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

Pennsylvania Research Activities

Collaring White-tailed deer fawn as part of a study of fawn survival, Pennsylvania.

Unit personnel conduct interdisciplinary applied and basic research in fish and wildlife management and contribute to graduate education. The Unit's research emphasis is on (1) integrating ecology and management of terrestrial and aquatic habitats, (2) evaluating the effects of human activities on wildlife, fish, and their habitats, and (3) providing guidelines for restoring and maintaining important terrestrial and aquatic communities.

Projects

Project	Completion Date
Landscape genetics of white-tailed deer to assess population structure for surveillance of chronic wasting disease	June 2017	Research on surveillance strategies, that consider demographic and environmental factors, is lacking in most states CWD has not been found. Developing surveillance strategies to maximize efficiency of sampling white-tailed deer has been recommended but requires knowledge of deer behavior, movements, and spatial connectivity of populations. Landscape genetics can provide the necessary framework to understand landscape features, dispersal characteristics of deer, and transmission and spread of CWD through assessment of population structure throughout a region.	Research on surveillance strategies, that consider demographic and environmental factors, is lacking in most states CWD has not been found. Developing surveillance strategies to maximize efficiency of sampling white-tailed deer has been recommended but requires knowledge of deer behavior, movements, and spatial connectivity of populations. Landscape genetics can provide the necessary framework to understand landscape features, dispersal characteristics of deer, and transmission and spread of CWD through assessment of population structure throughout a region.
Characterization of habitat for pheasant in wild pheasant recovery areas of Pennsylvania	November 2014	Currently 4 Wild Pheasant Recovery Areas (WPRAs), with 10 study areas for pheasant research and monitoring, have been established<br>in Pennsylvania to investigate if the trap and transfer of wild pheasants from mid-west and western states can establish sustainable,<br>huntable populations of wild pheasants in Pennsylvania. The PGC has collected detailed habitat patch data that can be compared to<br>pheasant population densities to build a Predictive Pheasant Habitat Model (PPHM). However, the habitat patch data is not in a GIS<br>data base. The conversion of the habitat patch maps to a GIS, digital data base will allow robust and spatial analysis of the habitat data.<br>A more effective and predictive Pheasant Habitat Model can then be developed and applied across Pennsylvania. This will allow the<br>identification of potentially suitable pheasant habitat and identify the amount and location of habitat restoration needed to produce<br>sustainable and huntable pheasant populations. Project Deliverables: 1. A raster or polygon layer of habitats for each of the 160 buffered<br>circles with associated metadata to include latitude-longitude of sampling point, habitat category for each habitat patch to Anderson<br>Level IV codes or equivalent, and hectares for each habitat patch. 2. A KML file and ARC GIS Shape file for all habitat patches and<br>habitat circles. 3. Summary of habitat categories for all buffered circles included in the PGC Pheasant Model (developed land, cropland,<br>forest land, and hayland and pasture) for the 3 WPRAs provided by field operations.	Currently 4 Wild Pheasant Recovery Areas (WPRAs), with 10 study areas for pheasant research and monitoring, have been established in Pennsylvania to investigate if the trap and transfer of wild pheasants from mid-west and western states can establish sustainable, huntable populations of wild pheasants in Pennsylvania. The PGC has collected detailed habitat patch data that can be compared to pheasant population densities to build a Predictive Pheasant Habitat Model (PPHM). However, the habitat patch data is not in a GIS data base. The conversion of the habitat patch maps to a GIS, digital data base will allow robust and spatial analysis of the habitat data. A more effective and predictive Pheasant Habitat Model can then be developed and applied across Pennsylvania. This will allow the identification of potentially suitable pheasant habitat and identify the amount and location of habitat restoration needed to produce sustainable and huntable pheasant populations. Project Deliverables: 1. A raster or polygon layer of habitats for each of the 160 buffered circles with associated metadata to include latitude-longitude of sampling point, habitat category for each habitat patch to Anderson<br>Level IV codes or equivalent, and hectares for each habitat patch. 2. A KML file and ARC GIS Shape file for all habitat patches and<br>habitat circles. 3. Summary of habitat categories for all buffered circles included in the PGC Pheasant Model (developed land, cropland, forest land, and hayland and pasture) for the 3 WPRAs provided by field operations.
A decision support mapper for conserving stream fish habitats of the Northeast Climate Science Center region	June 2016	This project will develop a mapper for stream reaches in the NE U.S. to aid in climate change adaptation plans	The NE CSC region includes some of the most densely populated areas of the United States. Human impacts in the region, including urbanization, agriculture, and dams, have multiple effects on the region’s streams which also support economically valuable stream fishes in a range of unique fluvial habitats. Changes in climate are anticipated to lead to additional changes in stream habitats and the fish assemblages they support via multiple pathways (Allan 2004), including changing stream thermal regimes. Water temperature is one of the most important influences on aquatic ecosystems, and changes in temperatures can be an important indicator of disturbances to stream habitats (Poole and Berman 2001, Isaak et al. 2010). Accounting for current condition of and future changes in streams and understanding specific mechanisms by which streams are or may become impaired are essential for managing and conserving stream fishes and their habitats. To effectively manage streams of the NE CSC from current impacts and future threats, managers require region-wide information to aid in decision-making and implementation of proactive management strategies. Ideally, this information should identify current condition of stream habitats based on specific disturbances that limit stream fishes, future conditions that could result from changes in climate, and where possible, specific mechanisms (including changes in water temperature) by which streams may change with climate. With such information presented in an integrated, spatially-continuous, and scalable format for the entire NE CSC region, managers can more effectively conserve, protect, and restore stream fish and their habitats. Our project will meet that need by integrating results of a current condition assessment of stream habitats that accounts for fish response to human land use, water quality impairment, and fragmentation by dams with estimates of future stream habitats that may change with climate. Tailored current and future condition assessments for target species will be available for all stream reaches in the U.S. portion of the NE CSC via a web-based viewer, the Climate Change Visualization and Integration of Ecological and Watershed Resources (CCVIEWeR, described below). Objectives of our project include:
Snowshoe Hare Habitat Relationships in Response to Northern Forest Management	December 2015	The snowshoe hare is a game animal (34 Pa. CSA, § 102) and a species of “maintenance concern” in Pennsylvania’s Wildlife Action Plan due to its sensitivity to habitat changes and its importance for gene flow between states to the north and south in the Appalachians (Steele et al., 2010). The current limited distribution of snowshoe hares in western northcentral PA and the Poconos is thought to reflect the limited availability of critical habitat components in snowshoe hare range. In the Poconos, snowshoe hares inhabit high elevation wetlands and remaining pockets of scrub oak barrens. Hare abundance and distribution is thought to be directly related to the availability and spatial distribution of these high quality habitats. In northwestern Pennsylvania, hares are still relatively abundant in shrubby wetlands and nearby conifers. In both regions, these unique habitats are believed to serve as “reservoirs”, where hares can persist when adjacent habitats age and become unsuitable. Managers generally assume that forest disturbance such as fire, timber harvest, wind throw, or insect damage in these adjacent areas promotes dense shrub and young tree growth which benefit snowshoes hares and allows them to expand geographically. However, habitat studies in the southern fringe of the snowshoe hare’s range have been limited and the spatial relationships of critical habitats have yet to be described quantitatively. This research is proposed to aid in developing a comprehensive spatial understanding of snowshoe hare habitat relationships to better understand factors affecting snowshoe hare abundance and distribution in Pennsylvania. Additionally, we need to develop management guidelines to improve northern forest habitats, protect critical habitat features, and to conserve sustainable snowshoe hare populations. Project Objectives 1. To characterize the habitats used by snowshoe hare in northern hardwoods forests in Northwestern Pennsylvania and the scrub oak barrens in the Poconos region. 2. To estimate space use by hares and investigate how the spatial distribution of habitats influences home range size and movements. 3. Use the information gained from Objectives 1 and 2 to predict the effects of forest management on habitat use and distribution of snowshoe hares.	None
Structured Decision Making for Key Deer Management and Recovery	June 2014	The Key deer (O. v. clavium) is a well-known trust resource species for the U.S. Fish and Wildlife Service and the primary impetus for the formation of the National Key Deer Refuge (NKDR). With the establishment of the National Key Deer National Wildlife Refuge in 1957 along with years of targeted conservation efforts, the population has increased and their range has expanded. However, 75% of individuals of the species currently reside on Big Pine Key and No Name Key (the core of the range in terms of abundance and habitat availability), where more than 500 individual exist. There are still many obstacles to the recovery of Key deer, several of note include threats from disease, storm events, habituation, growth and development pressures, and global climate change (sea level rise). The species appears to be close to, and possibly above, biological carrying capacity in the core of the range (Big Pine Key and No Name Key). A negative aspect of the concentration of individuals on two islands is that “all eggs are in one basket,” where there is potentially limited resilience from any one threat described heretofore. An additional complication is the species listing status as federally endangered, which places limitations on certain elements of resource management. Concerns associated with this core population are also related to impacts on the ecosystem and the vegetation community due to their locally high abundance. In the core, rare and highly palatable plant species (including federally listed plants) are browsed by deer (which control the vegetation) with some evidence that East Indian hardwood species are now failing in recruitment. Balancing the habitat management to benefit the breadth of listed species (including listed plants, butterflies etc.) in the refuge is a consideration that needs to be evaluated in the long run within this core area. Deer ecology and management is further complicated by habituation issues and the full gamut of urban interface issues, not the least of which is human-provided foods to deer that affect their behavior and physiology. Several elements of this urban interface have been addressed through regulatory processes in Monroe County (e.g., Big Pine Key-No Name Key HCP; USFWS’s Biological Opinion for the Federal Emergency Management Agency’s administration of the National Flood Insurance Program; State and County Rate of Growth statutes and ordinances), but in many cases these processes have not been as successful as anticipated. Again, the concept that Key deer are listed as Endangered, as well as identified as at or above biological carrying capacity in a portion of their range, complicates management of the species relative to identified stressors and conflicts in the community. Structured Decision Making: Given the complexity of the issues briefly presented above, it seems appropriate to use a structured decision making (SDM) process to focus efforts of the U.S. Fish and Wildlife Service for their management responsibility for Key deer. Structured decision making is a way to prioritize goals and objectives given a well-defined problem. The benefit of the SDM process is that it provides a transparent basis for decision making and maximizes the chances that all alternative actions are identified and evaluated objectively. The SDM process requires that the primary decision maker be identified, which in this case is the Refuge Manager of Key Deer NWR on federal lands. However, there are numerous stakeholders including Monroe County, FDOT, FEMA, Florida agencies, and the public who must be part of any SDM process. Also, any decisions associated with the Endangered Species Act must involve other divisions within FWS, such as Ecological Services. Having subject matter experts in deer ecology and management participate in the SDM process would likely be useful. We propose the following activities in connection with this project: Plan and facilitate a series of SDM workshops to address a preliminary problem statement of “How to establish a healthy and wild Key deer population in the lower Keys.” We propose to develop and refine the problem statement with the refuge manager, who is the key decision maker, prior to the first workshop. For example, if “healthy” is going to be used in the problem statement it needs to be defined. Prior to the first workshop, Diefenbach and Wagner will visit the Florida Keys to meet with refuge staffs and other stakeholders and also learn more about the local community, ecology, and management issues facing the Key deer. Also, at this time we will work with stakeholders to schedule dates for the three workshops. We propose three SDM workshops attended by people identified as stakeholders, such as USFWS employees, representatives of federal, state, county, and local agencies, and experts in deer ecology and management. The stakeholder group will be identified with the assistance of refuge staff.	None
Linking fish health, contaminants, and population dynamics of smallmouth bass populations in the Susquehanna River, Pennsylvania	April 2017	Since 2005, diseased smallmouth bass have been detected throughout the Susquehanna River and its tributaries raising concern regarding the overall health of smallmouth bass and the Susquehanna River basin. In a collaborative effort with Pennsylvania Fish and Boat Commission, PA Department of Environmental Protection, U.S. Geological Survey, and Penn State University, this project aims to investigate a wide-range of variables (i.e., fish health analysis, contaminants, population modeling, radiotelemetry, etc.) to gain a better understanding of factors that could relate to disease in smallmouth bass. Preliminary and initial sampling began during Spring/Summer 2013. For fish health analysis, adult fish were collected during pre-spawn conditions at 6 sites within the Susquehanna River basin to investigate variables that could potentially influence offspring health (i.e., gonad condition, contaminant load, etc.). Following adult collection, benthic invertebrates (particularly aquatic worms) were collected for detection of parasites that could infect young of the year smallmouth bass. Sampling was concluded with collections of young of the year smallmouth bass for fish health analysis. Research will now focus on processing samples collected and identifying focal points for future research needs with fish health emphasis on the young of the year smallmouth bass.	None
Fall harvest rates of female wild turkeys in New York	March 2017	The primary form of population management for wild turkeys is by conducting a fall either-sex harvest. However, harvesting more than 10% of the fall population is believed to lead to a decrease in future turkey population abundance (Healy and Powell 1999). Currently, fall harvest rates in New York are unknown and harvest and survival rates likely vary according to management unit or physiographic region. To effectively manage wild turkey populations, without over harvesting the resource, it can be useful to know the rate at which hen turkeys are harvested in the fall. One difficulty with estimating fall harvest rates of wild turkeys is that substantial mortality occurs between the time of capture and the first hunting season. This is a problem for standard tag-recovery estimators of harvest rate because these models assume no mortality between date of capture and the first hunting season. Consequently, I will use an estimator developed by Buderman (2012) that uses survival of a sample of hens fitted with radio-transmitters to estimate the survival rate between tagging and harvest.	None
Deer abundance and its relationship to factors that affect forest vegetation conditions	June 2026	In the last decade, deer densities were reduced in many Wildlife Management Units (WMU) in Pennsylvania. These decisions to reduce deer densities were based on the assumption that forest conditions, especially regeneration, would improve with lower deer populations. Primarily anecdotal observations suggest forest regeneration has improved but the large-scale, quantitative Forest Inventory Analysis (FIA) monitoring program has failed to provide strong evidence for changes in tree regeneration. Consequently, the Pennsylvania Game Commission (PGC) has developed a decision model for deer harvest allocations based on deer browsing impact as measured by the FIA in addition to estimates of tree seedling density.<br><br>The ability to explain the lack of change in tree regeneration despite deer population reductions is critical to the credibility of the Pennsylvania Game Commission’s deer management program. In recent years, deer population reductions have caused the deer program to be sued by a sportsmen's group and audited by the legislature. Additionally, the application of the Deer Management Assistance Program (DMAP) on state forest lands has been questioned because DMAP has been used by the Pennsylvania Bureau of Forestry (BOF) to attempt to reduce the effect of deer browsing on forest vegetation.<br><br>The PGC needs a better understanding of how the deer browsing impact measure is related to deer densities and whether this measure is valuable for making deer harvest decisions. Similarly, the BOF needs to better understand how the application of the DMAP affects deer harvest and hunter behavior. Both agencies require a better understanding of how vegetation responds to changes in deer density in the context of existing monitoring programs and management activities.<br><br>This research proposes to stabilize deer populations at different densities on four study areas and quantify changes in vegetation with respect to other forest conditions (seed production, advanced tree regeneration, etc.) and management actions (e.g., herbicide to remove competing vegetation).	The forests of Pennsylvania have problems with tree regeneration and a lack of diversity in understory plant species. White-tailed deer herbivory has been identified as one problem source. However, other factors such as insect outbreaks, acid deposition, competitive effects among plant species, and lack of fire have been identified as other potential causes. <br><br>Deer populations were reduced by about 23% during 2002-2005 yet problems with forest plant diversity remains. An important question is whether deer populations require further reduction or other factors may be playing an important role in affecting forested ecosystems.<br><br>This study is a collaboration of the Pennsylvania Game Commission, Pennsylvania Bureau of Forestry, and the USGS Pennsylvania Cooperative Fish and Wildlife Research Unit at The Pennsylvania State University.<br><br>In this study we are monitoring changes in deer density and the response in forest understory vegetation. In addition, we are conducting experiments to study the relative importance of liming and using herbicide to reduce interspecific plant competition. The results of this research will inform the Pennsylvania Game Commission on how their habitat metrics used to make deer harvest recommendations respond to changes in deer density. In addition, this study will help the Bureau of Forestry refine their monitoring program on state forest lands used to make deer management decisions.
Allegheny Woodrat: Identifying Strategies to Conserve a Declining Species	September 2014	The Allegheny woodrat is an obligate inhabitant of forested, exposed rock habitats in the Appalachians and Interior Low Plateaus and has exhibited a long-term population decline and range contraction. Given that many other species of special concern also are linked to this habitat type, the woodrat is an excellent indicator of habitat conditions. Hypotheses regarding the decline of this species focus on food resources (forest conditions), disease, and habitat isolation. We propose to use datasets from throughout the range of the species to test predictions from these hypotheses and to identify risk factors. This analysis using existing datasets will help quantify a structured decision analysis that can be used to guide habitat management or population restoration actions. The results of the decision model will provide the foundation for a multi-state adaptive management program to maximize the effectiveness of ongoing management activities.	None
Using North American Breeding Bird Survey Data to Evaluate Portential Consequences of Energy Development and Other Land Use Changes on Bird Populations in the Northeast Appalachian Region	September 2014	Existing data from the BBS, linked to USGS land-use data and other spatially-explicit databases, will be used to develop spatially-explicit models of bird species abundance and distribution. Hierarchical modeling procedures used for the analysis of BBS data (Sauer and Link 2011) will be used, modified to incorporate spatial associations defined from grid cells or other spatial structuring (e.g., Thogmartin et al. 2004). These models can be used to evaluate covariates that influence species abundance at the route or grid-cell scale. These models for bird species will be used to predict the consequences of changes in land use due to urban development, climate change, and drilling in Marcellus shale on bird species abundance and distribution for specified time frames. Models will be developed for species with a variety of life histories and habitat requirements, and hypotheses will be developed regarding (1) covariates likely to influence abundance for the species and (2) the effects of habitat changes associated with alternative scenarios of energy development for the species. The modeling and prediction will permit evaluation of these hypotheses. We will also consider the possible use of stop-specific data from the BBS in the spatial models, as these data may provide a more local-scale evaluation of habitat influences on bird abundance. In addition to BBS data, Pennsylvania recently completed a statewide breeding bird atlas that has finer-scale bird data based on methods that attempted to account for imperfect detection of birds. This dataset could be used to compare results based on BBS data and serve as a tool to evaluate the robustness of model predictions.	None
Spatial analysis of large mammals to assess harvest vulnerability in relation to anthropogenic factors	December 2014	Successful management of large mammals is dependent upon availability of population to harvest in defined management units or season structures. Availability of the population to harvest is also dependent upon landowner distribution and hunter characteristics within management units that species occupy. The inherent changes in movements and populations size of black bear and elk coupled with landscape change and anthropogenic influences on populations requires a detailed assessment of range use and resource selection of both species in Pennsylvania. Many years of radiocollaring and monitoring has provided the necessary detailed locations needed to understand the change in distribution and use of public/private lands throughout the range of both species.	Successful management of large mammals is dependent upon availability of population to harvest in defined management units or season structures. Availability of the population to harvest is also dependent upon landowner distribution and hunter characteristics within management units that species occupy. The inherent changes in movements and populations size of black bear and elk coupled with landscape change and anthropogenic influences on populations requires a detailed assessment of range use and resource selection of both species in Pennsylvania. Many years of radiocollaring and monitoring has provided the necessary detailed locations needed to understand the change in distribution and use of public/private lands throughout the range of both species.
Surveillance and monitoring of river otter in Pennsylvania	December 2014	An effective surveillance strategy and estimate of population size is necessary to better understand river otter distribution and abundance in northeastern Pennsylvania and to develop methods to estimate and monitor river otter populations statewide. Non-invasive genetic sampling is feasible and efficient method to estimate population size of elusive species such as river otter. Although the condition of fecal DNA is of great importance, collection methods and season (i.e., fresh samples collected in winter) can improve quality of DNA used in population identification. Using the proper number of microsatellite loci (i.e., 8–10) can also enable identification of individual otter use of each latrine. Identification of individual otters will enable a genetic mark-recapture estimate of population size from scat sampling provided a thorough survey of latrines in a define area is conducted.	An effective surveillance strategy and estimate of population size is necessary to better understand river otter distribution and abundance in northeastern Pennsylvania and to develop methods to estimate and monitor river otter populations statewide. Non-invasive genetic sampling is feasible and efficient method to estimate population size of elusive species such as river otter. Although the condition of fecal DNA is of great importance, collection methods and season (i.e., fresh samples collected in winter) can improve quality of DNA used in population identification. Using the proper number of microsatellite loci (i.e., 8–10) can also enable identification of individual otter use of each latrine. Identification of individual otters will enable a genetic mark-recapture estimate of population size from scat sampling provided a thorough survey of latrines in a define area is conducted.
Characterization of spatial and temporal variability in fishes in response to climate change	August 2017	Predicting population responses to climate change requires an understanding of how population dynamics vary over space and time. Although variability has historically been viewed as an impediment to understanding population responses to ecological changes, it can provide an important signal, rather than just being viewed as noise. In this project, we will build upon recently completed analyses of fish population data in the Great Lakes basin to help predict how spatial and temporal variation in fish populations may respond to climate change and other important drivers. We suggest that shifting variance structure can be indicative of population-level responses to climate change. Our proposed research will help elucidate the extent to which quantifiable responses in spatial and temporal variability occur in different forms of fish population data.	The number of fish collected in routine monitoring surveys often varies from year to year, from lake to lake, and from location to location within a lake. Although some variability in fish catches is expected across factors such as location and season, we know less about how large-scale disturbances will influence population variability. Our objective was to evaluate spatial and temporal variation in fish catches from large freshwater lakes that have experienced large-scale changing conditions. This was a collaborative project, involving partners from around the Great Lakes region, and it relied on established data sets of fish catches, including from Oneida Lake in NY, Lake Michigan, and the Bay of Quinte in Lake Ontario. This research helps elucidate the extent to which quantifiable responses in spatial and temporal variability occur in fish population data, which can help managers develop adaptation strategies to prepare for decisions about monitoring and management of dynamic ecological systems.
