities throughout Alaskan National Parks. We will develop and apply new spatially-explicit statistical models to assimilate these data and improve our understanding the ecology and wildlife habitat in the region. <br><br>Why this research matters: This project leverages a huge field plot dataset collected over the past decade to learn the maximum amount that we can about the status and possible future trends in woody plant communities of northern Alaska that govern the distribution, character and quality of wildlife habitat across the eight very large national park units that comprise the Central Alaska and Arctic Networks of parks. <br><br>Partners: We collaborate on this project with the National Park Service and National Oceanic and Atmospheric Administration. <br><br>Research that informs decisions: Our work will provide statistically valid knowledge about the quality and quantity of wildlife habitat over these large naturally regulated landscapes to improve management and wildlife conservation efforts now and in the future.	Problem statement: Massive data sets have been collected over the past several decades on plant communities throughout Alaskan National Parks. We will develop and apply new spatially-explicit statistical models to assimilate these data and improve our understanding the ecology and wildlife habitat in the region. Why this research matters: This project leverages a huge field plot dataset collected over the past decade to learn the maximum amount that we can about the status and possible future trends in woody plant communities of northern Alaska that govern the distribution, character and quality of wildlife habitat across the eight very large national park units that comprise the Central Alaska and Arctic Networks of parks. Partners: We collaborate on this project with the National Park Service and National Oceanic and Atmospheric Administration. Research that informs decisions: Our work will provide statistically valid knowledge about the quality and quantity of wildlife habitat over these large naturally regulated landscapes to improve management and wildlife conservation efforts now and in the future.
Sea Turtle Monitoring	December 2014	TBA	TBA
Effects of habitat complexity on Rocky Mountain Brook Trout Populations	February 2016	Western U.S. rivers are currently influenced by legacy effects of reduced large wood (LW) loading and retention that has led to reduced in-stream habitat complexity. Historical land use practices such as tie-driving, snag removal, and beaver trapping have all contributed to declines in either input or retention of LW in mountain streams. Effects from these practices have persisted over a century after the activities ceased; suggesting streams have entered an alternative stable state. One that is characterized by loss of multi-thread stream reaches, reduced sediment and nutrient retention, steeper channel gradient, reduced pool volume and altered pool geometry, creating narrower and shallower streams with higher width to depth ratios, and overall decreased stream and valley complexity. Using one of the last remaining patches of old-growth forest on the Front Range of Colorado (USA) we compared population densities, individual growth rates, diet compositions, and annual prey consumption demand of brook trout Salvelinus fontinalis in streams across a gradient of wood volumes. Brook trout populations were sampled via multi-pass electrofishing events, while approximately 30 individuals at each site were sacrificed for growth and diet studies. Individual growth was back-calculated from otolith sections, and diet composition was estimated from stomach samples collected at each site. Average growth rates and diet compositions were then combined in a bioenergetics model that provided an estimate of the amount of prey resources needed to support observed growth and population densities. Trout population densities appear positively related to increasing number of pools, and standing stock biomass of aquatic insects. Yet, at different scales (square-meter vs valley-length) different variables were better at predicting trout biomass. At both the local (square-meter) and landscape (valley length) scales, standing stock biomass of aquatic insects was the best predictor variable chosen by model selection to predict trout biomass. However, at the valley scale, number of pools became more important in predicting trout biomass, as a combination of standing stock biomass of aquatic insects and number of pools held the most predictive power. Annual individual prey consumption demand did not differ between two sites of high and low wood volume and trout biomass. Therefore, total prey demand at a site is determined by population density, and less so by physical habitat. Between the two intensive sites, diet compositions were significantly different during the summer season. Fish at the high wood site were consuming more small aquatic insect larvae (e.g., Family Chironomidae and Simullidae) to support growth and fish biomass, whereas diet composition at the low wood site consisted of terrestrial insects (ants) and larger aquatic insect larvae. Individual growth rates of age-1 brook trout were negatively affected by increasing density. However, this pattern only held true for fish that were not the largest individuals, nor the smallest individuals, at each site. The largest fish at each site are presumably dominant individuals, and can out compete all other individuals for optimum foraging positions regardless of density, and are therefore not affected by density. While the smallest fish, presumably the most subordinate individuals, are outcompeted for resources at all densities, and are likewise also not affected by increasing density. Our results suggest that LW, in the correct geomorphic context, can drastically alter stream and valley habitat complexity. The creation of multi-thread stream reaches can greatly increase aquatic animal production by creating pool habitat preferred by trout and by prey resources that dramatically increase trout populations. The negative effects of historical land uses have persisted >100 years suggesting a resilience of streams to return to pre-perturbation states, and a loss of trout production in mountain watersheds due to land use over a century ago.	Western U.S. rivers are currently influenced by legacy effects of reduced large wood (LW) loading and retention that has led to reduced in-stream habitat complexity. Reduced habitat complexity is potentially related to declines in fish biomass and management of fish populations requires an understanding of the relationship between habitat complexity and fish biomass. The research was funded by the Colorado Water Center and the National Science Foundation. Collaborators were Colorado State University andthe USGS Fort Collins Science Center. Large amounts of annual fish production are lost in mountain watersheds due to reduced habitat complexity. Management of Large wood in the correct geomorphic context may be a strategy to mitigate and maintain fish production.
Distribution & Impacts of Gill Lice in Colorado	March 2017	TBA	TBA
Estimating the Role of National Wildlife Refuges	December 2014	Problem statement: Wildlife occurrence data are often collected throughout wildlife refuges, but are typically subject to measurement error associated with imperfect detection of species. Moreover, with amphibian and avian species, such data may be subject to both false negative and false positive errors. So What? Why this research matters: Traditionally, occupancy models to estimate wildlife occurrence and species distributions have only accommodated false negative errors, but false positives can affect the resulting statistical inference if they are not accounted for. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey. Research That Informs Decisions: Formal statistical models that account for both false negative and false positives help to reduce the uncertainty and bias associated with inferring species occupancy. Our new methodology will help better understand the role of management at wildlife refuges versus other non-federal lands in conserving amphibian species.	Problem statement: Wildlife occurrence data are often collected throughout wildlife refuges, but are typically subject to measurement error associated with imperfect detection of species. Moreover, with amphibian and avian species, such data may be subject to both false negative and false positive errors. So What? Why this research matters: Traditionally, occupancy models to estimate wildlife occurrence and species distributions have only accommodated false negative errors, but false positives can affect the resulting statistical inference if they are not accounted for. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey. Research That Informs Decisions: Formal statistical models that account for both false negative and false positives help to reduce the uncertainty and bias associated with inferring species occupancy. Our new methodology will help better understand the role of management at wildlife refuges versus other non-federal lands in conserving amphibian species.
Whirling Disease-Resistant Trout Evaluation	June 2012	TBA	TBA
Wildlife Corridor Identification	January 2016	Problem statement: Western carnivore species navigate a complex matrix of land types as they undergo their life history. In Colorado, several species are tracked with a variety of telemetry devices to understand vital rates and demographics, but relatively little was known the movement of these carnivores. So What? Why this research matters: The ability to formally make inferences about large-scale spatial and temporal movement of wild carnivores in Colorado helps us understand the natural history of the species and rigorously quantifies their space use and behavior. Collaboration/Partners: This project is in collaboration with scientists at the Colorado Parks and Wildlife and National Park Service. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in telemetry data help us make dependable inference about movement of large carnivores in Colorado that can help influence management decisions about landscape connectivity, development, and land use.	Problem statement: Western carnivore species navigate a complex matrix of land types as they undergo their life history. In Colorado, several species are tracked with a variety of telemetry devices to understand vital rates and demographics, but relatively little was known the movement of these carnivores. So What? Why this research matters: The ability to formally make inferences about large-scale spatial and temporal movement of wild carnivores in Colorado helps us understand the natural history of the species and rigorously quantifies their space use and behavior. Collaboration/Partners: This project is in collaboration with scientists at the Colorado Parks and Wildlife and National Park Service. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in telemetry data help us make dependable inference about movement of large carnivores in Colorado that can help influence management decisions about landscape connectivity, development, and land use.
Sage Grouse Connectivity & Gene Flow Modeling	July 2014	Problem statement: Wildlife genetic data are often collected, but the statistical methods to analyze such data parametrically are lacking. The greater sage-grouse is a species for which genetic data are collected, but sampling efforts are typically not optimal at the range-wide scale. Improved statistical models that can be useful to guide ongoing monitoring efforts. So What? Why this research matters: Improved statistical models for genetic data can be useful to improve our understanding of large-scale gene flow and guide ongoing monitoring efforts. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey and several western state agencies. Research That Informs Decisions: We developed formal parametric statistical models that allow for inference about gene flow using circuit theoretic concepts and environmental spatial data. Our new methodology guided the ongoing field data collection efforts to better understand gene flow for greater sage-grouse throughout the entire western U.S.	Problem statement: Wildlife genetic data are often collected, but the statistical methods to analyze such data parametrically are lacking. The greater sage-grouse is a species for which genetic data are collected, but sampling efforts are typically not optimal at the range-wide scale. Improved statistical models that can be useful to guide ongoing monitoring efforts. So What? Why this research matters: Improved statistical models for genetic data can be useful to improve our understanding of large-scale gene flow and guide ongoing monitoring efforts. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey and several western state agencies. Research That Informs Decisions: We developed formal parametric statistical models that allow for inference about gene flow using circuit theoretic concepts and environmental spatial data. Our new methodology guided the ongoing field data collection efforts to better understand gene flow for greater sage-grouse throughout the entire western U.S.
Spatial Risk Factors	August 2018	Problem statement: Data associated with wildlife disease monitoring are often spatially referenced, but the spatial information is not always utilized in formal statistical models for prediction and forecasting. So What? Why this research matters: The ability to formally make inferences about wildlife health at large spatial and temporal scales is challenging and new statistical methods are needed to incorporate existing data sources to improve our understanding of wildlife disease dyanmics. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey and Wisconsin Department of Natural Resources. Research That Informs Decisions: Formal statistical models that account for the spatio-temporal dynamics of disease spread can lead to be a better understanding of mechanisms and forecasts that aid in the management of wildlife populations.	Problem statement: Data associated with wildlife disease monitoring are often spatially referenced, but the spatial information is not always utilized in formal statistical models for prediction and forecasting. So What? Why this research matters: The ability to formally make inferences about wildlife health at large spatial and temporal scales is challenging and new statistical methods are needed to incorporate existing data sources to improve our understanding of wildlife disease dyanmics. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey and Wisconsin Department of Natural Resources. Research That Informs Decisions: Formal statistical models that account for the spatio-temporal dynamics of disease spread can lead to be a better understanding of mechanisms and forecasts that aid in the management of wildlife populations.
Adaptive Monitoring and Modeling of Sea Otters	September 2020	Problem statement: Data associated with reintroduced and/or invasive wildlife species are often collected, but are not typically optimal for desired inference. So What? Why this research matters: The ability to formally make inferences about, and forecast, spreading wildlife populations is critical for guiding future monitoring efforts and understanding the mechanisms associated with their dynamics. Collaboration/Partners: This project is in collaboration with scientists at the National Park Service and U.S. Geological Survey. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in monitoring populations can be developed and fit to existing data to provide forecasts that can then optimally be used to guide future decisions about monitoring efforts.	Problem statement: Data associated with reintroduced and/or invasive wildlife species are often collected, but are not typically optimal for desired inference. So What? Why this research matters: The ability to formally make inferences about, and forecast, spreading wildlife populations is critical for guiding future monitoring efforts and understanding the mechanisms associated with their dynamics. Collaboration/Partners: This project is in collaboration with scientists at the National Park Service and U.S. Geological Survey. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in monitoring populations can be developed and fit to existing data to provide forecasts that can then optimally be used to guide future decisions about monitoring efforts.
Fish Population Models	December 2021	Monitoring of the population status and dynamics of endangered humpback chub faces challenges that the population exists in remote locations (the Colorado and Little Colorado Rivers), where capture can only occur periodically, early life stages are difficult to tag, and fish are most accessible to capture only when spawning. Recently, arrays of PIT tag readers have been installed to increase the chance of tagged chub being detected. A model that integrates PIT tag detections with traditional recapture data is needed to better understand the population size and dynamics of humpback chub, including adult survival and reproductive rates, as well as juvenile recruitment and movement from the Little Colorado River to the Colorado River. In addition, for improved future monitoring a review of the sampling design and use of recapture and remote detections is needed. This project is a collaboration of the USGS-COCFWRU, the USGS Grand Canyon Monitoring and Research Center, and the USFWS. The results of the model of population size and vital rates will be used to better inform proposed management actions that affect the chub. Moreover, assessment of the sampling design itself will lead to more precise models and therefore better future management decisions.	Monitoring of the population status and dynamics of endangered humpback chub faces challenges that the population exists in remote locations (the Colorado and Little Colorado Rivers), where capture can only occur periodically, early life stages are difficult to tag, and fish are most accessible to capture only when spawning. Recently, arrays of PIT tag readers have been installed to increase the chance of tagged chub being detected. A model that integrates PIT tag detections with traditional recapture data is needed to better understand the population size and dynamics of humpback chub, including adult survival and reproductive rates, as well as juvenile recruitment and movement from the Little Colorado River to the Colorado River. In addition, for improved future monitoring a review of the sampling design and use of recapture and remote detections is needed. This project is a collaboration of the USGS-COCFWRU, the USGS Grand Canyon Monitoring and Research Center, and the USFWS. The results of the model of population size and vital rates will be used to better inform proposed management actions that affect the chub. Moreover, assessment of the sampling design itself will lead to more precise models and therefore better future management decisions.
Movement of Pinnipeds	June 2017	Problem statement: Data associated with marine mammal tracking are often collected but the measures associated with data and the underlying movement process make it challenging to understand space use, interaction among individuals, and learn about movement patterns. So What? Why this research matters: The ability to formally make inferences about marine mammal space use and movement can lead to improved understanding of these important aquatic species. Collaboration/Partners: This project is in collaboration with scientists at the National Oceanic and Atmospheric Administration. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in marine mammal telemetry data will lead to a better understanding of mechanisms that aid in the management of these aquatic wildlife populations.	Problem statement: Data associated with marine mammal tracking are often collected but the measures associated with data and the underlying movement process make it challenging to understand space use, interaction among individuals, and learn about movement patterns. So What? Why this research matters: The ability to formally make inferences about marine mammal space use and movement can lead to improved understanding of these important aquatic species. Collaboration/Partners: This project is in collaboration with scientists at the National Oceanic and Atmospheric Administration. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in marine mammal telemetry data will lead to a better understanding of mechanisms that aid in the management of these aquatic wildlife populations.
Graphics and Analysis for Marine Mammal Research	July 2018	Problem statement: Data associated with marine mammal tracking are often collected but the measures associated with data and the underlying movement process make it challenging to understand space use, interaction among individuals, and to visualize the movement patterns. So What? Why this research matters: The ability to formally make inferences about, and visualize, marine mammal space use and movement can lead to improved understanding of these important aquatic species. Collaboration/Partners: This project is in collaboration with scientists at the National Oceanic and Atmospheric Administration. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in marine mammal telemetry data will lead to a better understanding of mechanisms that aid in the management of these aquatic wildlife populations.	Problem statement: Data associated with marine mammal tracking are often collected but the measures associated with data and the underlying movement process make it challenging to understand space use, interaction among individuals, and to visualize the movement patterns. So What? Why this research matters: The ability to formally make inferences about, and visualize, marine mammal space use and movement can lead to improved understanding of these important aquatic species. Collaboration/Partners: This project is in collaboration with scientists at the National Oceanic and Atmospheric Administration. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in marine mammal telemetry data will lead to a better understanding of mechanisms that aid in the management of these aquatic wildlife populations.
Statistical Method to Estimate Boundaries	December 2018	Problem statement: Non-biological factors are often used to delineate management units for wildlife species. In cases where species distribution and movement information is available, functional boundaries may be preferred. So What? Why this research matters: The ability to formally delineate population boundaries based on the movement and space use of actual animals can aid in the effective management of wildlife populations. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey and U.S. Fish and Wildlife Service. Research That Informs Decisions: Formal statistical models that account for the phenology of sea ice in the north Atlanta and Bering seas on the movement of polar bears can help cluster individuals into sub-populations based on their space use. These sub-populations and estimated boundaries can help set future management decisions.	Problem statement: Non-biological factors are often used to delineate management units for wildlife species. In cases where species distribution and movement information is available, functional boundaries may be preferred. So What? Why this research matters: The ability to formally delineate population boundaries based on the movement and space use of actual animals can aid in the effective management of wildlife populations. Collaboration/Partners: This project is in collaboration with scientists at the U.S. Geological Survey and U.S. Fish and Wildlife Service. Research That Informs Decisions: Formal statistical models that account for the phenology of sea ice in the north Atlanta and Bering seas on the movement of polar bears can help cluster individuals into sub-populations based on their space use. These sub-populations and estimated boundaries can help set future management decisions.
Spatial Data for Gunnison Sage grouse	June 2017	Problem statement: Data associated with individual tracking of avian wildlife species are often collected using handheld telemetry equipment, but the measurement errors associated with such data are not often accommodated in statistical analyses, nor are the movements of individuals formally coupled with demography. So What? Why this research matters: The ability to formally make inferences about important species such as the Gunnison sage-grouse is critical for understanding the variation in space use associated with the demography of these populations. Collaboration/Partners: This project is in collaboration with scientists at Colorado Parks and Wildlife. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in tracking data while inferring the underlying individual-level movement can be coupled with demographic information to better understand the population so that effective management strategies can be developed.	Problem statement: Data associated with individual tracking of avian wildlife species are often collected using handheld telemetry equipment, but the measurement errors associated with such data are not often accommodated in statistical analyses, nor are the movements of individuals formally coupled with demography. So What? Why this research matters: The ability to formally make inferences about important species such as the Gunnison sage-grouse is critical for understanding the variation in space use associated with the demography of these populations. Collaboration/Partners: This project is in collaboration with scientists at Colorado Parks and Wildlife. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in tracking data while inferring the underlying individual-level movement can be coupled with demographic information to better understand the population so that effective management strategies can be developed.
The spatial distribution and impacts of endocrine disrupting compounds in the South Platte River basin, CO.	June 2017	TBA	TBA
Investigating Bacterial Coldwater Disease in Salmonids	June 2021	Aquaculture is one of the fastest growing industries worldwide and Bacterial Coldwater Disease (BCWD), caused by Flavobacterium psychrophilum (Fp), is one of the most important hatchery diseases. Outbreaks of BCWD can result in economic losses to producers of salmon and Rainbow Trout. Antibiotics are used for treatment for BCWD and concerns exist about the development of antibiotic resistance. The US Department of Agriculture (USDA) developed a selection program to create a Rainbow Trout strain that was genetically resistant to BCWD (the PRR strain in Colorado’s state hatchery system). BCWD resistant fish provide another management tool to reduce loss of Rainbow Trout due to BCWD outbreaks in aquaculture. A similar approach has been used to manage Rainbow Trout in the presence of whirling disease (WD). Colorado Parks and Wildlife (CPW) have developed WD resistant strains of Rainbow Trout that retain important wild characteristics, such as the ability to survive and breed in the wild. The state of Colorado has been using WD resistant Rainbow Trout to reestablish populations in the presence of Myxobolus cerebralis (Mc), the parasite that causes WD. Monitoring indicates that natural Rainbow Trout reproduction and recruitment are occurring. We are proposing to produce Rainbow Trout that are genetically resistant to both BCWD and WD. This would minimize the use of antibiotics to control BCWD and produce a fish capable of resisting WD. We propose to develop and evaluate a cross between Rainbow trout that are genetically resistant to BCWD and WD for managing both diseases concurrently.	Aquaculture is one of the fastest growing industries worldwide and Bacterial Coldwater Disease (BCWD), caused by Flavobacterium psychrophilum (Fp), is one of the most important hatchery diseases. Outbreaks of BCWD can result in economic losses to producers of salmon and Rainbow Trout. Antibiotics are used for treatment for BCWD and concerns exist about the development of antibiotic resistance. <br><br>We are proposing to produce Rainbow Trout that are genetically resistant to both BCWD and Whirling Disease (WD). This would minimize the use of antibiotics to control BCWD and produce a fish capable of resisting WD. <br><br>We are doing this research with Colorado Parks and Wildlife.<br><br>Our overarching goal is to develop a Rainbow Trout that will be genetically resistant to both BCWD and WD, allowing for better survival during hatchery production. Our approach will also provide an alternative disease management option for reestablishing Rainbow Trout fisheries. Economically, this should help aquaculture by lowering costs, improving survival, and providing alternative markets for Rainbow Trout.
Inferences on the Status of Raptors	January 2018	Raptors are key components of many ecosystems and numerous raptors in Colorado are species of conservation concern. Monitoring raptor populations is challenging due to their ecology and life history, and large-scale data sets of breeding raptor populations are rare and frequently incomplete. Scientists and volunteers throughout Colorado have been gathering data on raptor locations and abundance for decades using various survey techniques, including point counts, roost surveys, and nest surveys and monitoring. This project will investigate the potential of these combined data sources for assessing raptor populations at regional or statewide scales, and evaluate field protocols used to provide records for this database. The project is a collaboration between the USGS-COCFWRU and Colorado Parks and Wildlife avian researchers and raptor biologists. A model of eagle nest survival as a function of anthropogenic and landscape factors, as well as raptor species distribution, will be developed. In addition, recommendations for a design of nest survival and raptor distribution monitoring will inform future raptor assessment in Colorado.	Raptors are key components of many ecosystems and numerous raptors in Colorado are species of conservation concern. Monitoring raptor populations is challenging due to their ecology and life history, and large-scale data sets of breeding raptor populations are rare and frequently incomplete. Scientists and volunteers throughout Colorado have been gathering data on raptor locations and abundance for decades using various survey techniques, including point counts, roost surveys, and nest surveys and monitoring. This project will investigate the potential of these combined data sources for assessing raptor populations at regional or statewide scales, and evaluate field protocols used to provide records for this database. The project is a collaboration between the USGS-COCFWRU and Colorado Parks and Wildlife avian researchers and raptor biologists. A model of eagle nest survival as a function of anthropogenic and landscape factors, as well as raptor species distribution, will be developed. In addition, recommendations for a design of nest survival and raptor distribution monitoring will inform future raptor assessment in Colorado.
Stonecat Ecology in St. Vrain Creek, CO	June 2017	Stonecat Noturus flavus are a small-bodied native catfish found from southern Canada to the southern United States, and from the Appalachian Mountains to the Rocky Mountains. In Colorado, there are two remaining populations of Stonecat, including one geographically isolated population in St. Vrain Creek, which runs through the Front Range in Longmont, CO. There are five major drainages running through Colorado’s Front Range, which is where most of the state’s population is concentrated. As such, these streams are highly urbanized. When compared to the other four major Front Range streams, St. Vrain Creek contains a disproportionately high number of native fish species, including Colorado Species of Special Concern such as Stonecats. There has not yet been a quantitative analysis of population demographic parameters or individual habitat selection preferences of Stonecats. We sought to estimate both of these through a mark-recapture study using passive integrated transponder (PIT) tags. There are a number of assumptions associated with mark-recapture studies which we addressed through individual experiments, including tag loss, physical closure and detection probability of known tags. We evaluated tag loss under laboratory conditions. PIT tags were surgically implanted into the peritoneal cavity of Stonecats (n = 157) ranging from 71 mm to 213 mm through an incision closed with a single Braunamid suture and the fish were monitored for 120 weeks. After 120 weeks, there were fifteen lost tags (9.6%) and eight mortalities (5.0%). eevaluated our dataset of individual encounter histories and covariates including time since tagging, fish length and tag type in a multistate model framework using Program MARK. Time since tagging has an inverse effect on tag loss; if fish are going to lose tags, it will be relatively soon post-tagging. Additionally, fish length has a negative effect, with tag loss decreasing with fish length. These results support our assumption that using PIT tags to individually mark Stonecats is an appropriate method, and we now have a better understanding of tag loss rates over a long-term study period. We evaluated population demographic parameters and individual habitat selection preferences of Stonecats in a field experiment. PIT tags were surgically implanted in Stonecats (n = 679) ranging from 70 mm to 230 mm. We monitored tagged Stonecats with both static and mobile PIT antennae. Our results from the static antennae show that the proportion of Stonecat encounters are higher at night and during the summertime. From the mobile PIT antenna results, we determined Stonecats prefer coarse substrate at an intermediate velocity (0.29 m/s) and intermediate depth (0.3 m). Conclusions from this study will be used to inform future urban stream management in conjunction with managing for sensitive fishes such as Stonecats.	Stonecat Noturus flavus are a small-bodied native catfish found from southern Canada to the southern United States, and from the Appalachian Mountains to the Rocky Mountains. In Colorado, there are two remaining populations of Stonecat, including one geographically isolated population in St. Vrain Creek, which runs through the Front Range in Longmont, CO. There has not yet been a quantitative analysis of population demographic parameters or individual habitat selection preferences of Stonecats and these are important to help manage native fish populations in urban environments. We collaborated with Colorado Parks and Wildlife and the city of Longmont during the study. W now understand some of the meso and micro-habitat requirements of Stonecats in an urban setting.In the face of increased population growth and the associated increase in urbanization, streams across Colorado’s Front Range face challenges in managing for both human concerns (i.e. health, safety, flood mitigation and recreation) and for aquatic ecosystems, but understanding habitat requirements and increasing connectivity may ensure the longevity of some imperiled fishes.
Inferences on the Status of Raptors	June 2017	TBA	TBA
Mountain Lion Population Modeling	June 2014	TBA	TBA
Lynx & Cougar Movement	June 2017	Problem statement: Western carnivore species navigate a complex matrix of land types as they undergo their life history. In Colorado, several species are tracked with a variety of telemetry devices to understand vital rates and demographics, but relatively little was known the movement of these carnivores. So What? Why this research matters: The ability to formally make inferences about large-scale spatial and temporal movement of wild carnivores in Colorado helps us understand the natural history of the species and rigorously quantifies their space use and behavior. Collaboration/Partners: This project is in collaboration with scientists at the Colorado Parks and Wildlife. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in telemetry data help us make dependable inference about movement of large carnivores in Colorado that can help influence management decisions about landscape connectivity, development, and land use.	Problem statement: Western carnivore species navigate a complex matrix of land types as they undergo their life history. In Colorado, several species are tracked with a variety of telemetry devices to understand vital rates and demographics, but relatively little was known the movement of these carnivores. So What? Why this research matters: The ability to formally make inferences about large-scale spatial and temporal movement of wild carnivores in Colorado helps us understand the natural history of the species and rigorously quantifies their space use and behavior. Collaboration/Partners: This project is in collaboration with scientists at the Colorado Parks and Wildlife. Research That Informs Decisions: Formal statistical models that account for the various sources of uncertainty in telemetry data help us make dependable inference about movement of large carnivores in Colorado that can help influence management decisions about landscape connectivity, development, and land use.