Trans-boundary management and conservation: linking large-scale dynamics to ecological monitoring and management	September 2014	A central challenge to natural resource management is to understand and predict ecological responses to management and environmental change over large spatial scales. It is recognized, however, that the management and conservation of many important ecological systems and the services they provide must be addressed at spatial scales that transcend jurisdictional and political boundaries. For example Landscape Conservation Cooperatives (LCCs) recognize that managing natural resources is complex and requires landscape-scale (i.e., trans-boundary) approaches. Although trans-boundary approaches are necessary to understand large-scale phenomenon (e.g., species range), it remains unclear in many cases how best to address the inherent complexities in managing ecosystems at large (e.g., regional) spatial scales. In addition to challenges associated with performing trans-boundary research, it is often unclear how to link large-scale system dynamics with on-the-ground decision-making processes, which are often done using adaptive management principles. For example, a critical component for successfully implementing adaptive management is the development of a rigorous monitoring program, which provides a critical feedback loop for learning about system dynamics. It is unclear, however, how the interplay between components acting at different, hierarchical scales will affect the ability of natural resource managers to detect changes in important state variables (e.g., animal abundance, occupancy, etc.) at trans-boundary spatial scales. Thus, our overarching objective is to use freshwater stream fish populations as model systems to develop a framework and tools for addressing the inherent challenges in performing trans-boundary research and for linking large-scale dynamics to ecological monitoring and management.	None
Fish Community Assessment in the Eastern Rivers and Mountains Network and Integration with Existing Monitoring Data	May 2015	The National Park Service (NPS) has initiated a long-term ecological monitoring program, known as “Vital Signs Monitoring”, to provide the minimum infrastructure to allow more than 270 national park system units to identify and implement long-term monitoring of their highest-priority measurements of resource condition. The Eastern Rivers and Mountains Network (ERMN) includes nine parks in New York, New Jersey, Pennsylvania, and West Virginia which together encompass nearly 91,000 ha of land area and more than 600 stream and river miles within the parks’ authorized boundaries. A primary objective of the ERMN monitoring program is to evaluate status and trends in the condition of tributary watersheds flowing into and through member parks. Currently, the monitoring of fish communities is not part of the monitoring program. Consequently, methodology is needed to estimate the current condition of fish communities in ERMN wadeable streams in a rigorous and repeatable manner. Estimates of the current fish community’s condition at ERMN stream sites will complement data collected on an annual basis (i.e., Vital Signs Monitoring) and enable an integrated measure of ecosystem condition that can be monitored over time. The specific objectives of this study are to: (1) characterize fish communities in selected ERMN stream reaches, and (2) combine fish community data with existing monitoring data (e.g., macroinvertebrates) to provide an integrated measure of stream ecological condition.	None
Developing an adaptive management approach for potential surveillance and spread of chronic wasting disease in white-tailed deer in Pennsylvania	December 2014	Research on surveillance strategies, that consider demographic and environmental factors, is lacking in most states CWD has not been found. Developing surveillance strategies to maximize efficiency of sampling white-tailed deer has been described in an endemic area of Colorado (Walsh and Miller 2010) and in initial stages of CWD occurrence in Saskatchewan (Rees et al. 2011). Predictive models of pathways of CWD spread would also be beneficial to states that have CWD at their borders. Predictive models, based on previous research on deer demographics and environmental contributors to disease, could provide focused efforts on surveillance strategies in the short- and long-term for state agencies.	Research on surveillance strategies, that consider demographic and environmental factors, is lacking in most states CWD has not been found. Developing surveillance strategies to maximize efficiency of sampling white-tailed deer has been described in an endemic area of Colorado (Walsh and Miller 2010) and in initial stages of CWD occurrence in Saskatchewan (Rees et al. 2011). Predictive models of pathways of CWD spread would also be beneficial to states that have CWD at their borders. Predictive models, based on previous research on deer demographics and environmental contributors to disease, could provide focused efforts on surveillance strategies in the short- and long-term for state agencies.
The effects of cross-scale interactions on freshwater ecosystem state across space and time	May 2016	Understanding cross-scale interactions (CSIs) is a critical research frontier in macrosystems ecology that extends across all environmental sciences. A CSI exists where a driver at one scale, such as local land use, interacts with a driver at another scale, such as regional climate. These CSIs can lead to nonlinear and often unexpected relationships between drivers and responses. Unfortunately, general properties of CSIs, such as the conditions in which they occur, are largely unknown, partly because they have been quantified in only a few instances. We use lakes and their major nutrients (phosphorus, nitrogen, and organic carbon) as a model system because lakes are affected by many of the main classes of drivers postulated to be a part of CSIs (e.g., connectivity, land use, and climate), and because there is a wealth of existing data and knowledge from small-scale studies regarding possible mechanisms through which drivers could interact across scales.	None
Modeling species response to environmental change: development of integrated, scalable Bayesian models of population persistence	March 2014	Estimating species response to environmental change is a key challenge for ecologists and a core mission of the USGS. Effective forecasting of species response requires models that are detailed enough to capture critical processes and at the same time general enough to allow broad application. This tradeoff is difficult to reconcile with most existing methods. This project will extend and combine existing models that operate at different scales and with different levels of data complexity into a modeling framework that will allow robust estimation of population response to environmental change across a species’ range.	None
Harvest Rates of Hen Wild Turkeys in Pennsylvania	June 2014	This project will estimate fall harvest rates of hen turkeys using a cross-over design where two management units change between a 3-week to 2-week fall season. This study is designed to help the PA Game Commission understand the effect of changing fall season length on harvest rates of hen turkeys.	None
Developing An Adaptive Management Approach For Meeting Deer And Forest Management Objectives	September 2013	Forest vegetation conditions are affected by a number of factors, such as deer browsing, light conditions, soil characteristics, competing vegetation, and seed sources. All these factors are considered by foresters when making forest management decisions but not in a formal manner. In addition, there is controversy regarding which factor may have the greatest influence on future forest conditions. This project will formalize decision models to learn about the relative effect of key factors that influence future vegetation conditions on state forests. In addition, management experiments will be identified that may help learn faster about the response of forest vegetation conditions to management actions.	None
Lake Trout (Salvelinus namaycush) Reproduction, Habitat Use, and Movement Dynamics in the Niagara River/Niagara Bar, Lake Ontario	September 2013	Lake trout were extirpated from Lake Ontario in the late 19th century, and since the early 1970s stocking efforts have been attempting to re-establish a naturally reproducing population. Restoration efforts face many challenges including high mortality rates of yearlings during the first few days of stocking, reduced egg survival due to Early Mortality Syndrome (EMS) and predation by non-native fishes, and degraded spawning habitats due to sedimentation and introduced dreissenid mussels, among others. Lake Ontario is currently stocked with two hatchery strains: Seneca strain and the Traverse Island/Lake Superior strain (Lantry and Lantry 2008), but low numbers of wild lake trout also exist in the basin. Although some lake trout are naturally reproducing in the lake and Niagara River, there are still uncertainties related to strain-specific contributions to natural reproduction and the timing and location of spawning within the river. This study aims to genetically characterize the lake trout hatchery strains which could contribute to natural reproduction in Lake Ontario, and to evaluate the contribution of these strains to reproduction being documented in the Niagara River. Based on the genetic differences between hatchery strains, and incorporating any wild lake trout sampled from near the spawning area, assessment of the source(s) of lake trout natural reproduction in the Niagara River area will be assessed. If hatchery lake trout are reproducing successfully in the Niagara River, evaluation of the particular strain can be used to inform stocking practices or strain selections necessary to increase natural reproduction in Lake Ontario. In addition, lake trout will be tagged with radio transmitters and tracked to assess lake trout movement, with focus on strain-specific reproductive patterns and behaviors.	None
Comparative Energetics of Lake Trout Morphotypes	June 2013	Lake trout (Salvelinus namaycush) are deep water apex predators native to North America that inhabit glacially formed lakes including the Great Lakes region. During the late 19th century and early to mid-20th century, lake trout populations began to decline throughout the Great Lakes due to lamprey parasitism, overfishing, and poor water conditions. Lake trout management and restoration efforts are focused on stocking and restoring lake trout populations. Lake trout management, however, is complicated by the presence of multiple body forms or morphotypes. The three main morphotypes are lean, humper, and siscowet lake trout which vary in many characteristics, including depth preference, lipid content, body shape, and spawning time. Bioenergetics modeling is often used as tool to guide management decisions using information about the organism’s utilization of habitat (i.e. prey consumed, oxygen usage, etc.). Current lake trout bioenergetics models are based primarily off of the lean morphotype. The main objective of this study is to refine lake trout bioenergetics models to include morphotype variability. A better understanding of potential variability in lake trout morphotype bioenergetics is important for predicting potential future environmental changes on lake trout populations.	None
Defining oxythermal performance metrics for use in physiologically guided abundance models of diverse coregonid ecotypes	May 2026	Recruitment failures have led to declines of Lake Whitefish (<i>Coregonus clupeaformis</i>) and Cisco (<i>C. artedi sensu lato</i>) throughout the Great Lakes and in inland lakes. Maintaining, restoring, and the re-establishment of coregonid populations requires understanding environmental drivers of population processes and how population-specific biology may need to be integrated into hatchery-based culturing and stocking practices. This project will quantify the oxythermal performance of coregonid populations and examine whether populations from different environments exhibit habitat-relevant differences in physiology.	None
Zebra mussel impacts on fish mercury concentrations	December 2025	Recent work has shown that invasive Dressenid mussels can increase mercury (a neurotoxin) in fish tissues, but it is unknown how widespread these effects are. This work assesses this zebra mussel effect at a large scale and provides explicit predictions of mercury concentrations in important fisheries. We will produce mercury risk maps that can be used to guide monitoring towards potential mercury hot spots. This work will enhance our understanding of zebra mussels as a driver of variation in mercury bioaccumulation and ensure that future monitoring is allocated strategically–mitigating a significant impact of a highly problematic invader.<br>	None
The use of riparian buffer best management practices to reduce thermal stress on trout populations	September 2025	Riparian buffers are one of several best management practices used as part of watershed management plans developed for improving stream habitat for cold-water species of fish, including recreationally important trout. However, how riparian buffer development over time affects trout population viability is understudied. Critically, individual trout health has received almost no attention due to the lack of effective assessment tools. This study will assess thermal stress of trout living in streams with different age riparian buffers. To accomplish this, we will use a cutting-edge technique that involves quantifying the level of expression of thousands of genes. This research will help inform the effectiveness of riparian buffers at reducing thermal stress in trout populations.	Riparian buffers are one of several best management practices used as part of watershed management plans developed for improving stream habitat for cold-water species of fish, including recreationally important trout. However, how riparian buffer development over time affects trout population viability is understudied. Critically, individual trout health has received almost no attention due to the lack of effective assessment tools. This study will assess thermal stress of trout living in streams with different age riparian buffers. To accomplish this, we will use a cutting-edge technique that involves quantifying the level of expression of thousands of genes. This research will help inform the effectiveness of riparian buffers at reducing thermal stress in trout populations.
Nations Fish Habitat at Multiple Spatial Scales in a Rapidly Changing Climate	September 2014	Throughout its native range in the Eastern U.S., the brook trout is a culturally and economically important species that is sensitive to warming stream temperatures and habitat degradation. The purpose of this project is to determine what impacts projected future land use and climate changes might have on the condition of stream habitat to support self-sustaining brook trout populations. The study region encompasses the historic native range of brook trout which includes the northeastern states and follows the Appalachian Mountains south to Georgia, where the distribution is limited to higher elevation streams with suitable water temperatures (streams < ~24 C maximum summer temperature). Relationships between recent observations of brook trout and predicted stream temperature, land use, and a number of potential habitat stressors will be used to make predictions regarding the condition of the habitat in each stream reach for supporting self-sustaining brook trout now and under future climate and land use change scenarios.	None
Methods of estimating deer abundance at Gettysburg National Military Park: Testing model assumptions	December 2011	1. Test whether the proportion of the deer population sighted during spotlight surveys at GNMP-ENHS has changed since these sighting probabilities were estimated in the 1980s and 1990s. 2. Test the assumption that roads can serve as transects when using distance sampling to estimate abundance. 3. Investigate the accuracy, precision, and logistical feasibility of other population estimators that use data collected during deer population reduction efforts to estimate abundance.	None
Spatial and Temporal Components of Variation in Great Lake Percid Populations	June 2011	The purpose of this project is to provide monitoring recommendations for fishery-independent surveys of percid populations in the Great Lakes basin. The specific objectives of the research are to: (1) determine relative magnitudes of spatial and temporal components of variation in percid relative abundance data and how these variance structures may differ among systems in the Great Lakes basin, (2) determine whether variance structure itself is responsive to large-scale ecological perturbations, (3) develop recommendations for the design of monitoring programs and analysis of resulting data to support management of important percid fisheries within the Great Lakes region.	The purpose of this project is to provide monitoring recommendations for fishery-independent surveys of percid populations in the Great Lakes basin. The specific objectives of the research are to: (1) determine relative magnitudes of spatial and temporal components of variation in percid relative abundance data and how these variance structures may differ among systems in the Great Lakes basin, (2) determine whether variance structure itself is responsive to large-scale ecological perturbations, (3) develop recommendations for the design of monitoring programs and analysis of resulting data to support management of important percid fisheries within the Great Lakes region.
Evaluation of Wild Trout Resources and Restoration Efforts in Pennsylvania	June 2015	In collaboration with the Pennsylvania Fish and Boat Commission and the US Fish and Wildlife Service, we are examining movement dynamics and habitat use of wild brook and brown trout in headwater streams.	None
Distribution of PCB Congeners in Pennsylvania Streams and Fish: Implications for Risk Assessment and Fish Health	December 2011	Polychlorinated biphenyls (PCBs) are a group of man-made organic chemicals that have been widely used in industry throughout the world. PCBs have adverse health effects on organisms, including disrupting the immune, reproductive, endocrine, and nervous systems. Although banned in the United States in the late 1970s, PCBs remain a global threat to environmental and human health. The deleterious effects of PCBs are largely due to the properties of these chemicals including, (1) their long lifetimes (persistence) in the environment (including water, sediment and organisms), (2) their ability to reach high concentrations in predatory species, including fish (i.e. bioaccumulate), and (3) their potential for long-range transport through air and water. Because a primary sink of PCB deposition is in aquatic environments, the effects of these chemicals on aquatic life and the potential threat to human health through fish consumption remains a concern. Although PCBs have been extensively studied over the past several decades, there remains uncertainty regarding the dynamics of specific PCB congeners in aquatic organisms. Much of this uncertainty stems from earlier studies relying on measures of total PCBs to assess health effects instead of evaluating individual congener dynamics. Therefore, the objectives of this study are to: 1. Quantify the effects of lipid depletion on PCB congener dynamics and the subsequent effects on the health of channel catfish. 2. Reassess streams that were historically contaminated with PCBs and quantify any remaining PCB congeners in both stream sediments and fish communities. This research will advance knowledge of PCB congener dynamics in fish and in the environment as well as inform future environmental health policy.	None
Dispersal of female white-tailed deer in Pennsylvania	May 2012	Characteristics of dispersal of female white-tailed are not well studied because females exhibit a high degree of philopatry to natal home ranges. However, dispersal does occur and can be over long distances (>30 miles). We will use data on radio-collared female deer since 2005 to study dispersal rates, timing, and distances in Pennsylvania. In addition, we will investigate how dispersal may be influenced by landscape characteristics.	None
Effects of shrub removal on breeding grassland sparrows	December 2012	Grasslands throughout the United States have been lost at incredible rates, and most grassland obligate bird species also have experienced significant downward trends. While the reasons for these declines are many, habitat loss has played a substantial role. Grasslands in Pennsylvania, created through coal surface-mining reclamation activities, provide an important habitat for grassland birds: notably Grasshopper (Ammodramus savannarum) and Henslow’s Sparrows (A. henslowii). These reclaimed grasslands, however, are being lost to successional processes as woody plant species recolonize these areas. Grassland sparrow abundance and fitness are thought to decline with increasing woody vegetation; although this evidence is based on observation and correlation and has largely been measured in grasslands with little woody vegetation. With these ideas in mind I implemented a large-scale manipulative experiment in the spring of 2009 to measure the influence of woody vegetation on the abundance and fitness of grassland birds. After collecting avian baseline and vegetation data on eight 50-ac plots during 2009, we will remove all woody vegetation from half of those plots during the winter of 2010. By monitoring these plots for the following two years, I will be able to link habitat structure and composition with territory shifts, return rates, nestling growth rate, survival, and changes in population size. Finally, I will conduct multiple grassland bird surveys at hundreds of grassland sites across western Pennsylvania. I will model occupancy rates and develop a population estimate for grassland sparrows in western Pennsylvania. Taking what we learn from the woody vegetation removal experiment, I will be able to estimate the percent of grasslands in western Pennsylvania that contain viable populations of grassland birds.	None
Dispersal rates, timing, and distances of Pennsylvania black bears	June 2011	This project was developed to document dispersal timing, rates and distances for juvenile black bears from tagging and recovery information gathered in Pennsylvania from 1980-2008. Data have been gathered by the Pennsylvania Game Commission with bears being marked using individually numbered ear tags. Bears tagged as cubs or yearlings <15 months of age will be used for analysis and >1400 individual bears have been identified.	None
Movement and habitat use of sika and white-tailed deer on Assateague Island National Seashore	August 2008	This research project was conducted to describe habitat use of sika deer (Cervus nippon) and white-tailed deer (Odocoileus virginianus) and possibly attribute the effects of ungulate herbivory to specific deer species, if spatial separation in habitat use could be identified. Sturm (2007) conducted an exclosure study to document the effect of feral horse (Equus caballus) herbivory, deer herbivory, and horse and deer herbivory combined on plant communities. Sturm (2007) found that ungulate herbivory reduced plant species richness, evenness, and diversity in the maritime forest and affected species composition in all habitats studied. Sturm (2007) also found that herbivory on some species could be directly attributable to either horse or deer. However, the effects of sika and white-tailed deer herbivory could not be separated via an exclosure study design because of the difficulty of passively excluding one deer species but not the other.	None
Incorporating radio telemetry data in tag-return studies	May 2013	White-tailed deer have been captured and either ear-tagged with reward tags or radio collars. Because capture occurs in winter (Jan-Apr) and harvest doesn't occur until autumn, mortality between capture and harvest is estimated from radio-collared deer. We are evaluating how these data can be combined to provide more accurate and precise estimates of harvest rates.	None
Evaluation of the PA Sex-Age-Kill Model for White-tailed Deer	May 2010	Readily available harvest data is frequently incorporated in models used to estimate abundance of game species. However, appropriateness of parameter estimates and assumptions using these data is rarely evaluated. This project used data across 10 years from >1,500 VHF and GPS collared white-tailed deer to provide parameter estimates and evaluate methods used to estimate white-tailed deer abundance in Pennsylvania. In addition, this project investigated spatial, temporal, and demographic patterns in harvest rates.	Accurately monitoring population trends is an essential component of game species management. This is especially true for white-tailed deer (Odocoileus virginianus) in Pennsylvania where the Pennsylvania Sex-Age-Kill (PASAK) model is used to estimate annual abundance. Historically, the PASAK model only provided point estimates of abundance. However, statistically valid estimates of precision are needed to quantify uncertainty. Additionally, assumption violations can incorporate bias into estimates, the extent of which is unknown. I estimated survival and harvest rates based on data from 1,131 radio- or GPS-collared white-tailed deer and obtained harvest data (number killed, age-sex structure, etc.) to (1) evaluate assumptions of the PASAK model, (2) develop a method to estimate precision, and (3) evaluate model sensitivity and robustness. The PASAK model input parameters for the mature (≥2.5 years old) male harvest rate, yearling (1.5 years old) male harvest rate, and percent yearling females in the adult (≥1.5 years old) female population did not meet required assumptions. Mature male harvest rates differed by as much as 32.8% among wildlife management units (WMUs) studied. However, this spatial variability could be reliably modeled using a hunting effort index as a covariate. I found difficulties in the current method used to estimate yearling male harvest rates. However, direct yearling male harvest rate estimates from radiocollar data, which differed by <16.5% among WMUs studied, provided a suitable alternative estimate. In addition, variation in hunting effort was related to spatial variability in yearling male harvest rates. Yearling female deer were nearly 50% more likely to be harvested than mature female deer, which caused the PASAK model to underestimate population size. Mean coefficient of variation (CV) estimates by WMU, 14.1% in year t, were slightly above benchmarks recommended for managing game species populations (≤ 12.8%). Doubling reporting rates by hunters or doubling the number of deer checked by personnel in the field would improve mean CVs in year t to recommended levels. The PASAK model was robust to variability and bias in estimates for mature male harvest rate, female harvest rate, and non-harvest mortality. However, model estimates were sensitive to variability and bias in yearling male harvest rates. Consequently, yearling male harvest rate estimates had the greatest influence on the accuracy of population estimates. Few studies have monitored spatial and temporal variability in male white-tailed deer harvest rates. My results support the hypothesis that the majority of variability in mature male white-tailed deer harvest rates can be explained by variation in hunting effort. Similar variability exists in yearling male harvest rates, however, antler point restrictions (APRs) in Pennsylvania limit the extent of variability. Although minimized by APRs, yearling male harvest rate variability has profound influences on PASAK model estimates. Because harvest rates in the PASAK model are assumed constant across years, potential influences of regulation changes or shifts in hunting practices that alter male harvest rates will have profound influences on model performance. Yearling male harvest estimates are similarly important, and research to evaluate their accuracy will improve reliability of PASAK model estimates. Increasing harvest reporting rates by hunters may be the most efficient approach to improve precision of harvest estimates, whereas similar improvements by increasing the number of deer checked and aged may be more difficult or expensive to achieve. Independent estimates for the percent of yearling males in the adult male population will reduce the importance of yearling male harvest rate and harvest estimates.
Testing Assumptions of Distance Sampling to Estimate Abundance of White-tailed Deer	December 2011	This project is taking place at Gettysburg National Military Park and Eisenhower National Historic Site in Pennsylvania. White-tailed deer (Odocoileus virginianus) were captured from January-March 2008 using rocket-nets and modified clover traps and fitted with ear tags and GPS-collars. Over the next two years, I will perform 7 distance sampling surveys using transects selected from existing roads within a 2862 hectare or 11 square-mile study area that includes both the park and private lands surrounding the park. I will be collecting intensive GPS locations from marked deer during the distance sampling survey to model habitat use. Results from this habitat-use model will allow me to estimate the proportion of the population that was actually near roads during surveys, to quantify the bias introduced when using roads, and to correct population estimates.	None
Quantifying per- and polyfluoroalkyl substances in aquatic environments	July 2023	Per- and polyfluoroalkyl substances (PFAS) have received national attention because of potential human-health concerns. PFAS are ubiquitous in the environment, having been observed in surface water, groundwater, and drinking water, with many having the potential to accumulate in aquatic organisms. In collaboration with state agencies this project seeks to understand the potential transfer and accumulation of PFAS within aquatic food webs, with the goal of informing risk to ecological systems and to human health through consumption of recreationally important sportfish.	Per- and polyfluoroalkyl substances (PFAS) have received national attention because of potential human-health concerns. PFAS are ubiquitous in the environment, having been observed in surface water, groundwater, and drinking water, with many having the potential to accumulate in aquatic organisms. In collaboration with state agencies this project seeks to understand the potential transfer and accumulation of PFAS within aquatic food webs, with the goal of informing risk to ecological systems and to human health through consumption of recreationally important sportfish.