Survival of rainbow trout fry in the wild: a comparison of two whirling disease resistant strains	June 2017	Many animal populations have experienced population declines due to a broad range of factors such as habitat loss and degradation, invasive species, disease, and climate change. Introduced pathogens are known to have dramatic effects on populations. Following the establishment of the parasite that causes whirling disease (Myxobolus cerebralis) in Colorado, Colorado Parks and Wildlife (CPW) developed a whirling disease resistant Rainbow Trout (Oncorhynchus mykiss) for stocking known as the GRxCRR. The GRxCRR is a cross between the wild, susceptible Colorado River Rainbow (CRR) and the domesticated, resistant German Rainbow (GR) trout strains. It was thought that the GRxCRR would exhibit survival and reproduction similar to that of the CRR, overcome potential disadvantages associated with the history of domestication of the GR, and maintain the genetic resistance to whirling disease of the GR. One disadvantage to stocking GRxCRR is the potential for outcrossing and backcrossing that could decrease resistance to whirling disease. Stocking pure GR was not considered a viable option because it was thought that they would not survive well in a natural environment. However, in a laboratory study the GR and GRxCRR strains showed few physiological differences, indicating that the GR may be a candidate for stocking in whirling disease positive streams. We undertook a laboratory and field experiment to compare fry survival between the two strains. The field experiment was conducted in three drainages (Cache la Poudre River, Middle Fork of the South Platte River, and Colorado River), and three streams were selected in each drainage. One-mile reaches of each stream were stocked in August 2014 with 5,000 GRxCRR, identified with coded wire tags, and 5,000 untagged GR. In October 2014, April 2015 and August 2015, population estimates were conducted, providing an estimate of apparent survival for each strain. Two laboratory experiments were also conducted. In the first experiment, a 50:50 mix of GRxCRR and GR were stocked into large open mesocosms with one wild Brown Trout (Salmo trutta) predator. Survival was estimated over a 24-hour time period. The second experiment was similar, but I added treatments with or without cover. The field experiment revealed that apparent survival and growth rate was influenced by strain, stream, and primarily average temperature within the first year after stocking. After two months in the wild, the GRxCRR exhibited a higher growth rate than the GR, opposite of what is seen in the hatchery. However, after 12 months there was no significant difference in apparent survival or growth rate between the GR and GRxCRR. Laboratory experiments revealed that there were no differences in survival between the strains when confronted with Brown Trout predation. My results indicate that the GR may be a viable alternative for stocking in streams that contain M. cerebralis.	Following the establishment of the parasite that causes whirling disease (Myxobolus cerebralis) in Colorado, Colorado Parks and Wildlife (CPW) developed a whirling disease resistant Rainbow Trout (Oncorhynchus mykiss) for stocking known as the GRxCRR. The GRxCRR is a cross between the wild, susceptible Colorado River Rainbow (CRR) and the domesticated, resistant German Rainbow (GR) trout strains. It was thought that the GRxCRR would exhibit survival and reproduction similar to that of the CRR, overcome potential disadvantages associated with the history of domestication of the GR, and maintain the genetic resistance to whirling disease of the GR. One disadvantage to stocking GRxCRR is the potential for outcrossing and backcrossing that could decrease resistance to whirling disease. Stocking pure GR was not considered a viable option because it was thought that they would not survive well in a natural environment. To understand what strain was a better option for re-establishing rainbow trout fisheries, we undertook a laboratory and field experiment to compare fry survival between the two strains. The project was conducted with Colorado Parks and Wildlife. Our results indicate that the pure resistant rainbow (GR) may be a viable alternative for stocking in streams that contain M. cerebralis and my avoid issues of backcrossing and loss of resistance.
Colorado Plains Fish Optimal Monitoring	June 2016	Problem statement: Plains fishes in Eastern Colorado represent and important set of aquatic species that are undergoing population changes due to ongoing land use and environmental changes. So What? Why this research matters: The ability to formally make inferences about large-scale spatial distributions of these fishes is critical for understanding their ranges and for future monitoring efforts. Collaboration/Partners: This project was in collaboration with scientists at the Colorado Parks and Wildlife. Research That Informs Decisions: We reconciled a massive data set collected by Colorado Parks and Wildlife to estimate and understand the influences on Colorado Plains fishes and developed a statistical rigorous monitoring strategy for ongoing field sampling of these species in Colorado.	Problem statement: Plains fishes in Eastern Colorado represent and important set of aquatic species that are undergoing population changes due to ongoing land use and environmental changes. So What? Why this research matters: The ability to formally make inferences about large-scale spatial distributions of these fishes is critical for understanding their ranges and for future monitoring efforts. Collaboration/Partners: This project was in collaboration with scientists at the Colorado Parks and Wildlife. Research That Informs Decisions: We reconciled a massive data set collected by Colorado Parks and Wildlife to estimate and understand the influences on Colorado Plains fishes and developed a statistical rigorous monitoring strategy for ongoing field sampling of these species in Colorado.
Preliminary evaluation of Santa Ana Sucker responses to Waste Water Treatment Plant Effluent in the Santa Ana River.	June 2019	The Santa Ana sucker (Catostomus santaanae) is a federally threatened fish to the larger streams of southern California’s Los Angeles Basin: the Los Angeles, San Gabriel, and Santa Ana River watersheds in Los Angeles, Orange, Riverside, and San Bernardino counties. The Santa Ana Sucker was listed as an endangered species in 2000 and the primary threat to its continued presence is hydrological modifications that degrade and reduce available habitat (USFWS 2014). Water quality is also considered a high priority concern (priority 2). The Santa Ana River is heavily influenced by wastewater treatment plant (WWTP) effluent and WWTP effluent comprises the majority of the flow in the river throughout most of the year (Allen 2002, 2003). It is crucial to begin to understand how Santa Ana Suckers are responding to both acute and chronic exposure to WWTP effluents and the potential population consequences of exposure. Many WWTPs discharge to the environment a mixture of endocrine disrupting contaminants (EDCs), particularly estrogens and estrogen mimics (Kolpin et al. 2002). Long-term exposure to low-dosages of estrogenic EDCs can have adverse effects on survival, reproduction, and population viability (Mills and Chichester 2005, Schwindt et al. 2015), and removal of estrogenic contaminants can improve population recovery (Barber et al. 2012, Blanchfield et al. 2015). The Santa Ana sucker may be particularly vulnerable to the effects of WWTP-derived EDCs. Many estrogenic EDCs bioconcentrate in stream biofilms (Writer et al. 2011), resulting in elevated exposure of benthic grazing organisms like the Santa Ana sucker (Greenfield et al. 1970). Surface waters of the Santa Ana River have been demonstrated to be estrogenic in vivo in the mosquitofish, and in vitro in yeast-based estrogen screen assay (Jenkins et al. 2009). However, biomarkers of endocrine disruption have not yet been evaluated in Santa Ana suckers inhabiting these WWTP effluent impacted habitats. The preliminary work outlined in this proposal will evaluate histological and molecular biomarker responses to estrogenic EDCs. The presence or absence of biomarker responses will inform managers on the potential for EDC-induced reproductive impairment as a contributor to population recovery, and inform future management and research options.	The Santa Ana sucker (Catostomus santaanae) is a federally threatened fish to the larger streams of southern California’s Los Angeles Basin: the Los Angeles, San Gabriel, and Santa Ana River watersheds in Los Angeles, Orange, Riverside, and San Bernardino counties. The Santa Ana Sucker population in the Santa Ana River is living in an effluent dominated system and current habitat restoration efforts may not be sufficient to overcome the negative consequences of WWTP effluent exposure. Ourstudy will provide a preliminary assessment of potential negative effects of exposure to waste water effluent, particularly exposure to estrogenic compounds. The project is being conducted with U.S. Fish and Wildlife Service, the San Bernadino Valley Municipal Water District, University of Colorado, and the Environmental Protection Agency. Understanding the potential influence of water quality on Santa Ana Suckers is a high priority for the recovery and management of this endangered species and , the conservation group has concerns about long term reproductive health and the stability of the Santa Ana River sucker population. It is essential that managers have a firm understanding of the potential reproductive consequences of waste water exposure on the Santa Ana Sucker.
Breeding Ecology of Cinnamon Teal Within the San Luis Valley, CO	December 2019	The USFWS Service Regulations Committee (SRC) in 2009 requested an assessment of the harvest potential of three North American teal species; one of which was the cinnamon teal. The assessment, as envisioned by the SRC, included five areas of interest one of which was a description of the population dynamics of each species (Teal Assessment Team 2013). The cinnamon teal is one of the least studied waterfowl species in North America. Reliable, accurate demographic information is needed to determine population status and responses to harvest and habitat management. Little monitoring information is available for cinnamon teal, so as a first step to evaluating recruitment, this project is focused on estimating reproductive parameters (nest survival, hen success and fidelity, and duckling survival) and how they relate to habitat variables, in a major breeding area, Monte Vista NWR in the San Luis Valley, CO. Results will proved baseline demographic data for this population of teal, and will inform refuge managers about the effects of conditions created by refuge management and water availability on cinnamon teal. This project is a collaboration among the COCFWRU, USFWS Region 6, Migratory Birds, Colorado Parks and Wildlife, and the USFWS Monte Vista NWR.	The USFWS Service Regulations Committee (SRC) in 2009 requested an assessment of the harvest potential of three North American teal species; one of which was the cinnamon teal. The assessment, as envisioned by the SRC, included five areas of interest one of which was a description of the population dynamics of each species (Teal Assessment Team 2013). The cinnamon teal is one of the least studied waterfowl species in North America, and reliable, accurate demographic information, including reproductive parameters, is needed to determine population status and responses to harvest and habitat management. This project is a collaboration with USFWS Region 6, Migratory Birds, Colorado Parks and Wildlife, and the USFWS Monte Vista NWR. Results will proved baseline demographic data for this population of teal, and will inform refuge managers about the effects of conditions created by refuge management and water availability on cinnamon teal.
Demography of Black-footed and Laysan Albatross: Vital Rates in Support of the Surrogate Species Approach to Strategic Habitat Conservation	July 2020	The black-footed (BFAL) and Laysan (LAAL) albatrosses are long-lived seabirds of conservation concern to the USFWS. Specifically, a petition to list the BFAL under the Endangered Species Act has recently been submitted to USFWS. Furthermore, over 65% of the world population of these albatross species nest on remote island refuges in the Pacific. Although Southern Hemisphere albatross species are well-studied, through intensive research projects conducted by multiple countries, relatively little is known about the life history, survival, breeding frequency, and reproductive success of Northern Hemisphere albatross species. Such information is important, given the variety of threats that these species face (e.g., fishery bycatch, plastics ingestions, contaminants, loss of breeding habitat due to sea level rise). A banding/recapture program to monitor the vital rates of these species, under protocols developed by the Principal Investigator and collaborators, was initiated by USFWS on Midway Atoll and Tern Island in 2004, and on Laysan Island in 2005, thus encompassing the vast majority of each of these species. Designing, developing, and maintaining this monitoring program of these globally significant populations has been an ongoing collaboration among the USGS (Patuxent Wildlife Research Center before 2010 and the Colorado Cooperative and Wildlife Research Unit since), the USGS Bird Banding Lab, the USFWS Pacific and Remote Refuges, and the USFWS Region 1 Division of Migratory Birds and Habitat Programs. The main purpose of this project is to, based on the first 10 years of this data collection, (1) to assess the life history and demographic parameters (survival, recruitment probabilities, breeding probabilities, reproductive success, variability in these metrics across populations) of these Northern Hemisphere species. The parameter estimates and variability from this effort can be incorporated into a stage-based population model, to inform status assessment and provide predictions for candidate conservation actions. (2) Review whether the level of sampling effort recommended in the monitoring protocols has produced inferences with sufficient precision for management purposes (i.e., whether effort should be increased, or could be reduced).	The black-footed (Phoebastria nigripes; BFAL) and Laysan (Phoebastria immutabilis; LAAL) albatrosses are long-lived seabirds of conservation concern to the USFWS, and a petition to list the BFAL under the Endangered Species Act has recently been submitted to USFWS. Furthermore, over 65% of the world population of these albatross species nest on remote low island refuges in the Pacific, and in smaller numbers in the main Hawaiian Islands. Relatively little is known about the life history, survival, and breeding frequency of Northern Hemisphere albatross species, and in how this compares between the low islands of the Northwestern Hawaiian Islands and the main Hawaiian Islands. Such information is important, given the variety of threats that these species face (e.g., fishery bycatch, plastics ingestions, contaminants, loss of breeding habitat due to sea level rise). The project is a collaboration with the USFWS Region 1 Migratory Bird and Habitat and Inventory and Monitoring programs, the Marine National Monuments of the Pacific, and the USGS Bird Banding Laboratory. A model for annual survival and breeding probability for albatross will be developed for Midway Atoll and Laysan Island, allowing these processes to be connected with threats such as overlap with long-line fishing and other environmental factors. A vetted banding database will be provided for future analyses and recommendations for future monitoring intensity will also be provided to Refuge personnel.

Research Publications

Research Publications	Publication Date
Zimmerman, G. S., B. A. Milsap, F. Abadi, J. V. Gedir, W. L. Kendall, and J. R. Sauer. 2022. An integrated population model to inform exploitation management for bald eagles. Journal of Wildlife Management 86:e22158, https://doi.org/10.1002/jwmg.22158. \| Abstract	January 2022	Effectively managing take of wildlife resulting from human activities poses a major challenge for applied conservation. Demographic data essential to decisions regarding take are often expensive to collect and are either not available or based on limited studies for many species. Therefore, modeling approaches that efficiently integrate available information are important to improving the scientific basis for sustainable take thresholds. We used the prescribed take level (PTL) framework to estimate allowable take for bald eagles (Haliaeetus leucocephalus)in the conterminous United States. We developed an integrated population model (IPM) that incorporates multiple sources of information and then use the model output as the scientific basis for components of the PTL framework. Our IPM is structured to identify key parameters needed for the PTL and to quantify uncertainties in those parameters at the scale at which the United States Fish and Wildlife Service manages take. Our IPM indicated that mean survival of birds >1 year old was high and precise (0.91, 95% CI = 0.90–0.92), whereas mean survival of first‐year eagles was lower and more variable(0.69, 95% CI = 0.62–0.78). We assumed that density dependence influenced recruitment by affecting the probability of breeding, which was highly imprecise and estimated to have declined from approximately 0.988 (95% CI = 0.985–0.993) to 0.66 (95% CI = 0.34–0.99) between 1994 and 2018. We sampled values from the posterior distributions of the IPM for use in the PTL and estimated that allowable take (e.g., permitted take for energy development, incidental collisions with human made structures, or removal of nests for development) ranged from approximately 12,000 to 20,000 individual eagles depending on risk tolerance and form of density dependence at the scale of the conterminous United States excluding the Southwest. Model‐based thresholds for allowable take can be inaccurate if the assumptions of the underlying framework are not met, if the influence of permitted take is under‐estimated, or if undetected population declines occur from other sources. Continued monitoring and use of the IPM and PTL frameworks to identify key uncertainties in bald eagle population dynamics and management of allowable take can mitigate this potential bias, especially where improved information could reduce the risk of permitting non‐sustainable take.
Zhao, Q*., G. Scott Boomer, and W. L. Kendall. 2018. The non-linear, interactive effects of population density and climate drive the geographical patterns of waterfowl survival. Biological Conservation 221:1-9.	May 2018
Zendt, J. S., and E. P. Bergersen. 2000. Distribution and abundance of the aquatic oligochaete host Tubifex tubifex for the salmonid whirling disease parasite Myxobolus cerebralis in the Upper Colorado River Basin. North American Journal of Fisheries Management 20:502-512.	January 2000
Xiao X., E.P. White, M.B. Hooten, and S.L. Durham. (2011). On the use of log-transformation vs. nonlinear regression for analyzing biological power-laws. Ecology, 92: 1887-1894.	December 2011
Wolfe, L. L., Conner, M. M., Baker, T. H., Dreitz, V. J., Burnham, K. P., Williams, E. S., Hobbs, N. T., and Miller, M. W. 2002. Evaluation of antermortem sampling to estimate chronic wasting disease prevalence in free-ranging mule deer. Journal of Wildlife Management 66:564-573.	August 2002
Wolfe, B.A., B.M. Johnson, A.R. Breton, P.J. Martinez, and D.L. Winkelman. In press. Origins and movements of invasive piscivores determined from the strontium isotope (87Sr/86Sr) ratio of otoliths. Canadian Journal of Fisheries and Aquatic Sciences. \| Download	April 2012
Winkelman, D.L. and A.R. Schwindt. A common wastewater contaminant can disrupt fish survival, reproduction, and population dynamics. Colorado Water Newsletter	August 2014
Winkelman, D.L. 2011. Evaluation of the Flathead Catfish Population and Fishery on Lake Carl Blackwell, OK, with emphasis on the effects of Noodling. Pages 209-218 in P.H. Michaletz and V.H. Travniceck, editors. Conservation, ecology, & management of catfish: the second international symposium. American Fisheries Society, Symposium 77, Bethesda, MD.	August 2011
Winkelman, D. L., and C. Sager. Managing Hybrid Bluegill Fisheries: estimating and predicting the effects of young anglers. Pages 207-214 in M. J. Nickum, P. M. Mazik, J. G. Nickum and D. D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society Symposia 44, American Fisheries Society, Bethesda, Maryland.	July 2004
Williams, P.J., M.B. Hooten, J.N. Womble, G.G. Esslinger, and M.R. Bower. (2018). Monitoring dynamic spatio-temporal ecological processes optimally. Ecology, 99: 524-535.	May 2018
Williams, P.J., M.B. Hooten, J.N. Womble, G.G. Esslinger, M.R. Bower, and T.J. Hefley. (2017). Estimating occupancy and abundance using aerial images with imperfect detection. Methods in Ecology and Evolution, 8: 1679-1689.	July 2017
Williams, P.J., M.B. Hooten, J.N. Womble, G.G. Esslinger, M.R. Bower, and T.J. Hefley. (2017). An integrated data model to estimate spatio-temporal occupancy, abundance, and colonization dynamics. Ecology, 98: 328-336.	March 2017
Williams, P.J., M.B. Hooten, G.G. Esslinger, J.N. Womble, J. Bodkin, and M.R. Bower. (2019). The rise of an apex predator following deglaciation. Diversity and Distributions, 25: 895-908.	May 2019
Williams, P.J. and M.B. Hooten. (2016). Combining statistical inference and decisions in ecology. Ecological Applications, 26: 1930-1942.	December 2016
Williams, P. J., and W. L. Kendall. A guide to multi-objective optimization for ecological problems with an application to cackling goose management. Ecological Modelling, in press.	October 2016
Williams, P. J., W. L. Kendall, and M. B. Hooten. 2019. Choosing ecological models using multi-objective optimization. Ecological Modelling 404:21-26.	July 2019
Wikle, C.K., W.B. Leeds, and M.B. Hooten. (2016). Models for ecological models: Ocean primary productivity. Chance, 29 (2): 23.	December 2016
White, G. C., and Burnham, K. P., 1999. Program MARK: Survival estimation from populations of marked animals. Bird Study 46 (Supplement):S120-139.	May 1999
White, G. C., K. P. Burnham, and R. J. Barker. 2009. Evaluation of a Bayesian MCMC random effects inference methodoly for capture-mark-recapture date, pp 1119-1127 in Modeling Demographic Processes in Marked Populations, Environmental and Ecological Statistics 3. Thomson, D. L., E. G. Cooch, and M. J. Conroy (Eds. ). Springer, New York, NY.	December 2008
Wampole, E.M., Farris, Z.J., Razafy, P. and Gerber, B.D. (2023), Forest carnivores living on the edge with invasive predators. Animal Conservation. https://doi.org/10.1111/acv.12926 \| Download	December 2023
Walsh, M. G., and D. L. Winkelman. 2004. Short-term retention of floy anchor tags by stream-dwelling smallmouth bass. Proceedings of the Annual Conference of the Southeastern Association of Fish and Wildlife Agencies 58:38-43.	May 2004
Walsh, M. G., and D. L. Winkelman. 2004. Fish assemblage structure in an Oklahoma Ozark stream before and after rainbow trout introduction. Pages 413-426 in M. J. Nickum, P. M. Mazik, J. G. Nickum, and D. D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society, Symposium 44, American Fisheries Society, Bethesda, Maryland.	October 2004
Walsh, M. G., and D. L. Winkelman. 2004. Anchor and Visible Implant Elastomer Tag Retention by Hatchery Rainbow Trout Stocked into an Ozark Stream. North American Journal of Fisheries Management 24:1425-1429.	February 2004
Walsh, M. G., D. L. Winkelman, and R. J. Bahr. 2004. Short-term mortality and electrofishing injury in hatchery-reared rainbow trout stocked into an Ozark stream. North American Journal of Fisheries Management 24:316-321.	January 2004
W. D. Walter, D.P. Walsh, M.L. Farnsworth, D.L. Winkelman, and M.W. Miller. 2011. Soil clay content underlies prion infection odds. Nature Communications:2:200 doi: 10.1038 / ncomms1203	January 2011
Ver Hoef, J.M., E.M. Hanks, and M.B. Hooten. (2018). On the relationship between conditional (CAR) and simultaneous (SAR) autoregressive models. Spatial Statistics, 25: 68-85.	July 2018
Ver Hoef, J.M., E.E. Peterson, M.B. Hooten, E.M. Hanks, and M-J. Fortin. (2018). Spatial autoregressive models for statistical inference from ecological data. Ecological Monographs, 88: 36-59.	March 2018
Vanausdall, R. A., W. L. Kendall, D. P. Collins, and Q. R. Hays. 2024. Time of year and weather influence departure decisions of sandhill cranes at a primary stopover. Frontiers in Ecology and Evolution 12:1279279, doi: 10.3389/fevo.2024.1279279.	March 2024
Twining, JP, Zalewski, A, Cove, MV, Birks, J, Wearn, O, Haysom, J, Wereszczuk, A,Manzo, E, Bartolommei, P, Mortelli, A, Evans, B, Gerber, BD, McGreevy, TJ,Ganoe, L, Masseloux, J, Mayer, A, Wierzbowska, I, Akins, J, Drummey, D, McShea,W, Kays, R, Schuttler, S, Pardo, L, Boyce, A, Trujillo, AJV, L´opez-Gonz´alez, C, Lara-D´ıaz, NE, Sukmasuang, R, Whatton, M, Cosby, O, Giman, B, Ragai, RB, Li, S, Bu,H, Wang, D, Wang, F, Waggershauser, C, Bamber, J, Stewart, F, Fisher, J, Fuller,A, Perkins, K, Sutherland, C, and Powell, RA. In Press. Sociality in unexpected places: Using global remote camera data to evaluate the drivers of social complexity.Proceedings of the National Academy of Science. 121, e2312252121. \| Abstract \| Download \| Publisher Website	March 2024	The social system of animals involves a complex interplay between physiology, natural history, and the environment. Long relied upon discrete categorizations of “social” and “solitary” inhibit our capacity to understand species and their interactions with the world around them. Here, we use a globally distributed camera trapping dataset to test the drivers of aggregating into groups in a species complex (martens and relatives, family <i>Mustelidae</i>, Order <i>Carnivora</i>) assumed to be obligately solitary. We use a simple quantification, the probability of being detected in a group, that was applied across our globally derived camera trap dataset. Using a series of binomial generalized mixed-effects models applied to a dataset of 16,483 independent detections across 17 countries on four continents we test explicit hypotheses about potential drivers of group formation. We observe a wide range of probabilities of being detected in groups within the solitary model system, with the probability of aggregating in groups varying by more than an order of magnitude. We demonstrate that a species’ context-dependent proclivity toward aggregating in groups is underpinned by a range of resource-related factors, primarily the distribution of resources, with increasing patchiness of resources facilitating group formation, as well as interactions between environmental conditions (resource constancy/winter severity) and physiology (energy storage capabilities). The wide variation in propensities to aggregate with conspecifics observed here highlights how continued failure to recognize complexities in the social behaviors of apparently solitary species limits our understanding not only of the individual species but also the causes and consequences of group formation.
Tredennick, A.T., M.B. Hooten, and P.B. Adler. (2017). Do we need demographic data to forecast the state of plant populations? Methods in Ecology and Evolution, 8: 541-551.	June 2017
Tredennick, A.T., M.B. Hooten, C.L. Aldridge, C.G. Homer, A. Kleinhesselink, and P.B. Adler. (2016). Forecasting climate change impacts on plant populations over large spatial extents. Ecosphere,7: e01525.	December 2016
Tipton, J.R., M.B. Hooten, C. Nolan, R.K. Booth, and J. McLachlan. (2019). Predicting paleoclimate from compositional data using multivariate Gaussian process inverse prediction. Annals of Applied Statistics, 13: 2363-2388.	February 2019
Tipton, J., M.B. Hooten, and S. Goring. (2017). Reconstruction of spatio-temporal temperature from sparse historical records using robust probabilistic principal component regression. Advances in Statistical Climatology, Meteorology and Oceanography, 3: 1-16.	January 2017
Tipton, J., M.B. Hooten, N. Pederson, M. Tingley, and D. Bishop. (2016). Reconstruction of late Holocene climate based on tree growth and mechanistic hierarchical models. Environmetrics, 27: 42-54.	December 2016
Thomas, L., Laake, J. L., Strindberg, S., Marques, F. F. C., Buckland, S. T., Borchers, D. L., Anderson, D. R., Burnham, K. P., Hedley, S. L., and Pollard, J. H. 2002. Distance 5. 0. Release 2. Research Unit for Wildlife Population Assessment, University of St. Andrews, UK. http://www. ruwpa. st-and. ac. uk/distance/	November 2002
Thomas, L., Burnham, K. P. Buckland, S. T. 2004. Temporal inferences from distance sampling surveys, pp 71-107 (Chapter 5) in Advanced Distance Sampling (Buckland et al. editors), Oxford University Press, Oxford, UK.	April 2005
Thomas, L, Buckland, S. T., Burnham, K. P., Anderson, D. R., Laake, J. L., Borchers, D. L., Strindberg, S. 2002. Distance sampling. Pp 544-552. Volume 1, in Encyclopedia of Environmetrics, El-Shaarawi, A. H., Piegorsh, W. W., Wiley, John and Sons Ltd. Chichester.	October 2002
Tatarenkov, A., F. Barreto, D. L. Winkelman, and J. C. Avise. 2006. Genetic monogamy in the channel catfish, Ictalurus punctatus, a species with uniparental nest guarding. Copeia 2006:735-741.	November 2006
Stoelting, R. E., R. J. Gutiérrez, W. L. Kendall, and M. Z. Peery. 2015. Life history trade-offs and reproductive cycles in Spotted Owls? The Auk: Ornitholigical Advances 132:46-64.	October 2014
Steger, C., B. Butt, and M.B. Hooten. (2017). Safari Science: Assessing the reliability of citizen science data for wildlife surveys. Journal of Applied Ecology, 54: 2053-2062.	October 2017
Stauffer, G. E., J. J. Rotella, R. A. Garrott, and W. L. Kendall. 2014. Environmental correlates of temporary emigration for female Weddell seals and consequences for recruitment. Ecology 95:2526-2536.	October 2014
Stanley, T. R., and Burnham, K. P. 1999. A goodness-of-fit test for capture-recapture model Mt under closure. Biometrics 55:366-375.	August 1999
Stanley, T. R., and Burnham, K. P. 1999. A closure test for time-specific closed-population capture-recapture data. Environmental and Ecological Statistics 6:197-209.	September 1999
Smith, D. R., K. P. Burnham, D. M. Kahn, X. He, C. J. Goshorn, K. A. Hattala, and A. Kahnle. 2000. Bias in survival estimates from tag-recovery models where catch-and-release is common, with an example from Atlantic striped bass (Morone Saxatilis). Canadian Journal of Fisheries and Aquatic Science 57:886-897.	January 2000
Small, R.J., B.M. Brost, M.B. Hooten, M. Castellote, and J. Mondragon. (2017). Anthropogenic noise in Cook Inlet beluga critical habitat: Potential for spatial displacement. Endangered Species Research, 32: 43-57.	February 2017
Shamon, Hila, Roi Maor, Michael V. Cove, Roland Kays, Jessie Adley, Peter D. Alexander, David N. Allen, et al. 2024. “ SNAPSHOT USA 2021: A Third Coordinated National Camera Trap Survey of the United States.” Ecology e4318. https://doi.org/10.1002/ecy.4318	May 2024
Setash, C. M., W. L. Kendall, and D. Olson. 2020. Nest site selection influences cinnamon teal nest survival in Colorado. Journal of Wildlife Management 84:542-552.	January 2020
Setash, C. M., W. L. Kendall, and D. Olson. 2020. Nest attendance patterns during incubation influence reproductive success of a ground-nesting bird. Ibis DOI: 10.1111/ibi.12838.	March 2020
Schwindt, AR and DL Winkelman, K Keteles, M. Murphy, A.M. Vajda. 2014. An Environmental oestrogen disrupts fish population dynamics through direct and transgenerational effects on survival and fecundity. Journal of Applied Ecology 51:582-591. \| Download	May 2014
Schwindt, A.R. and D.L. Winkelman. Stochastic population growth rate is reduced by an environmental estrogen and is highly sensitive to fecundity and juvenile survival of a short-lived fish	June 2016
Schmelter, M.L., P. Wilcock, M.B. Hooten, and D.K. Stevens. (2015). Multi-fraction Bayesian sediment transport model. Journal of Marine Science and Engineering, 3: 1066-1092.	September 2015
Schmelter, M.L., M.B. Hooten, and D.K. Stevens. (2011). Bayesian sediment transport model for uni-size bedload. Water Resources Research, 47: W11514.	December 2011
Schisler, G. J., and E. P. Bergersen. 2002. Evaluation of risk of high elevation Colorado waters to the establishment of M. cerebralis. Pages 33-42 in Whirling Disease: reviews and current topics, J. L. Bartholomew and J. C. Wilson (Eds. ). American Fisheries Society Symposium 29, Bethesda, Maryland.	July 2002
Schisler, G. J., E. P. Bergersen, P. G. Walker, J. Wood and J. K. Epp. 2001. Comparison of single-round polymerase chain reaction (PCR) and pepsin-trypsin digest (PTD) methods for detection of Myxobolus cerebralis. Diseases of Aquatic Organisms 45:109-114.	June 2001
Schisler, G. J., E. P. Bergersen and P. G. Walker. 2000. Effects of multiple stressors on morbidity and mortality of fingerling rainbow trout infected with Myxobolus cerebralis. Transactions of the American Fisheries Society 129:859-865.	January 2000
Schaub, M. and W. L. Kendall (eds.). 2012. Proceedings "Euring Analytical Conference 2009". Journal of Ornithology 152 (Supplement 2).	February 2012
Scharf, H.R., M.B. Hooten, and D.S. Johnson. (2017). Imputation approaches for animal movement modeling. Journal of Agricultural, Biological, and Environmental Statistics, 22: 335-352.	June 2017
Scharf, H.R., M.B. Hooten, R.R. Wilson, G.M. Durner, T.C. Atwood (2019). Accounting for phenology in the analysis of animal movement. Biometrics, 75: 810-820.	September 2019
Scharf, H.R., M.B. Hooten, D.S. Johnson, and J. Durban. (2018). Process convolution approaches for modeling interacting trajectories. Environmetrics, 29: e2487.	February 2018
Scharf, H.R., M.B. Hooten, B.K. Fosdick, D.S. Johnson, J.M. London, and J.W. Durban. (2016). Dynamic social networks based on movement. Annals of Applied Statistics,10: 2182-2202.	December 2016
Schaffler, J. J., and D. L. Winkelman. 2008. Temporal and spatial variability in trace element signatures of juvenile striped bass from two spawning locations in Lake Texoma, Oklahoma-Texas. Transactions of the American Fisheries Society 137:818-829.	August 2008
Sauer, J. R., W. A. Link, W. L. Kendall, D. D. Dolton, and D. K. Niven. 2010. Mourning dove population change in North America, 1966-2007: indexes based on doves seen and heard can tell different stories. Journal of Wildlife Management 74:1059-1069.	July 2010
Sauer, J. R., M. Otto, W. L. Kendall, and G. S. Zimmerman. 2011. Monitoring bald eagles using lists of nests: a response to Watts and Duerr. Journal of Wildlife Management 75:509-512.	June 2011
Sagar, C. R., and D. L. Winkelman. 2006. Effects of increased feeding frequency on growth of hybrid bluegill in ponds. North American Journal of Aquaculture 68:313-316.	October 2006
Ruzicka, R. E., D. Rollins, W. L. Kendall, and P. F. Doherty, Jr. 2024. Effects of release strategy, source population, and age on reintroduced scaled quail reproduction. Journal of Wildlife Management, DOI: 10.1002/jwmg.22660.	August 2024
Ruzicka, R. E., D. Rollins, P. F. Doherty, Jr., and W. L. Kendall. 2023. Longer holding times decrease dispersal bur increase mortality of translocated scaled quail. Journal of Wildlife Management 2023;e22498, DOI: 10.1002/jwmg.22498.	September 2023
Ruiz-Gutierrez, V., W. L. Kendall, J. F. Saracco, and G. C. White. 2016. Modeling dynamics for resident and transient individuals: a case study using uncertain state models for migratory birds. Journal of Applied Ecology, DOI: 10.1111/1365-2664.12655	April 2016
Ruiz-Gutierrez, V., M.B. Hooten, and E.H. Campbell Grant. (2016). Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias. Methods in Ecology and Evolution, 7: 900-909.	August 2016
Ross, B.E., M.B. Hooten, and D.N. Koons. (2012). An accessible method for implementing hierarchical models with spatio-temporal abundance data. PLoS One, 7: e49395.	November 2012
Ross, B.E., M.B. Hooten, J-M. DeVink, and D.N. Koons. (2015). Combined effects of climate, predation, and density dependence on Greater and Lesser Scaup population dynamics. Ecological Applications, 25: 1606-1617.	September 2015
Rosenstock, S. S., D. R. Anderson, K. G. Kiesen, T. Leukering, and M. F. Carter. 2002. Landbird counting techniques: current practices and an alternative. The Auk 119:46-53.	January 2002
Rogers, K. B., and E. P. Bergersen. 1999. Utility of synthetic structures for concentrating adult northern pike and largemouth bass. North American Journal of Fisheries Management 19:1054-1065.	November 1999
Rockweit, JT, JM Jenkins, JE Hines, JD Nichols, KM Dugger, AB Franklin, PC Carlson, WL Kendall, DB Lesmeister, C McCafferty, SH Ackers, LS Andrews, LL Bailey, JB, KP Burnham, T Chestnut, MM Conner, KE Dilione, RJ Davis, ED Forsman, EM Glenn, SA Gremel, KA Hamm, DR Herter, JM Higley, RB Horn, DW Lamphear, TL McDonald, JA Reid, CJ Schwarz, DC Simon, SG Sovern, JK Swingle, JD Wiens, H Wise, and CB Yackulic. 2022. Range-wide Sources of Variation in Reproductive Rates of Northern Spotted Owls. Ecological Applications 000:000-000, doi:10.1002/eap.2726.	August 2022
Roberts, J.J., K.D. Fausch, D.P. Peterson, and M.B. Hooten. (2013). Fragmentation and thermal risks from climate change interact to affect persistence of native trout in the Colorado River basin. Global Change Biology, 19: 1383-1398.	March 2013
Rivera, K., Garcia-Quijano, C., Sonnet, V., & Gerber, B. D. (2024). Applying a hierarchical Bayesian framework to reveal how fear and animal ownership drive human's valuation of and interactions with coyotes. Conservation Science and Practice, e13177. https://doi.org/10.1111/csp2.13177 \| Download	August 2024
Riepe, T.B., V. Vincent, Vicki Milano, E.R. Fetherman, and D.L. Winkelman. Evidence for the use of mucus swabs to detect Renibacterium salmoninarum in Brook Trout. Pathogens 10, 460. https://doi.org/10.3390/ pathogens10040460 \| Download	April 2021
Riepe, T.B., E.R. Fetherman, B. Neuschwanger, T. Davis, A. Perkins, and D.L. Winkelman. 2023. Vertical Transmission of Renibacterium salmoninarum in Cutthroat Trout (Oncorhynchus clarkii). Journal of Fish Diseases DOI:10.1111/jfd13745 \| Download	December 2022
Riepe, T.B., B.W. Avila, and D.L. Winkelman. 2022. Effects of 17a-ethinylestradiol and Density on Juvenile Fathead Minnow Growth and Survival. Journal of Aquatic Pollution and Toxicology 6:60 DOI:10.21767/2581-804X.22.6.60 \| Download	October 2022
Reichert, B. E., W. L. Kendall, R. J. Fletcher, Jr., and W. M. Kitchens. Spatio-temporal variation in age structure and abundance of the endangered snail kite: a declining, aging population in South Florida. Plos One DOI:10.1371/journal.pone.0162690: 1-18.	September 2016
Reichert, B. E., J. M. Martin, W. L. Kendall, C. E. Cattau, and W. M. Kitchens. 2010. Interactive effects of senescence and natural disturbance on the annual survival probabilities of snail kites. Oikos 119:972-979.	May 2010
Reichert, B. E., C. E. Cattau, R. J. Fletcher, Jr., W. L. Kendall, and W. E. Kitchens. 2012. Extreme weather and experience influence reproduction in an endangered bird. Ecology 93:2580-2589.	October 2012
Raiho, A., M.B. Hooten, S. Bates, and N.T. Hobbs. (2015). Forecasting the effects of fertility control on overabundant ungulates: White-tailed deer in the National Capital region. PLoS One, 10: e0143122.	December 2015
Péron, G., J. E. Hines, J. D. Nichols, W. L. Kendall, K. A. Peters, and D. S. Mezrahi. 2013. Age-specific superpopulation capture-recapture models for the estimation of the number of bird and bat fatalities at wind-power plants. Journal of Applied Ecology 50:902-911.	August 2013
Peñaloza, C. L., W. L. Kendall, and C. A. Langtimm. Reducing bias in survival under non-random temporary emigration. Ecological Applications 24:1155-1166.	July 2014
Peterson, E.E., E.M. Hanks, M.B. Hooten, J.M. Ver Hoef, and M.-J. Fortin. (2019). Spatially structured statistical network models for landscape genetics. Ecological Monographs, 89: e01355.	April 2019
Pepin, K. M., T. J. Smyser, A. J. Davis, R. S. Miller, K. C. VerCauteren, W. L. Kendall, and C Slootmaker. 2020. Optimal spatial prioritization of control resources for elimination of invasive species under demographic uncertainty. Ecological Applications, in review.	March 2020
Pepin, K. M., A. J. Davis, R. S. Epanchin-Niell, A. M. Gormley, J. L. Moore, T. J. Smyser, B. Shaffer, W. L. Kendall, K. Shea, M. C. Runge, and S. McKee. 2022. Optimizing management of invasions in an uncertain world using dyamic spatial models. Ecological Applications 32:e2628. https://doi.org/10.1002/eap.2628.	April 2022
Pejchar, L., M.B. Hooten, and G.Daily. (2018). Unique effects of large-scale forest restoration on native and exotic birds in Hawaii. Diversity and Distribution, 24: 811-819.	May 2018
Pearson, K. N., W. L. Kendall, D. L. Winkelman, and W. R. Persons. Tradeoffs between physical captures and PIT tag antenna array detections: a case study for the Lower Colorado River Basin population of humpback chub (Gila cypha). Fisheries Research 183:263-274..	November 2016
Pearson, K. N., W. L. Kendall, D. L. Winkelman, and W. R. Persons. 2015. Evidence for skipped spawning in the endangered humpback chub (Gila cypha) with implications for demographic parameter estimates. Fisheries Research 170:50-59	October 2015
Paschoal, A. M. O., R. L. Massara, L. L. Bailey, W. L. Kendall, P. F Doherty, Jr., A. Hirsch, A G. Chiarello, and A. P. Paglia. Use of Atlantic forest protected areas by free-randing dogs: estimating abundance and persistence of use. Ecosphere 7 (Article e01480):1-15.	October 2016
Parmenter, R. R., T. L. Yates, D. R. Anderson, K. P. Burnham, J. L. Dunnum, A. L. Franklin, M. T. Friggens, B. C. Lubow, M. Miller, G. S. Olson, C. A. Parmenter, J. Pollard, E. A. Rexstad, T. M. Shenk, T. R. Stanley, and G. C. White. 2002. Small mammal density estimation: a field comparison of grid-based versus web-based density estimators. Ecological Monographs 73:1-26.	March 2002
Oyler-McCance, S. J., Kahn, N. W., Burnham, K. P., Braun, C. E., Quinn, T. W. 1999. A population genetic comparison of large and small-bodied sage grouse in Colorado using microsatellite and mitochondrial DNA markers. Molecular Ecology 8:1457-1466.	June 1999
Oyler-McCance, S. J., K. P. Burnham, and C. E. Braun. 2000. Modeling management and conservation strategies for Gunnison sage grouse in Colorado. Pp. 305-307 in Wildlife, Land, and People: Priorities for the 21st Century, R. Fields, R. Warren, H. Okarma, and P. Sievert (Editors). Proceedings of the Second International Wildlife Management Congress. The Wildlife Society, Bethesda, Maryland.	December 2002
Oyler-McCance, S. J., K. P. Burnham and C. E. Braun. 2001. Influence of changes in sagebrush on Gunnison sage grouse in southwestern Colorado. The Southwestern Naturalist 46:323-331.	October 2001
Northrup, J.M., M.B. Hooten, C.R. Anderson, and G. Wittemyer. (2013). Practical guidance on characterizing availability in resource selection functions under a use-availability design. Ecology, 94: 1456-1463. Ecology, In Press.	July 2013
Northrup, J.M., C.R. Anderson, M.B. Hooten, and G. Wittemyer. (2016). Movement reveals scale-dependence in habitat selection of a large ungulate. Ecological Applications, 26: 2746-2757.	January 2016
Nichols, J. D., W. L. Kendall, and G. S. Boomer. 2019. Accumulating evidence in ecology: once is not enough. Ecology and Evolution. DOI: 10.1002/ece3.5836	November 2019
Nichols, J. D., M. K. Oli, W. L. Kendall, and G. S. Boomer. 2021. A better approach for dealing with reproducibility and replicability in science. Proceedings of the National Academy of Sciences 118(7): e2100769118. https://doi.org/10.1073/pnas.2100769118	February 2021
Nehring, B.R., B. Hancock, M. Catanese, M.E.T. Stinson, D. Winkelman, J. Wood, and J. Epp. 2013. Reduced Myxobolus cerebralis actinospore production in a Colorado reservior may be linked to changes in Tubifex tubifex population structure.	August 2013
Milsap, B. A., G. S. Zimmerman, W. L. Kendall, ,J. G. Barnes, M. A. Braham, B. E. Bedrosian, D. A. Bell, P. H. Bloom, R. H. Crandall, R. Domenech, D. Driscoll, A. E. Duerr, R. Gerhardt, S. E. J. Gibbs, A. R. Harmata, K. Jacobson, T. E. Katzner, R. N. Knight, J. M. Lockhart, C. McIntyre, R. K. Murphy, S. J. Slater, B. W. Smith, J. P. Smith, D. W. Stahlecker, and J. W. Watson. 2022. Age-specific survival rates, causes of death, and allowable take of golden eagles in the western United States. Ecological Applications 32:e2544, https://doi.org/10.1002/eap.2544.	April 2022
Mezebish Quinn, T., P. W. Paton, B. D. Gerber, J. E. Kilburn, and S. R. McWilliams. 2024. Habitat selection of non-breeding American black ducks in an urban estuary. Journal of Wildlife Management e22649. https://doi.org/10.1002/jwmg.22649 \| Download	August 2024
Meredith, C.S., P. Budy, and M. Hooten, and M. O. Prates. 2016. Assessing abiotic conditions influencing the longitudinal distribution of exotic brown trout in a mountain stream: a spatially-explicit modeling approach. Biological Invasions. DOI 10.1007/s10530-016-1322-z. USGS IP-069503 \| Abstract	November 2016	Trout species often segregate along elevational gradients, yet the mechanisms driving this pattern are not fully understood. On the Logan River, Utah, USA, exotic brown trout (Salmo trutta) dominate at low elevations but are near-absent from high elevations with native Bonneville cutthroat trout (Onchorhynchus clarkii utah). We used a Bayesian, spatial modeling approach to evaluate abiotic conditions (describing mechanisms related to temperature and physical habitat) potentially influencing the distribution of brown trout in this system. We also considered the influence of propagule pressure, including the intensity of past stocking pressure and distance from a concentrated stocking area. The distribution of brown trout was best explained by models describing: 1) average summer temperature interacting with unit stream power, our measure of gravel availability for spawning (R2=0.54), and 2) the prevalence of anchor ice between each reach and a high-intensity stocking area, also interacting with our measure of gravel availability (R2=0.52). Based on these findings, effects of cold summer temperatures on age-0 survival and/or the lack of movement upstream due to anchor ice are likely mechanisms contributing to low abundance of brown trout at high elevations. The potential role of anchor ice in affecting longitudinal distributions of brown trout has not been well-explored in other research. These findings have implications for future brown trout expansion upstream given some evidence suggesting anchor ice prevalence on the Logan River has decreased significantly over the last several decades, likely in response to climatic changes.
McGree, M.M., D.L. Winkelman, N.K. Vieira, and A. Vajda. 2009. Reproductive failure of the red shiner after acute exposure to an exogenous estrogen. Canadian Journal of Fisheries and Aquatic Sciences 67:1730-1743. \| Download \| Publisher Website	October 2010
McGowan, C.P., J.E. Hines, J.D. Nichols, J.E. Lyons, D.R. Smith, K. Kalasz, L.J. Niles, A. Dey, N.A. Clark, P.W. Atkinson, C.D.T. Minton, W. Kendal. 2011. Demographic consequences of migratory stopover: linking red knot survival to horseshoe crab spawning abundance. Ecosphere 2: art 69.	June 2011
McClintock, B.T., D.S. Johnson, M.B. Hooten, J.M. Ver Hoef, and J.M. Morales. (2014). When to be discrete: the importance of time formulation in understanding animal movement. Movement Ecology, 2: 21.	October 2014
McClintock, B. T., J. D. Nichols, L. L. Bailey, D. I. MacKenzie, W. L. Kendall, and A. B. Franklin. 2010. Seeking a second opinion: uncertainty in disease ecology. Ecology Letters 13:659-674.	June 2010
McClintock, B. T., G. C. White, K. P. Burnham. 2006. A robust design mark-resight abundance estimator allowing heterogeneity in resighting probabilities. Journal of Agricultural, Biological and Environmntal Statistics. 11:231-248.	September 2006
McClintock, B. T., G. C. White, K. P. Burnham, and M. A. Pryde. 2009. A generalized mixed effects model of abundance for mark-resight data when sampling is without replacement, pp 271-289 in Modeling Demographic Porcesses in Marked Populations, Environmental and Ecological Statistics 3, Thomson, D. L., E. G. Cooch, and M. J. Conroy (Eds. ). Springer, New York, NY.	December 2008
Mayer, A. E., Ganoe, L. S., Brown, C., & Gerber, B. D. (2023). Diel activity structures the occurrence of a mammal community in a human-dominated landscape. Ecology and Evolution, 13, e10684. https://doi.org/10.1002/ece3.10684 \| Download	November 2023
Martin, J. M., A. F. O’Connell, W. L. Kendall, M. C. Runge, T. R. Simons, A. H. Waldstein, S. A. Schulte, S. J. Converse, G. W. Smith, M. Rikard, and E. F. Zipkin. 2010. Optimal control of native predators. Biological Conservation 143:1751-1758.	July 2010
Lyons, J. E., W. L. Kendall, J. A. Royle, S. J. Converse, B. A. Andres, and J. B. Buchanan. 2015. Population size and stopover duration estimation using mark-resight data and Bayesian analysis of a superpopulation model. Biometrics DOI: 10.1111/biom.12393.	December 2015
Lukacs, P. M., and K. P. Burnham. 2005. Review of capture-recapture methods applicable to noninvasive genetic sampling. Molecular Ecology 14:3909-3919	July 2005
Lukacs, P. M., and K. P. Burnham, 2005. Estimating population size from DNA-based closed capture-recapture data incorporating genotyping error. Journal of Wildlife Management 69:396-403.	January 2005
Lukacs, P. M., W. L. Thompson, W. L. Kendall, W. R. Gould, P. F. Doherty, K. P. Burnham, D. R. Anderson. 2007. Concerns regarding a call for pluralism. Journal of Applied Ecology 44:456-460	March 2007
Lukacs, P. M., L. S. Eggert, K. P. Burnham. 2007. Estimating population size from dung-based DNA capture-recapture data. Wildlife Biology in Practice 3:83-92. A web publication http://www. socpvs. org/journals/index. php/wbp	August 2007
Lukacs, P. M., K. P. Burnham, B. P. Dreher, K. T. Scribner, S. R. Winterstein. 2009. Extending the robust design for DNA-based capture-recapture date incorporating genotyping error and laboratory date, pp 711-726 in Modeling Demographic Processes in Marked Populations, Environmental and Ecological Statistics 3. Thomson, D. L., E. G. Cooch, and M. J. Conroy (Eds. ). Springer, New York, NY.	December 2008
Lukacs, P. M., Dreitz, V. J., Knopf, F. L., Burnham, K. P., 2004. Estimating survival probabilities of unmarked dependent young when detection is imperfect. The Condor 106:926-931.	October 2004
Lukacs, P. M., D. R. Anderson, K. P. Burnham. 2005. Evaluation of trapping-web designs. Wildlife Research 32:103-110.	April 2005
Lu, X., P.J. Williams, M.B. Hooten, J.A. Powell, J.N. Womble, and M.R. Bower. (2020). Nonlinear reaction-diffusion process models improve inference for population dynamics. Environmetrics, 31: e2604.	February 2020
Lepak, J.M., M.B. Hooten, and B.M. Johnson. (2012). The influence of marine subsidies on diet, growth, and Hg concentrations of freshwater sport fish: tertiary impacts on fisheries and human health. Ecotoxicology, 21: 1878-1888.	October 2012
Lepak, J.M., M.B. Hooten, C.A. Eagles-Smith, M.A. Lutz, M.T. Tate, J.T. Ackerman, J.J. Willacker Jr., D.C. Evers, J. Davis, C.F. Pritz, J.G. Wiener. (2016). Assessing mercury concentrations in fish across western Canada and the United States: potential health risks to fish and humans. Science of the Total Environment, 571: 342-354.	December 2016
Lepak, J.M., C.N. Cathcart, and M.B. Hooten. (2012). Otolith weight as a predictor of age in kokanee salmon (Oncorhynchus nerka) from four Colorado reservoirs. Canadian Journal of Fisheries and Aquatic Sciences, 69: 1569-1575.	October 2012
Krzystan, A. M., T. A. Gowan, W. L. Kendall, J. Martin, J. G. Ortega-Ortiz, K. Jackson, A. R. Knowlton, P. Naessig, M. Zani, D. W. Schulte, and C. R. Taylor. 2018. Characterizing residence patterns of North Atlantic right whales in the southeastern U.S. with a multistate open robust design model. Endangered Species Research 36:279-295 DOI: https://doi.org/10.3354/esr00902.	May 2018
Kowalski, D. A., and E. P. Bergersen. 2002. The toxicity of Bayluscide and TFM to Tubifex tubifex: implications for chemical control of the oligochaete host of whirling disease. North American Journal of Fisheries Management 65(3):171-178.	August 2002
Khalighifar, A., B. S. Gotthold, E. Adams, J. Barnett, L. O. Beard, E. R. Britzke, P. A. Burger, K. Chase, Z. Cordes, P. M. Cryan, E. Ferrall, C. T. Fill, S. E. Gibson, G. Scott Haulton, K. M. Irvine, L. S. Katz, W. L. Kendall, C. A. Long, O. M. Aodha, T. McBurney, S. McCarthy, M. W. McKown, J. O'Keefe, L. D. Patterson, K. A. Pitcher, M. Rustand, J. L. Segers, K. Seppanen, J. L. Siemers, C. Stratton, B. R. Straw, T. J. Weller, and B. E. Reichert. 2022. NABat ML: Utilizing deep learning to enable crowdsourced development of automated, scalable solutions for documenting North American bat populations. Journal of Applied Ecology 59:2849-2862, doi:10.1111/1365-2664.14280.	November 2022
Ketz, A.C., T.L. Johnson, R.J. Monello, J. Mack, J.L. George, B.R. Kraft, M.A. Wild, M.B. Hooten, and N.T. Hobbs. (2018). Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements. Ecological Applications, 28: 816-825.	January 2018
Ketz, A.C., T.L. Johnson, M.B. Hooten, and N.T. Hobbs. (2019). A hierarchical Bayesian approach for handling missing classification data. Ecology and Evolution, 9: 3130-3140.	January 2019
Kendall, W. L., S. Stapleton, G. C. White, J. I. Richardson, K. N. Pearson, and P. Mason. 2019. A multistate open robust design: population dynamics, reproductive effort, and phenology of sea turtles from tagging data. Ecological Monographs 89: e01329.	January 2019
Kendall, W. L., R. J. Barker, G. C. White, M.S. Lindberg, C. A. Langtimm, and C. L. Peñaloza. 2013. Combining tag recovery, auxiliary observations, and robust design data to estimate demographic parameters from marked individuals. Methods in Ecology and Evolution 4:828-835. \| Abstract	September 2013	1. When estimating demographic parameters for wild populations, using multiple data sources can increase robustness through greater precision, reducing bias, and permitting the estimation of otherwise confounded parameters. 2. We present a method and software that combines recapture data from marked individuals, collected at a single study site, under a robust design framework, with dead recoveries and auxiliary resightings collected at any time and place. This model permits the joint modeling of survival, permanent, and temporary emigration from the study area. 3. We demonstrate that the usefulness of this model is compelling in the case of long-lived species with substantial rates of temporary emigration, to mitigate bias in survival at the end of the time series and to permit conservation decisions based on more current information. We use the case of Florida manatees as an example. 4. Our model can easily be extended to account for an arbitrary number of phenotypic states and account for state uncertainty.
Kendall, W. L., J. E. Hines, J. D. Nichols, and E. H. Grant. 2013. Relaxing the closure assumption in single-season occupancy models: staggered arrival and departure times. Ecology 94(3):610-617.	March 2013
Kendall, W. L., G. C. White, J. E. Hines, C. A. Langtimm, and J. Yoshizaki. 2012. Estimating parameters of hidden Markov models based on marked individuals: use of robust design data. Ecology 93:913-920.	April 2012
Kendall, W. L. and C. T. Moore. 2012. Maximizing the utility of monitoring to the adaptive management of natural resources. Pages 74-98 in R. A. Gitzen, J. J. Millspaugh, A. B. Cooper, and D. S. Licht, editors. Design and analysis of long-term ecological monitoring studies. Cambridge University Press, Cambridge, UK.	July 2012
Kays, R., Snider, M. H., Hess, G., Cove, M. V., Jensen, A., Shamon, H., McShea, W. J., Rooney, B., Allen, M. L., Pekins, C. E., Wilmers, C. C., Pendergast, M. E., Green, A. M., Suraci, J., Leslie, M. S., Nasrallah, S., Farkas, D., Jordan, M., Grigione, M., … Parsons, A. (2024). Climate, food and humans predict communities of mammals in the United States. Diversity and Distributions, 00, e13900. https://doi.org/10.1111/ddi.13900 \| Download	July 2024
Kasparian, M. A., E. C. Helgren, S. M. Ginger, L. P. Levesque, J. E. Clark, D. L. Winkelman, and D. M. Engle 2004. Population characteristics of Virginia opossum in the cross timbers during raccoon reduction. American Midland Naturalist 151:154-163.	January 2004
Johnson, D.S., P.B. Conn, M.B. Hooten, J. Ray, and B. Pond. (2013). Spatial occupancy models for large data sets. Ecology, 94: 801-808.	April 2013
Johnson, D.S., M.B. Hooten, and C.E. Kuhn. (2013). Estimating animal resource selection from telemetry data using point process models. Journal of Animal Ecology, 82: 1155-1164.	November 2013
Itter, M.S., A.O. Finley, M.B. Hooten, P.E. Higuera, J.R. Marlon, R. Kelly, and J.S. McLachlan. (2018). A model-based approach to wildland fire reconstruction using sediment charcoal records. Environmetrics, 22: e2450.	April 2018
Iannarilli, F., Gerber, B. D., Erb, J., & Fieberg, J. R. (2024). A ‘how-to’ guide for estimating animal diel activity using hierarchical models. Journal of Animal Ecology, 00, 1–13. https://doi.org/10.1111/1365-2656.14213 \| Abstract \| Download	November 2024	Animal diel activity patterns can aid understanding of (a) how species behaviour-ally adapt to anthropogenic and natural disturbances, (b) mechanisms of speciesco-existence through temporal partitioning, and (c) community or ecosystem ef-fects of diel activity shifts.2. Activity patterns often vary spatially, a feature ignored by the kernel density es-timators (KDEs) currently used for estimating diel activity. Ignoring this source ofheterogeneity may lead to biased estimates of uncertainty and misleading conclu-sions regarding the drivers of diel activity. Thus, there is a need for more flexiblestatistical approaches for estimating activity patterns and testing hypotheses re-garding their biotic and abiotic drivers.3. We illustrate how trigonometric terms and cyclic cubic splines combined withhierarchical models can provide a valuable alternative to KDEs. Like KDEs, thesemodels accommodate circular data, but they can also account for site-to-site andother sources of variability, correlation amongst repeated measures, and variablesampling effort. They can also more readily quantify and test hypotheses relatedto the effects of covariates on activity patterns.4. Through empirical case studies, we illustrate how hierarchical models can quan-tify changes in activity levels due to seasonality and in response to biotic and abi-otic factors (e.g. anthropogenic stressors and co-occurrence). We also describefrequentist and Bayesian approaches for quantifying site- specific (conditional)and population-averaged (marginal) activity patterns.5. We provide guidelines and tutorials with detailed step-by-step instructions forfitting and interpreting hierarchical models applied to time-stamped data, such asthose recorded by camera traps and audio recorders. We conclude that this ap-proach offers a viable, flexible, and effective alternative to KDEs when modellinganimal activity patterns.