Targeted surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wildlife	October 2025	This study will be coordinated with targeted surveillance studies led by partner institutions so that similar designs are used and the data can be analyzed as one large dataset. The targeted surveillance data for SARS-CoV-2 will be analyzed at USDA/APHIS/WS-National Wildlife Research Center in risk assessment analyses.	The project was initiated to conduct collaborative, targeted surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer (WTD) populations. Targeted surveillance will involve placing GPS tracking devices on deer in the Established Area of Disease Management Area 2 from the same population chronic wasting disease has been detected, and sampling the same deer multiple times where possible. We will also leverage additional ongoing studies by the state where deer are being tracked with GPS collars to collect samples from those populations as well. Targeted surveillance data will complement opportunistic surveillance data that are being collected by state agencies and Wildlife Services management through hunter and agency harvest. While harvest data serve to determine the distribution of SARS-CoV-2 in deer, the data collected here will allow for: (1) Recording sample locations, (2) determining infection status over time in nature for the same individual (when possible) and within the same population, (3) identifying how deer movement determines infection status, (4) understanding the relative role of human-deer spillover versus deer-to-deer transmission, (5) estimating epidemiological parameters (i.e., force of infection), (6) identifying and understanding factors that lead to persistence and reservoir status of SARS-CoV-2 in deer, and (7) understanding the potential impacts of SARS-CoV-2 on deer populations.
Putting the sampling design to work: enhancing monitoring programs for improved management and inference of ecological responses to changes in climate.	December 2025	Studying the impacts of climate on important ecological responses is a priority of monitoring programs throughout the Northeast. Established sampling protocols for data collection, whether to inform estimates of abundance or occupancy, were designed to evaluate the effects of non-climate stressors and related management actions. Traditional modeling approaches, such as generalized linear models, may not accurately identify important relationships between species and climate nor elicit useful information on how these species will be impacted by a changing climate. This project is a collaboration between the U.S. Geological Survey, the Virginia Department of Wildlife Resources, the Maryland Department of Natural Resources, the West Virginia Division of Natural Resources, the Pennsylvania Fish and Boat Commission, and the National Park Service. The goal of this work is to develop statistical methods to enhance and/or modify existing monitoring programs' abilities to understand climate effects on fish and wildlife populations. Specifically, given existing monitoring programs, our objectives are to (1) develop statistical models that quantify and account for the impacts of the sampling design in understanding the relationship between climate and species abundance or occupancy, and (2) develop an optimal supplemental sampling design that factors in spatial and temporal effects, precision, and cost tradeoffs to enhance the monitoring program’s ability to track climate change and provide early indicators for fish and wildlife responses.	Studying the impacts of climate on important ecological responses is a priority of monitoring programs throughout the Northeast. Established sampling protocols for data collection, whether to inform estimates of abundance or occupancy, were designed to evaluate the effects of non-climate stressors and related management actions. Traditional modeling approaches, such as generalized linear models, may not accurately identify important relationships between species and climate nor elicit useful information on how these species will be impacted by a changing climate. This project is a collaboration between the U.S. Geological Survey, the Virginia Department of Wildlife Resources, the Maryland Department of Natural Resources, the West Virginia Division of Natural Resources, the Pennsylvania Fish and Boat Commission, and the National Park Service. The goal of this work is to develop statistical methods to enhance and/or modify existing monitoring programs' abilities to understand climate effects on fish and wildlife populations. Specifically, given existing monitoring programs, our objectives are to (1) develop statistical models that quantify and account for the impacts of the sampling design in understanding the relationship between climate and species abundance or occupancy, and (2) develop an optimal supplemental sampling design that factors in spatial and temporal effects, precision, and cost tradeoffs to enhance the monitoring program’s ability to track climate change and provide early indicators for fish and wildlife responses.
Assessment of movement of prions across the captive-wild interface	August 2023	Pennsylvania has detected chronic wasting disease (CWD) in captive and wild white-tailed deer since 2012. Since first detection occurred in the same year in both captive and wild deer, it is difficult to ascertain the role the captive-wild interface has on disease transmission in the state. Since 2012, over 10 captive facilities and 250 wild deer have tested positive for CWD. Considering Pennsylvania is second only to Texas in the number of captive facilities statewide, assessment of various components of the captive-wild interface appears warranted. Previous studies have documented crows were able to transmit infectious prions responsible for CWD in a controlled laboratory setting but field evaluation of this possibility has yet to be tested. Furthermore, limited information exists as to species’ use of captive facilities or areas surrounding these facilities to evaluate the role these species play, if any, of movement of prions around the landscape.	Pennsylvania has detected chronic wasting disease (CWD) in captive and wild white-tailed deer since 2012. Since first detection occurred in the same year in both captive and wild deer, it is difficult to ascertain the role the captive-wild interface has on disease transmission in the state. Since 2012, over 10 captive facilities and 250 wild deer have tested positive for CWD. Considering Pennsylvania is second only to Texas in the number of captive facilities statewide, assessment of various components of the captive-wild interface appears warranted. Previous studies have documented crows were able to transmit infectious prions responsible for CWD in a controlled laboratory setting but field evaluation of this possibility has yet to be tested. Furthermore, limited information exists as to species’ use of captive facilities or areas surrounding these facilities to evaluate the role these species play, if any, of movement of prions around the landscape.
Modeling the risk of West Nile virus to ruffed grouse populations	June 2022	Since its arrival in North America in 1999, West Nile virus (WNV) has had unprecedented adverse effects on the health of native birds across numerous taxa. In Pennsylvania, WNV was first documented statewide in 2002, with concurrent and precipitous population declines in ruffed grouse (<i>Bonasa umbellus</i>). Recovery of grouse populations has not since been observed. Infected grouse may experience mortality rates as high as 70% or greater. The ongoing influence of WNV can be seen in statewide population indices such as hunter flush rates and late-summer brood sighting survey data. Recent analysis indicates that WNV and availability of young forest on the landscape synergistically influence colonization, persistence and extinction of local grouse populations. Susceptibility of ruffed grouse to ongoing cycles of high-WNV prevalence has important implications for managing this species. Monitoring vector species abundance can assist in understanding areas of the landscape that pose a risk to sustaining grouse populations.	Since its arrival in North America in 1999, West Nile virus (WNV) has had unprecedented adverse effects on the health of native birds across numerous taxa. In Pennsylvania, WNV was first documented statewide in 2002, with concurrent and precipitous population declines in ruffed grouse (<i>Bonasa umbellus</i>). Recovery of grouse populations has not since been observed. Infected grouse may experience mortality rates as high as 70% or greater. The ongoing influence of WNV can be seen in statewide population indices such as hunter flush rates and late-summer brood sighting survey data. Recent analysis indicates that WNV and availability of young forest on the landscape synergistically influence colonization, persistence and extinction of local grouse populations. Susceptibility of ruffed grouse to ongoing cycles of high-WNV prevalence has important implications for managing this species. Monitoring vector species abundance can assist in understanding areas of the landscape that pose a risk to sustaining grouse populations.
Muskrat ecology and disease	August 2023	Wildlife disease surveillance is important for understanding wildlife health and can also provide insight into human and domestic animal health. Monitoring wildlife for diseases can be used to initiate preventative measures or management efforts against outbreaks in other wildlife, domestic animals, and humans. Passive surveillance involves investigation of mortality events to determine the cause(s) of disease. Results of passive surveillance give researchers insight into what is currently causing or has previously caused morbidity and mortality. Active surveillance consists of targeted investigations of pathogens, toxicants, and diseases through systematic collections of animals or their samples. Through various surveillance frameworks, researchers can assess current and future risk to outbreaks and diseases.	Wildlife disease surveillance is important for understanding wildlife health and can also provide insight into human and domestic animal health. Monitoring wildlife for diseases can be used to initiate preventative measures or management efforts against outbreaks in other wildlife, domestic animals, and humans. Passive surveillance involves investigation of mortality events to determine the cause(s) of disease. Results of passive surveillance give researchers insight into what is currently causing or has previously caused morbidity and mortality. Active surveillance consists of targeted investigations of pathogens, toxicants, and diseases through systematic collections of animals or their samples. Through various surveillance frameworks, researchers can assess current and future risk to outbreaks and diseases.
Parturition timing and calf survival in Pennsylvania elk	June 2023	Novel methods are available to understand the ecology of large mammals in various regions of the US. From the use of global positioning technology (GPS) for movements to vaginal implant transmitters (VITs) to document parturition, information on various life stages of elk can be determined. This project focuses on using improvements in technology or novel methods to assess elk diet, reproduction, genetics, and survival.	Novel methods are available to understand the ecology of large mammals in various regions of the US. From the use of global positioning technology (GPS) for movements to vaginal implant transmitters (VITs) to document parturition, information on various life stages of elk can be determined. This project focuses on using improvements in technology or novel methods to assess elk diet, reproduction, genetics, and survival.
Distribution and Habitat Associations of Snowshoe Hares in Pennsylvania	June 2025	Pennsylvania encompasses the southernmost range of snowshoe hares. Changes in climate or habitat conditions could result in hares becoming extirpated from Pennsylvania. Our study will be essential to the Pennsylvania Game Commission as it attempts to implement any management actions to offset potential effects of habitat changes and global climate change. Identifying if and how the distribution has changed and what habitat conditions impact those changes for hares in Pennsylvania will provide the PGC with the necessary information to make appropriate management decisions for harvest regulations, identify priority areas for conservation and management action, and to protect and manage existing habitat.<br> <br>In year one, we will evaluate how distribution of snowshoe hares has changed by replicating the 2004 track and fecal pellet methods used by Diefenbach et al. (2016). We will delineate the geographic distribution and large-scale habitat associations of snowshoe hares across northern Pennsylvania by collecting fecal pellet groups deposited by cottontails and hares and then extract DNA from fecal pellets to discern the presence of snowshoe hares. If snow is present, tracks will also be used to identify presence of snowshoe hares and hares may be visually detected. Technicians will navigate to pre-selected sampling locations and sampling sites will be searched for sign of cottontails and hares, and fecal pellet groups will be collected and stored in ethanol. DNA will be extracted at the Pennsylvania Cooperative Fish and Wildlife Research Unit genetics lab. Genetic analyses will be conducted by the Nucleic Acid Facility, Life Sciences Consortium, Pennsylvania State University. Mitochondrial DNA will be extracted from epithelial cells found in fecal pellets and gene sequences unique to each species of lagomorph will be used to identify the presence or absence of snowshoe hare, cottontail rabbit, and Appalachian cottontail. Additional genetic analyses will use microsatellite markers to investigate the spatial structure of genetic diversity to estimate levels of gene flow and identify isolated populations.<br><br>To ensure a representative sample of hare habitats, we will use a probability-based sampling design to select areas to search for fecal pellets. Repeated samples will be taken from a portion of the sample sites to obtain estimates of detectability, and hence correct for errors attributed to the failure to detect hares when they are in fact present. For each sampled site, we will use a geographic information system (GIS) with vegetation cover types and other digital layers to identify habitat characteristics associated with the presence of snowshoe hares. To suggest a plausible model for the effects of habitat characteristics, a logistic regression will initially be fit to the presence/absence data for snowshoe hares. However, logistic regression does not take into account non-detection errors, and so can lead to under-estimates of the probability that hares are present. Logistic regression is based on the untenable assumption that observations are independent and not spatially correlated. Therefore, new geostatistical methods shall be developed to correct for non-detection errors, to account for spatial dependence in the data, and to predict whether or not hares are present at unsampled sites. Once we have identified habitat or landscape characteristics associated with the presence or absence of hares we can use a GIS, coupled with the newly developed geostatistical procedures, to map the distribution of hares across Pennsylvania. Estimates of uncertainty of model predictions will be an essential component of our analyses.<br><br>In year two, we will identify focal areas in McKean, Cameron, and Elk counties to evaluate fine scale habitat features influence on local snowshoe hare population density and potentially population connectivity. Features we will evaluate include stem density of mid and understory vegetation, height of midstory, deer browse, and coarse woody debris among others. One-mi<sup>2</sup> focal areas will be identified within this core Pennsylvania hare range that was identified by Diefenbach et al (2016). Specific areas will be selected for landscape features such as scale of timber sales, aspect, cover type, and stand age.	Pennsylvania encompasses the southernmost range of snowshoe hares. Changes in climate or habitat conditions could result in hares becoming extirpated from Pennsylvania. Our study will be essential to the Pennsylvania Game Commission as it attempts to implement any management actions to offset potential effects of habitat changes and global climate change. Identifying if and how the distribution has changed and what habitat conditions impact those changes for hares in Pennsylvania will provide the PGC with the necessary information to make appropriate management decisions for harvest regulations, identify priority areas for conservation and management action, and to protect and manage existing habitat.<br><br>In year one, we will evaluate how distribution of snowshoe hares has changed by replicating the 2004 track and fecal pellet methods used by Diefenbach et al. (2016). We will delineate the geographic distribution and large-scale habitat associations of snowshoe hares across northern Pennsylvania by collecting fecal pellet groups deposited by cottontails and hares and then extract DNA from fecal pellets to discern the presence of snowshoe hares. If snow is present, tracks will also be used to identify presence of snowshoe hares and hares may be visually detected. Technicians will navigate to pre-selected sampling locations and sampling sites will be searched for sign of cottontails and hares, and fecal pellet groups will be collected and stored in ethanol. DNA will be extracted at the Pennsylvania Cooperative Fish and Wildlife Research Unit genetics lab. Genetic analyses will be conducted by the Nucleic Acid Facility, Life Sciences Consortium, Pennsylvania State University. Mitochondrial DNA will be extracted from epithelial cells found in fecal pellets and gene sequences unique to each species of lagomorph will be used to identify the presence or absence of snowshoe hare, cottontail rabbit, and Appalachian cottontail. Additional genetic analyses will use microsatellite markers to investigate the spatial structure of genetic diversity to estimate levels of gene flow and identify isolated populations.<br><br>To ensure a representative sample of hare habitats, we will use a probability-based sampling design to select areas to search for fecal pellets. Repeated samples will be taken from a portion of the sample sites to obtain estimates of detectability, and hence correct for errors attributed to the failure to detect hares when they are in fact present. For each sampled site, we will use a geographic information system (GIS) with vegetation cover types and other digital layers to identify habitat characteristics associated with the presence of snowshoe hares. To suggest a plausible model for the effects of habitat characteristics, a logistic regression will initially be fit to the presence/absence data for snowshoe hares. However, logistic regression does not take into account non-detection errors, and so can lead to under-estimates of the probability that hares are present. Logistic regression is based on the untenable assumption that observations are independent and not spatially correlated. Therefore, new geostatistical methods shall be developed to correct for non-detection errors, to account for spatial dependence in the data, and to predict whether or not hares are present at unsampled sites. Once we have identified habitat or landscape characteristics associated with the presence or absence of hares we can use a GIS, coupled with the newly developed geostatistical procedures, to map the distribution of hares across Pennsylvania. Estimates of uncertainty of model predictions will be an essential component of our analyses.<br><br>In year two, we will identify focal areas in McKean, Cameron, and Elk counties to evaluate fine scale habitat features influence on local snowshoe hare population density and potentially population connectivity. Features we will evaluate include stem density of mid and understory vegetation, height of midstory, deer browse, and coarse woody debris among others. One-mi<sup>2</sup> focal areas will be identified within this core Pennsylvania hare range that was identified by Diefenbach et al (2016). Specific areas will be selected for landscape features such as scale of timber sales, aspect, cover type, and stand age.
Collaborative Research: RAPID: lake ecosystem responses to fire along gradients of burn characteristics and hydrologic connectivity	February 2024	Although wildfire activity is increasing across the US and concern is mounting over fire effects on water resources, few studies have documented fire effects on lake ecosystems. At 10844 ha, the 2021 Greenwood Fire in Superior National Forest was the largest lightning-caused Minnesota wildfire in 10 years and covered all or parts of 28 lake watersheds through October 2021. This fire event presents an unprecedented opportunity to study lake responses to fire in an especially lake-rich landscape, which may represent a harbinger of ecological change in northern forests that are expected to experience more warm, dry fire weather under climate change. This study will evaluate the physical, chemical, and biological responses of northern Minnesota lakes to the Greenwood Fire.	Although wildfire activity is increasing across the US and concern is mounting over fire effects on water resources, few studies have documented fire effects on lake ecosystems. At 10844 ha, the 2021 Greenwood Fire in Superior National Forest was the largest lightning-caused Minnesota wildfire in 10 years and covered all or parts of 28 lake watersheds through October 2021. This fire event presents an unprecedented opportunity to study lake responses to fire in an especially lake-rich landscape, which may represent a harbinger of ecological change in northern forests that are expected to experience more warm, dry fire weather under climate change. This study will evaluate the physical, chemical, and biological responses of northern Minnesota lakes to the Greenwood Fire. Partners involved in this research include several academic institutions and state and federal land and resource management agencies.
Aquatic food web changes to invasive Flathead Catfish along an invasion gradient	January 2024	Biological invasions have the potential to significantly alter the structure and function of aquatic communities. By altering energy transfer through the food web, invasive species also have the potential to affect the accumulation of contaminants in other food fish species. This study seeks to understand the effects of an invasive catfish (the flathead catfish; <i>Pylodictis olivaris</i>) on a riverine food web and resulting changes in the trophodynamics of per- and polyfluoroalkyl substances (PFAS). PFAS have the potential to be harmful to aquatic organisms and the accumulation of PFAS in fish species targeted by recreational anglers raises concerns for human health through consumption. This project is a collaboration between the U.S. Geological Survey, The Pennsylvania State University, and the Pennsylvania Fish and Boat Commission (PFBC). The results of this study will provide important information on the food web consequences of flathead catfish invasion and PFAS trophodynamics that will help fisheries management and risk assessments of invasive flathead catfish.	Biological invasions have the potential to significantly alter the structure and function of aquatic communities. Invasive predatory fish species are known to restructure food webs – since predatory fishes have a dominant influence on community structure in freshwater systems. This research is focusing on understanding the food web changes to invasive Flathead Catfish <i>Pylodictis olivaris</i> along an invasion gradient in the Susquehanna River Basin, PA. This research is collaboration with state and federal partners, including the PA Fish & Boat Commission and the US Geological Survey. Information on the food web consequences of invasion can help inform formal decision-making processes, and thus this research will help reduce an important uncertainty related to the management of invasive Flathead Catfish.
Landscape Transcriptomics as a new tool for natural and agricultural resource management	August 2023	The implications of climate change for Earth’s biota and agricultural systems remains uncertain. We will address this uncertainty by characterizing connections between an organism’s genotype, phenotype, and environmentally determined fitness in the context of a changing climate. Specifically, this approach connects landscape-level variables to gene expression patterns (transcriptomes). Working with state fisheries agencies, the US Geological Survey, and the US Fish & Wildlife Service, we will use a combination of landscape transcriptomics and experimental manipulations to identify markers of stress reactivity and resilience to warming streams, a key risk to brook trout <i>Salvelinus fontinalis</i> population persistence. This information will help guide the conservation and management of this iconic species.	The implications of climate change for Earth’s biota and agricultural systems remains uncertain. We will address this uncertainty by characterizing connections between an organism’s genotype, phenotype, and environmentally determined fitness in the context of a changing climate. Specifically, this approach connects landscape-level variables to gene expression patterns (transcriptomes). Working with state fisheries agencies, the US Geological Survey, and the US Fish & Wildlife Service, we will use a combination of landscape transcriptomics and experimental manipulations to identify markers of stress reactivity and resilience to warming streams, a key risk to brook trout <i>Salvelinus fontinalis</i> population persistence. This information will help guide the conservation and management of this iconic species.
Wild Turkey Harvest Management Decision Making	June 2026	Fall and spring turkey hunting is popular in Pennsylvania, but the fall harvest is dominated by females and poults, which may reduce reproductive output of the population the following spring. Therefore, maximizing fall hunting opportunity has the potential to negatively affect spring harvests. Turkey research on the effect of fall hunting seasons, along with population modeling, has suggested that careful regulation of fall hunting seasons is necessary to ensure sufficient reproductive output the following spring and prevent the fall harvest from negatively affecting spring harvest via reduced turkey abundance.<br>Identifying an optimal fall harvest strategy, however, has been difficult because turkey population dynamics are highly variable because of the effect of spring weather conditions on reproduction and mast abundance on fall harvest rates. Identifying an optimal fall harvest strategy requires estimates of fall population size with measures of uncertainty, because the harvest strategy depends on the size of the population and how certain we are that the estimate is a good representation of the population.<br>An integrated population model (IPM) has been developed to estimate turkey population size by WMU, which requires band-recovery data of males, spring and fall harvest estimates by sex-age class (Game Take Survey and report cards), and reproductive rates (summer sighting survey). The IPM has been demonstrated to provide population estimates as well as derive important parameters that aren’t monitored with data (e.g., fall harvest rates of females and poults). However, the IPM has only been implemented in a spreadsheet to show proof of concept. Developing the IPM in a Bayesian framework using Markov Chain Monte Carlo (MCMC) methods provides multiple advantages: 1) the IPM will provide measures of precision of estimated population parameters, 2) the model can be directly integrated with databases managed by the Pennsylvania Game Commission (PGC), and 3) the model can evaluate the effects of different levels of sampling effort (e.g., how increasing the number of turkeys leg banded affects precision of population estimates).	Fall and spring turkey hunting is popular in Pennsylvania, but the fall harvest is dominated by females and poults, which may reduce reproductive output of the population the following spring. Therefore, maximizing fall hunting opportunity has the potential to negatively affect spring harvests. Turkey research on the effect of fall hunting seasons, along with population modeling, has suggested that careful regulation of fall hunting seasons is necessary to ensure sufficient reproductive output the following spring and prevent the fall harvest from negatively affecting spring harvest via reduced turkey abundance.<br>Identifying an optimal fall harvest strategy, however, has been difficult because turkey population dynamics are highly variable because of the effect of spring weather conditions on reproduction and mast abundance on fall harvest rates. Identifying an optimal fall harvest strategy requires estimates of fall population size with measures of uncertainty, because the harvest strategy depends on the size of the population and how certain we are that the estimate is a good representation of the population.<br>An integrated population model (IPM) has been developed to estimate turkey population size by WMU, which requires band-recovery data of males, spring and fall harvest estimates by sex-age class (Game Take Survey and report cards), and reproductive rates (summer sighting survey). The IPM has been demonstrated to provide population estimates as well as derive important parameters that aren’t monitored with data (e.g., fall harvest rates of females and poults). However, the IPM has only been implemented in a spreadsheet to show proof of concept. Developing the IPM in a Bayesian framework using Markov Chain Monte Carlo (MCMC) methods provides multiple advantages: 1) the IPM will provide measures of precision of estimated population parameters, 2) the model can be directly integrated with databases managed by the Pennsylvania Game Commission (PGC), and 3) the model can evaluate the effects of different levels of sampling effort (e.g., how increasing the number of turkeys leg banded affects precision of population estimates).