Hyde, M., E. Payan, J. Barragan, D. Stasiukynas, S. Rincon, W. L., Kendall, J. Rodriguez, K. R. Crooks, S. W. Breck, and V. Boron. 2023. Tourism-supported working lands sustain a growing jaguar population in the Colombian Llanos. Scientific Reports 13, 10408 (2023). https://doi.org/10.1038/s41598-023-36935-2.	June 2023
Hubert, W. A., and E. P. Bergersen. 1999. Approaches to habitat analysis. Chapter 2, Pages 7-10 in Aquatic habitat assessment: common methods. M. B. Bain and N. J. Stevenson, editors. American Fisheries Society, Bethesda, MD.	November 1999
Horton, G. E., B. H. Letcher, and W. L. Kendall. 2011. A multi-state capture-recapture modeling strategy to separate true survival from permanent emigration for a passive integrated transponder tagged population of stream fish. Transactions of the American Fisheries Society 140:320-333.	April 2011
Hooten, M.B., X. Lu, M.J. Garlick, and J.A. Powell. (2020). Animal movement models with mechanistic selection functions. Spatial Statistics, 37: 100406.	February 2020
Hooten, M.B., W.B. Leeds, J. Fiechter, and C.K. Wikle. (2011). Assessing first-order emulator inference for physical parameters in nonlinear mechanistic models. Journal of Agricultural, Biological, and Environmental Statistics, 16: 475-494.	December 2011
Hooten, M.B., M.J. Garlick, and J.A. Powell. (2013). Computationally efficient statistical differential equation modeling using homogenization. Journal of Agricultural, Biological and Environmental Statistics, 18: 405-428.	September 2013
Hooten, M.B., J.M. Ver Hoef, and E.M. Hanks. (2019). Simultaneous autoregressive (SAR) model. Wiley StatsRef: Statistics Reference Online.	September 2019
Hooten, M.B., H.R. Scharf, and J.M. Morales. (2019). Running on empty: Recharge dynamics from animal movement data. Ecology Letters, 22: 377-389.	January 2019
Hooten, M.B., H.R. Scharf, T.J. Hefley, A. Pearse, and M. Weegman. (2018). Animal movement models for migratory individuals and groups. Methods in Ecology and Evolution, 9: 1692-1705.	January 2018
Hooten, M.B., F.E. Buderman, B.M. Brost, E.M. Hanks, and J.S. Ivan. (2016). Hierarchical animal movement models for population-level inference. Environmetrics, 27: 322-333.	December 2016
Hooten, M.B., E.M. Hanks, D.S. Johnson, and M.W. Alldredge. (2014). Temporal variation and scale in movement-based resource selection functions. Statistical Methodology, 17: 82-98.	March 2014
Hooten, M.B., E.M. Hanks, D.S. Johnson, and M.W. Alldredge. (2013). Reconciling resource utilization and resource selection functions. Journal of Animal Ecology, 82: 1146-1154.	April 2013
Hooten, M.B., D.S. Johnson, B.T. McClintock, and J.M. Morales. (2017). Animal Movement: Statistical Models for Telemetry Data. Chapman and Hall\CRC.	February 2017
Hooten, M.B., B.E. Ross, and C.K. Wikle. (2012). Optimal spatio-temporal monitoring designs for characterizing population trends. Gitzen, R.A., J.J. Millspaugh, A.B. Cooper, and D.S. Licht (eds). In: Design and Analysis of Long-Term Ecological Monitoring Studies. Cambridge University Press.	May 2012
Hooten, M.B. and T.J. Hefley. (2019). Bringing Bayesian Models to Life. Chapman & Hall/CRC.	June 2019
Hooten, M.B. and N.T. Hobbs. (2015). A guide to Bayesian model selection for ecologists. Ecological Monographs. 85: 3-28.	February 2015
Hooten, M.B. and E. Cooch. (2019). Comparing ecological models. Marcot, B., A. Tri, and L. Brennan (eds). In: Quantitative Analysis in Wildlife Science. Johns Hopkins University Press.	August 2019
Hooten, M.B. and D.S. Johnson. (2019). Modeling Animal Movement. Gelfand, A.E., M. Fuentes, and J.A. Hoeting (eds). In Handbook of Environmental and Ecological Statistics. Chapman & Hall/CRC.	January 2019
Hooten, M.B. and D.S. Johnson. (2017). Basis function models for animal movement. Journal of the American Statistical Association, 112: 578-589.	October 2017
Hooten, M.B. (2011). The State of Spatial and Spatio-Temporal Statistical Modeling. In: Predictive Modeling in Landscape Ecology. Drew A., F. Huettman, and Y. Wiersma (eds). In: Predictive Modeling in Landscape Ecology.	December 2011
Hobbs, N.T., C. Geremia, J. Treanor, R. Wallen, P.J. White, M.B. Hooten, and J.C. Rhyan. (2015). State-space modeling to support adaptive management of brucellosis in the Yellowstone bison population. Ecological Monographs, 85: 525-556.	November 2015
Hobbs, N.T. and M.B. Hooten. (2015). Bayesian Models: A Statistical Primer for Ecologists. Princeton University Press.	December 2015
Herdrich, A.T., D.L. Winkelman, M.P. Venarsky, D.M. Walters, and E. Wohl. 2018. The Loss of Large Wood Affects Rocky Mountain Trout Populations. Ecology of Freshwater Fish 2018;00:1-14 https://doi.org/10.1111/eff.12412 \| Abstract	March 2018	Western U.S. rivers are currently influenced by legacy effects of reduced large wood (LW) loading and retention that has substantially reduced in-stream habitat complexity. Large wood is typically associated with streams in undisturbed old-growth forest and in the correct geomorphic context can drastically alter stream and valley habitat complexity. Streams with LW are typically multichannel and depositional, while streams lacking LW, due to relatively recent wildfire or logging (<200 years ago), are usually single channelled and erosional. We compared population biomass and individual growth rates of Brook Trout <i>Salvelinus fontinalis</i> in streams across a gradient of wood volumes. At both the square metre and valley length scales, standing stock biomass of aquatic invertebrates was the best predictor of trout biomass. However, at the valley scale, the number of pools was important in predicting trout biomass in combination with standing stock biomass of aquatic invertebrates. Individual growth rates of age-1 Brook Trout were negatively affected by increasing density; however, growth rates for the largest and smallest individuals at each site were unaffected by density. Our results suggest the pool habitat created by LW acts synergistically with prey availability to dramatically increase trout populations. However, in streams lack- ing LW, negative effects of detrimental land use practices have persisted >100 years, suggesting that recovering lost animal production in mountain stream networks will only occur at decadal to century time scales.
Hefley, T.J., M.B. Hooten, R.E. Russell, D.P. Walsh, and J. Powell. (2017). When mechanism matters: Forecasting the spread of disease using ecological diffusion. Ecology Letters, 20: 640-650.	September 2017
Hefley, T.J., M.B. Hooten, J.M. Drake, R.E. Russell, and D.P. Walsh. (2016). When can the cause of a population decline be determined? Ecology Letters, 19: 1353-1362.	December 2016
Hefley, T.J., M.B. Hooten, E.M. Hanks, R.E. Russell, and D.P. Walsh. (2017). Dynamic spatio-temporal models for spatial data. Spatial Statistics, 20: 206-220.	March 2017
Hefley, T.J., M.B. Hooten, E.M. Hanks, R.E. Russell, and D.P. Walsh. (2017). The Bayesian spatial group lasso. Journal of Agricultural, Biological, and Environmental Statistics, 22: 42-59.	February 2017
Hefley, T.J., K.M. Broms, B.M. Brost, F.E. Buderman, S.L. Kay, H.R. Scharf, J.R. Tipton, P.J. Williams, and M.B. Hooten. (2017). The basis function approach to modeling dependent ecological data. Ecology, 98: 632-646.	March 2017
Hefley, T.J., B.M. Brost, and M.B. Hooten. (2017). Bias correction of bounded location errors in presence-only data. Methods in Ecology and Evolution, 8: 1566-1573.	January 2017
Hefley, T.J. and M.B. Hooten. (2016). Hierarchical species distribution models. Current Landscape Ecology Reports, 1: 87-97.	December 2016
Hefley, T.J. and M.B. Hooten. (2015). On the existence of maximum likelihood estimates for presence-only data. Methods in Ecology and Evolution, 6: 648-655.	December 2015
Harris, R. B., and K. P. Burnham. 2002. On estimating wildlife densities from line transect data. Acta Zoologica Sinica [Dongwu Xuebao] 48:812-818 (in Chinese. ) (This journal is sometimes referred to as The Chinese Journal of Zoology. )	March 2002
Hanks, E.M., M.B. Hooten, and M. Alldredge. (2015). Continuous-time discrete-space models for animal movement. Annals of Applied Statistics, 9: 145-165.	March 2015
Hanks, E.M., M.B. Hooten, and F.A. Baker. (2011). Reconciling multiple data sources to improve accuracy of large-scale prediction of forest disease incidence. Ecological Applications, 24: 1173-1188.	December 2011
Hanks, E.M., M.B. Hooten, S.A. Knick, S.J. Oyler-McCance, J.A. Ficke, T.B. Cross, and M.K. Schwartz. (2016). Latent spatial models and sampling design for landscape genetics. Annals of Applied Statistics, 10: 1041-1062.	June 2016
Hanks, E.M., M.B. Hooten, D.S. Johnson, and J. Sterling. (2011). A velocity-based approach for linking animal telemetry data to environmental drivers of movement. PLoS One, 6(8), e22795.	December 2011
Hanks, E.M., E. Schliep, M.B. Hooten, and J.A. Hoeting. (2015). Restricted spatial regression in practice: Geostatistical models, confounding, and robustness under model misspecification. Environmetrics. 26: 243-254.	December 2015
Hanks, E.M., D.S. Johnson, and M.B. Hooten. (2017). Reflected stochastic differential equation models for constrained animal movement. Journal of Agricultural, Biological, and Environmental Statistics, 22: 353-372.	September 2017
Hanks, E.M. and M.B. Hooten. (2013). Circuit theory and model-based inference for landscape connectivity. Journal of the American Statistical Association, 108: 22-33.	March 2013
Haas, S.E., M.B. Hooten, D. Rizzo, and R.K. Meentemeyer. (2011). Forest species diversity reduces disease risk in a generalist plant pathogen invasion. Ecology Letters, 14: 1108-1116.	December 2011
Green, A.W., M.B. Hooten, E.H.C. Grant, and L.L. Bailey. (2013). Evaluating breeding and metamorph occupancy and vernal pool management effects for wood frogs using a hierarchical model. Journal of Applied Ecology, 50: 1116-1123.	February 2013
Gibson-Reinemer, D. K., B. M. Johnson, P. J. Martinez, D. L. Winkelman, A. E. Koenig, and J. D. Woodhead. 2009. Elemental signatures in otoliths of hatchery trout: distinctiveness and utility for detecting origins and movement. Canadian Journal of Fisheries and Aquatic Sciences 66:513-524.	March 2009
Gerber, B.D., M.B. Hooten, C.P. Peck, M.B. Rice, J.H. Gammonley, A.D. Apa, and A.J. Davis. (2019). Extreme site fidelity as an optimal strategy in an unpredictable and homogeneous environment. Functional Ecology, 33: 1695-1707. \| Download	August 2019
Gerber, B.D., M.B. Hooten, C.P. Peck, M.B. Rice, J.H. Gammonley, A.D. Apa, and A.J. Davis. (2018). Accounting for location uncertainty in azimuthal telemetry data improves ecological inference. Movement Ecology, 6: 14.	January 2018
Gerber, B. D., and W. L. Kendall. Adaptive management of animal populations with significant unknowns and uncertainties: a case study. Ecological Applications 28:1325-1341, https://doi.org/10.1002/eap.1734. \| Download	April 2018
Gerber, B. D., and W. L. Kendall. 2017. Evaluating and improving count-based population inference: A case study from 31 years of monitoring sandhill cranes. The Condor: Ornithological Applications 119:191-206	January 2017
Gerber, B. D., and W. L. Kendall. 2016. Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane. Biological Conservation 200:228-239. \| Download	August 2016
Gerber, B. D., W. L. Kendall, M. B. Hooten, J. A. Dubovsky, and R. C. Drewien. 2015. Optimal population prediction of sandhill crane recruitment based on climate-mediated habitat limitations. Journal of Animal Ecology, DOI: 10.1111/1365-2656.12370	May 2015
Gerber, B. D., Devarajan, K., Farris, Z. J., & Fidino, M. (2024). A model-based hypothesis framework to define and estimate the diel niche via the ‘Diel.Niche’ R package. Journal of Animal Ecology, 00, 1–15. https://doi.org/10.1111/1365-2656.14035 \| Abstract \| Download	January 2024	How animals use the diel period (24-h light–dark cycle) is of fundamental importance to understand their niche. While ecological and evolutionary literature abound with discussion of diel phenotypes (e.g. diurnal, nocturnal, crepuscular, cathemeral), they lack clear and explicit quantitative definitions. As such, inference can be confounded when evaluating hypotheses of animal diel niche switching or plasticity across studies because researchers may be operating under different definitions of diel phenotypes. We propose quantitative definitions of diel phenotypes using four alternative hypothesis sets (maximizing, traditional, general and selection) aimed at achieving different objectives. Each hypothesis set is composed of mutually exclusive hypotheses defined based on the activity probabilities in the three fundamental periods of light availability (twilight, daytime and night-time). We develop a Bayesian modelling framework that compares diel phenotype hypotheses using Bayes factors and estimates model parameters using a multinomial model with linear inequality constraints. Model comparison, parameter estimation and visualizing results can be done in the Diel.Niche R package. A simplified R Shiny web application is also available.We provide extensive simulation results to guide researchers on the power to discriminate among hypotheses for a range of sample sizes (10–1280). We also work through several examples of using data to make inferences on diel activity, and include online vignettes on how to use the Diel.Niche package. We demonstrate how our modelling framework complements other analyses, such as circular kernel density estimators and animal movement modelling.Our aim is to encourage standardization of the language of diel activity and bridge conceptual frameworks and hypotheses in diel research with data and models. Lastly, we hope more research focuses on the ecological and conservation importance of understanding how animals use diel time.
Garlick, M.J., J.A. Powell, M.B. Hooten, and L. McFarlane. (2011). Homogenization of large-scale movement models in ecology. Bulletin of Mathematical Biology, 73: 2088-2108.	December 2011
Garcia-Cruz, M. A., M. Lampo, C. L. Penaloza, W. L. Kendall, G. Sole, and K. M. Rodriguez-Clark. 2015.Population trends and survival of nesting green sea turtles (Chelonia mydas) on Aves Island, Venezuela. Endangered Species Research 29:101-116.	December 2015
Ganoe, L. S., Mayer, A. E., Brown, C., & Gerber, B. D. (2024). Mesocarnivore sensitivity to natural and anthropogenic disturbance leads to declines in occurrence and concern for species persistence. Ecology and Evolution, 14, e70043. https://doi.org/10.1002/ece3.70043 \| Download	July 2024
Ganoe, L, Mayer, AE, Brown, C, and Gerber, BD. 2024. Fisher activity patterns show potential for behavioral adaptations to human modified landscapes. Global Ecology and Conservation, e03225, https://doi.org/10.1016/j.gecco.2024.e03225 \| Abstract \| Download	October 2024	Animals alter their diel activity in response to physiological constraints and ecological conditions. Fisher (<i>Pekania pennanti</i>) activity is known to vary through the diel cycle and change in response to cold stress and generally through both the climatic and biological seasons. However, less is known whether thermoregulatory effects impact fisher activity in milder climates and in areas of high human disturbance. We focused on two distinct research objectives to understand the 1) physiological constraints, and 2) ecological components of fisher activity in a highly disturbed landscape with a relatively mild climate. We used accelerometer data from 34 individual live-captured fisher in Rhode Island, USA from 2021-2023. We found that fisher activity patterns were primarily driven by diel cycle with higher activity levels at night than during the day. We did not observe any physiological influence of ambient temperature on fisher activity; daily minimum temperatures did not constrain fisher activity in the colder months, nor did daily maximum temperatures in warmer months. We did find that female activity levels differed by breeding status with non-pregnant females having higher activity levels than pregnant females. Considering ecological components, we found fisher decreased activity levels in higher road density areas during warmer months that coincide with higher traffic volumes. For fisher living in areas with lower road densities, we saw higher activity in the breeding season and summer than in winter. In contrast, fisher living in areas with high road densities had lower activity in the breeding season and summer than in winter. We conclude that fisher largely do not shift their activity to mitigate thermoregulatory costs in areas where temperatures do not reach extremes for extended periods of time. However, our findings suggest that behavioral shifts in activity are impacted by human disturbance and fisher minimize activity in risky areas.
Freilich, J., K. P. Burnham, C. M. Collins, and C. A. Garry. 2000. Factors affecting population assessments of desert tortoises. Conservation Biology 14:1479-1489.	October 2000
Freilich, J., Burnham, K. P., Collins, C. M., and Garry, C. A. 2000. Factors affecting population assessments of desert tortoises. Conservation Biology 14:1479-1489.	August 1999
Fraser, G.S., K.R. Bestgen, D.L. Winkelman, and K.G. Thompson. Temperature-not flow-predicts native fish reproduction with implications for climate change. Transactions of the American Fisheries Society 148:509-527. DOI: 10.1002/tafs.10151 \| Download	January 2019
Fraser, G.S., D.L. Winkelman, K.R. Bestgen, and K.G. Thompson. Submitted. Tributary Use by Flannelmouth and Bluehead Suckers in the Upper Colorado River Basin. Transactions of the American Fisheries Society	September 2017
Franklin, A. B., T. M. Shenk, D. R. Anderson, and K. P. Burnham. 2001. Statistical model selection: the alternative to null hypothesis testing. Pp. 75-90 in T. M. Shenk and A. B. Franklin, editors. Modeling in Natural Resource Management: Development, Interpretation, and Application. Island Press, Washington, D. C.	May 2001
Franklin, A. B., D. R. Anderson, and K. P. Burnham. 2002. Estimation of long-term trends and variation in avian survival probabilities using random effects models. Pp. 267-287 in Statistical Analysis of Data from Marked Bird Populations, Morgan, B. J. T., and Thomson, D. L. (Eds). Journal of Applied Statistics 29, numbers 1-4.	February 2002
Franklin, A. B., D. R. Anderson, R. J. Gutierrez, and K. P. Burnham. 2000. Climate, habitat quality, and fitness in Northern Spotted Owl populations in northwest California. Ecological Monographs 70:539-590.	November 2000
Franklin, A. B., D. R. Anderson, E. D. Forsman, K. P. Burnham, and F. F. Wagner. 1996. Methods for collecting and analyzing demographic data on the northern spotted owl. Studies in Avian Biology 17:12-20.	September 1996
Francis, C. M., Bart, J., E. H. Dunn, K. P. Burnham, and C. J. Ralph. 2005. Enhancing the value of the breeding bird survey: Reply to Sauer et. al. 2005. Journal of Wildlife Management 69:1327-1332	November 2005
Fitzpatrick, R.M., D.L. Winkelman, and B.M. Johnson. Using isotopic data to evaluate Esox lucius (Linnaeus, 1758) natal origins in a hydrologically complex river basin. 2021. Fishes 2021, 6, 67. https://doi.org/10.3390/fishes6040067 \| Abstract \| Download	November 2021	Otolith microchemistry has emerged as a powerful technique with which to identifythe natal origins of fishes, but it relies on differences in underlying geology that may occur over large spatial scales. An examination of how small a spatial scale on which this technique can be implemented, especially in water bodies that share a large proportion of their flow, would be useful for guiding aquatic invasive species control efforts. We examined trace isotopic signatures in northern pike (<i>Esox lucius</i>) otoliths to estimate their provenance between two reservoirs in the Upper Yampa River Basin, Colorado, USA. This is a challenging study area as these reservoirs are only 11-rkm apart on the same river and thus share a high proportion of their inflow. We found that three isotopes (86Sr, 137Ba, and 55Mn) were useful in discriminating between these reservoirs, but their signatures varied annually, and the values overlapped. Strontium isotope ratios (87Sr/86Sr) were different between sites and relatively stable across three years, which made them an ideal marker for determining northern pike provenance. Our study demonstrates the usefulness of otolith microchemistry for natal origin determination within the same river over a relatively small spatial scale when there are geologic differences between sites, especially geologic differences underlying tributaries between sites.
Fetherman, E.R., D.L. Winkelman, M.R. Baerwald, and G.J. Schisler. 2014. Survival and reproduction of Myxobolus cerebralis-resistant rainbow trout introduced to the Colorado River and increased resistance of age-0 progeny. PLoS ONE 9(5):e96954. doi:10.1371/journal.pone.0096954. \| Download	May 2014
Fetherman, E.R., D.L. Winkelman, L.L. Bailey, G.J Schisler, and K. Davies. Brown Trout removal effects on short-term survival and movement of Myxobolus cerebralis-resistant rainbow trout. Transactions of the American Fisheries Society 144:610-626. doi=10.1080/00028487.2015.1007166 \| Download \| Publisher Website	April 2015
Fetherman, E.R., B.W. Avila, and D.L. Winkelman. Raft and Floating RFID Antenna Systems for Detecting PIT-tagged Fish in Rivers. North American Journal of Fisheries Management 34:1065-1077. \| Download \| Publisher Website	October 2014
Fetherman, E. R., D. L. Winkelman, G. J. Schisler, and M.F. Antolin. 2012. Genetic basis of differences in myxospore count between whirling disease resistant and susceptible strains of rainbow trout. Diseases of Aquatic Organisms 102:97-106	December 2012
Fetherman, E. R., D. L. Winkelman, G. J. Schisler, and C. A. Myrick. In press. The effects of Myxobolus cerebralis on the physiological performance of whirling disease resistant and susceptible strains of rainbow trout (Oncorhynchus mykiss). Journal of Aquatic Animal Health. \| Download	November 2011
Farnsworth, M. L., Wolfe, L. L., Hobbs, N. T., Burnham, K. P., and Miller, M. W. (2004). Communication: Human land use influences chronic wasting disease prevalence in mule deer. Ecological Applications 14.	July 2005
Farnsworth, M. L., W. L. Kendall, P. F. Doherty, Jr., R. S. Miller, G. C. White, J. D. Nichols, and A. B. Franklin. 2011. Targeted surveillance for highly pathogenic avian influenza in migratory waterfowl and geese across the United States. Pages 143-155 in Pandemic Influenza Viruses: Sceience, Surveillance and Public Health. S. K. Majumdar et al., eds, The Pennsylvania Academy of Science.	July 2011
Farnsworth, M. L., L. L. Wolfe, N. T. Hobbs, K. P. Burnham, E. S. Williams, D. M. Theobald, M. M. Conner, and M. W. Miller. 2005. Human land use influences chronic wasting disease prevalence in mule deer. Ecological Applications 15:119-126.	March 2005
Farnsworth, M. L., J. A. Hoeting, N. T. Hobbs, M. M. Conner, K. P. Burnham, L. L. Wolfe, E. S. Williams, D. M. Theobold, and M. W. Miller. 2007. The role of geographic information systems in wildlife landscape epidemiology: models of chronic wasting disease in Colorado mule deer. Veterinaria Italiana 43:581-593.	November 2007
Ekman, D.R., K. Keteles, J. Beihoffer, J.E. Cavallin, K. Dahlin, J.M. Davis, A. Jastrow, J.M. Lazorchak, M. Mills, M. Murphy, D. Nguyen, A.M. Vajda, D.L. Villeneuve, D.L. Winkelman, And T.W. Collette. Evaluation of Targeted and untargeted effects-based monitoring tools to assess contaminants of emerging concern on fish in the South Platte River, CO. Environmental Pollution 239:706-713. \| Download	April 2018
Dzul, Maria Christina, William Louis Kendall, Charles Brandon Yackulic, Dana L. Winkelman, David Randall Haverbeke, and Michael Yard. 2021. Partial migration and spawning movements of humpback chub in the Little Colorado River are better understood using data from autonomous PIT tag antennas. Canadian Journal of Fisheries and Aquatic Sciences 78:1057-1072. https://doi.org/10.1139/cjfas-2020-0291 \| Download	February 2021
Dzul, M. C., W. L. Kendall, C.B. Yackulic, D.R. Van Haverbeke, P. Mackinnon, K. Young, M. Pillow, P. Rinker, and J. Thomas. 2024. Estimating migration timing and abundance of both residents and migrants in partial migratory systems by integrating continuous antenna detections with physical captures. Journal of Animal Ecology, DOI: 10.1111/1365-2656.14076.	April 2024
Dzul, M. C., C. B. Yackulic, W. L. Kendall, D. L. Winkelman, M. Connor, and M. Yard. 2021. Incorporating antenna detections into abundance estimates of fish. Canadian Journal of Fisheries and Aquatic Sciences, https://doi.org/10.1139/cjfas-2021-0003	August 2021
Devineaux, O., W. L. Kendall, P. F. Doherty, Jr., T. M. Shenk, G. C. White, P. M. Lukacs, and K. P. Burnham. 2014. Increased flexibility for modeling telemetry and nest-survival data using the multistate framework. Journal of Wildlife Management 78:224-230.	February 2014
Davis, A.J., M.B. Hooten, R.S. Miller, M. Farnsworth, J. Lewis, M. Moxcey, and K.M. Pepin. (2016) Inferring invasive species abundance using removal data from management actions. Ecological Applications, 26: 2339-2346.	January 2016
Davis, A.J., M.B. Hooten, M.L. Phillips, and P.F. Doherty. (2014). An integrated modeling approach to estimating Gunnison sage-grouse population dynamics: Combining index and demographic data. Ecology and Evolution, 4: 4247-4257.	October 2014
Dalgleish, H.J., D.N. Koons, M.B. Hooten, C.A. Moffet, and P.B. Adler. (2011). The influence of climate on the demography of three dominant sagebrush steppe plants. Ecology, 92: 75-85.	January 2011
D. B. Fenner, D. L. Winkelman and M. G. Walsh. 2004. Diet overlap of introduced rainbow trout and three native fishes in an Ozark stream. Pages 475-482 in M. J. Nickum, P. M. Mazik, J. G. Nickum and D. D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society Symposia 44, American Fisheries Society, Bethesda, Maryland.	July 2004
D'Amico, T.W., D.L. Winkelman, T.R. Swarr, and C.A. Myrick. Retention of Passive Integrated Transponder tags in a small-bodied catfish. North American Journal of Fisheries Management 41:187-195. DOI: 10.1002/nafm.10550 \| Download	January 2021
Cruz, S.M., M.B. Hooten, K.P. Huyvaert, C. Proano, D.J. Anderson, J. Fox, and M. Wikelski. (2013). At–sea behavior varies with lunar phase in a nocturnal pelagic seabird, the swallow-tailed gull. PLoS One, 8: e56889.	February 2013
Crockett, J. G., C. Brown, and B. D. Gerber. 2024. Muskrat occurrence in Rhode Island shows little evidence of land use change driving declines. Journal of Wildlife Management e22668. https://doi.org/10.1002/jwmg.22668 \| Abstract \| Download \| Publisher Website	October 2024	Muskrat (<i>Ondatra zibethicus</i>) populations have been in apparent decline across their native range in North America for decades. Several hypotheses exist for the causes of these declines, including loss of wetlands. We used time-to-detection data from 925 surveys from 276 sites across Rhode Island, USA, between 2021–2023 to fit an occupancy model that related the probability of muskrat occupancy at a site to land cover classification. We found that muskrat occupancy was higher in areas with more open water, urban land cover, or a second-order or larger stream, and lower in areas with salt water. We estimated changes in wetland area throughout Rhode Island using the National Land Cover Database classifications from 2001 and 2019 and found a net loss in wetland cover of 219 ha. We calculated the distance between wetland patches in each of these periods and found that patches were closer together than the dispersal distance of muskrats, suggesting isolation is unlikely to be driving muskrat declines. Additionally, when we used our model to predict changes in muskrat occupancy between 2001 and 2019, both mean and median predicted occupancy changed by <0.005. These results indicate that muskrat declines are not driven by habitat loss, and suggest future research is needed that focuses on other hypothesized mechanisms of muskrat declines such as disease, declining habitat quality, predation, and competition.