Landscape Genetics of white-tailed deer in Minnesota	September 2022	Minnesota’s CWD infection appears to be in a relatively early stage of development. This provides hope that an effective control strategy might protect the state’s white-tailed deer resource. This project will leverage existing MNDNR plans and infrastructure to control occurrence and distribution of CWD in Minnesota utilizing targeted removal of deer groups at locations where CWD positive deer have been found. The intent of the proposed work is to use agency culling as a fine-scale management tool to increase the likelihood of removing additional CWD positive animals from the affected landscape, reduce deer density around locations of CWD positive animals, and use genetic information from sampled deer to better understand social network structure of deer most likely exposed to CWD. Understanding familial relationship of culled deer will assist in understanding if related individual deer are being remove at designated removal sites.	<b>Problem Statement:</b> Social structure and the interactions among groups of conspecific individuals are important when considering the dynamics of disease transmission and potential means of disease management. White-tailed deer are known to associate in relatively stable matrilineal or dominant-female groups and female white-tailed deer generally associate more closely with relatives than with nonrelatives.<br><br><b>Why it matters: </b>We can bring this collective genetic information together by determining both haplotypes and pairwise relatedness in order to quantify social group membership at a fine spatial scale. More specifically we can quantify the numbers of close relatives of CWD positive deer removed from culling efforts and haplotype diversity among known CWD-infected deer.<br><br><b>Partners:</b><br>Dr. Christopher Jennelle, Minnesota Department of Natural Resources, Forest Lake, MN 55025<br><br><b>How it will be used:</b> These statistics can be used as a baseline for creating an index of the ability of agency culling efforts to remove high-risk social groups in a given spatial location. Another potential management application is to track this type of information for all deer harvested in close spatial proximity to CWD-positive detections to quantify the degree to which CWD exposed matrilines (a broader-scale proxy for infected social groups) are being removed from fine spatial scale locations.
Establishing a national tissue and reagents repository for chronic wasting disease	September 2023	Management of chronic wasting disease (CWD) has been limited because the infectious proteins, called prions, responsible for CWD in wild cervids in 26 US states, are difficult to study. Tracking CWD as it progressed across the US since it’s discovery in the early 1980s has been hampered because studies of distinct strains of CWD has been lacking. Identification of distinct prion strains can inform management by targeting areas known to harbor CWD, thus prioritizing management of cervid populations with prion strains that have greater infection potential and those that are able to infect new species. Although the biology of prions has been well studied (they are responsible for mad cow disease), prion researchers have been unable to study prion strains throughout the US because samples have not been available for study. Therefore, a virtual repository to link CWD tissue sample locations would provide this important resource to researchers to aid management agencies in the US.	<b>Problem Statement:</b> The overall goal of this program is to establish a national CWD tissue and reagents repository.<br><br><b>Why it matters: </b>The significance of this program is multifold. First, a repository of CWD field isolates from a wide-ranging geographic location in North America will allow, for the first time, the means to begin to assess the distribution and frequency of CWD strains in North America. Since prion strains can differ in pathogenicity and host range, this is essential data for the determination for risk of interspecies prion transmission to humans and to domestic livestock and wildlife. Second, this repository can provide uniform standardized CWD-infected and uninfected sources of tissue for diagnostic development, mitigation testing and for basic research purposes. Finally, the implementation of the repository will facilitate cooperation between the various state agencies that could lead to new collaborative efforts.<br><br><b>Partners:</b><br>Jason Bartz<i>, </i>Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178<br><br><b>How it will be used: </b>This virtual repository will be accessible by researchers throughout the world to request samples to achieve study objectives involving prion strain type and prion protein genotypes. Important metadata will be linked to each tissue type that would include: coordinates for collection location, species, sex, age, tissue type (e.g. retropharyngeal lymph node, obex), prion protein genotype, physical location of stored sample, and contact information of organization housing the sample. All of this metadata for each tissue sample will be housed in a single virtual repository accessible to researchers throughout the world.
Linking Genetics to Movements of White-tailed deer to Assist Surveillance for CWD Epidemiology	August 2024	Surveillance for chronic wasting disease (CWD) in deer is often in response to finding a new disease foci with direction of surveillance controlled by some arbitrary distanced buffer around a diseased animal. Understanding large-scale gene flow across a region can identify the most likely transmission path of CWD because gene flow identifies historic ancestry of deer across a landscape. Combining landscape genetics with CWD surveillance would provide natural resource agencies a more structured approach to surveillance by providing disease units more reflective of the underlying subpopulation structure of deer in a region.	<b>Problem Statement:</b> The purpose of the proposed research is to identify the frequency and distribution of prion gene variants within white-tailed deer populations across multiple regions with varying histories of CWD infection. In addition, use of microsatellite genotypes collected from free-ranging white-tailed deer can provide details on the landscape genetics of white-tailed deer across multiple areas with differing CWD exposure histories.<br><br><b>Why it matters: </b>Assess and compare PRNP genotypes of individuals in samples from areas experiencing various times since establishment of CWD in white-tailed deer populations:CWD apparently established within the past decade (Maryland/Pennsylvania/Virginia; n = 100 samples collected 2014–2018)CWD not present (New York; n = 133 samples collected 2010–2016).<br>Assess broad- and fine-scale landscape genetics using microsatellite markers/mitochondrial DNA within core areas to identify likely pathways of CWD transmission.<br><br><b>Partners:</b><br>Krysten L. Schuler,Wildlife Disease Ecologist - Cornell Wildlife Health Lab, 240 Farrier Road, Ithaca, NY 14853; ks833@cornell.edu; 607-253-3629<br>Chris Rosenberry, Bureau of Wildlife Management, Pennsylvania Game Commission, Harrisburg, Pennsylvania; chrosenber@pa.gov, 717-433-4062<br><br><b>How it will be used:</b> This project will increase understanding of the potential genetic basis of disease risk and potential disease transmission pathways at the landscape level for several areas of known or anticipated CWD occurrence.
Landscape transcriptomics as a new tool for natural resources management	December 2021	How does habitat connectivity and composition affect genetic diversity and adaptive potential? Landscape genetics combines population genetic (using DNA sequence variation) and landscape ecology analyses to address this question. However, a DNA sequence only approach ignores the differences in relative expression of genes that also differ between populations, and importantly, covaries with variables such as stress or other physiological responses. These snapshots of gene expression patterns ("transcriptomes") add key information about an organism's condition. We believe it is time for a new field of "landscape transcriptomics". Landscape transcriptomics could address similar questions as landscape genetics, but also tackle issues such as how landscape features affect stress and health of populations. This project will develop this field with a focus on applications to fisheries conservation and management, response of organisms to rapidly changing environments, and response of bee populations to nutritional resources, parasites, and pesticides.	Species genetic diversity, persistence, and adaptive potential are all affected by the degree of connectivity between habitat patches and the characteristics of those patches, whether it be water temperature for fish or flower species diversity for bees. To better inform management and conservation efforts and provide insights about adaptation potential, it is important to know not only how populations differ from one another across the landscape, but also how populations differ in their response to dynamic environmental conditions. Examining a snapshot of the whole genome gene expression (a transcriptome) is one way to accomplish this need. However, currently there is not a formal field in ecology that explicitly explores the benefits, limits, and quantitative challenges associated with this approach at landscape scales. This project will develop this new subdiscipline of ecology, which we refer to as landscape transcriptomics. This research will be performed with partners from Penn State University, USGS, and other academic institutions.
Forecasting Aquatic Invasions in Rivers: Using Riverscapes Genetics to Inform Invasive Fish Species Management at Regional Scales	August 2025	Invasive species have significant, negative effects on ecosystem structure and function, and predicting and limiting the spread of invasive organisms a priority for environmental managers. Invasive species management is particularly challenging in aquatic habitats, where higher invasion velocities and stronger interactions with native biota result in more significant disruptions to ecosystem structure and function. In particular, through competition, predation, and disruption to nutrient and energy flows, invasive species often lead to a reduction and/or loss of native populations and can decrease ecosystem resiliency to disturbance. In collaboration with state fisheries management agencies and Penn State University, we will apply a novel quantitative framework for riverscape genetics to better understand and predict the invasion potential of invasive flathead catfish in the Susquehanna River Basin. This research will identify management scenarios that can be used to limit future invasion and we will develop a web viewer to communicate the efficacy of different management scenarios to stakeholders and managers.	Invasive species have significant, negative effects on ecosystem structure and function, and predicting and limiting the spread of invasive organisms a priority for environmental managers. Invasive species management is particularly challenging in aquatic habitats, where higher invasion velocities and stronger interactions with native biota result in more significant disruptions to ecosystem structure and function. In particular, through competition, predation, and disruption to nutrient and energy flows, invasive species often lead to a reduction and/or loss of native populations and can decrease ecosystem resiliency to disturbance. In collaboration with state fisheries management agencies and Penn State University, we will apply a novel quantitative framework for riverscape genetics to better understand and predict the invasion potential of invasive flathead catfish in the Susquehanna River Basin. This research will identify management scenarios that can be used to limit future invasion and we will develop a web viewer to communicate the efficacy of different management scenarios to stakeholders and managers.
Surveillance Optimization Project for Chronic Wasting Disease: Streamlining a Web Application for Disease Visualization and Data-Driven Decisions	August 2022	The overarching goal is to build a CWD-community science and management communication platform to improve coordination, planning, and knowledge sharing. Efficient CWD surveillance, response, monitoring, and management requires coordination between neighboring states. Starting with the development of the shared data system and the continuance of partnership among stage wildlife agencies and non-government organization in the collaborative process, we can pool our resources and knowledge to improve our understanding of the ecology, epidemiology, and ultimately, management of CWD. The proposed product will be hosted by the CWD Alliance for long-term viability with a steering committee directing future products and tools. Our commitment to continued coordination with other interested parties will make this product a “one-stop shop” with the long-term aim to serve the entire U.S. and Canada.<br>However, efficient CWD information sharing and strategic coordination between neighboring states requires an established infrastructure, or “data language”, with which to communicate efficiently. By engaging a computer scientist, we can program linkages between various components and ensure there is full functionality between each piece. This will require custom software development to connect the state agency data to the Data Warehouse, which will then feed through a computational pipeline to the CWD Dashboard and back to state wildlife agencies for planning recommendations and progress reports.	The overarching goal is to build a CWD-community science and management communication platform to improve coordination, planning, and knowledge sharing. Efficient CWD surveillance, response, monitoring, and management requires coordination between neighboring states. Starting with the development of the shared data system and the continuance of partnership among stage wildlife agencies and non-government organization in the collaborative process, we can pool our resources and knowledge to improve our understanding of the ecology, epidemiology, and ultimately, management of CWD. The proposed product will be hosted by the CWD Alliance for long-term viability with a steering committee directing future products and tools. Our commitment to continued coordination with other interested parties will make this product a “one-stop shop” with the long-term aim to serve the entire U.S. and Canada.<br>However, efficient CWD information sharing and strategic coordination between neighboring states requires an established infrastructure, or “data language”, with which to communicate efficiently. By engaging a computer scientist, we can program linkages between various components and ensure there is full functionality between each piece. This will require custom software development to connect the state agency data to the Data Warehouse, which will then feed through a computational pipeline to the CWD Dashboard and back to state wildlife agencies for planning recommendations and progress reports.
North American interdisciplinary chronic wasting disease research consortium: NC1209	September 2024	NC1209: North American interdisciplinary chronic wasting disease research consortium: Research across multiple disciplines is needed to fully address the complexities of CWD and acquire the knowledge needed to limit or eliminate its spread. Research programs are emerging and maturing at multiple universities and government agencies. These are developing in parallel with little coordination. For example, within institutions of higher education located in the Midwest alone, three large studies have been initiated within the last two years to investigate the role of movement behavior in shaping epidemiological models of CWD. Our intent is to form a multistate consortium designed to improve information exchange among universities and researchers with common goals, but different backgrounds and knowledge bases. Increased collaboration would improve research quality and avoid duplication of work at a critical time when effective solutions are needed quickly.<br>Previous ID: NCDC234: North American interdisciplinary chronic wasting disease consortium	Research across multiple disciplines is needed to fully address the complexities of CWD and acquire the knowledge needed to limit or eliminate its spread. Research programs are emerging and maturing at multiple universities and government agencies. These are developing in parallel with little coordination. For example, within institutions of higher education located in the Midwest alone, three large studies have been initiated within the last two years to investigate the role of movement behavior in shaping epidemiological models of CWD. Our intent is to form a multistate consortium designed to improve information exchange among universities and researchers with common goals, but different backgrounds and knowledge bases. Increased collaboration would improve research quality and avoid duplication of work at a critical time when effective solutions are needed quickly.
Regional assessment of cause-specific mortality in white-tailed deer populations, and influence of landscape attributes and deer density on CWD spread through juvenile deer dispersal and seasonal movements	August 2021	Collaborator providing GPS locations from white-tailed deer in the Mid-Atlantic Region and Lead Role in identifying definition of dispersal and risk of infection across the landscape	Results from a multitude of adult white-tailed deer survival studies across the Upper Midwest have been published in peer-reviewed journals. However, the scope of inference was limited because data from each study represented only one or two areas, and the variation in timing among research projects has not allowed a meta-analysis. Recently initiated concurrent research projects in Michigan, Minnesota, Pennsylvania and Wisconsin related to the discovery and spread of chronic wasting disease (CWD) has afforded an opportunity to combine information to make more robust and larger-scale spatial inference about deer survival.<br>This proposal attempts to harness data from the concurrent CWD research activities being undertaken by states’ wildlife management agencies. These various research projects each entail annually marking adult deer with GPS collars in Michigan (Lansing and Upper Peninsula), southeastern Minnesota, Pennsylvania, and southwestern Wisconsin for at least 2 years. Additional data may be available from radiocollared deer in study areas representing central and northcentral Pennsylvania.
A standardized, high-throughput genetic resource to inform white-tailed deer population and disease management	August 2021	Current techniques to manage genetic data of white-tailed deer and disease have significant limitations, including high costs, slow results and difficulty in standardization. This study will design a new suite of efficient, cost-effective, collaborative genomic resources for white-tailed deer that will be commercially available to wildlife managers and researchers at roughly half the current cost.	The majority of ecological genetic studies that have been conducted on white-tailed deer have employed 10-15 microsatellite markers to investigate population structure and relatedness or Sanger sequencing/targeted SNP assays to investigate variation at the PRNP gene. However, a number of genetic technologies have been developed over the last few years that could significantly decrease costs and increase resolution of ecological genetic analysis in deer. Dr. Chris Seabury at Texas A&M has sequenced hundreds of full whitetail deer genomes and is currently developing high-density SNP arrays containing hundreds of thousands of SNPs using these data. These sequence data could be used to develop a smaller and more cost-effective panels for parentage/population structure analyses and PRNP genotyping. Principal Investigators have identified three new approaches that could be used to conduct genetic analysis in deer: (1) genomic analyses using thousands of SNPs to investigate fine-scale population structure and local adaptation, (2) SNP panel analysis using hundreds of SNPs to investigate coarse population structure, conduct parentage analysis, and identify PRNP variation, and (3) PRNP genotyping using amplicon sequencing.
Scale, Space, and Time: A Unifying Approach to Aquatic Invasions	December 2026	Species invasions are a major catalyst in the global biodiversity crisis, with particularly acute effects in river ecosystems. Yet despite decades of research, ecology still faces a glaring paradox: Many invasion theories are at odds with one another, but each is supported by strong empirical evidence. The paradox exists because studies have been constrained in three key dimensions: <i>scale, space, and time</i>. Using riverine fishes as a model system, the project team will integrate invasion theories to develop a more unified framework of species invasions. Because this research will be broadly applicable to other systems and taxa, it will support our partners, including state and federal fish and wildlife agencies, in their management decision making processes designed to prevent, manage, and predict the spread of invasive species.	Species invasions are a major catalyst in the global biodiversity crisis, with particularly acute effects in river ecosystems. Yet despite decades of research, ecology still faces a glaring paradox: Many invasion theories are at odds with one another, but each is supported by strong empirical evidence. The paradox exists because studies have been constrained in three key dimensions: <i>scale, space, and time</i>. Using riverine fishes as a model system, the project team will integrate invasion theories to develop a more unified framework of species invasions. Because this research will be broadly applicable to other systems and taxa, it will support our partners, including state and federal fish and wildlife agencies, in their management decision making processes designed to prevent, manage, and predict the spread of invasive species.
Quantifying the impacts of climate change on fish growth and production to enable sustainable management of diverse inland fisheries	August 2022	Fisheries managers in Midwestern lakes and reservoirs are tasked with balancing multiple management objectives related to the abundance and growth of several priority fish species across a landscape of diverse lakes. Growth rates of fish are indicators of population status, and directly influence the effectiveness of regulations designed to protect spawning fish or to promote trophy fishing opportunities. Growth, combined with reproduction and survival, also determines the amount of fish biomass available for harvest, known as population production. Changing water temperatures can influence growth and production of managed fish species in multiple and complex ways, increasing the opportunity for harvest in certain locations and decreasing it in others. In this project, we will quantify how climate change influences growth and productivity of priority fish species in lakes and reservoirs throughout the Midwest. This information will enable managers to adapt management objectives to take advantage of increased growth and harvest potential in certain places, while implementing protective actions where climate change is likely to have negative effects. Such work is particularly important given that climate change impacts on fish populations are often indirect, influencing species interactions, growth rates, and recruitment in ways that are often counterintuitive and vary across the landscape of Midwestern Lakes and reservoirs.	Climate change is altering all aspects of freshwaters, with important implications for managed fisheries. Both individual growth and population production are fundamental metrics for designing and evaluating effective regulations. Partners in this research include state fisheries management agencies of Iowa, Michigan, Minnesota, Missouri, and Wisconsin, in addition to USGS National Climate Adaptation Center, the University of Minnesota, University of Wisconsin, Michigan State University, and the University of Missouri. Results of this project will be used to inform managers about the effectiveness of length-based regulations under changing climates, in addition to providing managers with a tool to identify populations most likely to have experienced declines in population productivity.
Changes in forest composition through time due to charcoal production for the iron industry, tree harvest, and deer browse	September 2021	Historic charcoal production is an example of abrupt change across northern Appalachian forest ecosystems that we hypothesize has had a lasting effect on forests; forest managers can be better prepared to adapt to future abrupt change by studying this model system of past abrupt change.<br><br>Abrupt changes in a forest ecosystem, whether natural or anthropogenic, are changes that occur over short time periods; such disturbance has the potential to drive state changes and alter forest resilience. Understanding how present-day abrupt forest change may alter ecosystem services is becoming more important due to ever-growing anthropogenic stresses.<br><br>This project is a collaboration of researchers at Penn State University with expertise in soils, forests, and white-tailed deer.<br><br>Forest managers trying the adapt to anthropogenic stress can benefit from the study and quantification of past abrupt changes in forests, especially when the legacy of past disturbance is still evident.	Historic charcoal production is an example of abrupt change across northern Appalachian forest ecosystems that we hypothesize has had a lasting effect on forests; forest managers can be better prepared to adapt to future abrupt change by studying this model system of past abrupt change.<br><br>Abrupt changes in a forest ecosystem, whether natural or anthropogenic, are changes that occur over short time periods; such disturbance has the potential to drive state changes and alter forest resilience. Understanding how present-day abrupt forest change may alter ecosystem services is becoming more important due to ever-growing anthropogenic stresses.<br><br>This project is a collaboration of researchers at Penn State University with expertise in soils, forests, and white-tailed deer.<br><br>Forest managers trying the adapt to anthropogenic stress can benefit from the study and quantification of past abrupt changes in forests, especially when the legacy of past disturbance is still evident.
Snowshoe hare habitat relationships in response to prescribed burn and northern forest management	June 2022	In the face of climate change, land development, and the ephemeral nature of early successional habitats, the Pennsylvania Game Commission needs to develop a comprehensive spatial understanding of snowshoe hare habitat relationships to better understand factors affecting snowshoe hare abundance and distribution in Pennsylvania.<br><br>The snowshoe hare is classified as a game animal (34 Pa. CSA, § 102) and was listed as a species of maintenance concern on Pennsylvania’s 2005 State Wildlife Action Plan due to sensitivity to habitat alteration, apparent decline, and potential importance of Pennsylvania’s population for gene flow between states to the north and south. Currently, the distribution is thought to be limited to mountainous sections of the northern half of Pennsylvania (Merritt 1987) and in small, isolated populations in higher elevations of southern parts of the state (Boyd 2015) in areas where suitable habitats exist (Diefenbach et al. 2016).<br><br>This project is a collaboration with the Pennsylvania Game Commission.<br><br>The findings from this research will help to develop guidelines for habitat managers to consider and implement when managing northern forest habitats, habitats managed with prescribed fire, and for protecting critical habitat features to conserve and expand sustainable snowshoe hare populations.	In the face of climate change, land development, and the ephemeral nature of early successional habitats, the Pennsylvania Game Commission needs to develop a comprehensive spatial understanding of snowshoe hare habitat relationships to better understand factors affecting snowshoe hare abundance and distribution in Pennsylvania.<br><br>The snowshoe hare is classified as a game animal (34 Pa. CSA, § 102) and was listed as a species of maintenance concern on Pennsylvania’s 2005 State Wildlife Action Plan due to sensitivity to habitat alteration, apparent decline, and potential importance of Pennsylvania’s population for gene flow between states to the north and south. Currently, the distribution is thought to be limited to mountainous sections of the northern half of Pennsylvania (Merritt 1987) and in small, isolated populations in higher elevations of southern parts of the state (Boyd 2015) in areas where suitable habitats exist (Diefenbach et al. 2016).<br><br>This project is a collaboration with the Pennsylvania Game Commission.<br><br>The findings from this research will help to develop guidelines for habitat managers to consider and implement when managing northern forest habitats, habitats managed with prescribed fire, and for protecting critical habitat features to conserve and expand sustainable snowshoe hare populations.