Conner, M. M, M. W. Miller, M. R. Ebinger, K. P. Burnham. 2007. A spatial, meta-BACI approach for evaluating effects of chronic wasting disease in free-ranging mule deel. Ecological Applications 17:140-153	April 2007
Conn, P.B., Johnson, D.S., J.M. Ver Hoef, M.B. Hooten, J.M. London, and P.L. Boveng. (2015). Using spatio-temporal models to estimate animal abundance and infer ecological dynamics from survey counts. Ecological Monographs. 85: 235-252.	December 2015
Conn, P.B., D.S. Johnson, P.J. Williams, S. Melin, and M.B. Hooten. (2018). A guide to Bayesian model checking for ecologists. Ecological Monographs, 88: 526-542.	January 2018
Collins, D. P., G. S. Zimmerman, S. A. Carleton, W. L. Kendall, and C. L. Coxen. 2023. Survival rates of band-tailed pigeon in New Mexico estimated using passive integrated transponder tags. Journal of Wildlife Management 87:e22385, https://doi.org/10.1002/jwmg.22385.	February 2023
Christianson, K.R., B.M. Johnson, M.B. Hooten, and J.J. Roberts. (2019). Estimating lake-climate responses from sparse data: An application to high elevation lakes. Limnology and Oceanography, 64: 1371-1385.	April 2019
Christianson, K.R., B.M. Johnson, M.B. Hooten, and A.S. Denning. (2020). Compound effects of water clarity, inflow, wind, and climate warming on mountain lake thermal regimes. Aquatic Sciences, 82: 6.	February 2020
Chambert, T., W. L. Kendall, J. E. Hines, J. D. Nichols, P. Pedrini, J. H. Waddle, G. Tavecchia, S. C. Walls, and S. Tenan. 2015. An open dynamic occupancy model to estimate shifts in the distribution and phenology of imperfectly detectable species. Methods in Ecology and Evolution 6:638-647	June 2015
Cavallin, J.E., W.A. Battaglin, J. Beihoffer, B.R. Blackwell, P.M. Bradley, A.R. Cole, D.R. Ekman, R. Hofer, J. Kinsey, K. Keteles, R. Weissinger, D.L. Winkelman, D.L. Villeneuve. Effects-Based Monitoring of Bioactive Chemicals Discharged to the Colorado River Before and After a Municipal Wastewater Treatment Plant Replacement. Environmental Science and Technology 55:974-984. https://doi.org/10.1021/acs.est.0c05269 \| Publisher Website	January 2021
Cavallin, J.E., J. Beihoffer, B.R. Blackwell, A.R. Cole, D.R. Ekman, R. Hofer, A. Jastrow, J. Kinsey, K. Keteles, E.M. Maloney, J. Parman, D.L. Winkelman, D.L. Villeneuve. In review. Effects-Based Monitoring of Bioactive Compounds Associated with Municipal Wastewater Treatment Plant Effluent Discharge to the South Platte River, Colorado, USA. Environmental Pollution. \| Abstract	August 2021	Previous studies have detected numerous organic contaminants and in vitro bioactivities in surface water from the South Platte River near Denver, Colorado, USA. To evaluate the temporal and spatial distribution of selected contaminants of emerging concern, water samples were collected throughout 2018 and 2019 at 11 sites within the S. Platte River and surrounding tributaries with varying proximities to a major wastewater treatment plant (WWTP). Water samples were analyzed for pharmaceuticals, pesticides, steroid hormones, and wastewater in- dicators and screened for in vitro biological activities. Multiplexed, in vitro assays that simultaneously screen for agonistic activity against 24 human nuclear receptors detected estrogen receptor (ER), peroxisome proliferator activated receptor-gamma (PPARγ), and glucocorticoid receptor (GR) bioactivities in water samples near the WWTP outflow. Targeted in vitro bioassays assessing ER, GR, and PPARγ agonism corroborated bioactivities for ER (up to 55 ± 9.7 ng/L 17β-estradiol equivalents) and GR (up to 156 ± 28 ng/L dexamethasone equivalents), while PPARγ activity was not confirmed. To evaluate the potential in vivo significance of the bioactive contaminants, sexually-mature fathead minnows were caged at six locations upstream and downstream of the WWTP for 5 days after which targeted gene expression analyses were performed. Significant up-regulation of male hepatic vitellogenin was observed at sites with corresponding in vitro ER activity. No site-related differences in GR-related transcript abundance were detected in female adipose or male livers, suggesting observed environ- mental concentrations of GR-active contaminants do not induce a detectable in vivo response. In line with the lack of detectable targeted in vitro PPARɣ activity, there were no significant effects on PPARɣ-related gene expression. Although the chemicals responsible for GR and PPAR-mediated bioactivities are unknown, results from the present study provide i relative to short-term in situ fish exposures.
Cannell, B. L., W. L. Kendall, J. Tyne, M. Bunce, Y. Hetzel, D. Murray, and B. Radford. 2023. Marine heatwaves affect breeding, diet and population size but not body condition of a range-edge Little Penguin colony. Marine Ecology Progress Series DOI: https://doi.org/10.3354/meps14425.	November 2023
Burton, A.C., Beirne, C., Gaynor, K.M. et al. Mammal responses to global changes in human activity vary by trophic group and landscape. Nat Ecol Evol (2024). https://doi.org/10.1038/s41559-024-02363-2 \| Download	March 2024
Burnham, K. P., and G. C. White. 2002. Evaluation of some random effects methodology applicable to bird ringing data. Pp. 245-264 in Statistical Analysis of Data from Marked Bird Populations, Morgan, B. J. T., Thomson, D. L. (Eds). Journal of Applied Statistics 29, numbers 1-4.	April 2002
Burnham, K. P., and G. C. White. 2002. Evaluation of some random effects methodology applicable to bird ringing data. Journal of Applied Statistics 29(1-4):245-264.	February 2002
Burnham, K. P., and D. R. Anderson. 2004. Multimodel inference: understanding AIC and BIC in model selection. Sociological Methods and Research 33:261-305.	June 2005
Burnham, K. P., and D. R. Anderson. 2002. Model selection and multimodel inference: A practical information-theoretical approach (2nd Edition). Springer-Verlag, New York, NY. 488pp.	October 2002
Burnham, K. P., and D. R. Anderson. 2001. Kullback-Leibler information as a basis for strong inference in ecological studies. Wildlife Research 28:111-119.	May 2001
Burnham, K. P., Buckland, S. T., Laake, J. L., Borchers, D. L., Barques, T. A. 2004. Further topics pp 307-392 (Chapter 11) in Advance Distance Sampling (Buckland et al., editors) Oxford University Press, UK	February 2005
Burnham, K. P. 2004. Foreword (invited), in the book, "Sampling Rare or Elusive Species: Concepts, Designs and Techniques for Estimating Population Parameters. Thompson, W. L. (Editor). Island Press, Washington, D. C.	November 2004
Burnham, K. P. 2002. Invited discussion comments on the paper "Bayesian measures of model complexity and fit, " Spiegelhalter et al. Journal of the Royal Statistical Society, Series B 64:1-629.	November 2002
Buderman, F.E., M.B. Hooten, M.W. Alldredge, E.M. Hanks, and J.S. Ivan. (2018). Time-varying predatory behavior is primary predictor of fine-scale movement of wildland-urban cougars. Movement Ecology, 6: 22.	January 2018
Buderman, F.E., M.B. Hooten, J.S. Ivan, and T.M. Shenk. 2016. A functional model for characterizing long distance movement behavior. Methods in Ecology and Evolution 7(3): 264–273.	March 2016
Buderman, F.E., M.B. Hooten, J. Ivan, and T. Shenk. (2018). Large-scale movement behavior in a reintroduced predator population. Ecography, 41: 126-139.	January 2018
Buckland, S. T., D. R. Anderson, K. P. Burnham, J. L. Laake, D. L. Borchers, and L. J. Thomas. 2001. An introduction to distance sampling: estimation abundance of biological populations. Oxford University Press, Oxford, UK. 448pp.	August 2001
Buckland, S. T., Anderson, D. R., Burnham, K. P. Laake, J. L. Borches, D. L., Thomas, L. J. (Editors). 2004. Advanced Distance Sampling - Estimating Abundance of Biological Populations. Oxford University Press, Oxford, UK.	September 2005
Brost, B.M., M.B. Hooten, and R.J. Small. (2020). Model-based clustering reveals patterns in central place use of a marine top predator. Ecosphere, 11: e03123.	May 2020
Brost, B.M., M.B. Hooten, and R.J. Small. (2017). Leveraging constraints and biotelemetry data to pinpoint repetitively used spatial features. Ecology, 98: 12-20.	January 2017
Brost, B.M., M.B. Hooten, E.M. Hanks, and R.J. Small. (2015). Animal movement constraints improve resource selection inference in the presence of telemetry error. Ecology, 96: 2590-2597.	December 2015
Broms, K.M., M.B. Hooten, and R.M. Fitzpatrick. (2016). Model selection and assessment for multispecies occupancy models. Ecology, 97: 1759-1770.	December 2016
Broms, K.M., M.B. Hooten, and R. Fitzpatrick. (2015). Accounting for imperfect detection in Hill numbers for biodiversity studies. Methods in Ecology and Evolution. 6: 99-108.	December 2015
Broms, K.M., M.B. Hooten, D.S. Johnson, L.L. Conquest, and R. Altwegg. (2016). Dynamic occupancy models for explicit colonization processes. Ecology, 97: 194-204.	January 2016
Breton, A.R., D.L. Winkelman, J.A. Hawkins, and K.R. Bestgen. Population trends of smallmouth bass in the upper Colorado River basin with an evaluation of removal effects.	August 2014
Breton, A., J. Hawkins, and D.L. Winkelman. 2013. Correcting length-frequency distributions for imperfect detection. North American Journal of Fisheries Management 33:1156-1165. \| Download	November 2013
Borchers, D. L., Burnham, K. P. 2004. General formulation for distance sampling, pp 6-30 (Chapter 2) in Advanced Distance Sampling (Buckland et al. editors), Oxford University Press, Oxford, UK.	September 2005
Bergstedt, R. A., McDonald, R. B., Mullett, K. M., Wright, G. M., Swink, W. D., Burnham, K. P. 2003. Mark-recapture population estimates of parasitic sea lampreys (Petromyzon marinus) in Lake Huron. Journal of Great Lakes Research 29 (sup1):226-239.	July 2003
Bergersen, E. P., and P. J. Martinez. 2003. The use of a pattern recognition model to assess fish habitat in two Colorado reservoirs. Lake and Reservoir Management 19(1):55-63.	April 2003
Bergersen, E. P. 2001. Colorado's experience with Northern Pike. Lake Line 21(3):33-36.	September 2001
Bellier, Edwige, Dylan C. Ferreira, David M. Kalb, Laken S. Ganoe, Amy E. Mayer, and Brian D. Gerber. 2024. A Statistical Population Reconstruction Model for Wildlife Populations: A Case Study with White-Tailed Deer and Fisher. Ecosphere 15(6): e4878. https://doi.org/10.1002/ecs2.4878 \| Download	July 2024
Baum, C.M., D.L. Winkelman, and R.M. Fitzpatrick. 2023. Temperature and winter duration requirements for reproductive success in johnny darter Etheostoma nigrum in the South Platte River Basin, Colorado. Freshwater Biology DOI: 10.1111/fwb.14100	May 2023
Bart, J., Burham, K. P., Dunn, E. H., Francis, C., Ralph, C. J. 2004. Goals and strategies for estimating trends in landbird abundance. Journal of Wildlife Management 68: 611-623.	March 2005
Barker, R. J., Burnham, K. P., White, G. C. 2004. Encounter history modeling of joint mark-recapture, tag-resighting and tag-recovery data under temporary migration. Statistica Sinica 14:1037-1055.	September 2004
Baker, D., W. F. Andelt, K. P. Burnham and W. D. Shepperd. 1999. Effectiveness of hot sauce and deer away repellents for deterring elk browsing of aspen sprouts. Journal of Wildlife Management 63:1327-1336.	November 1999
Bailey, L. L., S. J. Converse, and W. L. Kendall. 2010. Bias, precision, and parameter redundancy in complex multistate models with unobservable states. Ecology 91:1598-1604	October 2010
Avila, B.W., K.P. Huyvaert, D.L. Winkelman, and E.R. Fetherman. Factors affecting post-challenge survival of Flavobacterium psychrophilum in susceptible Rainbow Trout. Pathogens 2022, 11, 1318 DOI:10.3390/pathogens11111318 \| Download	August 2022
Avila, B.W., D.L. Winkelman, and E.R. Fetherman. Survival of Whirling Disease Resistant Rainbow Trout Fry in the Wild: A Comparison of Two Strains. Journal of Aquatic Animal Health 30:280-290. DOI: 10.1002/aah.10040 \| Download	November 2018
Avila, B.W., D.L. Winkelman, and E.R. Fetherman. Biotic and abiotic factors affecting survival of two Rainbow Trout strains. North American Journal of Fisheries Management 43:786-793. DOI:10.1002/nafm.10895 \| Download	March 2023
Avila B.W., D.L. Winkelman, and E.R. Fetherman. 2022. Dual Resistance to Flavobacterium psychrophilum and Myxobolus cerebralis in Rainbow Trout (Oncorhynchus mykiss, Walbaum) . Journal of Fish Diseases DOI:10.1111/jfd.13605 \| Abstract \| Download	February 2022	Aquatic pathogens are a major concern for fish hatchery production, fisheries management, and conservation, and disease control needs to be addressed. Two important salmonid pathogens are <i>Myxobolus cerebralis</i> and <i>Flavobacterium psychrophilum</i> that cause whirling disease and bacterial coldwater disease (BCWD), respectively. Innate disease resistance is a potential option for reducing disease-related mortality in hatchery-reared rainbow trout (<i>Oncorhynchus mykiss</i>, Walbaum). Two experiments were conducted to assess pathogen resistance of first-generation (F1) rainbow trout created by crossing <i>M. cerebralis</i>- and <i>F. psychrophilum</i>-resistant strains. In the first experiment, we exposed two rainbow trout strains and one F1 cross to six treatments: control (no exposure), mock injection, F. psychrophilum only, <i>M. cerebrali</i>s only, <i>F. psychrophilum</i> then <i>M. cerebralis</i>, and <i>M. cerebralis</i> then <i>F. psychrophilum</i>. Results indicated that the F1 cross was not resistant to either pathogen. In the second experiment, we exposed five rainbow trout strains and four rainbow trout crosses to <i>F. psychrophilum</i>. The second experiment indicated that at least one rainbow trout cross was <i>F. psychrophilum</i>-resistant. Achieving dual resistance may be possible using selective breeding but only some multigenerational strains are suitable candidates for further evaluation.
Anthony, R. G., E. D. Forsman, A. B. Franklin, D. R. Anderson, K. P. Burnham, G. C. White, C. J. Schwarz, J. D. Nichols, J. E. Hines, G. S. Olson, S. H. Ackers, S. L. Andrews, B. L. Biswell, P. C. Carlson, L. V. Diller, K. M. Dugger, K. E. Fehring, T. L. Fleming, R. P. Gerhardt, S. A. Gremel, R. J. Gutierrez, P. J. Happe, D. R. Herter, J. M. Higley, R. B. Horn, L. L. Irwin, P. J. Loschl, J. A. Reid, S. G. Sovern. 2006. Status and trends in demography of northern spotted owls, 1985-2003. Wildlife Monographs 163:1-47.	September 2006
Anderson, J.R. and D.L. Winkelman. 2018. Differences in vitellogenin production between laboratory-raised and wild fathead minnows: potential consequences for understanding estrogenic exposure in wild populations. Integrated Environmental Assessment and Management 2018:418-423 DOI:10.1002/ieam.4047 \| Download	April 2018
Anderson, D. R., and K. P. Burnham. 2002. Avoiding pitfalls when using information-theoretic methods. Journal of Wildlife Management 66:912-918.	October 2002
Anderson, D. R., and K. P. Burnham. 2001. Commentary on models in ecology. Bulletin of the Ecological Society of America 82:160-161.	November 2001
Anderson, D. R., and K. P. Burnham. 1999. Understanding information criteria for selection among capture-recapture or ring recovery models. Bird Study 46 (Supplement):S14-21.	November 1999
Anderson, D. R., and K. P. Burnham. 1999. General strategies for the analysis of ringing data. Bird Study 46 (Supplement): S261-270.	November 1999
Anderson, D. R., W. A. Link, D. H. Johnson, and K. P. Burnham. 2001. Suggestions for presenting the results of data analyses. Journal of Wildlife Management 65:373-378.	August 2001
Anderson, D. R., K. P. Burnham, and W. L. Thompson. 2000. Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management 64:912-923.	October 2000
Anderson, D. R., K. P. Burnham, G. W. Gould, and S. Cherry. 2001. Concerns about finding effects that are actually spurious. Wildlife Society Bulletin 29:311-316.	April 2001
Anderson, D. R., K. P. Burnham, B. C. Lubow, L. Thomas, P. S. Corn, P. A. Medica, and R. W. Marlow. 2001. Field trials of line transect methods applied to estimation of desert tortoise abundance. Journal of Wildlife Management 65:583-597.	August 2001
Anderson, D. R., K. P. Burnham, A. B. Franklin, R. J. Guti�rrez, E. D. Forsman, R. J. Anthony, G. C. White, and T. M. Shenk. 1999. A protocol for conflict resolution in analyzing empirical data related to natural resource controversies. Wildlife Society Bulletin 27:1050-1058.	September 1999
Anderson, D. R., Burnham, K. P., Lubow, B. C., Thomas, L., Corn, P. S., Medica, P. A., Marlow, R. W. 2001. Field trials of line transect methods applied to estimation of desert tortoise abundance. Journal or Wildlife Management 65:583-597.	August 2001
Anderson, D. R. 2001. The need to get the basics right in wildlife field studies. Wildlife Society Bulletin 29:1294-1297.	December 2001
Allen, M. B. and E. P. Bergersen. 2002. Factors influencing the distribution of Myxobolus cerebralis, the causative agent of whirling disease, in the Cache la Poudre River, Colorado. Diseases of Aquatic Organisms 49:51–60.	April 2002
Adams, C.M., D.L. Winkelman, and R.M. Fitzpatrick. 2023. Impact of wastewater treatment plant effluent on the winter thermal regime of two urban Colorado South Platte tributaries. Frontiers in Environmental Science 11:1120412. DOI: 10.3389/fenvs.2023.1120412. \| Download	March 2023
Adams, C.M., D.L. Winkelman, P.A. Schaffer, D.L. Villeneuve, J.E. Cavallin, M. Ellman, K.S. Rodriguez, and R.M. Fitzpatrick. 2022. Elevated winter stream temperatures below wastewater treatment plants shift reproductive development of female Johnny Darter Etheostoma nigrum: A field and histological approach. Fishes:7-361 DOI: 10.3390/fishes7060361. \| Download	November 2022
A.B. Franklin, K.M. Dugger, D.B. Lesmeister, R.J. Davis, J.D. Wiens, G.C. White, J.D. Nichols, J.E. Hines, C.B. Yackulic, C.J. Schwarz, S.H. Ackers, L.S. Andrews, L.L. Bailey, R. Bown, J. Burgher, K.P. Burnham, P.C. Carlson, T. Chestnut, M.M. Conner, K.E. Dilione, E.D. Forsman, E.M. Glenn, S.A. Gremel, K.A. Hamm, D.R. Herter, J.M. Higley, Rob B. Horn, J.M. Jenkins, W.L. Kendall, D.W. Lamphear, C. McCafferty, T.L. McDonald, J.A. Reid, J.T. Rockweit, D.C. Simon, S.G. Sovern, J.K. Swingle, and H. Wise. 2021. Range-wide declines of Northern Spotted Owls populations in the Pacific Northwest: a meta-analysis. Biological Conservation Volume 259, DOI: 10.1016/j.biocon.2021.109168.	May 2021
A. Jastrow, D.A. Gordon, K.M. Auger, E.C. Punska, K.F. Arcaro, K. Keteles, D.L. Winkelman, D. Lattier, A. Biales, J.L. Lazorchak. Tools to Minimize Inter-Laboratory Variability in Vitellogenin Gene Expression Monitoring Programs	August 2017

Presentations

Presentations	Presentation Date
Winkelman, D.L., C.M. Adams, C.M. Baum, and R.M. Fitzpatrick. An overview of elevated winter water temperature effects on fish reproduction. 154th annual meeting of the American Fisheries Society. Honolulu, HI.	September 2024	Our empirical data and models can be used to gain insight into the magnitude and downstream extent of the impact of effluent temperature on small urban streams in winter and provide a baseline for models in other watersheds and at larger scales.
Stack, T., A. Harris, S. Oyler-McCance, J. Fike, M. Fairchild, C. Kennedy, D. Preston, D. Winkeman, and Y. Kanno. Influences of wildfire on trout abundance and genetic diversity in Rocky Mountain headwater streams. 154th Meeting of the American Fisheries Society, Honolulu, HI. September 23.	September 2024	With current trends of larger and more frequent wildfires, understanding the impacts of fire-related disturbance on trout abundance and genetic diversity is important for informing management strategies and predicting the resilience of populations to environmental change.<br>
Zhao, Q., G. S. Boomer, and W. L. Kendall. 2016. Partitioning the effects of hunting and climate on waterfowl survival. North American Ornithological Conference, Washington, DC.	August 2016	In this work the effects of both climate and density dependence on mallard survival are modeled, while accounting for variability in hunter effects. We find that adult female survival is most subject to these non-hunting factors.
Womble, J.N., P.J. Williams, M.B. Hooten, G.G. Esslinger, L. Taylor-Thomas, M.R. Bower, and H. Coletti. (2017). Combining Contemporary Spatiotemporal Models and Aerial Photographic Techniques to Estimate Sea Otter Colonization and Abundance in Glacier Bay, Alaska. Society for Marine Mammalogy Meetings, Halifax, Nova Scotia.	October 2017	This talk describes a method for using aerial imagery over large spatial regions to estimate abundance.
Womble, J.N., P.J. Williams, M.B. Hooten, G.G. Esslinger, M.R. Bower, and H. Colletti. National Park Service Centennial Science and Stewardship Symposium. 2016. Fairbanks, AK (contrib. talk). Title: Contemporary models and aerial photographic monitoring methods for a new vital sign: Sea otters in Glacier Bay National Park.	October 2016	This talk presents methodology for monitoring sea otters in Glacier Bay, AK.
Winkelman, D.L., M.M. McGree, A.R. Schwindt, and J. Anderson. Estrogenic exposure: Reproduction, survival, and the future of eastern plains native fishes. Regional Aquatic Days February 11, 2016. Colorado Parks and Wildlife. Denver, CO	February 2016	Our indicate that exposure to environmentally relevant concentrations of estrogen can result in complete reproductive failure and this may have population consequences. There appear to be transgenerational effects of exposure, mediated through parental exposure. Field caging experiments show that fish are being exposed to exogenous estrogens at levels that could indicate risk for reproductive failure.
Winkelman, D.L., K. Thompson, and J. Terrell. 2006. The role of sediment size and other habitat factors in the abundance and relative dominance of Tubifex tubifex lineages. 12th annual Whirling Disease Symposium. Denver, CO.	February 2006
Winkelman, D.L., K. Thompson, and C. Clapp. 2008. Investigating the introduction of resistant lineage T. tubifex as a potential biological control of whirling disease. 14th Annual Whirling Disease Symposium: Solving the Puzzle. Denver, CO.	February 2008
Winkelman, D.L., K. Thompson, C. Clapp, A. Gigliotti. 2010. Investigating the introduction of resistant lineage T. tubifex as a potential biological control of whirling disease. Annual meeting of the Western Division of the American Fisheries Society. Salt Lake City, UT.	April 2010
Winkelman, D.L., Jordan Anderson, Alan Vajda, and Aaron Jastrow. Evaluating wastewater effluent exposure in wild fishes using insights from laboratory and wild populations. Society of Ecological Toxicology and Chemistry North America 39th annual meeting. November 7, 2018	November 2018	Our results indicate that the response of VTG production in laboratory raised FHM is more sensitive to estrogen exposure than VTG production in wild FHM, demonstrating that wild FHM seem to be acclimated or adapted to living in WWTP effluent compared to the naïve laboratory population. These results have consequences for the potential inferences being made between laboratory and wild populations and indicates that more research needs to be done to understand the differences between wild and lab
Winkelman, D.L., B. Johnson, J. Schafler, R. Fitzpatrick, D. Gibson-Reinemer. 2006. Temporal variation in otolith elemental signatures: limitations for using otolith microchemistry to identify recruitment sources. Annual meeting of the American Fisheries Society Western Division. Bozeman, MT.	May 2006
Winkelman, D.L., A.R. Schwindt, K. Keteles, and M. McGree. Waste water effluent, estrogenic exposure, and the future of eastern plains native fishes. 2014 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 4-6, Laramie, WY.	March 2014	Our results suggest that acute exposure to exogenous estrogens may cause reproductive failure, fish may not recover from early life exposure, and the population consequences could be catastrophic. Field caging experiments in waste water effluent in the South Platte River clearly show that previously unexposed fathead minnows are being exposed to exogenous estrogens at levels that could indicate risk for reproductive failure.
Winkelman, D.L. and R. Fitzpatrick. 2006. Estimating sources of northern pike (Esox lucius) recruitment in the Yampa River, using otolith microchemistry. Upper Colorado River Researchers annual meeting. Moab, UT.	February 2006
Winkelman, D.L. and R. Fitzpatrick 2005. Estimating sources of northern pike (Esox lucius) recruitment in the Yampa River, using otolith microchemistry. Upper Colorado River Working Group annual meeting. Grand Junction, CO.	February 2005
Winkelman, D.L. and D. Walters. Rocky Mountain Streams Past and Present: The Influence of Forest Stand Age and Wood Deposition on Trout and Insect Biomass. Colorado Water Center. April 20, 2015. Fort Collins, CO	April 2015	The deposition of large wood influences brook trout and aquatic macroinvertebrate biomass.
Winkelman, D.L. and A.R. Schwindt. Using stochastic stage-structured models to evaluate the effects of estrogenic exposure on population growth rate in a short-lived fish.	November 2014	Despite the recent use of population models in ecotoxicology, few models incorporate variance in vital rates or evaluate the importance of variation on population dynamics. Our modeling indicates that estrogens significantly influence stochastic PGR even though empirical data may indicate that some vital rates are not influenced by exposure. We also demonstrate that adult fecundity and juvenile survival are most important for sustaining populations of fathead minnows (Pimephales promelas), an
Winkelman, D.L. and A. Schwindt. 21 August, 2012. Understanding population level responses to EDC exposure on fish population dynamics. 142nd annual meeting of the American Fisheries Society, Minneapolis-St. Paul, MN.	August 2012
Winkelman, D.L. Overview of Cooperative Fish and Wildlife Unit Aquatic Research Projects. Annual Researchers Meeting of the Colorado Division of Wildlife. December 16, 2015. Fort Collins, CO	December 2015	A complete overview of the Colorado Unit Aquatic program to state cooperator.
Winkelman, D.L. 2016, K. Keteles , A.R. Schwindt, and J. Anderson. Estrogenic exposure: Reproduction, Survival, and the future of eastern plains native fishes. Annual meeting of the Western Division of the American Fisheries Society. May 24, 2018. Anchorage, AK	May 2018	Our data indicate that exposure to environmentally relevant concentrations of estrogen can result in complete reproductive failure and this may have population consequences. There appear to be transgenerational effects of exposure, mediated through parental exposure. Field caging experiments show that fish are being exposed to exogenous estrogens at levels that could indicate risk for reproductive failure.
Winkelman, D.L. 2016, K. Keteles , A.R. Schwindt, and J. Anderson. Estrogenic exposure: Reproduction, Survival, and the future of eastern plains native fishes. 41st Annual meeting of the Western Division of the American Fisheries Society. April 22, 2016. Reno, NV.	March 2016	Our data indicate that exposure to environmentally relevant concentrations of estrogen can result in complete reproductive failure and this may have population consequences. There appear to be transgenerational effects of exposure, mediated through parental exposure. Field caging experiments show that fish are being exposed to exogenous estrogens at levels that could indicate risk for reproductive failure.
Winkelman, D.L. 2010. Evaluation of the Flathead Catfish Population and Fishery on Lake Carl Blackwell, OK, with emphasis on the effects of Noodling. Conservation, Ecology, and Management of Catfish: The Second International Symposium	June 2010
Winkelman, D. L., W. L. Kendall, and M. C. Dzul. 2019. Introduction to the symposium on the use of autonomous PIT tag antennas for modeling vital rates and movement. American Fisheries Society and The Wildlife Society 2019 Joint Annual Conference, Reno, Nevada, 29 Sep - 3 Oct 2019.	October 2019	This work provides an overview of the realized and potential contribution of the use of autonomous PIT tag readers to modeling vital rates and movement of fish.
Winkelman D.L., C. Clapp, and K. Thompson. 2006. Investigating competition among lineages of T. tubifex and the potential for biological control of whirling disease in natural streams. 12th annual whirling disease symposium. Denver, CO.	February 2006
Winkelman D.L. 26 February, 2004. Age and growth of flathead catfish in relation to exploitation in Oklahoma reservoirs. The American Fisheries Society Southern Division annual mid-year meeting. Oklahoma City, OK.	February 2004
Windell, B, Gerber, BD, Titcomb, G, Malmberg, J, Parrie, L, Nordeen, T, and Bailey, L. March 2025. Assigning probability of infection for ecological studies of chronic wasting disease. Colorado Chapter of The Wildlife Society. Fort Collins, CO.	March 2025	Chronic wasting disease (CWD) is a fatal cervid prion disease. There are uncertainties in assigning infection probability to live deer with current tests. We evaluate a Bayesian multi-scale occupancy model in estimating infection probability while incorporating multiple tests and their physiological dependencies.
Williams, P.J., M.B. Hooten, J.N. Womble, G.G. Esslinger, and M.R. Bower. Joint Statistical Meetings: ASA. Baltimore, MD (contrib. talk, 2nd author), 2017, Title: Optimal dynamic sampling of a spreading population.	August 2017	This talk describes how to optimally monitor sea otters in Glacier Bay.
Williams, P.J., M.B. Hooten, J.N. Womble, G.G. Esslinger, and M.R. Bower. (2016). Contributed talk, Joint Statistical Meetings, Chicago, IL. Title: A spatio-temporal model for ecological colonizations.	August 2016	This talk describes a modeling approach for sea otters in Glacier Bay that is dynamic and can be fused with an adaptive monitoring design.
Williams, P., M.B. Hooten, J.N. Womble, G.G. Esslinger, and M.R. Bower. International Statistical Ecology Conference. 2016. Seattle, WA. Contributed talk: A Spatio-Temporal Model to Infer Colonization Dynamics of Sea Otters in Glacier Bay, Alaska.	June 2016	This talk presents research on spatio-temporal modeling of sea otter population spread in Glacier Bay.
Williams, P. J., C. R. Ely, W. L. Kendall, M. B. Hooten, and J. A. Schmutz. 2014. Population dynamics and management of Cackling Geese. 21st Annual Conference of The Wildlife Society, Pittsburgh, PA.	October 2014	This work integrates data sources for Cackling Geese into a population model that is then further integrated with management objectives to provide a decision framework for managing this species. Integrating harvest, subsistence, and crop depredation objectives has not been done before.
White, G. C., and D. R. Anderson. September 2000. Advanced statistical principles for wildlife graduate students: Web-based learning approaches. 7th Annual Conference of The Wildlife Society, Nashville, TN.	September 2000
Vigil, E., J. Lepak, and D.L. Winkelman. Status and Life History Traits of Gill Lice Salmincola californiensis in Colorado	August 2015	Understanding impacts gill lice have on fish populations will help managers in the state mitigate the negative consequences of gill lice infestations.
Vigil, E., J. Lepak, and D.L. Winkelman. Distribution, Prevalence and Intensity of Gill Lice Salmincola Californiensis in Colorado	August 2015	Relatively little information is known about gill lice, and a better understanding of their distribution and life history traits will help managers determine which fish populations may be most at risk of experiencing detrimental effects due to gill lice infestation, as well as mitigate the negative consequences due to these infections.
Vigil, E., J. Lepak, D. Dreiling, D.L. Winkelman. Distribution and Life History Traits of Gill Lice Salmincola californiensis in Colorado	February 2015	Distribution and Life History Traits of Gill Lice Salmincola californiensis in Colorado
Vigil, E., D.L. Winkelman, and G. Schisler. Interactions of the parasitic Gill Louse, Salmincola californiensis and salmonids in Colorado. 41st Annual meeting of the Western Division of the American Fisheries Society. April 23, 2016. Reno, NV.	April 2016	Relatively little information is known about gill lice, and a better understanding of their distribution and life history traits will help managers determine which fish populations may be most at risk of experiencing detrimental effects due to gill lice infestation, as well as mitigate the negative consequences due to these infections.
Victoria J. Dreitz, N. Thompson Hobbs, Thomas H. Baker, Lisa L. Wolfe, Kenneth P. Burnham, Mary M. Conner, and Michael W. Miller. July 2002. Land-use impacts on the prevalence of chronic wasting disease in Colorado mule deer populations. Preparing for Emerging Diseases, 51st Annual Meeting of the Wildlife Diseases Association, Humboldt State University, Arcata, California.	July 2002
Vanausdall, R. A., W. L. Kendall, and D. P. Collins. 2023. Time of year and weather influence departure decisions of sandhill cranes at a stopover area in south-central Colorado. 30th Annual Conference of The Wildlife Society. Louisville, KY, 5-9 November 2023.	November 2023	We evaluated factors driving the phenology of departure from the major stopover area of Rocky Mountain Population sandhill cranes in fall and spring. We found no particular trend in phenology but found in fall winds, barometric pressure, and surface water drove phenology whereas in spring barometric pressure and crosswinds were important.
Vanausdall, R. A., W. L. Kendall, D. P. Collins, and Q. R. Hays. 2022. Greater sandhill crane roost selection and distribution during stopover in Colorado: implications for management in an arid system. 29^th Annual Conference of The Wildlife Society, Spokane, WA, 6-10 November, 2022.	November 2022	Understanding sandhill crane habitat use for foraging and roosting in the San Luis Valley, their most important stopover site for fall and spring migration, is crucial to decisions for providing habitat and water. This work evaluates the habitat they prefer and how roost sites and foraging sites relate in terms of accessibility to one another, allowing for carrying capacity models.
Tipton, J., M.B. Hooten, and S. Goring. Joint Statistical Meetings: ASA. Baltimore, MD (contrib. talk, 2nd author), 2017, Title: Reconstruction of Spatio-Temporal Temperature from Sparse Historical Records Using Robust Probabilistic Principal Component Regression.	August 2017	This talk describes how to reconstruct temperature from historical observational data.
Tipton, J., M.B. Hooten, R. Booth, C. Nolan. Joint Statistical Meetings, Chicago, IL (2016). Multivariate Bayesian networks for modelling multispecies ecological communities and paleoclimate reconstruction. Contributed Talk.	August 2016	This talk describes how to model microorganism data from bogs to reconstruct historical water levels.
Terrell, J. W., and E. P. Bergersen. 2003. Predicting streambed particle size distributions that limit oligochaete densities. 9th Annual Whirling Disease Symposium, Managing the Risk, Seattle, Washington.	February 2003
Sipher, C. and E. Bergersen. March 2001. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. Annual American Fisheries Society, Colorado/Wyoming Chapter Meeting, Cheyenne, WY.	March 2001
Sipher, C. R., and E. P. Bergersen. March 2001. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. Front Range Student Ecology Symposium, Fort Collins, CO.	March 2001
Sipher, C. R., and E. P. Bergersen. March 2001. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. Annual American Fisheries Society, Colorado/Wyoming Chapter Meeting, Cheyenne, WY.	March 2001
Sipher, C. R., and E. P. Bergersen. February 2002. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. 8th Annual Whirling Disease Symposium, Putting a Fresh Spin on Whirling Disease, Denver, Colorado.	February 2002
Sipher, C. R., and E. P. Bergersen. February 2001. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. 7th Annual Whirling Disease Symposium, Salt Lake City, UT.	February 2001
Sipher, C. R., and E. P. Bergersen. April 2001. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. Colorado Division of Wildlife Aquatics Section Meeting, Montrose, CO.	April 2001
Shaffler, J. J., and D. L. Winkelman. 23 February 2005. Temporal and spatial variability in trace element signatures of juvenile striped bass otoliths. 16th Graduate Research Symposium, Oklahoma State University, Stillwater, OK.	February 2005
Shaffler, J. J., and D. L. Winkelman. 25 February 2005. Temporal and spatial variability in trace element signatures of juvenile striped bass. Annual Meeting of the Oklahoma Chapter of the American Fisheries Society, Broken Bow, OK.	February 2005
Setash, C.M., W. L. Kendall, and D. Olson. 2017. Adaptive nest site selection influences Cinnamon Teal nest survival in Colorado. 24th Annual Conference of The Wildlife Society, Albuquerque, NM.	September 2017	This work provides much needed baseline nesting ecology information for the modeling of cinnamon teal populations, and informs Monte Vista NWR management of wetlands and duck habitat.
Setash, C., W. L. Kendall, and D. Olson. 2018. Cinnamon teal nest attendance influences nest survival during incubation. 25th Annual Conference of The Wildlife Society, Cleveland, OH.	October 2018	Little is known about the cinnamon teal, a harvested species. This paper partitions attendance patterns at the nest as incubation progresses and identifies effects on nest survival and thus productivity.
Setash, C., W. L. Kendall, and D. Olson. 2016. Cinnamon teal breeding ecology in the San Luis Valley, Colorado. Annual Meeting of the Colorado Chapter of The Wildlife Society, Fort Collins, CO.	February 2017	This work adds to the little information available on Cinnamon Teal nesting ecology and vital rates.
Setash, C., W. L. Kendall, and D. Olson. 2016. Cinnamon teal breeding ecology in the San Luis Valley, Colorado. 23rd Annual Conference of The Wildlife Society, Raleigh, NC.	October 2016	Information on cinnamon teal ecology to inform management decisions is limited. The breeding ecology parameters estimated in this work will contribute to population modeling of this species.
Schisler, G., P. Walker, E. P. Bergersen, T. James, and C. Smith. 2003. Evaluation of oxytetracycline, dimilin, malarone and quinine for control of Myxobolus cerebralis. 9th Annual Whirling Disease Symposium, Managing the Risk, Seattle, Washington.	February 2003
Schisler, G. J., and E. P. Bergersen. February 2001. Evaluation of risk of high elevation waters to the establishment of Myxobolus cerebralis, the causative agent of whirling disease. 7th Annual Whirling Disease Symposium, Salt Lake City, UT.	February 2001
Schisler, G. J. and E. P. Bergersen. February 2000. Evaluation of single round polymerase chain reaction and pepsin-trypsin digest methods for the detection of Myxobolus cerebralis. 6th Annual Whirling Disease Symposium, Coeur d' Alene, ID.	February 2000
Scharf, H.R., M.B. Hooten, B.K. Fosdick, D.S. Johnson, J.M. London, and J.W. Durbin. (2016). ISEC, Seattle, WA. Dynamic social networks based on movement.	June 2016	This talk describes a social network modeling approach based on telemetry data.
Scharf, H.R., M.B. Hooten, B.K. Fosdick, D.S. Johnson, J.M. London, and J.W. Durban. (2016). Joint Statistical Meetings, Chicago, IL. Title: Dynamic social networks based on movement.	August 2016	This talk describes a statistical approach to using telemetry data to identify dynamic social networks in killer whale populations.
Scharf, H.J., M.B. Hooten, R.R. Wilson, G.M. Durner, and T.C. Atwood. (2018). Accounting for phenology in the analysis of animal movement. International Statistical Ecology Conference.	July 2018	This presentation describes a statistical approach for clustering populations given underlying movement and environmental phenology.
Scharf, H., M.B. Hooten, D.S. Johnson, and J. Durban. Joint Statistical Meetings: ASA. Baltimore, MD (topic contrib. talk, 2nd author), 2017, Title: Process convolution approaches for modeling interacting trajectories.	August 2017	This talk presents a method for analyzing telemetry data from multiple individuals simultaneously.
Schaffler, J.J. 15 March 2004. Do fish use discharge as a cue for spawning? Larval fish abundance in the Red and Washita rivers. 15th Graduate Research Symposium, Oklahoma State University, Stillwater, OK.	March 2004
Schaffler, J. J., and D. L. Winkelman. 7 November 2003. Larval striped bass distribution and abundance in Lake Texoma. 92nd annual meeting of Oklahoma Academy of Science, Chickasha, OK.	November 2003
Schaffler, J. J., and D. L. Winkelman. 27 February 2004. Larval striped bass distribution and abundance in Lake Texoma, Oklahoma-Texas. 12th annual spring meeting of the Southern Division of the American Fisheries Society, Oklahoma City, OK.	February 2004
Ruzicka, R. E., B. L. Walker, and W. L. Kendall. 2024. Addressing uncertainty in greater sage-grouse daily lek attendance and inter-lek movement. Western Association of Fish and Wildlife Agencies 34th Biennial Sage and Columbian Sharp-Tailed Grouse Workshop, Wenatchee, Washington, 5-8 August 2024.	August 2024	This work is important to accurately estimating survival and lek attendance rates for sage grouse, and in informing the interpretation of lek counts as a monitoring method.
Ruiz-Gutierrez, V., W. L. Kendall, and J. Saracco. 2014. Overwintering dynamics of migratory birds: how to infer movement patterns using open multi-state models. 2014 Joint Meeting of the American Ornithologists Union, the Cooper Ornithological Society, and the Society of Canadian Ornithologists, Estes Park, CO.	September 2014	This work advances the ability to model transience in populations and its biological interpretation, by implementing new capture-recapture models.
Ruiz-Gutierrez, V., W. L. Kendall, G. C. White, and J. Saracco. 2013. On the use of multistate open robust design state uncertainty models to account for and directly estimate transience under various definitions. Euring 2013 Analytical Conference.	May 2013	Estimation of the proportion of a population that are transients is of interest, whether to remove their influence from a population model, or to assess resource needs of individuals using an area. This work shows how to estimate this under various definitions of transience.
Ross, B.E., M.B. Hooten, and D.N. Koons. 2017. Evaluating the inference from dynamic occupancy models relative to population abundance. American Ornithology 2017, Michigan.	July 2017	We compare inference between parameters in dynamic occupancy models to population abundance for lesser and greater scaup from 1957-2015. Our results indicate that decreases in abundance may not be detected using occupancy models.
Rohwer, K., A.T. Herdrich, D.L. Winkelman. The Effects of Land Use, In-stream Wood and Insect Populations on Salvelinus fontinalis Density, Growth and Diet	February 2015	The increased fish density places greater pressure on the invertebrate populations, leading to a decrease in invertebrate density. The data we have establishes that in-stream wood affects the percent of lipids stored; however we would like to collect data from additional streams to establish a definite pattern.
Response of fathead minnow populations to an exogenous estrogen used in human birth control.	May 2011
Response of fathead minnow populations to an exogenous estrogen used in human birth control.	February 2011
Presented, Burnham and White, Evaluation of some Bayesian MCMC random effects inference applicable to bird ringing data, and Burnham, 'Computing issues concerning hierarchical models.' Presented a poster, "Profile likelihood intervals: a new feature of program MARK to solve a problem of 'standard theory'."	October 2003
Pettigrew, E.J., D.L. Winkelman, D. Walters, M. Venarsky, A. Herdrich. Effects of in-stream large wood on fish diets.	February 2015	Analyses of insect biomass and production are ongoing; however, it appears that differences in diet can at least partially be explained by differences in insect community between the sites. It appears that fish consumption may help explain differences in fish biomass and individual growth observed between the sites and will aid in understanding how large wood influences ecosystem function.
Peck, C., B.D. Gerber, and M.B. Hooten. Joint Statistical Meetings: ASA. Baltimore, MD (contrib. talk, 3rd author), 2017, Title: Hierarchical Bayesian models for azimuthal telemetry data.	August 2017	This talk presents a method for analyzing VHF telemetry data.
Pearson, K., W. Kendall, D.L. Winkelman, and W Persons. Spawning probability of humpback chub, Gila cypha, in the Little Colorado River, Arizona. 2014 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 4-6, Laramie, WY.	March 2014	Understanding the spawning strategy of humpback chub in the LCRB is essential to accurately estimate demographic parameters because, as our research indicates, humpback chub are not annually present in the LCR.
Pearson, K., W. Kendall, D. Winkelman, and W. Persons. 2014. Spawning strategy of the endangered humpback chub in the Little Colorado River with implications for estimability of demographic parameters necessary for species recovery. Society for Conservation Biology Conference, Missoula, MT.	July 2014	This work provides unbiased estimates of adult survival, breeding probability, and breeding population size for the endangered humpback chub. Models of population dynamics can now be more robust.
Participated in the technical meeting EURING 2003, Oct. 6-10, 2003 in Radolfzell, Germany. The Quantitative Study of Marked Individuals in Ecology, Evolution and Conservation Biology.	October 2003
Orabutt, D., and E. Bergersen. 2003. Northern pike and trout interactions in high elevation trout reservoirs in Colorado. American Fisheries Society Esocids Technical Committee Meeting, Minaqua, Minnesota.	July 2003
Orabutt, D., Jr., and E. P. Bergersen. Northern pike in high elevation reservoir trout fisheries. American Fisheries Society Student Chapter Meeting, Colorado State University, Fort Collins, Colorado.	January 2003
Nambiar, R., D. L. Winkelman, D. M. Leslie, Jr., and T. Boyer. 7 November 2003. Zooplankton community structure in ephemeral wetlands on the Tallgrass Prairie Preserve, Pawhuska, Oklahoma. 92nd annual meeting of Oklahoma Academy of Science, Chickasha, OK.	November 2003
Multimodel inference: Understanding AIC and BIC in model selection. Conference on New Developments of Statistical Analysis in Wildlife, Fisheries and Ecological Research (The Fifth Winemiller Symposium), October 13-16, 2004 at the University of Missouri. Sponsored by NSF and the University of Missouri and hosted by the University of Missouri Department of Statistics.	October 2004
Millsap, B., G. S. Zimmerman, W. L. Kendall, F. Abadi, and J. V. Gedir. 2020. An integrated population model to inform management of permitted take of bald eagles in the United States. Ecological Society of America Annual Conference, Salt Lake City Utah, 2 August to 7 August, 2020.	August 2020	This work demonstrates a tool for integrating multiple monitoring data streams to model the dynamics of bald eagles and implications for incidental take and permitting decisions.
Milhous, R. T., J. W. Terrell, and E. P. Bergersen. 2002. Sediment as habitat for worms associated with whirling disease. Annual Meeting of Rocky Mountain Hydrologic Research Center, Denver, Colorado.	December 2002
Mezebish Quinn, T, Paton, P, Gerber, BD, Kilburn, J, and McWilliams Scott. Habitat selection of American black ducks wintering in an urban estuary with increasing shellfish aquaculture. North American Duck Symposium; Feb 2024; Oregon	February 2024	We deployed backpack-style GPS-GSM transmitters during winter 2020-2021 to monitor the movements of adult American black ducks (female n = 14, male n = 16) in coastal Rhode Island. Black ducks had bimodal movement distributions dominated by short steps that indicated movement between either coastal or inland waterbodies but also including longer steps that reflected shifts in locale between coastal and inland waterbodies.
McGree, Michelle, D.L. Winkelman, and N. Viera. 2008. An estrogenic endocrine disruptor alters reproductive behaviors and fecundity of the red shiner. Annual Meeting of the Western Division of AFS. Portland, OR.	May 2008
McGree, M.M., D.L. Winkelman, and N. Vieira. 2009. Exposure to 17β-estradiol reduces reproductive success of the Adult Red Shiner (Cyprinella lutrensis). 2nd International Conference on Occurrence, Fate, Effects, and Analysis of Emerging Contaminants in the Environment. Fort Collins, CO.	August 2009
McGree, M., D.L. Winkelman, and N. Viera. 2008. An estrogenic endocrine disruptor alters reproductive behaviors and fecundity of the red shiner. Annual Meeting of CO-WY Chapter of the American Fisheries Society. Cheyenne, WY.	February 2008
McGree, M. M., D. L. Winkelman, and N. K. Vieira. 2007. The effects of an estrogenic endocrine disruptor on male red shiner reproduction: behavior, secondary sexual traits, and development. Rocky Mountain Society of Toxicology and Chemistry, Golden, CO (April).	April 2007
McGree, M. M., D. L. Winkelman, and N. K. Vieira. 2007. The effects of an estrogenic endocrine disruptor on male red shiner reproduction: behavior, secondary sexual traits, and development. Colorado/Wyoming Meeting of the American Fisheries Society, Fort Collins, CO (March).	March 2007
McGree, M. M., D. L. Winkelman, and N. K. Vieira. 2007. The effects of an estrogenic endocrine disruptor on male red shiner (Cyprinella lutrensis) reproduction: behavior, secondary sexual traits, development, and productivity. National Meeting of the American Fisheries Society, San Francisco, CA (September).	September 2007
McGree, M. M., D. L. Winkelman, and N. K. M. Vieira. 2008. An estrogenic endocrine disruptor alters the reproductive behaviors and fecundity of the red shiner. Colorado State University Department of Fish, Wildlife, and Conservation Biology Departmental Seminar, Fort Collins, CO (March).	March 2008
Mauck, M., and D. L. Winkelman. 7 November 2003. Survival and condition of age-0 striped bass in Lake Texoma. 92nd annual meeting of the Oklahoma Academy of Science, Chickasha, OK.	November 2003
Mauck, M., and D. L. Winkelman. 27 February 2004. Factors influencing first year recruitment of striped bass in Lake Texoma. 12th annual spring meeting of the Southern Division of the American Fisheries Society, Oklahoma City, OK.	February 2004
Mauck M. and D.L. Winkelman. 2005. Factors Influencing First Year Recruitment of Striped Bass in Lake Texoma. 59th annual meeting of the Southeastern Association of Fish and Wildlife Agencies. St. Louis, MO.	October 2005
Malachowski, C., W. L. Kendall, R. Swift, E. Flint, J. L. McKay, M. Rogosky, M. Naughton, M. Romano, J. Yoshizaki, and P. F. Doherty, Jr. 2023. Trade-offs between survival and reproduction in two species of North Pacific albatrosses. 50th Annual Meeting of the Pacific Seabird Group, 15-17 February 2023, Lajolla, CA.	February 2023	This paper is the first comprehensive demographic analysis of a major breeding population of black-footed and Laysan albatrosses, from Tern Island, French Frigate Shoals. Little is known about population dynamics of Northern Hemisphere albatrosses.
Malachowski, C., W. L. Kendall, D. Collins, K. Kraii, J. Olszak, and L. Reynolds. 2022. Survival, recovery, and post-breeding movements in the Western Gulf Coast Population of mottled ducks. 29th Annual Conference of The Wildlife Society, Spokane, WA, 6-10 November, 2022.	November 2022	This work examines the effects of harvest regulations and climate variables on the survival and movement of this declining population of ducks. The results can be used by population and habitat managers to improve populations.
Malachowski, C. M., W. L. Kendall, J. Plissner, R. Swift, and E. Flint. 2025. An integrated population model for Black-footed and Laysan albatrosses in the Northwestern Hawaiian Islands. 2025 Joint Meeting of the Pacific Seabird Group and The Waterbird Society, La Ribera de Belen Heredia, Costa Rica, 6-9 January, 2025.	January 2025	This paper demonstrates the relative value of different monitoring programs for modeling the dynamics of albatross populations in the Northwestern Hawaiian Islands.
Lukacs, P.M., and K. P. Burnham. Statistical aspects of using genetic markers for individual identification in capture-recapture studies. 10th Annual Wildlife Society Conference, Burlington, Vermont.	September 2003
Lukacs, P.M. and Burnham, K.P. 2003. Statistical aspects of using genetic markers for individual identification in capture-recapture studies. 3rd International Wildlife Management Congress, Christchurch, New Zealand.	September 2003
Lukacs, P.M. and Burnham, K.P. 2003 Statistical aspects of using genetic markers for individual identification in capture-recapture studies. EURING Technical Meeting, Radolfzell, Germany.	September 2003
Lisa L. Wolfe, Mary M. Conner, Thomas H. Baker, Victoria J. Dreitz, Kenneth P. Burnham, Elizabeth S. Williams, N. Thompson Hobbs, and Michael W. Miller. July 2002. Evaluation of tonsillar biopsy data for estimating chronic wasting disease prevalence in free-ranging mule deer. Preparing for Emerging Diseases, 51st Annual Meeting of the Wildlife Diseases Association, Humboldt State University, Arcata, California.	July 2002
Larkin, K and D.L. Winkelman. 2009. Colorado River cutthroat trout restoration: conservation planning and watershed prioritization tools for today’s managers. Annual meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Fort Collins, CO.	February 2009
Lambert, S. M., P. Ersts, M. Alldredge, W. L. Kendall, and R. Beveridge. 2021. Methods and applications for integrating A.I. photo-filtering software into camera surveys. 2021 Annual Meeting of the Colorado Chapter of The Wildlife Society (virtual).	February 2021	Trail cameras provide a wealth of information on species presence, relative abundance, and age-structure, but extracting information from hundreds of thousands of photos is very time-consuming and therefore budgetarily expensive. This work demonstrates the power of machine learning approaches to automate the extraction of information to reduce time and effort considerably, and allow the use of this data for research and management in a timely manner.
Kowalski, D., and E. P. Bergersen. February 2002. Toxicity of bayluscide and TFM to different lineages of Tubifex Tubifex: implications for the chemical control of oligochaetes. 8th Annual Whirling Disease Symposium, Putting a Fresh Spin on whirling Disease, Denver, Colorado.	February 2002
Kowalski, D. and E. Bergersen. March 2001. Preliminary investigations on the efficacy of chemical control of Tubifex tubifex on the incidence of whirling disease in Colorado hatcheries. Annual American Fisheries Society, Colorado/Wyoming Chapter Meeting, Cheyenne, WY.	March 2001
Kowalski, D. and E. Bergersen. February 2001. Preliminary investigations on the efficacy of chemical control of Tubifex tubifex on the incidence of whirling disease in Colorado hatcheries. 7th Annual Whirling Disease Symposium, Salt Lake City, UT.	February 2001
Kowalski, D. and E. Bergersen. April 2001. Preliminary investigations on the efficacy of chemical control of Tubifex tubifex on the incidence of whirling disease in Colorado hatcheries. Colorado Division of Wildlife Aquatic Section Meeting, Montrose, CO.	April 2001
Keteles, K., D.L. Winkelman, J. Lazorchak, D. Villeneuve, D. Ekman, A. Vajda, and T. Collette. Use of bioactivity tools to measure estrogenic mixtures below WWTPs with differing treatment technologies. SETAC North America 36th annual meeting, Salt Lake City, UT.	November 2015	Biomonitoring of vtg expression appears to be a useful screening tool to determine exposure to estrogenic mixtures especially when used in concert with metabolomics and in vitro tools.