Changes in stream fish distribution and occurrence in seven National Park Service units of the Eastern Rivers and Mountains Network	December 2023	The National Park Service (NPS) mission to preserve, protect, and maintain the integrity of park ecosystems for the enjoyment of future generations relies upon access to science-based information regarding the status and trends of ecosystem condition. The Eastern Rivers and Mountains Network (ERMN) includes nine parks located in four states: New York, New Jersey, Pennsylvania, and West Virginia ranging in size from approximately 66 to 30,000 hectares with over 690 km of rivers and streams. The ERMN documents long-term change in the ecological integrity of one of the most abundant surface water ecosystems types in the network (high gradient, wadeable streams) by monitoring stream fish communities. Assessment of changes in fish community composition, occupancy and abundance is necessary in order to ensure the NPS mission is achieved. The project is a collaboration of researchers from USGS, NPS, and Pennsylvania State University. The statistical models developed during this project will inform decision making processes for the management of park ecosystems.	The National Park Service (NPS) mission to preserve, protect, and maintain the integrity of park ecosystems for the enjoyment of future generations relies upon access to science-based information regarding the status and trends of ecosystem condition. The Eastern Rivers and Mountains Network (ERMN) includes nine parks located in four states: New York, New Jersey, Pennsylvania, and West Virginia ranging in size from approximately 66 to 30,000 hectares with over 690 km of rivers and streams. The ERMN documents long-term change in the ecological integrity of one of the most abundant surface water ecosystems types in the network (high gradient, wadeable streams) by monitoring stream fish communities. Assessment of changes in fish community composition, occupancy and abundance is necessary in order to ensure the NPS mission is achieved. The project is a collaboration of researchers from USGS, NPS, and Pennsylvania State University. The statistical models developed during this project will inform decision making processes for the management of park ecosystems.
Determining the consequences of land management actions on fish population dynamics and distributions	May 2025	Better understanding the drivers and stressors affecting fish health, fish habitat and aquatic conditions remains a significant management need in cool and warmwater rivers. Quantifying the effects of land management activities on aquatic ecosystems plays an important role in environmental management and decision-making. This research will address stakeholder needs related to understanding the effects of land management actions on stream and river habitat conditions – habitat that is critical for supporting socioeconomically and ecologically important fish communities throughout the Chesapeake Bay Watershed. The project is a collaboration of researchers across multiple agencies and includes the USGS and state fisheries management agencies across the Chesapeake Bay Watershed. Through the development of several modeling frameworks, this research will focus on quantifying the effects of land management actions on population-level outcomes that are relevant to managers, including effects on abundance, recruitment, the number of spawners, and size structure.	Better understanding the drivers and stressors affecting fish health, fish habitat and aquatic conditions remains a significant management need in cool and warmwater rivers. Quantifying the effects of land management activities on aquatic ecosystems plays an important role in environmental management and decision-making. This research will address stakeholder needs related to understanding the effects of land management actions on stream and river habitat conditions – habitat that is critical for supporting socioeconomically and ecologically important fish communities throughout the Chesapeake Bay Watershed. The project is a collaboration of researchers across multiple agencies and includes the USGS and state fisheries management agencies across the Chesapeake Bay Watershed. Through the development of several modeling frameworks, this research will focus on quantifying the effects of land management actions on population-level outcomes that are relevant to managers, including effects on abundance, recruitment, the number of spawners, and size structure.
Fish habitat restoration to promote adaptation: resilience of sport fishing in lakes of the Upper Midwest	July 2025	Climate change is influencing fish communities in lakes throughout the upper Midwest. Popular sport fish such as walleye are declining in many lakes, while warmwater species such as largemouth bass are increasing. However, not all lakes or fish species respond in the same way, even when they experience the same conditions. In some cases, local management actions such as restoration or protection of lake habitat can slow down or mitigate the negative effects of climate change on economically and ecologically important fish species. This project aims to understand how multiple fish species (walleye, yellow perch, northern pike, largemouth and smallmouth bass, and cisco) with different temperature preferences respond to climate change, and how their responses are affected by lake habitat conditions. Researchers will develop models to predict responses to climate change in tens of thousands of lakes in the upper Midwest. By identifying habitat factors that make certain lakes more or less vulnerable to climate change, this research will enable lake and watershed managers to prioritize management actions aimed at reducing the negative effects of climate change. At the same time, lakes where certain species are unlikely to exist under future conditions will also be identified, which will enable managers and citizens to prepare for shifts in fish community composition. Project results will be communicated to managers and the public using online data visualization and communication tools to demonstrate how lakes in the Midwest are affected by climate change and identify lakes where local actions may be effective in preserving cold- and coolwater fish species as the climate warms.<br><br>The project is a collaboration of researchers across multiple agencies and includes the University of Minnesota, University of Missouri, USGS, Wisconsin DNR, Minnesota DNR, Midwest Glacial Lakes Partnership, and Michigan DNR.	Climate change is influencing fish communities in lakes throughout the upper Midwest. Popular sport fish such as walleye are declining in many lakes, while warmwater species such as largemouth bass are increasing. However, not all lakes or fish species respond in the same way, even when they experience the same conditions. In some cases, local management actions such as restoration or protection of lake habitat can slow down or mitigate the negative effects of climate change on economically and ecologically important fish species. This project aims to understand how multiple fish species (walleye, yellow perch, northern pike, largemouth and smallmouth bass, and cisco) with different temperature preferences respond to climate change, and how their responses are affected by lake habitat conditions. Researchers will develop models to predict responses to climate change in tens of thousands of lakes in the upper Midwest. By identifying habitat factors that make certain lakes more or less vulnerable to climate change, this research will enable lake and watershed managers to prioritize management actions aimed at reducing the negative effects of climate change. At the same time, lakes where certain species are unlikely to exist under future conditions will also be identified, which will enable managers and citizens to prepare for shifts in fish community composition. Project results will be communicated to managers and the public using online data visualization and communication tools to demonstrate how lakes in the Midwest are affected by climate change and identify lakes where local actions may be effective in preserving cold- and coolwater fish species as the climate warms.<br><br>The project is a collaboration of researchers across multiple agencies and includes the University of Minnesota, University of Missouri, USGS, Wisconsin DNR, Minnesota DNR, Midwest Glacial Lakes Partnership, and Michigan DNR.
Diet composition of invasive Flathead Catfish in the Susquehanna River Basin: quantifying impacts on native and migratory fishes and recreational fisheries	January 2022	Flathead Catfish are an indiscriminate predator of other fish and an expanding invader to large river systems outside of its native range, including the Susquehanna River Basin in Pennsylvania. Research efforts are beginning to provide insight on the distribution of this invader in the Susquehanna River Basin, however, there is considerable uncertainty about the potential ecological impacts of Flathead Catfish. In particular, there are concerns about their impacts on native and migratory fish species and on economically important recreational fisheries. To begin understanding the ecological effects of Flathead Catfish invasion, we propose a comprehensive diet study on Flathead Catfish in the Susquehanna River Basin. We will quantify Flathead Catfish diet composition using morphology and molecular identification of ingested prey items. Our study will help inform future fisheries management in the Susquehanna River Basin by increasing our understanding about the predatory effects and potential ecological consequences of invasive Flathead Catfish. The project is in collaboration with the Pennsylvania Fish and Boat Commission and Penn State University.	Flathead Catfish are an indiscriminate predator of other fish and an expanding invader to large river systems outside of its native range, including the Susquehanna River Basin in Pennsylvania. Research efforts are beginning to provide insight on the distribution of this invader in the Susquehanna River Basin, however, there is considerable uncertainty about the potential ecological impacts of Flathead Catfish. In particular, there are concerns about their impacts on native and migratory fish species and on economically important recreational fisheries. To begin understanding the ecological effects of Flathead Catfish invasion, we propose a comprehensive diet study on Flathead Catfish in the Susquehanna River Basin. We will quantify Flathead Catfish diet composition using morphology and molecular identification of ingested prey items. Our study will help inform future fisheries management in the Susquehanna River Basin by increasing our understanding about the predatory effects and potential ecological consequences of invasive Flathead Catfish. The project is in collaboration with the Pennsylvania Fish and Boat Commission and Penn State University.
Quantifying the Roles of Changing Watershed Conditions and Biotic Interactions in Structuring Pennsylvania Stream Fish Communities	January 2022	Understanding and predicting fish community interactions and their response to environmental stressors is of utmost importance for fisheries and water resource management. For example, state agencies and other water resource agencies rely on knowledge of stream and river fish communities for assessment programs, many of which have regulatory ramifications and implications for water and fisheries management and aquatic resource use activities. However, traditional fish community studies fail to accommodate potential interactions that exist among the entire fish assemblage and thus represent an overly simplistic view of community dynamics. This is important because treating species independently when quantifying and predicting their responses to changing watershed conditions ignores potential dependencies between species due to biotic interactions and can lead to erroneous predictions. Therefore, the overarching goal of this research is to help inform fisheries and water resource management and conservation by improving our understanding of the relative roles of fish species interactions, environmental factors, and how species traits influence a species’ response to changing watershed conditions in Pennsylvania streams and rivers. The project is in collaboration with the Pennsylvania Fish and Boat Commission, the Pennsylvania Department of Environmental Protection, the Susquehanna River Basin Commission, and Penn State University.	Understanding and predicting fish community interactions and their response to environmental stressors is of utmost importance for fisheries and water resource management. For example, state agencies and other water resource agencies rely on knowledge of stream and river fish communities for assessment programs, many of which have regulatory ramifications and implications for water and fisheries management and aquatic resource use activities. However, traditional fish community studies fail to accommodate potential interactions that exist among the entire fish assemblage and thus represent an overly simplistic view of community dynamics. This is important because treating species independently when quantifying and predicting their responses to changing watershed conditions ignores potential dependencies between species due to biotic interactions and can lead to erroneous predictions. Therefore, the overarching goal of this research is to help inform fisheries and water resource management and conservation by improving our understanding of the relative roles of fish species interactions, environmental factors, and how species traits influence a species’ response to changing watershed conditions in Pennsylvania streams and rivers. The project is in collaboration with the Pennsylvania Fish and Boat Commission, the Pennsylvania Department of Environmental Protection, the Susquehanna River Basin Commission, and Penn State University.
Comparison of age and growth parameters of Flathead Catfish in invasive and native populations: A meta-analysis with implications for invasive species management in Pennsylvania	January 2020	Flathead catfish (Pylodictis olivaris) are a long-live apex predator native to the Mississippi, Mobile and Rio Grande drainages, and the Laurentian Great Lakes region. These fish have been introduced into most of the East Coast and areas of the Western US. Introduced Flathead Catfish populations often have detrimental effects on native fauna. In the Atlantic Slope portions of Pennsylvania the status of flathead catfish has not been adequately documented. Several large to medium-sized river systems in Pennsylvania have yet to be surveyed so the residency status of flathead catfish in those systems remains unknown. The primary objective of the project will be to determine flathead catfish distribution, and estimate abundance and population characteristics for both native and introduced populations in Pennsylvania. Much of the focus of the analysis will include age and growth analysis and modeling to put the current population status in the introduced range in a larger regional context for management purposes moving forward. Several other Atlantic Slope drainage have encountered similar invasions in recent decades so comparison with Pennsylvania populations with those will help to predict what to expect moving forward with existing populations as well as in areas where they have not yet invaded.	Flathead catfish (Pylodictis olivaris) are a long-live apex predator native to the Mississippi, Mobile and Rio Grande drainages, and the Laurentian Great Lakes region. These fish have been introduced into most of the East Coast and areas of the Western US. Introduced Flathead Catfish populations often have detrimental effects on native fauna. In the Atlantic Slope portions of Pennsylvania the status of flathead catfish has not been adequately documented. Several large to medium-sized river systems in Pennsylvania have yet to be surveyed so the residency status of flathead catfish in those systems remains unknown. The primary objective of the project will be to determine flathead catfish distribution, and estimate abundance and population characteristics for both native and introduced populations in Pennsylvania. Much of the focus of the analysis will include age and growth analysis and modeling to put the current population status in the introduced range in a larger regional context for management purposes moving forward. Several other Atlantic Slope drainage have encountered similar invasions in recent decades so comparison with Pennsylvania populations with those will help to predict what to expect moving forward with existing populations as well as in areas where they have not yet invaded.
Bobcat population dynamics on Cumberland Island National Seashore	December 2020	Bobcats were reintroduced to Cumberland Island National Seashore in 1988-1989 to restore a native predator. The reintroduction of bobcats has reduced the deer population and allowed natural regeneration of live oaks and other plant species. Although bobcats bobcat populations are secure throughout their range, most felid species are threatened or endangered. The population on Cumberland Island can be considered equivalent to an endangered population (<30 individuals) because natural immigration is extremely rare. We are studying the population dynamics and monitoring the genetic status of bobcats on the island to better understand when this population undergoes genetic bottlenecks and whether conservation actions are warranted to ensure the sustainability of the population on the island.<br><br>This research is supported by the Pennsylvania Game Commission and the National Park Service.	Bobcats were reintroduced to Cumberland Island National Seashore in 1988-1989 to restore a native predator. The reintroduction of bobcats has reduced the deer population and allowed natural regeneration of live oaks and other plant species. Although bobcats bobcat populations are secure throughout their range, most felid species are threatened or endangered. The population on Cumberland Island can be considered equivalent to an endangered population (<30 individuals) because natural immigration is extremely rare. We are studying the population dynamics and monitoring the genetic status of bobcats on the island to better understand when this population undergoes genetic bottlenecks and whether conservation actions are warranted to ensure the sustainability of the population on the island.<br><br>This research is supported by the Pennsylvania Game Commission and the National Park Service.
Fawn survival and predator abundance in Pennsylvania	June 2020	Predation is the primary cause of white-tailed deer fawn mortality and is of concern to the hunting public. In this study we monitored survival and cause-specific mortality of fawns and the distribution and abundance of predators (black bear, coyote, and bobcat). The project was funded by the Pennsylvania Game Commission and conducted in collaboration with the USGS Pennsylvania Cooperative Fish and Wildlife Research Unit.	Predation is the primary cause of white-tailed deer fawn mortality and is of concern to the hunting public. In this study we monitored survival and cause-specific mortality of fawns and the distribution and abundance of predators (black bear, coyote, and bobcat). The project was funded by the Pennsylvania Game Commission and conducted in collaboration with the USGS Pennsylvania Cooperative Fish and Wildlife Research Unit.
An investigation into the role of groundwater as a point source of emerging contaminants to smallmouth bass in the Susquehanna River basin	March 2018	There is currently a paucity of information on the role of groundwater discharge into surface waters as point sources of contaminants from polluted aquifers. This is critical to understand because the use of groundwater seeps are important for smallmouth bass, particularly during spawning season, and there use is related to increased hatch success and survival of age 0 fish. In addition, previous work has shown smallmouth bass utilizing areas of groundwater upwelling for spawning in the Susquehanna River basin. Exposure to EDCs during this critical life-stage of egg development could have detrimental short- and long-term consequences on immune function and fish health. Therefore, the objective of this research is to investigate the role of groundwater as a point source of emerging contaminants to smallmouth bass in the Susquehanna River basin.	None
Preliminary determination of density and distribution of Flathead Catfish Pylodictis olivaris in the Susquehanna River and select tributaries	December 2017	The goal of this project is to estimate the relative abundance and age and growth characteristics of invasive Flathead Catfish in three reaches of the mainstem Susquehanna River with different degrees of population establishment. By examining river reaches with different degrees of population establishment, data collected during this study will serve to help understand current distribution and population characteristics (e.g., size distribution, growth rates). In addition, we will develop models (based on population vital rates and habitat use) to predict future changes in establishing populations as well as to evaluate potential impacts to areas where Flathead Catfish have not yet invaded. These models can be used to help inform management of Flathead Catfish and native species throughout the Susquehanna River Basin.	None
A macrosystems ecology framework for continental-scale prediction and understanding of lakes	September 2023	In the past decade, our understanding of how inland waters influence regional, continental, and global biogeochemical cycles has fundamentally changed. We have moved from discounting their contributions, to now recognizing these ecosystems as significant hotspots for the storage and transformation of nitrogen, phosphorus, and carbon. This realization has come about through careful and labor-intensive collection, integration, and synthesis of often-scattered data sources, combined with a variety of different approaches to extrapolate site-level measures to unsampled sites across regions and continents. Today, although this view of the role of inland waters in large-scale cycling is supported by numerous studies, substantial gaps in our understanding remain. Estimates for the same flux (e.g., organic carbon burial in lakes) often differ substantially among studies. Further, most attempts to quantify continental or global fluxes or pools come with caveats regarding the often high– and often unknown– uncertainty associated with these estimates. To better understand the role of inland waters in macroscale nutrient cycling, new approaches are needed to reduce uncertainty in extrapolating site-level estimates to larger geographical scales. The overarching goal of this research is to understand and predict nutrient patterns for ALL continental US lakes to inform estimates of lake contributions to continental and global cycles of nitrogen (N), phosphorus (P), and carbon (C), while also providing locally valuable information about conditions in unsampled lakes.	Inland waters are significant hotspots for the storage and transformation of nitrogen, phosphorus, and carbon and influence regional, continental, and global biogeochemical cycles. However, most attempts to quantify continental or global fluxes or pools come with caveats regarding the often high– and often unknown– uncertainty associated with these estimates. To better understand the role of inland waters in macroscale nutrient cycling, new approaches are needed to reduce uncertainty in extrapolating site-level estimates to larger geographical scales. The project is a collaboration of researchers across multiple agencies and includes the USGS, Michigan State University, The Pennsylvania State University, University of Wisconsin, and the University of Missouri. The overarching goal of this research is to understand and predict nutrient patterns for all continental US lakes to inform estimates of lake contributions to continental and global cycles of nitrogen (N), phosphorus (P), and carbon (C), while also providing locally valuable management information about conditions in unsampled lakes. This work will improve understanding of the role of inland waters in macroscale nutrient cycling.
Establishing a strategy for assessing risk of endocrine-disrupting compounds to aquatic and terrestrial organisms	September 2019	Endocrine disruption is a national and global concern that affects fish, wildlife and human populations. Through interactions with neural, endocrine, and immune systems, endocrine disrupting compounds (EDCs) can influence growth, development, reproduction, disease, and mortality, with adverse outcomes for populations, communities, and ecosystems. Within the Chesapeake Bay, understanding the effects of EDCs on fish and wildlife populations has been identified as a priority to help inform natural resource management. Specifically, there is a need for assessing the risk of EDCs to fish and wildlife populations and their health. The risk assessment will integrate our understanding of the (1) population dynamics of the fish or wildlife species of interest, (2) mechanisms through which EDCs interact with individuals, and (3) exposure pathways between sources of EDCs, including hydrological conditions and land use practices, and fish and wildlife populations. This will help identify short and long-term impacts of compounds or classes of chemicals of concern, potential environmental conditions and stressors that may mediate the effects of EDCs, and how land use management practices may reduce exposure to EDCs.	None
Modeling potential habitat for pheasant population restoration	December 2017	The Pennsylvania Game Commission (PGC) has established several Wild Pheasant Restoration Areas (WPRAs) with specific population density goals (10 hen pheasants per square mile). Research being conducted on these areas provides an opportunity to evaluate under which habitat conditions wild pheasant populations have met established pheasant density goals. If additional WPRAs are going to be considered in Pennsylvania it would be useful to have a predictive model to assess existing landscapes to determine if pheasant restoration is possible or what habitat changes would be required to ensure success of the WPRA.	<b>Problem Statement:</b> Ring-necked pheasant (<i>Phasianus colchicus</i>) densities in Pennsylvania have declined from 15-30 birds/km<sup>2</sup> in 1970 to <1.5 birds/km<sup>2</sup> by the 1990s. Repeated population restoration efforts generally have failed. We used translocations of wild-caught birds released on 4 wild pheasant recovery areas (WPRA) to identify habitat and landscape characteristics associated with female densities of ≥3.86 females/km<sup>2</sup>.<br><br><b>So What? Why this research matters:</b> We used this information to identify locations in Pennsylvania that could be potential pheasant restoration areas. During 2013–2014, we mapped habitat characteristics within 0.56-km radius circles (25 May–11 July) at randomly selected sites where we estimated female pheasant densities.<br><br><b>Collaboration/Partners: </b>This project was a collaboration with the Pennsylvania Game Commission.<br><br><b>Research That Informs Decisions</b>: We identified 4 areas in Pennsylvania totaling 984 km<sup>2</sup> where <10% of land was developed, <7% was forest, and ≥8% of cropland could be enrolled in Conservation Reserve Enhancement Program (CREP). The lack of contiguous pheasant habitat, and even lack of potential habitat, that could sustain a population of wild pheasants suggests that restoration efforts may not be feasible without cooperation from private landowners to enroll ≥20,000 ha of cropland in programs that implement soil and water conservation practices, such as CREP.