Kendall, W. L., R. Y. Conrey, and J. H. Gammonley. 2020. Multistage nest survival: a hidden Markov model approach when nest age or stage is uncertain. The Wildlife Society 2020 Annual Conference, 28 Sep - 2 Oct 2020.	September 2020	The method for modeling nest survival in this work provides the ability to properly model nest survival when the age of the nest at discovery is not known. This is especially useful for raptor nests and others where eggs cannot be examined to determine age.
Kendall, W. L., R. C. Drewien, W. Brown, and B. D. Gerber. 2014. Pre- and post-harvest mortality sources and survival of the Rocky Mountain Sandhill Crane. 21st Annual Conference of The Wildlife Society, Pittsburgh, PA.	October 2014	This work illustrates for the first time that sandhill cranes have very low natural mortality rates (0.06), and that harvest mortality is compensatory for adults, in the face of low to moderate harvest pressure.
Kendall, W. L., M. C. Dzul, D. L. Winkelman, L. L. Bailey, and M. M. Conner. 2024. Modeling survival and movement of stream fishes using autonomous PIT tag antennas. 154th Annual Meeting of the American Fisheries Society, Honolulu, Hawaii, 15-19 September 2024.	September 2024	This work provides a framework for estimating survival and movement of fish where detections are on PIT tag arrays between reaches of interest. It accounts for the continuous nature of detection data, and informs the design of such studies.
Kendall, W. L., K. N. Pearson, P. H. Dutton, K. R. Stewart, and C. Lombard. 2018. Life history and demography of a nesting population of leatherback sea turtles (Dermochelys coriacea) at St. Croix, U. S. Virgin Islands, 1992-2013. 25th Annual Conference of The Wildlife Society, Cleveland, OH.	October 2018	Understanding the mechanism by which this threatened species is changing in population size, whether by change in survival or productivity, is important to its conservation. We partition these elements for a nesting population of leatherbacks.
Kendall, W. L., K. N. Pearson, P. H. Dutton, K. R. Stewart, and C. Lombard. 2017. Life history and demography of a nesting population of leatherback sea turtles (Dermochelys coriacea), U. S. Virgin Islands, 1992-2013. 37th Annual Symposium on Sea Turtle Biology and Conservation. Las Vegas, NV.	April 2017	This work identifies the population status of this threatened species, and life history patterns that could be influenced by environmental factors.
Kendall, W. L., G. C. White, and C. B. Yackulic. 2023. A multistate Jolly-Seber mark-recapture model for population dynamics or stopover phenology. 30th Annual Conference of The Wildlife Society. Louisville, KY, 5-9 November 2023.	November 2023	We provide a modeling framework for estimating either parameters of population dynamics for a population that occupies multiple states, or phenological parameters like residence, arrival, or departure times for a population at a stopover that uses multiple sites.
Kendall, W. L., G. C. White, L. Cordes, and B. W. Meixell. 2013. Estimating parameters under state uncertainty when events are seasonal. Euring 2013 Analytical Conference, Athens, Georgia.	May 2013	This work extends capture-recapture methodology to estimate demographic parameters in the face of uncertainty about phenotypic state, while acknowledging that indicators of state only occur seasonally. Thus bias in population models can be minimized.
Kendall, W. L., D. L. Winkelman, M. C. Dzul, and C. B. Yackulic. 2019. Estimating vital rates and movement using autonomous PIT tag antennas: a design and analysis framework. American Fisheries Society and The Wildlife Society 2019 Joint Annual Conference, Reno, NV.	October 2019	This work provides a framework for designing and robustly analyzing PIT tagging data for population parameters.
Kendall, W. L., C. Malachowski, R. Swift, E. Flint, J. L. McKay, and M. Rogosky. 2024. Trade-offs between survival and reproduction in two species of North Pacific albatrosses. 31st Annual Conference of The Wildlife Society. Baltimore, MD, 19-23 October 2024.	October 2024	This work is the first demographic analysis of recruitment, survival, and breeding probability for northern hemisphere albatross species, one of which is a USFWS species of concern.
Kendall, W. L., C. A. Langtimm, M. M. Lamont, M. Randall, R. S. Wells, K. M. Hart, C. A. Beck, and A. L. Teague. 2016. Assessing the potential of a monitoring network for the Gulf of Mexico based on large vertebrate species. 2016 Gulf of Mexico Oil Spill and Ecosystem Science Conference, Tampa, FL.	February 2016	This talk outlines how resighting data on a number of high profile species in the Gulf of Mexico could be integrated to assess system health of the Gulf, providing baseline or evaluation of impacts.
Kendall, W. L., C. A. Langtimm, C. A. Beck, K. A. Rood, S. L. Barton, and A. L. Teague. 2016. Using continuous-time resighting data to improve inference from multistate mark-recapture studies.	October 2016	The model presented here will provide a more flexible framework for incorporating auxiliary sighting data into analyses of mark-recapture data, increasing precision and in some cases improving the estimability of parameters.
Kendall, W. L. Robust demographic studies of sea turtles from an ensemble of data sources. 34th Annual Symposium on Sea Turtle Biology and Conservation. New Orleans, LA, USA.	April 2014	This paper indicates how data sources can be integrated into more robust inference, at a time when advances in technology are making demographic modeling of sea turtles ever more possible.
Kendall, W. L. 2020. Contributions of banding data to the development of avian demography and capture-recapture modeling. North American Ornithological Conference 2020, 11-16 August 2020.	August 2020	This presentation illustrates the value and contribution of the Bird Banding Laboratory and bird banding in general to the study of avian demography and the development of capture-recapture methodology for ecologists.
Kendall, W. L. 2017. The multistate model as an omnibus framework for robust inference from mark-recapture studies. 24th Annual Conference of The Wildlife Society, Albuquerque, NM.	September 2017	This talk lays out how multistate models provides a framework for modeling a wide variety of data and hypotheses within population studies.
Kendall, W. L. 2015. Robust inference from seabird demographic studies through a synergy among hypotheses, design, and analytical tools. 2nd World Seabird Conference, Cape Town, South Africa, October 26-30, 2015.	October 2015	This talk shows how the robustness and efficiency of seabird studies can be maximized by close attention to both the type of data to collect (design) and the types of models that can be useful (analysis).
James W. Rivers, Lindsay J. Adrean, Jennifer A. Bailey Guerrero, Jonathan Dachenhaus, Jennifer L. Fisher, Cecelia Frisinger, Marie-Sophie Garcia-Heras, Brian D. Gerber, Carolyn B. Meyer, S. Kim Nelson, Joseph M. Northrup, Daniel D. Roby, Jonathon Valente, Christopher Wolf, Ethan Woodis, Zhiqiang Yang, and Matthew G. Betts. Warming ocean conditions curtail breeding activity of the Marbled Murrelet, a most unusual forest-nesting bird. Oregon chapter of The Wildlife Society, February 2024.	February 2024	Projected increases in ocean heat waves, coupled with long-term reduction and fragmentation of murrelet nesting habitat, suggest that recovery of murrelet populations will remain a formidable challenge and require targeted conservation efforts in both marine and terrestrial environments.
J.E. Cavallin, W.A Battaglin, J. Beihoffer, B.R. Blackwell, P.M. Bradley, D.R. Eckman, J. Kinsey, K. Keteles, E.Lai, R. Weissinger, D.L. Winkelman, and D.L. Villeneuve. Effects-based monitoring of bioactive contaminants associated with exposure to a wastewater treatment plant discharge on the Colorado River. Society of Ecological Toxicology and Chemistry North America 39th annual meeting. November 6, 2018	November 2018	Results suggest rapid dilution of biologically-active contaminants downstream of the WWTP discharge and will be discussed relative to the potential effects of CECs in the Colorado River.
Itter, M., A. Finley, M.B. Hooten, P. Higuera, J. Marlon, and J. McLachlan. (2016) American Geophysical Union Annual Mtg. San Francisco, CA (contrib. talk, 3rd author). Title: A Model-Based Approach to Infer Shifts in Regional Fire Regimes Over Time Using Sediment Charcoal Records.	December 2016	This talk describes a statistical method for separating background and foreground historic fire events based on charcoal records.
Iannarilli, F, Gerber, BD, Erb, J, Wikelski, M, Fieberg, JR. A hierarchical modeling framework for estimating animal activity patterns: the effect of human presence on diel activity. The International Statistical Ecology Conference, Swansea, United Kingdom. 15-19, July 2024.	July 2024	We illustrate how trigonometric terms and cyclic cubic splines combined with hierarchical models (i.e., Generalized Linear Mixed Models, GLMMs) can be a valuable framework to estimate animal diel activity patterns. These patterns provide important information on how species adapt to both anthropogenic and natural disturbances, elucidate mechanisms of species co-existence through temporal partitioning, and assess broader effects of diel shifts at the community and ecosystem levels.
Hu, D, S. Gaughan, P.M. Kocovsky, M.E. Mather, K. Mayes, J. Perkin, J.S. Rogosch, D. Winkelman, M. Wuellner. 2022. AFS 151 Symposia Summaries. "Creating and implementing an ecosystem-wide integrated research agenda and conservation plan for prairie streams: A shared vision, next generation synthesis, and future action plan." Fisheries 47: 30. https://doi.org/10.1002/fsh.10708	November 2021	The symposium brought together scientists and managers across the Great Plains who shared their perspectives, research, existing resources, and anticipated roles in a collaborative network. Presentations were organized around several topics including a keynote address about prairie stream conservation, ongoing research, state agency perspectives, federal agency coordination, and opportunities for future collaboration.
Hooten, M.B., H.R. Scharf, T.J. Hefley, A.T. Pearse, M.D. Weegman. (2018). Animal movement models for migratory individuals and groups. The Wildlife Society Annual Meeting, Cleveland, OH. Invited Talk.	October 2018	This talk describes flexible animal movement models for telemetry data.
Hooten, M.B. and J.M. Morales. (2018). Animal movement models for recharge dynamics. International Statistical Ecology Conference.	July 2018	This presentation describes models for animal trajectories that rely on an underlying recharge process associated with obtaining and expending energy.
Hooten, M.B. and D.S. Johnson. Joint Statistical Meetings, Chicago, IL. (2016). Basis function approaches for continuous-time Lagrangian movement modeling. Invited Talk.	August 2016	This talk describes a new approach for modeling animal movement telemetry data by smoothing Brownian motion.
Hooten, M.B. (2015) IALE World Congress, Portland, OR. Invited Talk: Statistical dimension reduction and computation in spatial ecology.	July 2015	This talk covers different approaches for efficient statistical computation and model construction.
Hooten, M.B. (2014). Linking long-distance animal movement behavior and landscapes using multiscale functional models. Invited Presentation. Graybill Conference. Fort Collins, CO.	September 2014	This talk describes methods for better understanding long-distance behavior in animals using telemetry data.
Hooten, M.B. The International Environmetrics Society Meeting. (2016). A progression in G: time series, spatial statistics, and the trajectories of ecological particles. Invited Plenary Seminar.	July 2016	This talk describes statistical methods for analyzing animal movement telemetery data.
Hooten, M.B. (2018). Optimal adaptive monitoring: Past, present, and future. The Wildlife Society Annual Meeting, Cleveland, OH. Invited Talk.	October 2018	This talk describes the history and state of the art associated with optimal adaptive monitoring strategies in ecology.
Hooten, M.B. (2015) Joint Statistical Meetings, Seattle, WA. Invited Talk. Title: Linking Long-Distance Animal Movement Behavior and Landscapes Using Multiscale Functional Models.	August 2015	This talk describes functional modeling techniques for animal movement data.
Hooten, M.B. (2014). Fringe Benefits: The hidden utility of movement constraints in telemetry studies. Invited Presentation. International Statistical Ecology Conference. Montpellier, France.	July 2014	This presentation describes methods for utilizing telemetry data and natural constraints to movement to estimate and account for telemetry error in animal space use studies.
Herdrich, A.T., D.L. Winkelman, and D. Walters. Effects of large wood and log jams on eastern slope Rocky Mountain trout populations. 41st Annual meeting of the Western Division of the American Fisheries Society. April 23, 2016. Reno, NV.	August 2016	Large wood influences the amount of habitat available for insects and fish and increased trout density at sites with high amounts of large wood and is due to large wood modifying physical habitat. Our data indicates a potential loss in fish production in valleys with reduced channel complexity.
Herdrich, A.T., D.L. Winkelman, and D. Walters. Effects of large wood and log jams on eastern slope Rocky Mountain trout populations. 41st Annual meeting of the Western Division of the American Fisheries Society. April 23, 2016. Reno, NV.	April 2016	Large wood influences density of brook trout populations by creating pool habitat.
Herdrich, A.T., D.L. Winkelman, and D. Walters. Effects of Large Wood and Log Jams on Eastern Slope Rocky Mountain Trout Populations.	August 2015	Our results indicate potential losses in insect and fish production at sites historically cleared of large wood and suggests a minimum level of wood loading to ensure consistent fish densities.
Herdrich, A.T., D.L. Winkelman, D. Walters. Effects of Large Wood and Log Jams on Eastern Slope Rocky Mountain Trout Populations	February 2015	Our goals are to understand how LW influences trout biology and ultimately fish population density. Our results will be beneficial for managers in evaluating specific endpoints for stream restoration projects in high-elevation streams.
Herdrich, A.T., D. Walters, and D.L. Winkelman. Effects of Large Woody Debris and Log Jams on Eastern Slope Rocky Mountain Trout Populations. 2014 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 4-6, Laramie, WY.	March 2014	I examine how trout populations in high elevation, eastern slope streams along northern Colorado’s Front Range are affected by Large Woody Debris (LWD) by comparing streams with high amounts of in-stream LWD to streams with medium and low amounts of LWD. Trout densities were generally highest in streams with large quantities of LWD and lowest in streams in which LWD was minimal or absent.
Hefley, T.J., M.B. Hooten, E.M. Hanks, D.P. Walsh, and R.E. Russell. International Statistical Ecology Conference. 2016. Seattle, WA. (contributed talk) Title: Confounding in dynamic ecological processes.	June 2016	This presentation describes the importance of spatio-temporal dynamics in forming spatial ecological processes.
Hefley, T., M.B. Hooten, E.M. Hanks, D. Walsh, R. Russell. (2016). Contributed talk. Joint Statistical Meetings, Chicago, IL. Title: Dynamically induced spatial confounding.	August 2016	This talk describes a type of confounding that can complicate estimation in spatial statistical settings that arises due to latent dynamics.
Hefley, T., M.B. Hooten, D. Walsh, and R. Russell. (2017) Expansion and Growth of Chronic Wasting Disease in Wisconsin. Midwest Fish and Wildlife Conference. Lincoln, NE.	February 2017	This talk presents finding based on spatio-temporal modeling of CWD in Wisconsin.
Hart, A., W. L. Kendall, and M. Alldredge. 2024. Survival trade-offs of migratory and resident behavior in mule deer. 2024 Annual Meeting of the Colorado Chapter of The Wildlife Society, Pueblo, Colorado, 31 January – 2 February, 2024.	February 2024	This work compares survival and the factors that influence it for the migratory and resident components of a partially migratory population of mule deer. Their survival rates were partitioned using multistate models with state uncertainty.
Hart, A., G. Wittemyer, W. L. Kendall, and M. W. Alldredge. 2023. Influence of irrigated agriculture on mule deer movements in partially migratory herds. 30th Annual Conference of The Wildlife Society. Louisville, KY, 5-9 November 2023.	November 2023	This work examines the influence of irrigated agriculture on mule deer forage selection and movements. It demonstrates that mule deer will select for these irrigated fields when natural forage is mediocre to poor.
Grider, J. F., B. J. Udell, B. E. Reichert, W. F. Frick, T. L. Cheng, and W. L. Kendall. 2023. A novel method for estimating pathogen presence, prevalence, load, and dynamics at multiple scales during a disease outbreak. Euring Analytical Conference and Workshop, Montpellier, France, 17-21 April 2023.	April 2023	This paper improves on current naive methods for assessing prevalence of white-nose syndrome, which doesn't account for uncertainty in detecting the pathogen, and basic occupancy models that categorize PCR tests into detected or not. This paper's use of continuous measures from PCR tests utilizes more information and therefore produces unbiased and more precise estimates of prevalence.
Gibson-Reeinemer, D., B. Johnson, D.L. Winkelman. 2006. Use of otolith microchemistry to identify origin of hatchery-reared rainbow trout. . Annual meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Cheyenne WY.	January 2006
Gerber, BD, Devarajan, K, Farris, ZJ, and Fidino, M. A framework to define and estimate animal diel activity. The 103rd Annual American Society of Mammalogists Meeting. June 7-11, 2024. Boulder, CO, USA.	June 2024	We propose a quantitative framework that defines diel phenotypes and offers multiple hypotheses sets aimed to achieve different objectives. We evaluate this framework using simulations to guide researchers on evaluating diel phenotypes for a range of sample sizes (10–1280). We also apply our framework to a global camera trap data set to compare literature classifications with empirical estimates for 445 mammal species.
Gerber, BD, Devarajan, K, Farris, ZJ, and Fidino, M. A conceptual and statistical framework to define animal diel activity patterns and investigate species plasticity. The 31st Annual Wildlife Society Conference. October 19-23, 2024. Baltimore, MD, USA.	October 2024	We propose a quantitative framework that defines diel phenotypes and offers multiple hypotheses sets aimed to achieve different objectives. We evaluate this framework using simulations to guide researchers on evaluating diel phenotypes for a range of sample sizes (10–1280).
Gerber, B. Kendall, W. Hooten, M., Dubovsky, J., Drewien, R. Predicting Juvenile Sandhill Crane Production From Ecologically-Driven Hypotheses Using Statistical Regularization	October 2014	Presentation of dissertation work at the national annual Wildlife Society Conference. The authors demonstrate a predictive model of juvenile sandhill crane recruitment from the Rocky Mountain Population.
Gerber, B. D., W. L. Kendall, J. A. Dubovsky, R. C. Drewien, and M. B. Hooten. Annual variation of young of the year in the Rocky Mountain Population of Sandhill Cranes. 13th North American Crane Workshop. Lafayette, LA, USA.	April 2014	Relating recruitment to climatic variables will inform sandhill crane harvest management in the short term, and help predict the implications of climate change on cranes in the long term.
Gerber BD, BA Mosher, LL Bailey, E Muths, HJ Crockett, and SJ Converse. 2023. Optimal management decisions are robust to unknown dynamics in an amphibian metapopulation plagued by disease. The Wildlife Society Annual Conference, Louisville, Kentucky, USA. 5-9 November.	November 2023	We investigated the sensitivity of management decisions to unknown dynamics regarding colonization of sites by the pathogenic chytrid fungus using value of information and regret analyses. We found that, while uncertainty is substantial, the optimal decisions vary little, suggesting that little management value would be gained by reducing this uncertainty before moving to conserve the boreal toad.
Fraser, G., K.R. Bestgen, D.L. Winkelman. 2014. Use of Coal Creek,White River drainage by flannelmouth and bluehead sucker. 2014 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 4-6, Laramie, WY.	March 2014	Recapture data showed site fidelity, as reproductively ready suckers returned to Coal Creek the year after tagging. Antennae data also show that suckers leave Coal Creek immediately after they have been trapped and handled, which confounds our ability to estimate demographic parameters that require closed population assumptions. Our data show that tributaries are important for native suckers in the upper White River. Protecting and enhancing these habitats should be a priority conservation acti
Fraser, G., K.R. Besten, D.L. Winkelman, and K. Thompson. Flannelmouth and bluehead sucker tributary use in Coal Creek, CO.	January 2014	My project will enhance our understanding of the role that temperature plays in the life history of these species, the use of tributaries, spawning site fidelity and how handling influences fish behavior thus providing data to inform better decisions about the conservation of these native fish.
Franklin, A.B., Lukacs, P.M., Anderson, D.R. 2003. A new design to estimate density of trappable organisms: the trapping line transect. 3rd International Wildlife Management Congress, Christchurch, New Zealand.	April 2003
Franklin, A. B., K. P. Burnham, G. C. White, R. J. Anthony, E. D. Forsman, C. Schwarz, J. D. Nichols and J. Hines. November 1999. Range-wide status and trends in northern spotted owl populations. 1999 Raptor Research Foundation Annual Meeting, La Paz, Mexico.	November 1999
Franklin, A. B., D. R. Anderson, and K. P. Burnham. October 2000. Estimation of long-term trends and variation in avian survival probabilities using random effects models. EURING 2000, Marshal, CA.	October 2000
Fitzpatrick, R. and D.L. Winkelman. 2006. Identifying sources of northern pike recruitment in the Yampa River using otolith elemental signatures. 136th annual meeting of the American Fisheries Society. Lake Placid, NY.	September 2006
Fitzpatrick, R. and D.L. Winkelman. 2006. Identifying sources of northern pike (Esox lucius) recruitment in the Yampa River, using otolith microchemistry. Annual meeting of the Colorado-Wyoming Chapter of the American Fisheries Society annual meeting. Cheyenne WY.	January 2006
Fitzpatrick, R. M and D. L. Winkelman. September 2006. Estimation of recruitment sources and movement of northern pike (Esox lucius) using otolith microchemistry. American Fisheries Society National Meeting. Lake Placid, NY.	September 2006
Fitzpatrick, R. M and D. L. Winkelman. 27 February 2007. Estimation of recruitment sources and movement of northern pike (Esox lucius) using otolith microchemistry. Colorado/Wyoming meeting of the American Fisheries Society. Fort Collins, CO.	February 2007
Fitzpatrick, R. M and D. L. Winkelman. 15 February 2006. Estimation of recruitment sources and movement of northern pike (Esox lucius) using otolith microchemistry. Colorado/Wyoming meeting of the American Fisheries Society. Cheyenne, WY.	February 2006
Fitzpatrick, R. M and D. L. Winkelman. 15 February 2005. Estimation of recruitment sources and movement of northern pike (Esox lucius) using otolith microchemistry. Colorado/Wyoming meeting of the American Fisheries Society. Fort Collins, CO.	February 2005
Fetherman, E. and G. Schisler. 13 February 2007 Inheritance of Myxobolus cerebralis resistance among second generation crosses between the Hofer and Colorado River Rainbow trout strains. 13th annual Whirling Disease Symposium. Denver, CO.	February 2007
Fetherman, E. R., K. Davies, G. J. Schisler, K. Kehmeier, and D. L. Winkelman. 2011. Demented fish racists: Analyzing rainbow trout introductions in brown trout dominated streams. Great Plains Fishery Workers Association Meeting. Sidney, Nebraska. February 2, 2011.	February 2011
Fetherman, E. R., G. J. Schisler, and D. L. Winkelman. 2008. Whirling disease and the Colorado River. Special Meeting of the Chimney Rock Ranch Fishing Club. Denver, Colorado.	July 2008
Fetherman, E. R., G. J. Schisler, and D. L. Winkelman. 2007. Inheritance of Myxobolus cerebralis resistance among second generation crosses between the Hofer and Colorado River Rainbow trout strains. Annual meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Fort Collins, CO.	February 2007
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2011. Whirling disease resistant rainbow trout in Colorado: Introductions, monitoring, and brown trout removal. Annual Meeting of the Colorado Aquaculture Association. Mt. Princeton Hot Springs, Colorado.	January 2011
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2011. Brown trout removal in the Cache la Poudre River, Colorado: Managing whirling disease resistant rainbow trout introductions in brown trout dominated streams. National American Fisheries Society Annual Meeting. Seattle, Washington.	September 2011
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2010. Whirling disease resistant rainbow trout 2009 project update. Whirling Disease Symposium. 2010 Annual Meeting of the Western Division of the American Fisheries Society. Salt Lake City, Utah.	April 2010
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2010. Whirling disease resistant rainbow trout 2009 project update. 2010 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Laramie, Wyoming.	March 2010
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2009. Physiological effects of whirling disease and heritability of myxospore count in susceptible and resistant strains of rainbow trout. Annual Meeting of the Colorado Aquaculture Association. Mt. Princeton Hot Springs, Colorado.	January 2009
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2009. Physiological effects of whirling disease and heritability of myxospore count in susceptible and resistant strains of rainbow trout. 15th Annual Whirling Disease Symposium: Conserving Coldwater Fisheries. Denver, Colorado.	February 2009
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2009. Heritability of myxospore count and genetic correlations in whirling disease resistant and susceptible strains of rainbow trout. 2009 Annual Meeting of the Western Division of the American Fisheries Society. Albuquerque, New Mexico.	May 2009
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2009. Heritability of myxospore count and genetic correlations in whirling disease resistant and susceptible strains of rainbow trout. 2009 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Loveland, Colorado.	February 2009
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2008. The physiological effects of whirling disease in resistant and susceptible crosses of rainbow trout. 2008 Annual Meeting of the Western Division of the American Fisheries Society. Portland, Oregon.	May 2008
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2008. The physiological effects of whirling disease in resistant and susceptible crosses of rainbow trout. 2008 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Cheyenne, Wyoming.	March 2008
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2008. The physiological effects of whirling disease in resistant and susceptible crosses of rainbow trout. 14th Annual Whirling Disease Symposium: Solving the Puzzle. Denver, Colorado.	February 2008
Fetherman, E. R., D. L. Winkelman, and G. J. Schisler. 2008. The Physiological Effects of Whirling Disease in Resistant and Susceptible Crosses of Rainbow Trout. Annual Meeting of the Colorado Aquaculture Association. Mt. Princeton Hot Springs, CO.	January 2008
Fetherman, E. R., D. L. Winkelman, G. J. Schisler, L. Bailey, and W. L. Kendall. 2011. Multistate modeling approach for analyzing survival and movement of Radio Frequency Identification (RFID) PIT tagged trout in rivers. National American Fisheries Society Annual Meeting. Seattle, Washington.	September 2011
Fetherman, E. R., D. L. Winkelman, G. J. Schisler, K. Davies, and K. Kehmeier. 2011. Brown trout removal in the Cache la Poudre River: The next step in whirling disease resistant rainbow trout management. 2011 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society and the Colorado Chapter of The Wildlife Society. Fort Collins, Colorado.	February 2011
Fetherman, E. R. 2008. The physiological effects of whirling disease in resistant and susceptible crosses of rainbow trout. Departmental Seminar for the Department of Fish, Wildlife and Conservation Biology, Colorado State University. Fort Collins, Colorado.	September 2008
Drewien, R. C., W. L. Kendall, W. Brown, and B. D. Gerber. Survival of the Rocky Mountain Sandhill Crane. 13th North American Crane Workshop. Lafayette, LA.	April 2014	Evidence about survival processes from this work will directly inform the population and especially harvest management of sandhill cranes.
DeCoste, J, R. Y. Conrey, W. L. Kendall, and J. Gammonley. 2017. Nest survival of bald eagles in Colorado. Annual Meeting of the Colorado Chapter of the The Wildlife Society, Fort Collins, CO.	February 2017	This work provides estimates of nest survival of bald eagles in Colorado as a function of various putative factors. It also demonstrates the potential for bald eagle monitoring within the state of Colorado
D'Amico, T.W., T. Swarr, D.L. Winkelman, and C.M. Myrick. PIT tag retention in a small-bodied native catfish. 2018 Annual Meeting of the Western Division of the American Fisheries Society. Laramie, WY.	May 2018	Our best model included the covariates age, cohort (a proxy measure for technician experience with tagging), fish length, and tag type as well as the interaction between fish length and tag type. We also analyzed the individual effect of each of these covariates on tag expulsion. Results will be used to inform survival and movement estimation as well as habitat selection in our field study.
D'Amico, T.W., T. Swarr, D.L. Winkelman, and C.M. Myrick. PIT tag retention in a small-bodied native catfish. 2018 Annual Meeting of the Western Division of the American Fisheries Society, Anchorage, AK	February 2018	Our best model included the covariates age, cohort (a proxy measure for technician experience with tagging), fish length, and tag type as well as the interaction between fish length and tag type. We also analyzed the individual effect of each of these covariates on tag expulsion. Results will be used to inform survival and movement estimation as well as habitat selection in our field study.
D'Amico, T.W., T. Swarr, D.L. Winkelman, and C.M. Myrick. PIT tag retention in a small-bodied native catfish. 2018 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Laramie, WY.	February 2018	Our best model included the covariates age, cohort (a proxy measure for technician experience with tagging), fish length, and tag type as well as the interaction between fish length and tag type. We also analyzed the individual effect of each of these covariates on tag expulsion. Results will be used to inform survival and movement estimation as well as habitat selection in our field study.
D'Amico, T.W., D.L. Winkelman, and F.B. Wright. Habitat selection and movement of stonecat in St. Vrain Creek, CO. 2018 Annual Meeting of the Western Division of the American Fisheries Society. Laramie, WY.	May 2018	Initial analyses indicate that Stonecats can move long distances (up to 1.5 km) but most individuals are relatively sedentary, moving less than 100 meters. Stonecats appear to prefer riffle habitat at a depth of 1.01 feet, flow of 0.29 meters per second and large substrate. Understanding Stonecat movement patterns and habitat preferences are crucial for upcoming stream restoration and management.
D'Amico, T.W., D.L. Winkelman, and F.B. Wright. Habitat selection and movement of stonecat in St. Vrain Creek, CO. 2018 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Laramie, WY.	February 2018	Initial analyses indicate that Stonecats can move long distances (up to 1.5 km) but most individuals are relatively sedentary, moving less than 100 meters. Stonecats appear to prefer riffle habitat at a depth of 1.01 feet, flow of 0.29 meters per second and large substrate. Understanding Stonecat movement patterns and habitat preferences are crucial for upcoming stream restoration and management.
D'Amico, T. and D.L. Winkelman. Stone Cat Ecology in St. Vrain Creek. 42nd Annual Meeting of the Western Division the American Fisheries Society. Missoula, FT.	May 2017	We have PIT tagged Stonecats (n = 338; size range of 79 – 225 mm TL) and are using a combination of static and mobile PIT tag antennae to characterize their habitat preferences and movement ecology over an 5.3 km long section of St. Vrain Creek. To date, the greatest distance a Stonecat has moved is 2.4 km, and Stonecat prefer riffles (p = 0.652) to pools (p = 0.169) or runs (p = 0.179).
D'Amico, T. and D.L. Winkelman. Stone Cat Ecology in St. Vrain Creek. 2017 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Grand Junction, CO.	February 2017	We have PIT tagged Stonecats (n = 338; size range of 79 – 225 mm TL) and are using a combination of static and mobile PIT tag antennae to characterize their habitat preferences and movement ecology over an 5.3 km long section of St. Vrain Creek. To date, the greatest distance a Stonecat has moved is 2.4 km, and Stonecat prefer riffles (p = 0.652) to pools (p = 0.169) or runs (p = 0.179).
D'Amico, T, D.L. Winkelman, T. Swarr, and C. Myrick. PIT tag retention in a small-bodied native catfish (Noturus flavus). 42nd Annual Meeting of the Western Division the American Fisheries Society. Missoula, MT	May 2017	We evaluated retention rates in a laboratory setting to assess overall tag loss. We surgically implanted PIT tags in May 2015 and have been continuously measuring expulsion rates. Tag retention was approximately 85% at ten months.
D'Amico, T, D.L. Winkelman, T. Swarr, and C. Myrick. PIT tag retention in a small-bodied native catfish (Noturus flavus). 2017 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Grand Junction, CO.	February 2017	We evaluated retention rates in a laboratory setting to assess overall tag loss. We surgically implanted PIT tags in May 2015 and have been continuously measuring expulsion rates. Tag retention was approximately 85% at ten months.
Conrey, R. Y., J. DeCoste, W. L. Kendall, and J. H. Gammonley. 2019. Developing methods for nesting success of bald eagles in Colorado. Raptor Research Foundation Annual Conference, Fort Collins, CO, Nov 5-10, 2019.	November 2019	This work demonstrates the potential for bald eagle nest monitoring in Colorado, using both professional and citizen science effort, and indicates an approach to modeling nest success that accounts for the unknown age of raptor nests.
Cole, A.R., J. Beihoffer, B.R. Blackwell, J.E. Cavallin, D.R. Eckman, A. Jastrow, J. Kinsey, K. Keteles, J. Parman, D.L. Winkelman, and D.L. Villeneuve. Evaluating effects of bioactive contaminants related to waste water treatment plant effluent on the South Platte River. Society of Ecological Toxicology and Chemistry North America 39th annual meeting. November 6, 2018	November 2018	Results provide new insights into the significance of GR-and PPAR? active contaminants in this system.
Clapp C.M., D.L. Winkelman, K. Thompson. 2008. Investigating competition among lineages of Tubifex tubifex and the potential for biological control of whirling disease. Fisheries, Wildlife, and Conservation Biology Departmental Seminar.	January 2008
Clapp C, D.L. Winkelman, and K. Thompson. 2006. Investigating competition among lineages of T. tubifex and the potential for biological control of whirling disease in natural streams. Annual meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Cheyenne WY.	January 2006
Cannell, B., W. L. Kendall, J. Tyne, M. Bunce, Y. Hetzel, D. O. Muiri, and B. Radford. 2023. Marine heatwaves in Western Australia affect breeding, diet and population size but not body condition of a range-edge Little Penguin colony. 11th International Penguin Conference, Vina del Mar, Chile, 4 - 9 September 2023.	September 2023	This work demonstrates that the increasing phenomenon of marine heatwaves in the Antarctic region affects population parameters of penguins even as far north as Australia, at the edge of their range.
Cannell, B., W. L. Kendall, J. Tyne, M. Bunce, Y. Hetzel, D. Muiri, and B. Radford. 2023. Marine heatwaves in Western Australia affect breeding, diet and population size but not body condition of a range-edge Little Penguin colony. 11^th International Penguin Congress, Viña del Mar, Chile, 4-9 September 2023.	September 2023	This work demonstrates the effect of marine heatwaves on breeding and population size of a population of Little Penguins at the northern edge of their range. This work anticipates what could happen to other populations of the species if warming continues.
Cannell, B., J. Sinclair, S. Vardeh, W. L. Kendall, J. Tyne, and B. Sherwin. 2019. Is climate change to blame for the halving of a high conservation value Little Penguin colony over a mere 10 years? 10th International Penguin Conference, Dunedin, New Zealand, 24-28 August 2019.	August 2019	This work demonstrates the effect, or lack of it, of short term climate changes on little penguin demography.
Cannell, B. L., J. Tyne, J. J. K. Sinclair, W. B. Sherwin, and W. L. Kendall. 2021. Can a range edge colony of Little Penguins in Western Australia recover from an unprecedented marine heatwave followed by several years of warmer than average SST? 3rd Word Seabird Conference (virtual).	October 2021	This work demonstrates a decline in abundance and survival of a population of Little Penguins of conservation value, which coincided with a marine heatwave. Recovery from this heatwave has not yet been established.
Burnham, K. P. and G. C. White. October 2000. Evaluation of some random effects methodology applicable to bird ringing data. EURING 2000, Marshal, CA.	October 2000
Burnham, K. P. March 2000. Model testing and selection in wildlife data analysis. Wisconsin Cooperative Wildlife Research Unit, Madison, WI.	March 2000
Burnham, K. P. December 1999. A random effects model for band recovery and capture-recapture data. Estimating Animal Abundance and Related Parameters, Third Conference on Statistics in Ecology and Environmental Monitoring, Dunedin, New Zealand. (Keynote speaker)	December 1999
Buderman, Hooten, Ivan, Shenk (2015). The Wildlife Society Annual Meeting, Winnipeg, Canada. Contributed talk. Spatial ecology and movement of reintroduced Canada lynx.	October 2015	This talk describes a movement modeling approach and results pertaining to telemetry data from Canada Lynx.
Buderman, F.E., M.B. Hooten, and M. Alldredge. The Wildlife Society Annual Meeting. (2016). Mountain lion movement dynamics in the wildland-urban interface. Contributed Talk.	October 2016	This talk presents space use and movement of Colorado mountain lions.
Buderman, F.E., M.B. Hooten, and M. Alldredge. The Wildlife Society - CMPS meeting. (2016). Drivers of mountain lion movement in the Colorado Front Range. Contributed Talk.	August 2016	This talk describes space use and resource selection of mountain lions in Colorado.
Buderman, F.E. and M.B. Hooten. (2018). Basis functions for continuous-time models of animal movement. The Wildlife Society Annual Meeting, Cleveland, OH. Invited Talk.	October 2018	This talks provides an overview of continuous-time statistical models for animal telemetry data.
Brost, Hooten, Hanks, Small. (2015). The Wildlife Society Annual Meeting, Winnipeg, Canada. Invited Talk: Animal movement constraints improve resource selection inference in the presence of telemetry error.	October 2015	This paper describes a modeling technique for telemetry data that properly accounts for physical barriers to animal movement while providing resource selection inference.
Brost, B.M., M.B. Hooten, and R.J. Small. (2016). International Statistical Ecology Conference. Seattle, WA. Invited Talk. Title: Locating harbor seal haul-out sites from Argos satellite telemetry data using a Dirichlet process.	June 2016	This talk presents a method for using telemetry data to discover haul out sites for harbor seals.
Broms, K.M., M.B. Hooten, and R.M. Fitzpatrick. (2016). International Statistical Ecology Conference, Seattle, WA. Optimal adaptive sampling design for occupancy monitoring.	June 2016	This presentation describes an approach for optimal monitoring of ecological processes using adaptive design concepts and occupancy models.
Broms, K.M., M.B. Hooten, and R.M. Fitzpatrick. (2016). Ecological Society of America, Annual Meeting. Contributed talk. Title: Model selection and assessment for multi-species occupancy models.	August 2016	This presentation discusses the pros and cons of various model checking and comparison approaches for multispecies occupancy models.
Broms, K.M., M.B. Hooten, and R.M. Fitzpatrick. (2016). AFS Colorado/Wyoming Chapter Annual Meeting, Laramie, WY. Spatial monitoring design for plains fishes in the South Platte River Basin.	March 2016	This talk describes an optimal adaptive monitoring design for plains fishes in Colorado.
Broms, K.M., M.B. Hooten, R. Fitzpatrick, and J.M. Ver Hoef. Joint Statistical Meetings: ASA. Baltimore, MD (contrib. talk, 2nd author), 2017, Title: Bayesian spatial stream network models.	August 2017	This talk describes how to model ecological processes on stream networks.
Breton, A.R., D.L. Winkelman, K.R. Bestgen, and J.A. Hawkins. Population dynamics modeling of introduced smallmouth bass in the upper Colorado River basin. 2014 Upper Colorado River Basin Endangered Fish Recovery Program's Annual Researchers Meeting, Grand Junction, Colorado, January 14-15.	January 2014	Modeling results suggest that early season nest disturbance was most effective at reducing smallmouth bass densities and current spring electrofishing is preventing increases in smallmouth bass abundance in the Yampa River.
Breton, A.R., D.L. Winkelman, J.A. Hawkins, and K.R. Bestgen. Population trends of smallmouth bass in the upper Colorado River basin wit an evaluation of removal effects. 2014 Upper Colorado River Basin Endangered Fish Recovery Program's Annual Researchers Meeting, Grand Junction, Colorado, January 14-15.	January 2014	Despite the potential for post-removal bass population recovery in some reaches from recruitment and immigration, recent electrofishing removal effort (ca. 2008-2011) has resulted in declining smallmouth bass population trends.
Breton, A.R., D.L. Winkelman, J.A. Hawkins, K.R. Bestgen. Population trends of smallmouth bass in the upper Colorado River basin with an evaluation of removal effects.	February 2015	Despite the potential for post-removal population recovery recent electrofishing removal efforts have resulted in declining smallmouth bass population trends. Therefore, we recommend that removal efforts continue, especially in river reaches that are perceived to be production areas for smallmouth bass. We also suggest that other management options to reduce smallmouth bass populations be considered. For instance, it is clear that flow and temperature influence the spawning success of smallm
Betts, MG, Frey, SJK,Gerber, BD. Bird interspecific colonization and extinction dynamics are mediated by microclimate. Annual meeting of the American Ornithological Society. Estes Park, Colorado. October 1-5, 2024.	October 2024	We capitalized on a 14-year, landscape-scale dataset in a relatively stable old-growth forest environment to test the hypothesis that colonization by one species could affect either the local extinction or colonization by a phylogenetically related species. Counter to our hypothesis, we found that related species pairs more often showed colonization dynamics that were indicative of attraction rather than repulsion.
Bergersen, E. P. and K. B. Rogers. August 2000. Rocky Mountain Arsenal bass habitat use. American Fisheries Society Black Bass 2000 Symposium, St. Louis, MO.	August 2000
Belotti, MCTD, Gerber, B, Deng, Y, Zhao, W, Simmons, VF, Cheng, Z, Perez, G, Tielens, E, Maji, S, Sheldon, D, Kelly, JF, and Horton, KG. Comparison of swallow and martin trends from three large-scale data sources. Annual meeting of the American Ornithological Society. October 1 - 5, 2024.	October 2024	We describe a new approach to estimating avian trends using radar data and make regional comparisons across alternative data sets (BBS and eBird).
Bellier, E., McGreevy Jr., T.J., Petrullo, A. and Gerber. B.D. Evaluating the spatial count model to monitor the population dynamics of unmarked small mammals. Annual meeting of the Ecological society of America. August 4 - 9, 2024.	August 2024	We evaluate the utility of the spatial count model using simulation to estimate the abundance and density of unmarked animal populations. We apply this model to estimate the population size of the New England Cottontail on Patience Island, RI USA.
Avila, B.W., E.R. Fetherman, D.L. Winkelman. Raft and floating antenna systems for detecting PIT-tagged fish in rivers. 2014 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 4-6, Laramie, WY.	March 2014	Our portable antenna systems provide a noninvasive method that minimizes disturbance to individual fish for estimating PIT-tagged fish abundance and survival in both small (hundreds of m) and large (km) river reaches.
Avila, B.W., D.L. Winkelman, and E.R. Fetherman. Whirling disease resistant Rainbow Trout fry survival: a comparison of two strains. 2018 Annual Meeting of the Western Division of the American Fisheries Society. Anchorage, AK.	May 2018	The field experiment revealed that 2 month apparent survival and growth rate was influenced by strain and average temperature. However, after 12 months there was no significant difference in apparent survival or growth rate between the GR and GRxCRR.
Avila, B.W., D.L. Winkelman, and E.R. Fetherman. Quality vs. quantity: manipulating rearing density as a strategy for increasing survival of Rainbow Trout fry pre- and post-stocking. 2018 Annual Meeting of the Western Division of the American Fisheries Society. Anchorage, AK.	May 2018	Rearing fish at lower densities could be a low-cost management alternative for mitigating stress and water quality, and potentially reducing losses occurring from BCWD.
Avila, B.W., D.L. Winkelman, and E.R. Fetherman. Quality vs. quantity: manipulating rearing density as a strategy for increasing survival of Rainbow Trout fry pre- and post-stocking. 2018 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Laramie, WY.	March 2018	Rearing fish at lower densities could be a low-cost management alternative for mitigating stress and water quality, and potentially reducing losses occurring from BCWD.
Avila, B.W., D.L. Winkelman, E.R. Fetherman. Evaluation of resistant rainbow trout fry stocking in Colorado. 41st Annual meeting of the Western Division of the American Fisheries Society. April 22, 2016. Reno, NV.	April 2016	We did not detect differences in survival between strains of resistant rainbow trout stocked in Colorado streams. This indicates that pure resistant strains may be a management option.
Avila, B.W., D.L. Winkelman, E.R. Fetherman. Evaluation of resistant rainbow trout fry stocking in Colorado. 2016 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 1-4, Laramie, WY.	March 2016	Survival did not differ between resistant strains of rainbow trout, indicating that pure resistant strains may be used for stocking.
Avila, B.W., D.L. Winkelman, E.R. Fetherman. Evaluation of resistant Rainbow Trout fry stocking in Colorado	February 2015	Short-term results indicate that the GR strain may be a viable alternative for stocking in whirling disease endemic streams. However, longer-term monitoring is necessary before stocking recommendations can be made.
Avila, B. W., W. L. Kendall, C. B. Yackulic, and J. Korman. 2024. Sharing abundance: integrating count data with capture-recapture data in a marginalized, multistate Jolly-Seber framework. 154th Annual Meeting of the American Fisheries Society, Honolulu, Hawaii, 15-19 September 2024.	September 2024	This work provides a method for integrating extensive spatial capture-recapture data with even more extensive catch data to estimate site-specific abundance and recruitment even for years where there are no tagging data. We show how integrating long-term count data with capture-recapture data can improve inference to recruitment, which may be an important demographic parameter over time in some species.
Anderson, J.R., D.L. Winkelman, and A. Jastrow. Evaluating the distribution of estrogenic effects below wastewater treatment plants: estrogen persistence and fish movement. 42nd Annual Meeting of the Western Division of the American Fisheries Society. Missoula, MT.	May 2017	Analyses of downstream persistence of Vtg are ongoing, but we hypothesize that Vtg expression will decrease downstream due to degradation by organic or environmental processes.Laboratory and wild populations expressed similar increased levels of Vtg compared to controls. Similar expression of Vtg indicates that differences seen between fish in the field are likely due to avoidance of contaminants by wild fish.
Anderson, J.R., D.L. Winkelman, and A. Jastrow. Evaluating the distribution of estrogenic effects below wastewater treatment plants: estrogen persistence and fish movement. 2017 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Grand Junction, CO.	February 2017	Analyses of downstream persistence of Vtg are ongoing, but we hypothesize that Vtg expression will decrease downstream due to degradation by organic or environmental processes.Laboratory and wild populations expressed similar increased levels of Vtg compared to controls. Similar expression of Vtg indicates that differences seen between fish in the field are likely due to avoidance of contaminants by wild fish.
Anderson, J.R., D.L. Winkelman, A.M. Vajda, and A. Jastrow. Evaluating wastewater effluent exposure in wild fishes using insights from laboratory and wild populations. 2018 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society. Laramie, WY.	February 2018	Our results indicate that the response of VTG production in laboratory raised FHM is more sensitive to estrogen exposure than VTG production in wild FHM, demonstrating that wild FHM seem to be acclimated or adapted to living in WWTP effluent compared to the naïve laboratory population. These results have consequences for the potential inferences being made between laboratory and wild populations and indicates that more research needs to be done to understand the differences between wild and lab
Anderson, J and D.L. Winkelman. Evidence of estrogenic endocrine disruption at several municipal wastewater treatment plants within the South Platte watershed, Colorado. Annual Meeting of the Rocky Mountain Chapter of the Society for Ecological Toxicology and Chemistry April 8, 2016, Fort Collins, CO.	April 2016	An initial analysis of landscape level exposure indicated a high degree of variability in endocrine exposure across eastern Colorado.
Anderson, J and D.L. Winkelman. Evidence of estrogenic endocrine disruption at several municipal wastewater treatment plants within the South Platte watershed, Colorado. 2016 Annual Meeting of the Colorado-Wyoming Chapter of the American Fisheries Society, March 1-4, Laramie, WY.	March 2016	Endocrine exposure varies across the front range of Colorado.
Albright, S., W. L. Kendall, and R. Conrey. 2024. Occupancy, abundance, and productivity of burrowing owls nesting in eastern Colorado. 2024 Annual Meeting of the Colorado Chapter of The Wildlife Society, Pueblo, Colorado, 31 January – 2 February, 2024.	February 2024	The burrowing owl is a species of concern for Colorado. This work assesses the current status of these owls in the state, and the how the attributes of prairie dog colonies influences their distribution and reproductive success.
Albright, S., W. L. Kendall, and R. Conrey. 2022. Occupancy, abundance, and productivity of burrowing owls nesting in eastern Colorado. 29th Annual Conference of The Wildlife Society. Spokane, WA, 6-10 November 2022.	November 2022	This work updates information on the status of burrowing owls in Colorado, a species that has been in decline. Relating their presence and productivity to factors associated with prairie dog colony attributes will inform managers about future monitoring and habitat management.
D.L. Winkelman, and E.R. Fetherman. Introduction to the symposium on Fishing for solutions to economically and ecologically important salmonid diseases. 2018 Annual Meeting of the Western Division of the American Fisheries Society. Anchorage, AK.	May 2018	Infectious pathogens are a serious threat to fisheries and aquaculture production worldwide. The threats that pathogens pose to fisheries has stimulated research into control and management. Three main factors affect disease transmission and ultimately options for control. These factors consist of the environment, host, and pathogen and manipulating one of more these factors is necessary to reduce the prevalence and severity of a pathogen.

Theses and Dissertations

Theses and Dissertations	Publication Date
Tipton, J.R. (2016). Improved estimation and prediction for computationally expensive ecological and paleoclimate models. PhD Dissertation. Colorado State University. Fort Collins, CO.	August 2016
Schwindt, A.R. 2013. The population ecology of fathead minnows (Pimephales promelas) in estrogen contaminated environments. PhD Dissertation. Colorado State University. Fort Collins, CO.	November 2013
Ross, B.E. (2014). Assessing changes in waterfowl population and community dynamics. PhD Dissertation. Utah State University. Logan, UT.	May 2014
McGree, M. 2008. Exposure to 17beta-estradiol alters reproduction of the adult red shiner (cyprinella lutrensis). Department of Fish, Wildlife, and Conservation Biology, Master of Science, Colorado State University, Fort Collins, Colorado	May 2008
Herdrich, A.T. 2016. Effects of habitat complexity on eastern slope rocky mountain brook trout populations.	June 2016
Hanks, E.M. (2013). Statistical models for animal movement and landscape connectivity. PhD Dissertation. Colorado State University. Fort Collins, CO.	May 2013
Gerber, B., 2015. Sandhill Crane Population Monitoring, Modeling, and Harvest Decision Making. PhD Dissertation. Colorado State University, Fort Collins, USA.	August 2015
Garlick, M.J. (2012). Homogenization of large-scale movement models in ecology with application to the spread of chronic wasting disease in mule deer. PhD Dissertation. Utah State University. Logan, UT.	May 2012
Fraser, G.S. 2015. Movement patterns, reproduction, and potential impacts of climate change on three native fishes in the upper White River drainage, CO.	March 2015
Fitzpatrick, Ryan M. 2008. Use of otolith elemental signatures in estimating sources of northern pike recruitment in the Yampa River, Colorado. Master's Thesis. Colorado State University, Fort Collins, CO.	December 2008
Fetherman, Eric R. 2008. Heritability of myxospore count and the effects of Myxobolus cerebralis exposure on the physiological performance of whirling disease resistant and susceptible strains of rainbow trout. Master's Thesis. Colorado State University, Fort Collins, CO	December 2008
Fetherman, E.R. 2013. Introduction and management of Myxobolus cerebralis-resistant rainbow trout in Colorado. PhD Dissertation. Colorado State University, Fort Collins, CO	December 2013
D'Amico, T.W. Stonecat ecology in St. Vrain Creek, CO. Master's Thesis (88 pp), Colorado State University, Fort Collins, CO	August 2018
Clapp, Christine. 2009. Investigating competition among Myxobolus cerebralis resistant and susceptible mitochondrial lineages of Tubifex tubifex and the potential for biological control of whirling disease. Master's Thesis. Colorado State University, Fort Collins, CO.	May 2009
Buderman, F.E. (2017). Statistical methods for modeling the movement and space use of carnivores. PhD Dissertation. Colorado State University. Fort Collins, CO.	August 2017
Brost, B.M. (2016). Statistical models for animal telemetry data with applications to harbor seals in the Gulf of Alaska. PhD Dissertation. Colorado State University, Fort Collins, CO.	December 2017
Baum, C.M. Temperature and winter duration requirements for reproductive success in Johnny Darter Etheostoma nigrum in the South Platte River basin, CO. Master's Thesis (47 pp), Colorado State University, Fort Collins, CO	July 2021
Avila, Brian. 2016. Survival of rainbow trout in the wild: a comparison of two whirling disease resistant strains. Master's Thesis, Colorado State University, Fort Collins, Colorado.	October 2016
Avila, B.W. Bacterial Coldwater Disease Investigations. PhD Dissertation (1 33 pp), Colorado State University, Fort Collins, CO	July 2021

Technical Publications

Technical Publications	Publication Date
Winkelman, D.L., Kevin Thompson, and James Terrell. 2005. The role of sediment size distribution and other microhabitat factors in the abundance and relative dominance of various T. tubifex lineages. Final Report to the Montana Water Center, Whirling Disease Initiative.	December 2005
Sipher, C., and E. Bergersen. 2001. The effects of whirling disease on growth and survival of Snake River cutthroat and Colorado River rainbow trout fingerlings. Proceedings of the 7th Annual Whirling Disease Symposium, a Decade of Discovery:	February 2001
Miller, R.S., M. Farnsworth, W. Kendall, P. Doherty, J.D. Nichols, G.C. White, K.P. Burnham, A.B. Franklin, J. Freier. 2007. Risk-based Targeted Surveillance: Identifying Areas and Populations of Importance for Surviellance of High Path Avian Influenza in the United States. GisVet2007 Conference, held August 20-24,2007, in Copenhagen, Denmark. This is an accepted "Regular" paper; access at: http://www.gisvet.org/regular_papers_accepted.aspx	August 2007
Kowalski, D. and E. Bergersen. 2001. Preliminary investigations on the efficacy of chemical control of Tubifex tubifex on the incidence of whirling disease in Colorado hatcheries. Proceedings of the 7th Annual Whirling Disease Symposium, a Decade of Discovery: 71-72.	February 2001
Franklin, A. B., D. R. Anderson, and K. P. Burnham. 1998. Study of long-term trends in the annual probability of survival in North American birds. U. S. Geological Survey, Biological Resources Division Research Work Order 53, Denver, Colorado. 24pp.	September 1998
Farnsworth, M., W. Kendall, R. Miller, P. Doherty, J.D. Nichols, G.C. White, K.P. Burnham and A.B. Franklin. 2007. A preliminary sampling protocol for early detection of highly pathogenic avain influenza in environmental samples from migratory waterfowl in the United States for 2007. USDA-APHIS-WS National Wildlife Research Center, Colorado State University and USGS. (A report from the Sampling Design Committee for Detecting Avian Influenza in Environmental Samples, USDA, USGS and CSU).	April 2007
Brehme, C.S., K.P. Burnham, D.A. Kelt, A.R. Olsen, S.J. Montgomery, S.A. Hathaway, and R.N. Fisher. 2006. Stephen's Kangaroo Rat (Dipodomys stephensi) Monitoring Protocol for MCB Camp Pendleton (final report). Prepared for AC/S Environmental Security, Marine Corps Base, Camp Pendleton. DOI-USGS Western Ecological Research Center, San Diego, CA.	December 2006
Bergersen, E. P. 2001. Colorado's experience with Northern Pike. Lake Line 21(3):33-36.	October 2001
Anthony, R. G., E. D. Forsman, A. B. Franklin, D. R. Anderson, K. P. Burnham, G. C. White, C. J. Schwarz, J. Nichols, J. Hines, G. S. Olson, S. H. Ackers, S. Andrews, B. L. Biswell, P. C. Carlson, L. V. Diller, K. M. Dugger, K. E. Fehring, T. L. Fleming, R. P. Gerhardt, S. A. Gremel, R. J. Guti�rrez, P. Happe, D. R. Herter, J. M. Higley, R. B. Horn, L. L. Irwin, P. J. Loschl, J. A. Redi, and S. G. Sovern. 2004. Status and trends in demography of northern spotted owls. Report to Interagency Regional Monitori	September 2004

Data or Software Releases

Type	Citation	Publication Date
Software Release	Iannarilli, F, Gerber, B. D., Erb, J, and Fieberg, J. R. A ‘How-to’ Guide for Estimating Animal Diel Activity Using Hierarchical Models. 2024. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P13UTDBG	May 2024

Cooperative Fish and Wildlife Research Units Program: Colorado Education, Research and Technical Assistance for Managing Our Natural Resources

Colorado Research Activities

Cooperative Fish and Wildlife Research Units Program: Colorado
Education, Research and Technical Assistance for Managing Our Natural Resources