Can plasticity protect populations from rapid environmental fluctuation?	May 2018	Rates of population extirpation from habitat loss have reached unprecedented levels and climate change is predicted to be a leading cause of future species extinctions. Accordingly, conservation of emergent properties that promote resistance and resilience to environmental perturbation will be vital to future population persistence. Though it has been demonstrated that phenotypic plasticity increases resilience to habitat loss, the ability for plasticity to promote population persistence under climate change and habitat degradation has not been explored. If plasticity does increase survival, failure to conserve highly plastic genotypes could accelerate species extinction. This research focuses on an economically and socially important species, brook trout (Salvelinus fontinalis), to determine how the interactive effects of genetics and behavior influence differential survival of fish populations under a changing climate.	None

Research Publications

Research Publications	Publication Date
Yuan, S., J. Zhou, P-N., Tan, E. Fergus, T. Wagner, and P.A. Soranno. 2017. Multi-Level Multi-Task Learning for Nested Geospatial Data. The IEEE International Conference on Data Mining series (ICDM).	May 2018
Williamson, L. T., W. David Walter, S. R. Klinger, and D. R. Diefenbach. 2018. Incorporating detection probability to estimate pheasant density. Journal of Wildlife Management. 82(8):1680–1688; DOI: 10.1002/jwmg.21545 \| Download	September 2018
White, S.L., W.L. Miller, S.A. Dowell, M.L. Bartron, and T. Wagner. Accepted. Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking. Evolutionary Applications.	December 2018
White, S.L., T. Wagner, C. Gowand, and V.A. Braithwaite. 2017. Can personality predict individual differences in brook trout spatial learning ability? Behavioural Processes 141:220-228.	September 2016
White, S.L., M.S. Eackles, T. Wagner, M. Schall, G. Smith, J. Avery, and D.C. Kazyak. 2021. Optimization of a suite of flathead catfish (Pylodictis olivaris) microsatellite markers for understanding the population genetics of introduced populations in the northeast United States. BMC Research Notes 14:314.	August 2021
White, S.L., J. Keagy, S. Batchelor, J. Langlois, N. Thomas, and T. Wagner. 2024. Movement beyond the mean: decoupling sources of individual variation in brook trout movement across seasons.Environmental Biology of Fishes 106:2205-2218. https://doi.org/10.1007/s10641-023-01501-2	January 2024
White, S.L., E.M. Hanks, and T. Wagner. 2020. A novel quantitative framework for riverscape genetics. Ecological Applications. https://doi-org.ezaccess.libraries.psu.edu/10.1002/eap.2147	May 2020
White, S.L., D.A. DeMario, L.R. Iwanowicz, V.S. Blazer, and T. Wagner. 2020. Tissue distribution and immunomodulation in channel catfish (Ictalurus punctatus) following dietary exposure to polychlorinated biphenyl Aroclors and food deprivation. Int J Environ Res Public Health: 17(4). pii: E1228. doi: 10.3390/ijerph17041228	February 2020
White, S.L., B.C. Kline, N.P. Hitt, and T. Wagner. 2019. Individual behaviour and resource use of thermally stressed brook trout Salvelinus fontinalis portend the conservation potential of thermal refugia. Journal of Fish Biology 95:1061-1071.	September 2019
White, S.L. and T. Wagner. 2020. Behavior at short temporal scales drives dispersal dynamics and survival in a metapopulation of brook trout (Salvelinus fontinalis). Freshwater Biology.	November 2020
White, S., E. Faulk, C. Tzilkowski, A.S. Weber, M. Marshall, and T. Wagner. 2020. Predicting fish species richness and habitat relationships using Bayesian hierarchical multispecies occupancy models. Canadian Journal of Fisheries and Aquatic Sciences 77:602-610.	January 2020
White, S., D. DeMario, L. Iwanowicz, V. Blazer, and T. Wagner. 2020. Tissue distribution and immunomodulation in channel catfish (Ictalurus punctatus) following dietary exposure to polychlorinated biphenyl Aroclors and food deprivation. Int J Environ Res Public Health: 17(4). pii: E1228. doi: 10.3390/ijerph17041228	February 2020
Weiderholt, R., R. Fernandez-Duque, D. R. Diefenbach, and R. Rudran. 2010. Modeling the impacts of hunting on the population dynamics of red howler monkeys (Alouatta seniculus). Ecological Modelling 221:2482-2290. \| Abstract	August 2010	Overexploitation of wildlife populations occurs across the humid tropics and is a significant threat to the long-term survival of large-bodied primates. To investigate the impacts of hunting on primates and ways to mitigate them, we developed a spatially explicit, individual-based model for a landscape that included hunted and un-hunted areas. We used the large-bodied neotropical red howler monkey (Alouatta seniculus) as our case study species because its life history characteristics make it vulnerable to hunting. We modeled the influence of different rates of harvest and proportions of landscape dedicated to un-hunted reserves on population persistence, population size, social dynamics, and hunting yields of red howler monkeys. In most scenarios, the un-hunted populations maintained a constant density regardless of hunting pressure elsewhere, and allowed the overall population to persist. Therefore, the overall population was quite resilient to extinction; only in scenarios without any un-hunted areas did the population go extinct. However, the total and hunted populations did experience large declines over 100 years under moderate and high hunting pressure. In addition, when reserve area decreased, population losses and losses per unit area increased disproportionately. Furthermore, hunting disrupted the social structure of troops. The number of male turnovers and infanticides increased in hunted populations, while birth rates decreased and exacerbated population losses due to hunting. Finally, our results indicated that when more than 55% of the landscape was harvested at high (30%) rates, hunting yields, as measured by kilograms of biomass, were less than those obtained from moderate harvest rates. Additionally, hunting yields, expressed as the number of individuals hunted/year/km2, increased in proximity to un-hunted areas, and suggested that dispersal from un-hunted areas may have contributed to hunting sustainability. These results indicate that un-hunted areas serve to enhance hunting yields, population size, and population persistence in hunted landscapes. Therefore, spatial regulation of hunting via a reserve system may be an effective management strategy for sustainable hunting, and we recommend it because it may also be more feasible to implement than harvest quotas or restrictions on season length.
Walter,W.D. ,Fischer,J.W. Anderson,C.W., Marks,D.R., Deliberto,T., Robbe-Austerman,S., VerCauteren,K.C. 2013. Surveillance and movements of Virginia opossum (Didelphis virginiana) in the bovine tuberculosis region of Michigan. Epidemiology and Infection, Special Issue on TB, 141(7): 1498-1508. \| Abstract \| Publisher Website	June 2013	Wildlife reservoir hosts of bovine tuberculosis (bTB) include Eurasian badgers (Meles meles) and brushtail possum (Trichosurus vulpecula) in the UK and New Zealand, respectively. Similar species warrant further investigation in the northern lower peninsula of Michigan, USA due to the continued presence of bTB on cattle farms. Most research in Michigan, USA has focused on interactions between white-tailed deer (Odocoileus virginianus) and cattle (Bos taurus) for the transmission of the infectious agent of bTB, Mycobacterium bovis, due to high deer densities and feeding practices. However, limited data are available on medium-sized mammals such as Virginia opossum (Didelphis virginiana; hereafter referred to as opossum) and their movements and home range in Michigan near cattle farms. We conducted surveillance of medium-sized mammals on previously depopulated cattle farms for presence of M. bovis infections and equipped opossum with Global Positioning System (GPS) technology to assess potential differences in home range between farms inside and outside the bTB core area that has had cattle test positive for M. bovis. On farms inside the bTB core area, prevalence in opossum was comparable [6%, 95% confidence interval (CI) 2·0–11·0] to prevalence in raccoon (Procyon lotor; 4%, 95% CI 1·0–9·0, P = 0·439) whereas only a single opossum tested positive for M. bovis on farms outside the bTB core area. The prevalence in opossum occupying farms that had cattle test positive for M. bovis was higher (6·4%) than for opossum occupying farms that never had cattle test positive for M. bovis (0·9%, P = 0·01). Mean size of home range for 50% and 95% estimates were similar by sex (P = 0·791) both inside or outside the bTB core area (P = 0·218). Although surveillance efforts and home range were not assessed on the same farms, opossum use of farms near structures was apparent as was selection for farms over surrounding forested habitats. The use of farms, stored feed, and structures by opossum, their ability to serve as vectors of M. bovis, and their propensity to ingest contaminated sources of M. bovis requires additional research in Michigan, USA.
Walter, W.D., T.S. Evans, D. Stainbrook, B.D. Wallingford, C.S. Rosenberry, and D.R. Diefenbach. 2018. Heterogeneity of a landscape influences size of home range in a North American cervid. Scientific Reports 8:14667. DOI:10.1038/s41598-018-32937-7. \| Abstract \| Download \| Publisher Website	September 2018	Spatial heterogeneity, or composition and configuration of a landscape, plays a role in many biological and ecological processes. In spatial ecology, understanding movements of a species in relation to the landscape can assist wildlife managers in better understanding other processes, including habitat use and disease transmission. In the northeastern United States (Northeast), chronic wasting disease has been detected in populations of white-tailed deer (Odocoileus virginianus), and understanding the relationship between landscape and size of home range may provide a basis for disease surveillance and containment efforts. The objectives of our study were to (1) compare size of home range between sexes and among study areas for white-tailed deer occupying a continuum of forested landscapes from highly fragmented to contiguous and (2) investigate relationships between size of home range and measures of landscape composition and configuration. We observed differences in size of 95% home range between males (3.77 km2) and females (1.83 km2) across all study areas, as well as between deer in highly fragmented and contiguous landscapes. We developed 20 linear regression models that contained measures of landscape that were correlated with size of home range, and the best model showed that size of home range increased with connectivity of forest cover. Understanding this relationship may provide a foundation for disease surveillance efforts, because size of home range may represent the scale at which disease will spread. Therefore surveillance should be conducted in a manner that reflects connectivity of landscape at a local scale.
Walter, W.D., R. Smith, M. Vanderklok, and K.C. VerCauteren. 2014. Linking bovine tuberculosis on cattle farms to white-tailed deer and environmental variables using Bayesian hierarchical analysis. Plos ONE 9(3):e90925. \| Abstract	March 2014	Bovine tuberculosis is a bacterial disease caused by Mycobacterium bovis in livestock and wildlife with hosts that include Eurasian badgers (Meles meles) and brushtail possum (Trichosurus vulpecula) in Europe and white-tailed deer (Odocoileus virginianus) in North America. Basic risk-assessment efforts have been initiated on farms to minimize interactions of cattle with wildlife hosts but research of M. bovis on cattle farms has not investigated the spatial context of disease epidemiology. To incorporate spatially explicit data, initial likelihood of infection probabilities for cattle farms tested for M. bovis, prevalence of M. bovis in white-tailed deer, deer density, and environmental variables for each farm were modeled in a Bayesian hierarchical structure. We used geo-referenced locations of 757 cattle farms that have been tested for M. bovis since 1997 in the Modified Accredited Zone of the upper, lower peninsula of Michigan. We incorporated white-tailed deer prevalence and several environmental variables that may lead to long-term survival and viability of M. bovis on farms and surrounding habitats (i.e., soil type, habitat type). Bayesian hierarchical analyses identified deer prevalence and proportion of sandy soil within our sampling grid as the most supported model. Analysis of cattle farms tested for M. bovis identified that for every 1% increase in sandy soil resulted in an increase in odds of infection by up to 4%. Our analysis revealed that the influence of prevalence of M. bovis in white-tailed deer, although still a factor, has likely decrease in response to considerable efforts to prevent cattle interactions with white-tailed deer through on-farm mitigation and reduction in the deer population. Cattle farms test positive for M. bovis annually in our study area suggesting that the potential for an environmental source either on farms or in the surrounding landscape may contributing to new or re-infections with M. bovis. Our research provides an initial assessment of potential environmental factors that could be incorporated into additional modeling efforts as more knowledge of deer herd factors and cattle farm prevalence is documented.
Walter, W.D., J.W. Fischer, T.J. Zimmerman, S.E. Hygnstrom, J.A. Jenks, K.C. VerCauteren. 2013. Topographic home range of large mammals: is planimetric home range still a viable method? Prairie Naturalist 45(1): 21-27. \| Abstract	June 2013	Topography influences movement trajectories, quality of forages used, and behavioral response of large herbivores to anthropogenic disturbances, but research is lacking on the influence of terrain complexity on size of home range. Size of home range usually is based on planimetric area and therefore rarely accounts for the true surface area traversed by an animal. We conducted radiotelemetry on bighorn sheep (Ovis canadensis), Rocky Mountain elk (Cervus elaphus), mule deer (Odocoileus hemionus), and white-tailed deer (O. virginianus) equipped with VHF collars at 3 sites from 2002 to 2006 to document size of home range in areas that ranged from 400 m to 1,500 m in elevation with varying degrees of topographic ruggedness in the Great Plains. We used the fixed-kernel method to compare size of 95% home range between 2-dimensional (planimetric) and 3-dimensional (topographic) estimates. Mean (± SD) percent increase in size of home range from planimetric to topographic was 2.8% (± 0.19), 1.2 % (± 0.52), 1.0% (± 0.43), and 0.1% (± 0.40) for bighorn sheep, elk, mule deer, and white-tailed deer, respectively. We found little difference in size between planimetric and topographic home range for our species suggesting that planimetric home range techniques are likely valid in the Great Plains and similar regions but both home range methods should be compared in other regions with high topographic relief (e.g., Rocky Mountain region).
Walter, W.D., J.W. Fischer, M.A. Avery J.S. Humphrey, T.S. Daughtery, M.P. Milleson, and E.A. Tillman. 2012. Using three-dimensional flight patterns at airfields to identify hotspots for avian-aircraft collisions. Applied Geography 35:53-59. \| Download \| Publisher Website	June 2012
Walter, W.D., D.P. Onorato, and J.W. Fischer. 2015. Is there a single best estimator? Selection of home range estimators using area- under- the-curve. Movement Ecology \| Abstract \| Download	May 2015	1. Global positioning system technology for monitoring home range and movements of wildlife has resulted in datasets that are too numerous for traditional estimators of home range. 2. We used area-under-the-curve to explore the fit of 8 estimators of home range to data collected with global positioning system technology and concurrent very high frequency technology on a terrestrial mammal, the Florida panther Felis concolor coryi. 3. area-under-the-curve differed among several estimators with the highest area-under-the-curve scores occurring for Florida panthers equipped with global positioning systems technology. 4. For our study mammal, models identified number of locations, global positioning system schedule, and characteristics of study area influenced area-under-the-curve scores. 5. Synthesis and applications. Comparisons of fit of home range contours with locations collected would suggest that use of very high frequency technology should no longer be considered to estimate size of home range. Estimators of home range collected with global positioning system technology performed better than those estimated with very high frequency technology regardless of estimator used. Further, estimators that incorporate a temporal component (third-generation estimators) appeared to be the most reliable regardless of whether kernel-based or Brownian bridge-based algorithms and in comparison to first- and second-generation estimators. Third-generation estimators of home range should be defined as any estimator that incorporates time, space, animal-specific parameters, and habitat such as movement-based kernel density, Brownian bridge movement models and dynamic Brownian bridge movement models among others that have yet to be evaluated.
Walter, W.D., C.W. Anderson, and K.C. VerCauteren. 2012. Evaluation of remote delivery of passive infrared transponder (PIT) technology to mark large mammals. Plos ONE 7(9): e44838 \| Download \| Publisher Website	September 2012
Walter, W.D., C. W. Anderson, R. Smith, M. Vanderklok, J. Averill, and K.C. VerCauteren. 2012. On-farm mitigation of transmission of tuberculosis from white-tailed deer to cattle: literature review and recommendations. Veterinary Medicine International Article ID 616318. \| Download \| Publisher Website	September 2012
Walter, W.D. and J.W. Fischer. Manual of Applied Spatial Ecology. Online: \| Abstract \| Publisher Website	October 2014	Advances in data handling and manipulation, GIS capabilities, and methods of estimators for home range, movements, resource selection, and spatial epidemiology have occurred within the R environment. Considering that R is free to users, R also provides a platform to create and display spatial layers without the need for the variety of GUI software, free or otherwise. Furthermore, analyzing spatial data in R enables statistical analysis of data without the errors that may arise from bringing data from spreadsheet or GIS software to statistical programs. An online manual could be easily followed by researchers, biologists, or graduate students to analyze their data in R. We provide numerous citations throughout each section should the user choose to learn the theory
Walter, W.D. 2014. Use of stable isotopes to identify dietary differences and subpopulations of a free-ranging generalist herbivore. Isotopes in Environmental and Health Studies 50(3):399-413.	August 2014
Walter, W. D., B. Hanley, C. E. Them, C. I. Mitchell, J. Kelly, D. Grove, N. Hollingshead, R. C. Abbott, and K. L. Schuler. 2024. Predicting the odds of chronic wasting disease with Habitat Risk software. Spatial and Spatio-temporal Epidemiology 49:100650. \| Abstract	April 2024	Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (<i>Odocoileus virginianus</i>) populations across the US and Canada. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies have employed epidemiological models to understand long-term environmental risk. However, continued rapid spread of CWD into new regions of the continent has underscored the need for extension of these models into broader tools applicable for wide use by wildlife agencies. Additionally, efforts to semi-automate models will facilitate access of technical scientific methods to broader audiences. We introduce software (<i>Habitat Risk</i>) designed to link a previously published epidemiological model with spatially referenced environmental and disease testing data enabling agency personnel to make up-to-date, localized, data-driven predictions regarding the odds of CWD infection in surrounding areas after an outbreak is discovered. <i>Habitat Risk</i> requires pre-processing publicly available environmental datasets and standardization of disease testing (surveillance) data, after which an autonomous computational pipeline terminates in a user interface that displays an interactive map of disease risk. We demonstrated the use of the <i>Habitat Risk </i>software with surveillance data of white-tailed deer from Tennessee, US. Software to pre-process environmental data is openly available at <i>doi.org/10.7298/2tt1-yy48</i>, while <i>Habitat Risk</i> software is available at <i>doi.org/10.7298/rcz8-nw50</i>.
Wallingford, B. D., D. R. Diefenbach, E. S. Long, C. S. Rosenberry, and G. L. Alt. 2017. Biological and social outcomes of antler point restriction harvest regulations for white-tailed deer. Wildlife Monographs 196. \| Download	January 2017
Wagner, T., and J.A. Sweka. 2011.Evaluation of hypotheses for describing temporal trends in Atlantic salmon parr densities in Northeast U.S. Rivers. North American Journal of Fisheries Management 31:340–351. \| Abstract	May 2011	Atlantic salmon Salmo salar in the USA have declined dramatically and persistence is heavily dependent upon stocking juvenile fish, predominantly fry. The success of stocking hatchery fry is evaluated annually throughout New England by electrofishing surveys targeting age -1 parr. The objective of this study was to examine temporal trends in Atlantic salmon parr densities throughout New England and determine how trends vary among river basins. We fit generalized additive mixed models to investigate potential linear and nonlinear temporal trends in parr density. Akaike’s Information Criterion was used to evaluate competing hypotheses about how temporal trends vary regionally. The top-ranked model suggested two types of trends. The first type, (the Penobscot River) showed a nonlinear trend where parr densities increased until the 1990s and then rapidly decreased to the present time. The second type (all other rivers) showed a linear decrease throughout the time series. Parr density trends reflected trends in spawning escapement for each river group. We conclude that fry stocking has not been able to overcome the decrease in spawning escapement in altered stream ecosystems in New England and additional management strategies should be considered.
Wagner, T., and 7 coauthors. 2010. Spatial and temporal dynamics of lake whitefish (Coregonus clupeaformis) health measures: linking individual-based indicators to a management-relevant endpoint. Journal of Great Lakes Research 36:121-134. \| Abstract	May 2010	We examined the spatial and temporal dynamics of health indicators in four lake whitefish (Coregonus clupeaformis) stocks located in northern lakes Michigan and Huron from 2003 to 2006. The specific objectives were to (1) quantify spatial and temporal variability in health indicators; (2) examine relationships among nutritional indicators and stock-specific spatial and temporal dynamics of pathogen prevalence and intensity of infection; and (3) examine relationships between indicators measured on individual fish and stockspecific estimates of natural mortality. The percent of the total variation attributed to spatial and temporal sources varied greatly depending on the health indicator examined. The most notable pattern was a downward trend in the concentration of highly unsaturated fatty acids (HUFAs), observed in all stocks, in the polar lipid fraction of lake whitefish dorsal muscle tissue over the three study years. Variation among stocks and years for some indicators were correlated with the prevalence and intensity of the swimbladder nematode Cystidicola farionis, suggesting that our measures of fish health were related, at some level, with disease dynamics. We did not find relationships between spatial patterns in fish health indicators and estimates of natural mortality rates for the stocks. Our research highlights the complexity of the interactions between fish nutritional status, disease dynamics, and natural mortality in wild fish populations. Additional research that identifies thresholds of health indicators, below (or above) which survival may be reduced, will greatly help in understanding the relationship between indicators measured on individual fish and potential population-level effects.
Wagner, T., S.R. Midway, T. Vidal, B.J. Irwin, and J.R. Jackson. 2016. Detecting unusual temporal patterns in fisheries time series data. Transactions of the American Fisheries Society 145:786-794. \| Abstract \| Download	June 2016	Fishery-independent surveys are an important source of information for making inferences about the temporal dynamics of ecologically and recreationally important fisheries. For example, time-series of catch per effort data are often examined for the presence of long-term trends. However, it is also of interest to know if certain sampled locations are exhibiting temporal patterns that deviate from the overall pattern exhibited across all sampled locations. These ‘unusual’ sites may be the result of site-specific abiotic (e.g., habitat) or biotic (e.g., the presence of an invasive species) factors that cause them to respond differently to natural or anthropogenic drivers of population dynamics or to management actions. We present a Bayesian model selection approach that allows for detection of ‘unique’ sites—locations that display temporal patterns with documentable inconsistencies from the overall global average temporal pattern. We apply this modeling approach to long-term gillnet data for yellow perch in Oneida Lake, but the approach is also relevant to shorter time-series data. We used this approach to identify six unique temporal patterns among 15 sampled locations, and describe the magnitude of difference between these patterns and the lake-wide average. Detection of unique sites may be informative to management decisions related to prioritization of rehabilitation or restoration efforts, stocking decisions, determination of fishable areas, and to further understanding changes to ecosystem dynamics.
Wagner, T., P.A. Soranno, K.E. Webster, and K. Spence Cheruvelil. 2011. Landscape drivers of regional variation in the relationship between total phosphorus and chlorophyll in lakes. Freshwater Biology 56:1811-1824. \| Abstract	June 2011	1. For north temperate lakes, the well-studied empirical relationship between phosphorus (as measured by total phosphorus, TP), the most commonly limiting nutrient, and algal biomass (as measured by chlorophyll a, CHL) has been found to vary across a wide range of landscape settings. Variation in the parameters of these TP – CHL regressions has been attributed to such lake variables as nitrogen:phosphorus ratios, organic carbon and alkalinity, all of which are strongly related to catchment characteristics (e.g. natural land cover and human land use). Although this suggests that landscape setting can help to explain much of the variation in ecoregional TP – CHL regression parameters, few studies have attempted to quantify relationships at an ecoregional spatial scale. 2. We tested the hypothesis that lake algal biomass and its predicted response to changes in phosphorus are related to both local-scale features (e.g. lake and catchment), and ecoregional-scale features, all of which affect the availability and transport of co-varying solutes such as nitrogen, organic carbon, and alkalinity. Specifically, we expected that land use and cover, acting at both local and ecoregional scales, would partially explain the spatial pattern in TP – CHL regression parameters. 3. We used a multilevel modelling framework and data from 2,105 inland lakes spanning 35 ecoregions in six US states to test our hypothesis and identify specific local and ecoregional features that explain spatial heterogeneity in TP – CHL relationships. We include variables such as lake depth, natural land cover (for instance, wetland cover in the catchment of lakes and in the ecoregions) and human land use (for instance, agricultural land use in the catchment of lakes and in the ecoregions). 4. There was substantial heterogeneity in TP – CHL relationships across the 35 ecoregions. At the local scale, CHL was negatively and positively related to lake mean depth and percentage of wooded wetlands in the catchment, respectively. At the ecoregional scale, the slope parameter was positively related to the percentage of pasture in an ecoregion, indicating that CHL tends to respond more rapidly to changes in TP where there are high levels of agricultural pasture than where there is little. The intercept (i.e. the ecoregion-average CHL) was negatively related to the percentage of wooded wetlands in the ecoregion. 5. By explicitly accounting for the hierarchical nature of lake-landscape interactions, we quantified the effects of landscape characteristics on the response of CHL to TP at two spatial scales. We provide new insight into ecoregional drivers of the rate at which algal biomass respond to changes in nutrient concentrations. Our results also indicate that the direction and magnitude of the effects of certain land use and cover characteristics on lake nutrient dynamics may be scale-dependent and thus likely to represent different underlying mechanisms regulating lake productivity.
Wagner, T., P. McLaughlin, K.E. Faunce, S. Austin, K. Smalling. 2024. The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA. Environmental Toxicology and Chemistry. https://doi.org/10.1002/etc.5849	March 2024
Wagner, T., N.R. Lottig, M.L. Bartley, E.M. Hanks, E.M. Schliep, N.B. Wikle, K.B.S. King, I. McCullough, J. Stachelek, K.S. Cheruvelil, C.T. Filstrup, J.F. Lapierre, B. Liu, P.A. Soranno, P-N. Tan, Q. Wang, K. Webster, and J. Zhou. 2019. Increasing accuracy of lake nutrient predictions in thousands of lakes by leveraging water clarity data. Limnology and Oceanography Letters. https://doi.org/10.1002/lol2.10134	December 2019
Wagner, T., McLaughlin, P., Smalling, K., Breitmeyer, S., Gordon, S., and Noe, G.B., 2021. The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed, USA. Science of the Total Environment 812:152435. https://doi.org/10.1016/j.scitotenv.2021.152435	December 2021
Wagner, T., M.E. Benbow, T.O. Brenden, J. Qi, and R.C. Johnson. 2008. Buruli ulcer disease prevalence in Benin, West Africa: associations with land use/cover and the identification of disease clusters. International Journal of Health Geographics 7:25. \| Abstract	May 2008	Background: Buruli ulcer (BU) disease, caused by infection with the environmental mycobacterium M. ulcerans, is an emerging infectious disease in many tropical and sub-tropical countries. Although vectors and modes of transmission remain unknown, it is hypothesized that the transmission of BU disease is associated with human activities in or around aquatic environments, and that characteristics of the landscape (e.g., land use/cover) play a role in mediating BU disease. Several studies performed at relatively small spatial scales (e.g., within a single village or region of a country) support these hypotheses; however, if BU disease is associated with land use/cover characteristics, either through spatial constraints on vector-host dynamics or by mediating human activities, then large-scale (i.e., country-wide) associations should also emerge. The objectives of this study were to (1) investigate associations between BU disease prevalence in villages in Benin, West Africa and surrounding land use/cover patterns and other map-based characteristics, and (2) identify areas with greater and lower than expected prevalence rates (i.e., disease clusters) to assist with the development of prevention and control programs. Results: Our landscape-based models identified low elevation, rural villages surrounded by forest land cover, and located in drainage basins with variable wetness patterns as being associated with higher BU disease prevalence rates. We also identified five spatial disease clusters. Three of the five clusters contained villages with greater than expected prevalence rates and two clusters contained villages with lower than expected prevalence rates. Those villages with greater than expected BU disease prevalence rates spanned a fairly narrow region of south-central Benin. Conclusion: Our analyses suggest that interactions between natural land cover and human alterations to the landscape likely play a role in the dynamics of BU disease. For example, urbanization, potentially by providing access to protected water sources, may reduce the likelihood of becoming infected with BU disease. Villages located at low elevations may have higher BU disease prevalence rates due to their close spatial proximity to high risk environments. In addition, forest land cover and drainage basins with variable wetness patterns may be important for providing suitable growth conditions for M. ulcerans, influencing the distribution and abundance of vectors, or mediating vector-human interactions. The identification of disease clusters in this study provides direction for future research aimed at better understanding these and other environmental and social determinants involved in BU disease outbreaks.
Wagner, T., J.T. Deweber, J. Detar, and J.A. Sweka. 2013. Landscape-scale evaluation of asymmetric interactions between brown trout and brook trout using two-species occupancy models. Transactions of the American Fisheries Society 142:353-361. \| Download	January 2013
Wagner, T., J.T. Deweber, J. Detar, D. Kristine, and J.A. Sweka. 2014. Spatial and Temporal Dynamics in Brook Trout Density: Implications for Population Monitoring. North American Journal of Fisheries Management 34:258-269. \| Download	March 2014
Wagner, T., G.J.A. Hansen, E. Schliep, B. Bethke, A. Honsey, P. Jacobson, B.C. Kline, and S.L. White. 2020. Improved understanding and prediction of freshwater fish communities through the use of joint species distribution models. Canadian Journal of Fisheries and Aquatic Sciences 77(9): 1540-1551. https://doi.org/10.1139/cjfas-2019-0348	August 2020
Wagner, T., E.M. Schliep, J.S. North, H. Kundel, J.K. Ruzich, C.A. Custer, and G.J.A. Hansen. 2023. Predicting climate change impacts on poikilotherms using physiologically guided species abundance models. Proceedings of the National Academy of Sciences: 15: e2214199120 https://doi.org/10.1073/pnas.2214199120	April 2023
Wagner, T., D.R. Diefenbach, A.S. Norton, and S.A. Christensen. 2011. Using multilevel models to quantify heterogeneity in resource selection. Journal of Wildlife Management 75:1788-1796. \| Abstract \| Download	November 2011	Models of resource selection are being used increasingly to predict or model the effects of management actions rather than simply quantifying habitat selection. Multilevel, or hierarchical, models are becoming an increasingly popular method to analyze animal resource selection because they impose a relatively weak stochastic constraint to model heterogeneity in habitat use but also account for unequal sample sizes among individuals. However, few studies have taken advantage of the ability of multilevel models to model coefficients as a function of predictors that may influence habitat use at different scales or quantify differences in resource selection among groups. We use an example with white-tailed deer (Odocoileus virginianus) to illustrate how to model resource use as a function of distance to road that varies among deer by road density at the home range scale. Also, we use multilevel models with sika deer (Cervus nippon) and white-tailed deer to examine whether resource selection differs between species. Multilevel models can improve our understanding of how resource selection varies among individuals and provides an objective, quantifiable approach to assess differences or changes in resource selection.
Wagner, T., C.S. Vandergoot, and J. Tyson. 2009. Evaluating the Power to Detect Temporal Trends in Fishery-Independent Surveys: A Case Study Based on Gillnets Set in the Ohio Waters of Lake Erie for Walleye. North American Journal of Fisheries Management 29:805-816. \| Abstract	May 2009	Fishery-independent (FI) surveys provide critical information used for the sustainable management and conservation of fish populations. Because fisheries management often requires the effects of management actions to be evaluated and detected within a relatively short time-frame, it is important that research be directed towards FI survey evaluation, especially with respect to temporal trend detection capabilities. Using annual FI gillnet survey data for Lake Erie walleye collected from 1978 – 2006 as a case study, our goals were to (1) highlight the usefulness of hierarchical models for estimating spatial and temporal sources of variation in catch per effort (CPE); (2) demonstrate how resulting variance estimates can be used to examine the statistical power to detect temporal trends in CPE in relation to sample size, duration of sampling, and decisions regarding what data are most appropriate for analysis; and (3) discuss recommendations for the evaluation of FI surveys and the analysis of resulting data to support fisheries management. This case-study illustrated that the statistical power to detect temporal trends was low over relatively short sampling periods (e.g., 5 – 10 years), unless the annual decline in CPE reached 10 – 20%. For example, if 50 sites were sampled each year a 10% annual decline in CPE would not be detected with > 0.80 power until 15 years of sampling, and a 5% annual decline would not be detected with > 0.8 power for approximately 22 years. Because the evaluation of FI surveys is essential to ensure that trends in fish populations can be detected over management-relevant time periods, we suggest that a meta-analysis type approach be used across systems to quantify sources of spatial and temporal variation. This approach can be used to evaluate and identify sampling designs that increase the ability of managers to make inferences about trends in fish stocks.
Wagner, T., C.E. Fergus, C.A. Stow, K.S. Cheruvelil, and P.A. Soranno. 2016. The statistical power to detect cross-scale interactions at macroscales. Ecosphere. 7(7):e01417. \| Download	July 2016
Wagner, T., B. J. Irwin, J. R. Bence, and D.B. Hayes. 2013. Detecting temporal trends in freshwater fisheries surveys: statistical power and the important linkages between management questions and monitoring objectives. Fisheries 38:309-319. \| Download	July 2013
Wagner, T. and S.R. Midway. 2014. Modeling spatially varying landscape change points in species occurrence thresholds. Ecosphere 5(11):145.http://dx.doi.org/10.1890/ES14-00288.1 \| Download	November 2014
Wagner, T. and E.M. Schliep. 2018. Combining nutrient, productivity, and landscape-based regressions improves predictions of lake nutrients and provides insight into nutrient coupling at macroscales. Limnology and Oceanography 63:2372-2383.	August 2018
Wagner, T. J.B. Whittier, J.T. DeWeber, S.R. Midway, and C.P. Paukert. 2017. Annual changes in seasonal river water temperatures in the eastern and western United States. Water 9(2), 90; doi:10.3390/w9020090	February 2017
Vreeland, J. K., D. R. Diefenbach, and B. D. Wallingford. 2004. Survival rates, mortality causes, and habitats of Pennsylvania white-tailed deer fawns. Wildlife Society Bulletin 32:542-553.	July 2004
Vidal, T. E., B. J. Irwin, T. Wagner, L. G. Rudstam, J. R. Jackson, and J. R. Bence. 2017. Using Variance Structure to Quantify Responses to Perturbation in Fish Catches. Transactions of the American Fisheries Society 146:584-593. [Featured Article] \| Abstract	April 2017	Unexpected shifts in the state-space conditions of an ecosystem can result in unintended and undesirable conditions, jeopardizing conservation efforts and efficacy of natural resource management. Previous research has identified general statistical behaviors associated with major ecological shifts, yet reliable prediction of these events remains limited. Development of statistical indicators to detect and forecast large-scale change (i.e., regime shifts) in ecological systems could prove valuable for better understanding population dynamics, continuing effective monitoring of fisheries resources, and allowing for timely management actions. Changes in mean and variance have been previously associated with large-scale shifts in ecosystems; here we provide evidence that source components contributing to total variability may also be responsive to large-scale shifts and therefore have potential as new statistical indicators of ecological response to a changing environment. We present a case study from Oneida Lake in NY that evaluates walleye catch rates over time in response to changes to tropho-dynamics and an exotic species invasion. Our results indicate that variance structure provides insight into how an ecosystem changes across space and through time, and also may serve as an indicator of instability and transition into an alternate stable state.
Van Buskirk, A., C. S. Rosenberry, B. D. Wallingford, E. J. Domoto, M. E. McDill, P. Drohan, and D. R. Diefenbach. 2021. Modeling how to achieve localized areas of reduced white-tailed deer density. Ecological Modelling 442:109393 DOI: 10.1016/j.ecolmodel.2020.109393 \| Download	February 2021
Tucker, M. et al. 2018. Moving in the Anthropocene: Global reductions in terrestrial mammalian movements. Science 359:466-469. DOI: 10.1126/science.aam9712 \| Download	January 2018
Thompson, T.J., M.A. Briggs, P.J. Phillips, V.S. Blazer, K.L. Smalling, D.W. Kolpin, T. Wagner. 2020. Groundwater discharges as a source of phytoestrogens and other agriculturally derived contaminants to streams. Science of the Total Environment.	October 2020
Sweka, J.A., T. Wagner, J. Detar, and D. Kristine. 2012. Combining Field Data with Computer Simulations to Determine a Representative Reach for Brook Trout Assessment. Journal of Fish and Wildlife Management 3:209-222.	December 2012
Sweka, J.A., L.A. Davis, T. Wagner. 2017. Fall and winter survival of brook and brown trout in a North-Central Pennsylvania watershed. Transactions of the American Fisheries Society 146:744-752. \| Download	May 2017
Sweka, J.A. and T. Wagner. 2021. Influence of seasonal extreme flows on Brook Trout recruitment. Transactions of the American Fisheries Society. https://doi.org/10.1002/tafs.10347	December 2021
Stow, C.A., K.E. Webster, T. Wagner, N. Lottig, P.A. Soranno, C. YoonKynug. 2018. Small Values in Big Data: The Continuing Need for Appropriate Metadata. Ecological Informatics 45:26-30.	May 2018
Stedman, R., D. R. Diefenbach, C. B. Swope, J. C. Finley, A. E. Luloff, H. C. Zinn, G. A. Wang. 2004. Integrating wildlife and human dimensions research methods to study hunters. Journal of Wildlife Management 68:762-773.	December 2004
Stedman, R. C., P. Bhandari, A. E. Luloff, D. R. Diefenbach, and J. C. Finley. 2008. Deer hunting on Pennsylvania's public and private lands: a two-tiered system of hunters? Human Dimensions of Wildlife 13:222-233. \| Download	August 2008
Stauffer, G. E., M. R. Marshall, D. R. Diefenbach, and D. W. Brauning. 2010. Reclaimed surface mine habitat and grassland bird populations. Pages 86-96 in S. K. Majumdar, T. L. Master, M. C. Brittingham, R. M. Ross, R. S. Mulvihill, and J. E Huffman, eds. Avian Ecology and Conservation: A Pennsylvania focus with national implications. Pennsylvania Academy of Science, Easton, Pennsylvania, USA.	January 2010
Stauffer, G. E., D. R. Diefenbach, M. Marshall, and D. Brauning. 2011. Nest success of grassland sparrows on reclaimed surface mines. Journal of Wildlife Management 75:548-557. \| Abstract	May 2011	Grasslands resulting from surface mine reclamation support grassland songbird populations in several mid-western and eastern states in the USA, especially where reclaimed mines are large (>1000 ha). However, most reclaimed surface mines in Pennsylvania are small (<200 ha), and nest success is unknown. We evaluated nest success of grasshopper (GRSP; Ammodramus savannarum), Henslow's (HESP; Ammodramus henslowii), and Savannah sparrows (SAVS; Passerculus sandwichensis) on 4 reclaimed surface mines (50 - 180 ha) in western Pennsylvania, USA from 2006 - 2007. Overall nest success based on mean covariate values was 0.435 (95% CI = 0.376 - 0.504) for GRSP, 0.396 (95% CI = 0.295 - 0.533) for HESP, and 0.158 (95% CI = 0.063 - 0.392) for SAVS. These estimates of nest success are comparable to those on larger reclaimed mines and other habitats. GRSP and HESP nests that were well concealed were less likely to fail than highly visible nests, and nests in areas with surrounding deep litter were more likely to fail than nests in areas with shallow litter. SAVS nests in areas with high visual obstruction by vegetation were less likely to fail than nests in areas with sparse and short vegetation. Daily probability of survival for GRSP nests was greatest early and late in the breeding season, and SAVS nest survival followed a decreasing linear trend. Nest survival of HESP was greater on warm days, whereas for SAVS nest survival decreased on warm days and on days with rain, but for SAVS confidence intervals of weather effects included zero. We suggest that small reclaimed surface mine grasslands can provide valuable nesting habitat, and should be considered in conservation plans for grassland birds. Because nest success can increase in the latter part of the nesting season, agricultural disturbances or management activities should be delayed until late nesting attempts have concluded.
Stachelek, J. W. Weng, C.C. Carey, A.R. Kemanian, K.M. Cobourn, T. Wagner, K.C. Weathers, P.A. Soranno. 2020. Granular measures of agricultural land-use influence lake nitrogen and phosphorus differently at macroscales. Ecological Applications 30, e02123.	April 2020
Soranno, P.A., T. Wagner, S. Martin, L. McLean, L. Novitski,C. Provence, and A. Rober. 2011. Quantifying regional reference conditions for freshwater ecosystem management: A comparison of approaches and future research needs. Lake and Reservoir Management 27:138-148. \| Abstract	May 2011	Accurate and robust approaches for quantifying regional reference conditions are critical to the management and restoration of freshwater resources. We review four common approaches to quantify regional reference conditions. We consider approaches that have been developed for streams, lakes, or wetlands and for either biological or chemical waterbody features. The four approaches we discuss are: multimetric, multivariate, landscape-context statistical modeling, and paleolimnology. We focus on the major steps in the decision-making process that lead to the most appropriate approach. Based on this synthesis, we argue that there is a need to: (1)more explicitly quantify the spatial scale of waterbody variation within and across regions; (2) develop and use predictive classification models in a more explicit fashion to more effectively model this local and regional variation; (3) consider additional metrics with a focus on lakes and wetland responses to both individual and multiple anthropogenic stressors; and (4) continue to develop quantitative approaches to explicitly account for uncertainties in regional reference condition predictions.
Soranno, P.A., L.C. Bacon, M. Beauchene, K.E. Bednar, E.G. Bissell, C.K. Boudreau, M.G. Boyer, M.T. Bremigan, S.R. Carpenter, J.W. Carr and 70 co-authors. LAGOS-NE: A multi-scaled geospatial temporal database of lake ecological context and water quality for thousands of U.S. Lakes. In press. GigaScience.	October 2017
Soranno, P.A., K.S. Cheruvelil, T. Wagner, K.E. Webster, and M.T. Bremigan. 2015. Effects of land use on lake nutrients: The importance of scale, hydrologic connectivity, and region. PLoS ONE 10(8): e0135454. \| Download	August 2015
Soranno, P.A., K.S. Cheruvelil, B. Liu, Q. Wang, P-N. Tan, J. Zhou, K.B.S. King, I.M. McCullough, J. Stachelek, M. Bartley, C.T. Filstrup, E.M. Hanks, J-F. Lapierre, N.R. Lottig, E.M. Schliep, T. Wagner, K.E. Webster. 2020. Ecological prediction at macroscales using big data: Does sampling design matter? Ecological Applications 30:e02123.	September 2020
Soranno, P.A., K. Spence Cheruvelil, K.E. Webster, M.T. Bremigan, T. Wagner, and C.A. Stow. 2010. Freshwater Ecosystem Classification for Landscape-scale Management. BioScience 60:440-454.	June 2010
Soranno, P.A., K. Spence Cheruvelil, E. Bissell, M. Tate-Bremigan, J.A. Downing, C.E. Fergus, C. Filstrup, N.R. Lottig, E.N. Henry, E.H. Stanley, C.A. Stow, P.N. Tan, T. Wagner, and K.E. Webster. 2014. Cross-scale interactions: A conceptual framework for understanding multi-scaled cause-effect relationships in macrosystems. Frontiers in Ecology and the Environment 12:65-73. \| Download	February 2014
Soranno, P.A., E.G. Bissell, K.S. Cheruvelil, S.M. Collins, C.E. Fregus, C.T. Filstrup, J-F. Lapierre, N.R. Lottig, S.K. Oliver, C.E. Scott, N.J. Smith, S. Stopyak, S. Yuan, M.T. Bremigan, J.A. Downing, C. Gries, E.N. Henry, N.K. Skaff, E.H. Stanley, C.A. Stow, P-N. Tan, T. Wagner, and K.E. Webster. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse. GigaScience 4:28. \| Download	July 2015
Soranno, P.A., T. Wagner, S.M. Collins, J-F Lapierre, N.R. Lottig, and S.M. Oliver. 2019. Spatial and temporal variation of ecosystem properties at macroscales. Ecology Letters 22:1587-1598. (* co-leads)	September 2019
Smith, L.A., T. Wagner, M.L. Bartron. 2015. Spatial and temporal movement dynamics of brook Salvelinus fontinalis and brown trout Salmo trutta. Environmental Biology of Fishes 98:2049-2065. \| Download	July 2015
Smith, G.D., Massie, D.L., Perillo, J., Wagner, T. and Pierce, D., 2021. Range expansion and factors affecting abundance of invasive Flathead Catfish in the Delaware and Susquehanna rivers, Pennsylvania, USA. North American Journal of Fisheries Management 41:S205-S220. http://dx.doi.org/10.1002/nafm.10628	April 2021
Smalling, K.L., Romanok, K.M., Bradley, P.M, Morriss, M.C., Gray, J.L., Kanagy, L.K., Gordon, S.E., Williams, B.W., Breitmeyer, S.E., Jones, D.K., DeCicco, L.A., Eagles-Smith, C.A., and Wagner, T., 2023, Per- and Polyfluoroalkyl Substances (PFAS) in United States Tapwater: Comparison of Underserved Private-Well and Public-Supply Exposures and Associated Health Implications, Environment International, p. 108033, https://doi.org/10.1016/j.envint.2023.108033	June 2023
Smalling, K.L., O.H. Devereux, S. Gordon, P. Phillips, V.S. Blazer, M.L. Hladik, D.W. Kolpin, M.T. Meyer, A. Sperry, and T. Wagner. 2021. Environmental and anthropogenic drivers of contaminants in agricultural watersheds with implications for land management. Science of the Total Environment 145687.	February 2021
Shuter, B. J., R. F. Carline, and N. A. McGinn. 2002. An overview of the symposium. Pages xiii-xix, in N. A. McGinn, editor. Fisheries in a Changing Climate. American Fisheries Society Symposium 32.	August 2002
Schwabenlander, M.D., G. Rowden, S. Stone, R. Shoemaker, L.L. Lindsey, J.D. Oliver, L. Glaser, M. Carstensen, J.C. Bartz, W.D. Walter, R.J. Larsen, T.M. Wolf, P.A. Larsen. 2022. Implementing a veterinary forensics approach to investigate chronic wasting disease at a deer carcass disposal site. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022. \| Abstract	July 2022	Chronic wasting disease (CWD) is confirmed in 29 US states, three Canadian provinces, and in Sweden, Norway, Finland, and South Korea. Although its geographic origin is speculative, much of the disease spread in North America over the past seven decades is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD. Regulatory agencies provide guidance and proper disposal opportunities for the control of CWD in endemic areas and to reduce the risk of introduction to new areas. Upon the discovery of an illegal carcass dumping site associated with a CWD-positive captive cervid facility, we employed a veterinary forensics approach to investigate the existence of CWD-positive materials within the site. Animal remains were examined to determine species, age, sex, relatedness, and CWD status. We utilized advanced anatomic, entomologic, genetic, and prion amplification methods to discover CWD-positive remains across multiple age classes of white-tailed deer. CWD prions were detected via RT-QuIC in 13 of 49 carcass samples with 9 of 13 from fawns, 1 of 13 from a yearling, 2 of 13 from adults, and 1 of 13 from a deer of unknown age. We also identified CWD-positive fly larvae associated with positive remains. Our multi-methods approach provides the foundation for the veterinary forensic investigation of CWD spread by means of cervid carcasses.
Schneider, A.L., A.T. Gilbert, W.D. Walter, G.S. Vandeberg, J.R. Boulanger. 2019. Spatial Ecology of Urban Striped Skunks (Mephitis mephitis) in the Northern Great Plains: A Framework for Future Oral Rabies Vaccination Programs. Urban Ecosystems 22:539-552. \| Abstract	May 2019	Few studies have investigated the ecology of urban striped skunks (Mephitis mephitis) despite their role as a primary rabies vector species paired with an ability to thrive in these landscapes. Information on home range, nightly movements, and habitat selection, is important for informing rabies management decisions such as the placement of oral rabies vaccine (ORV) baits and for management of the species. Our aim was to obtain baseline ecological information with an emphasis on spatial ecology of urban striped skunks in the Northern Great Plains region that is lacking in the literature. We used radio telemetry to track 22 (4 M, 18 F) skunks from September 2016 to November 2016 and March 2017 to November 2017. Size of home range using kernel density estimation with smoothing by least squares cross validation identified males (x ̅ = 4.36 km2, SE ± 0.79) had larger home ranges than females (x ̅ = 1.79 km2, SE ± 0.24). Female skunk home ranges differed by season with the largest home ranges found in summer 2017. However, rate of nightly movements (m/hr) among female skunks did not differ within seasons (x ̅ = 184.79 m/hr, SE ± 0.53). Moreover, we found no evidence that use-availability was associated with habitat type among female skunks. The strongest predictor of habitat use was distance to water sources with female skunks more likely to be found closer to this habitat type; however, we found no association of use with road factors and geographic location within the study area. Targeting ORV efforts in areas near water may be warranted, but considering differences in habitat selection for skunk in urban areas, we caution that ORV baiting programs may not be one-size-fits-all, and a framework for effective bait placement would be most successful with studies similar to ours conducted beforehand.
Schall, M.K., V.S. Blazer, R.M. Lorantas, G.D. Smith, J.E. Mullican, B.J. Keplinger, T. Wagner. In press. Quantifying Temporal Trends in Fisheries Abundance using Bayesian Dynamic Linear Models: A Case-Study of Riverine Smallmouth Bass Populations. North American Journal of Fisheries Management.	April 2018
Schall, M.K., V.S. Blazer, H.L. Walsh, G.D. Smith, T. Wertz, and T. Wagner. Spatial and temporal variability of myxozoan parasite prevalence in young of the year smallmouth bass in the Susquehanna River Basin, Pennsylvania	August 2018
Schall, M.K., T. Wertz, G.D. Smith, V.S. Blazer, and T. Wagner. 2019. Movement dynamics of smallmouth bass (Micropterus dolomieu) in a large river-tributary system. Fisheries Management and Ecology 26:590-599.	July 2019
Schall, M.K., M.L. Bartron, T. Wertz, J. Niles, V.S. Blazer, and T. Wagner. 2017. Evaluation of genetic population structure of Smallmouth Bass in the Susquehanna River Basin, PA. North American Journal of Fisheries Management 37:729-740.	May 2017
Schall, M.K., G.D. Smith, V.S. Blazer, H.L. Walsh, Y. Li, and T. Wagner. 2020. A fishery after the decline: The Susquehanna River Smallmouth Bass story. Fisheries 45:576-584.	August 2020
Schall, M.K., G.D. Smith, V.S. Blazer, H.L. Walsh, T. Wertz, D. Shull, and T. Wagner. 2023. Assembling the right pieces: developing an interdisciplinary team to study disease, decline, and recovery of a world-class Smallmouth Bass fishery. Fisheries. https://doi.org/10.1002/fsh.10922	May 2023
Rosenberry, C. S., and D. R. Diefenbach. 2019. A comparison of spatial variation of deer harvests between small and large management units in Pennsylvania. Wildlife Society Bulletin. 43:71–76; DOI: 10.1002/wsb.939 \| Download	January 2019
Rosenberry, C. S., E. S. Long, H. M. Hassel-Finnegan, V. P. Buonaccorsi, D. R. Diefenbach, and B. D. Wallingford. 2009. Lack of mother–offspring relationships in white-tailed deer capture groups. Journal of Wildlife Management 73:357-361. \| Abstract	April 2009	Behavioral studies of white-tailed deer (Odocoileus virginianus) often assign mother–offspring relationships based on common capture of juveniles with adult deer, assuming that fawns associate closely with mothers. We tested this assumption using genetic parentage to assess mother–offspring relationships within capture groups based on data from 10 polymorphic microsatellite loci. At the 80% confidence level, we assigned maternity to 43% and 51% of juveniles captured with an adult female in 2 respective study areas. Capture with their mother did not differ by sex of juveniles in either study area, and limiting our analysis to capture groups that most represent family groups (i.e., one ad F with 1–3 juv) did not increase maternity assignment (35%). Our results indicate that common capture may be a poor indicator of mother–offspring relationships in many field settings. We recommend genetic verification of family relationships.
Rosenberry, C. S., D. R. Diefenbach, B. D. Wallingford. 2004. Reporting rate variability and precision of white-tailed deer harvest estimates in Pennsylvania. Journal of Wildlife Management 68:860-869.	December 2004
Rosenberry, C. S., A. S. Norton, D. R. Diefenbach, J. T. Fleegle, and B. D. Wallingford. 2011. White-tailed deer population trends and age ratios as herd management and predator impact measures in Pennsylvania. Wildlife Society Bulletin 35:461-468. \| Abstract \| Download	November 2011	A review of the Pennsylvania Game Commission's (PGC) deer management program and public concern about predator impacts on deer (Odocoileus virginianus) populations compelled the PGC to investigate the role of age ratios in developing management recommendations. Age ratios, such as proportion of juveniles in the antlerless harvest, may provide an index to population productivity and predator impacts. We estimated proportion of juveniles in the antlerless harvest from hunter-killed deer, population trends using the Pennsylvania (USA) sex–age–kill model, and reproduction from road-killed females. Using these estimates and a simulation model, we concluded that no single age-ratio value would serve as a reliable measure of population status. Wildlife Management Unit-specific trends in proportion of juveniles in the antlerless harvest and population trends provided the most relevant management information. We also provide an example decision chart to guide management actions in response to declining age ratios in the harvest. Although predator management activities and juvenile survival studies are often desired by the public, our decision-chart example indicated a number of deer management options exist before investing resources in predator management activities and juvenile survival studies.
Robinson, K.F., A.K. Fuller, M.V. Schiavone, B. Swift, D.R. Diefenbach, W.F. Siemer, and D.J. Decker. 2017. Addressing wild turkey (Meleagris gallapavo) population declines using structured decision making. Journal of Wildlife Management. DOI: 10.1002/jwmg.21220	February 2017
Robinson, K. F., D. R. Diefenbach, A. K. Fuller, J. E. Hurst, and C. S. Rosenberry. 2014. Can managers compensate for coyote predation of white-tailed deer? Journal of Wildlife Management 78:571–579. \| Download	April 2014
Rennie, M.D., M.P. Ebener, and T. Wagner. 2012. Can migration mitigate the effects of ecosystem change? Patterns of dispersal, energy acquisition and allocation in Great Lakes lake whitefish (Coregonus clupeaformis). Proceedings of the 10th Annual Coregonid Symposium. Advances in Limnology 63:455-476. \| Download	January 2012
Qui, Q., Y. Xu, S.S. Matsuzaki, K. Komatsu, Z. Liang, T. Wagner. 2021.A statistical framework to track temporal dependence of chlorophyll–nutrient relationships with implications for lake eutrophication management. Journal of Hydrology 603:127134. https://doi.org/10.1016/j.jhydrol.2021.127134	November 2021
Pregler, K.C., R.D. Hanks, E. Childress, N.P. Hitt, D.J. Hocking, B.H. Letcher, T. Wagner, and Y. Kanno. 2019. State-space analysis of power to detect regional brook trout population trends over time. Canadian Journal of Fisheries and Aquatic Sciences 76:2145-2155.	October 2019
Peterson, D. L. J. T. Peterson, and R. F. Carline. 2006. Effects of zooplankton density on survival of stocked walleye fry in five Pennsylvania reservoirs. Journal of Freshwater Ecology. 21:121-129.	May 2006
Perles, S. J., T. Wagner, B. J. Irwin, D. R. Manning, K. K. Callahan, and M. R. Marshall. 2014. Evaluation of a regional monitoring program's statistical power to detect temporal trends in forest health indicators. Environmental Management 54:641-655. doi:10.1007/s00267-014-0313-z \| Download	July 2014
Peoples, B., S.R. Midway, J.T. DeWeber, and T. Wagner. 2018. Catchment scale determinants of nonindigenous minnow richness in the eastern United States. Ecology of Freshwater Fish 27:138-145.	January 2017
Oliver, S.k., S.M. Collins, P.A. Soranno, T. Wagner, E.H. Stanley, J.R. Jones, C.A. Stow, and N.R. Lottig. 2017. Unexpected stasis in a changing world: Lake nutrient and chlorophyll trends since 1990. Global Change Biology 23:5455–5467 DOI: 10.1111/gcb.13810	August 2017
Oliver, S.K., P.A. Soranno, C.E. Fergus, T. Wagner, L.A. Winslow, C.E. Scott, K.E. Webster, J.A. Downing, and E.A. Stanley. 2016. Prediction of lake depth across a 17-state region in the U.S. Inland Waters 6:314-324. \| Download	June 2016
Oliver, S.K., C.E. Fergus, N.K. Skaff, T. Wagner, P-N. Tan, K.S. Cheruvelil, and P.A. Soranno. Strategies for effective collaborative manuscript development in interdisciplinary science teams. Ecosphere.	May 2018
Norton, A. S., D. R. Diefenbach, C. S. Rosenberry, and B. D. Wallingford. 2013. Incorporating Harvest Rates into the Sex-Age-Kill Model for White-tailed Deer. Journal of Wildlife Management. Journal of Wildlife Management 77:606-615. \| Download	April 2013
Norton, A. S., D. R. Diefenbach, B. D. Wallingford, C. S. Rosenberry. 2012. Spatio-Temporal Variation in Male White-Tailed Deer Harvest Rates in Pennsylvania: Implications for Estimating Abundance. Journal of Wildlife Management 76:136-143. \| Abstract \| Download	January 2012	The performance of two popular methods that use age-at-harvest data to estimate abundance of white-tailed deer is contingent on assumptions about variation in estimates of yearling (1.5 yr old) and adult (≥ 2.5 yr old) male harvest rates. Auxiliary data, e.g., estimates of survival or harvest rates from radiocollared animals, can be used to relax some assumptions, but unless these population parameters exhibit limited temporal or spatial variation these auxiliary data may not improve accuracy. Unfortunately maintaining sufficient sample sizes of radiocollared deer for parameter estimation in every wildlife management unit (WMU) is not feasible for most state agencies. We monitored the fates of 397 yearling and 225 adult male white-tailed deer across 4 WMUs from 2002-2008 using radio telemetry. We investigated spatial and temporal variation in harvest rates and investigated covariates related to the patterns observed. We found that most variation in harvest rates was explained spatially and that adult harvest rates (0.36–0.69) were more variable among study areas than yearling harvest rates (0.26–0.42). We found that hunter effort during the archery and firearms season best explained variation in harvest rates of adult males among WMUs, whereas hunter effort during the firearms season best explained harvest rates for yearling males. From a population estimation perspective, it is advantageous that most variation was spatial and explained by a readily obtained covariate (hunter effort). However, harvest rates may vary if hunting regulations or hunter behavior change, requiring additional field studies to obtain accurate estimates of harvest rates.
North, J.S., E.M. Schliep, G.J.A. Hansen, J. Kundel, C.A. Custer, P. McLaughlin, and T. Wagner. 2024. Accounting for spatiotemporal sampling variation in joint species distribution models. Journal of Applied Ecology 61:186-201. http://doi.org/10.1111/1365-2664.14547	November 2023
Niedringhaus, K.D, L.S. Ganoe, M. Lovallo, W.D. Walter, M.J. Yabsley, J.D. Brown. 2022. Fatal infection by Versteria sp. in a muskrat (Ondatra zibethicus) with implications for human health. Journal of Veterinary Diagnostic Investigations 34(2): 314–318. \| Abstract	March 2022	The <i>Taeniidae</i> tapeworms are a family of helminths that have a similar life cycle with intermediate hosts developing characteristic cysts in visceral organs. Recently, a new genus in this family, <i>Versteria,</i> has been implicated as the cause of severe morbidity and mortality in humans and animals in North America. This report describes a case of fatal <i>Versteria</i> infection in a muskrat (<i>Ondatra zibethicus</i>) which has not been previously reported to develop disease associated with infection. Postmortem examination revealed widespread tissue loss and replacement by solid-bodied cestode larvae with minimal adjacent inflammation in many visceral organs, most severe in the lungs, liver, and brain. Characteristic morphological features via histology included multiple cephalic structures and short rostellar hooklets, which are characteristic for the genus. Genetic characterization confirmed the cestode as being an undescribed lineage of <i>Versteria</i> that has been implicated as the cause of severe morbidity and mortality in humans and non-human primates in North America. Considering the zoonotic significance of this pathogen, this report expands on the limited literature regarding disease caused by <i>Versteria </i>and emphasizes the need to identify the causative tapeworm more accurately, especially in rodent intermediate hosts as all previous reports do not have molecular confirmation of species.
Navarro, N., D. R. Diefenbach, M. E. McDill, E. J. Domoto, C. S. Rosenberry, and P. J. Drohan. 2023. Species and physiographic factors drive Indian cucumber root and Canada mayflower plant chemistry: Implications for white-tailed deer forage quality. Journal of Environmental Management 326:11645 \| Download	January 2023
Murphy, A. M., D. R. Diefenbach, M. Ternent, M. Lovallo, D. Miller. 2021. Threading the needle: How humans influence predator-prey spatiotemporal interactions in a multiple-predator system. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13548 \| Download	January 2021
Moore, S. E., R. F. Carline, and J. Dillon, editors. Working together to ensure the future of wild trout. Proceedings of Wild Trout VIII Symposium -30th Anniversary, 2004 September 20-22; Yellowstone Park, Wyoming	June 2005
Mollenhauer, R., T. Wagner, M.V. Kepler, J.A. Sweka. 2013. Fall and early winter movement and habitat use of wild brook trout. Transactions of the American Fisheries Society 142:1167-1178. \| Download	July 2013
Millspaugh, J. J., J. R. Skalski, R. L. Townsend, D. R. Diefenbach, M. S. Boyce, L. P. Hansen, and K. Kammermeyer. 2009. An evaluation of Sex-Age-Kill (SAK) model performance. Journal of Wildlife Management 73:442-451. \| Abstract \| Download	June 2009	The sex-age-kill (SAK) model is widely used to estimate abundance of harvested large mammals, including white-tailed deer (Odocoileus virginianus). Despite a long history of use, few formal evaluations of SAK performance exist. We investigated how violations of the stable age distribution and stationary population assumption, changes to male or female harvest, stochastic effects (i.e., random fluctuations in recruitment and survival), and sampling efforts influenced SAK estimation. When the simulated population had a stable age distribution and k . 1, the SAK model underestimated abundance. Conversely, when k , 1, the SAK overestimated abundance. When changes to male harvest were introduced, SAK estimates were opposite the true population trend. In contrast, SAK estimates were robust to changes in female harvest rates. Stochastic effects caused SAK estimates to fluctuate about their equilibrium abundance, but the effect dampened as the size of the surveyed population increased. When we considered both stochastic effects and sampling error at a deer management unit scale the resultant abundance estimates were within 6121.9% of the true population level 95% of the time. These combined results demonstrate extreme sensitivity to model violations and scale of analysis. Without changes to model formulation, the SAK model will be biased when k 6¼ 1. Furthermore, any factor that alters the male harvest rate, such as changes to regulations or changes in hunter attitudes, will bias population estimates. Sex-age-kill estimates may be precise at large spatial scales, such as the state level, but less so at the individual management unit level. Alternative models, such as statistical age-at-harvest models, which require similar data types, might allow for more robust, broad-scale demographic assessments.
Miller-Butterworth, C. M., D. R. Diefenbach, J. E. Edson, L. A. Hansen, J. D. Jordan, T. M. Gingery, and A. L. Russell. 2021. Demography and loss of genetic diversity in two insular populations of the bobcat (Lynx rufus). Global Ecology and Conservation 26:e01547. https://doi.org/10.1016/j.gecco.2021.e01457 \| Abstract \| Download	January 2021	In the Felidae, only 6 of 38 species have stable or increasing populations, and most felid species are threatened by anthropogenic influences, especially habitat loss and fragmentation. We documented changes in genetic diversity in an isolated, reintroduced population of bobcats on Cumberland Island (CUIS), Georgia, USA, compared to another bobcat population on Kiawah Island, South Carolina that was naturally established and experiences limited immigration from the mainland. The CUIS population declined from 32 reintroduced bobcats in 1989 to 10–24 individuals during 2012–2019, and observed heterozygosity declined from 0.72 (SE = 0.024) to 0.63 (SE = 0.039). Observed heterozygosity of bobcats on Kiawah was 0.699 (SE = 0.026). We estimated that one bobcat immigrated to Kiawah Island every 5.3 years. We compared the predictions of a population viability analysis (PVA) to empirical estimates of abundance and genetic diversity on CUIS and used the PVA to identify management actions that are likely to support long-term viability. Mean heterozygosity from the PVA (0.588, SD = 0.065) was within 1 standard deviation of the empirical estimate. The PVA estimated the population would decline following population restoration due to loss of genetic diversity and inbreeding depression. Translocations of one female every four years would stabilize allele heterozygosity, but even translocations of two females every two years would not restore heterozygosity. The PVA predicted no management action would result in a one in five probability of extinction within 50 years of reintroduction, but all translocation strategies nearly eliminated extinction risk through 100 years.
Miller, W.M., C.M. Miller-Butterworth, D.R. Diefenbach, and W.D. Walter. 2020. Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease. Ecology and Evolution 10(9):3977–3990; https://doi.org/10.1002/ece3.6161 \| Download	May 2020
Miller, W.L., J. Edson, P. Pietrandrea, C. Miller-Butterworth, and W. David Walter. 2019. Identification and evaluation of a core microsatellite panel for use in white-tailed deer (Odocoileus virginianus). BMC Genetics 20:49.	June 2019
Miller, W.L. and W.D. Walter. 2020. Can genetic assignment tests provide insight on the influence of captive egression on the epizootiology of chronic wasting disease? Evolutionary Applications. 13:715–726; https://doi.org/10.1111/eva.12895. \| Publisher Website	March 2020
Miller, W.L. and W.D. Walter. 2017. CWDPRNP: a tool for cervid prion sequence analysis in program R. Bioinformatics. 33(19):3096–3097. \| Abstract	September 2017	Summary: Chronic wasting disease is a fatal neurological, disease caused by an infectious prion protein, which affects economically and ecologically important members of the family Cervidae. Single nucleotide polymorphisms within the prion gene have been linked to differential susceptibil-ity to the disease in many species. Wildlife managers are seeking to determine the frequencies of disease-associated alleles and genotypes and delineate spatial genetic patterns. The CWDPRNP package, implemented in program R, provides a unified framework for analyzing prion gene varia-bility and spatial structure. Availability and Implementation: The CWDPRNP package, manual, and example data files are available at http://ecosystems.psu.edu/research/labs/walter-lab. This package is available for all commonly used platforms.
Miller, W.L. and W. D. Walter. 2019. Spatial heterogeneity of prion gene polymorphisms in an area recently infected by chronic wasting disease. Prion 13: 65-76. \| Abstract	February 2019	Genetic variability in the prion protein (PRNP) gene influences host susceptibility to many pathogenic prion diseases. Understanding the distribution of susceptible PRNP variants and determining factors influencing spatial genetic patterns are important components of many chronic wasting disease mitigation strategies. Here, we describe PRNP variability in white-tailed deer (Odocoileus virginianus) from the Mid-Atlantic region of the United States of America, an area with a recent history of infection and low disease incidence. This population is characterized by lower rates of polymorphism and significantly higher frequencies of the more susceptible 96GG genotype compared to previously surveyed populations. The prevalence of the most susceptible genotypes at disease-associated loci did vary among subregions, indicating that populations have innate differences in genotype-dictated susceptibility.
Miksis-Olds, J. L. and T. Wagner. 2010. Behavioral response of manatees to variations in environmental sound levels. Marine Mammal Science 27: 130–148 \| Abstract	March 2010	Florida manatees (Trichechus manatus latirostris) inhabit coastal regions because they feed on the aquatic vegetation that grows in shallow waters, which are the same areas where human activities are greatest. Noise produced from anthropogenic and natural sources has the potential to affect these animals by eliciting responses ranging from mild behavioral changes to extreme aversion. Sound levels were calculated from recordings made throughout behavioral observation periods. An information theoretic approach was used to investigate the relationship between behavior patterns and sound level. Results indicated that elevated sound levels affect manatee activity and are a function of behavioral state. The proportion of time manatees spent feeding and milling changed in response to sound level. When ambient sound levels were highest, more time was spent in the directed, goal-oriented behavior of feeding, whereas less time was spent engaged in undirected behavior such as milling. This work illustrates how shifts in activity of individual manatees may be useful parameters for identifying impacts of noise on manatees and might inform population level effects.
Midway, S.R., T. Wagner, J.D. Zydlewski, B.J. Irwin, and C.P. Paukert. 2016. Transboundary Fisheries Science: Meeting the Challenges of Inland Fisheries Management in the 21st Century. Fisheries 41:537-546. \| Download	September 2016
Midway, S.R., T. Wagner, G.H. Burgess. 2019. Trends in global shark attacks. PLOSE ONE.\| https://doi.org/10.1371/journal.pone.0211049 F	February 2019
Midway, S.R., C.T. Hasler, T. Wagner, and C.D. Suski. 2017. Predation of freshwater fish in elevated carbon dioxide environments. Marine and Freshwater Resources 68:1585-1592.	February 2017
Midway, S.R. and T. Wagner. 2015. The first description of oarfish Regalecus glesne (Regalecidae) ageing structures. Journal of Applied Ichthyology.	December 2015
Midway, S., T. Wagner, B. H. Tracy, G. M. Hogue, and W.C. Starnes. 2015. Evaluating changes in stream fish species richness over a 50-year time-period within a landscape context. Environmental Biology of Fishes 98:1295-1309. \| Abstract	March 2015	Worldwide, streams and rivers are facing a suite of pressures that change water quality and degrade physical habitat, both of which can lead to changes in the composition and richness of fish populations. These potential changes are of particular importance in the southeast USA, home to one of the richest stream fish assemblages in North America. Using data from 83 sites sampled in the 1960's and the past decade, we used hierarchical Bayesian models to evaluate relationships between species richness and catchment land use and land cover (e.g., agriculture and forest cover). In addition, we examined how the rate of change in species richness over 50 years was related to catchment land use and land cover. We found a negative and positive correlation between forest land cover and agricultural land use and average species richness, respectively. After controlling for introduced species, a majority (66%) of stream sites showed an increase in native fish species richness, and the magnitude of the rate of increase was positively correlated to the amount of forested land cover in the catchment. Site-specific trends in species richness were not positive, on average, until the percentage forest cover in the network catchment exceeded about 55%. These results suggest that streams with catchments that have moderate to high (>55%) levels of forested land in upstream network catchments may be better able to increase the number of native species at a faster rate compared to less-forested catchments.
Midway, S. R., T. Wagner, S. Arnott, P. Biondo, F. Martinez-Andrade, and T. Wadsworth. 2015. Spatial and temporal variability in growth of southern flounder (Paralichthys lethostigma). Fisheries Research 167:323-332.	April 2015
Midway, S. M., T. Wagner. and Tracy, B. 2014. A hierarchical community occurrence model for North Carolina stream fish. Transactions of the American Fisheries Society 143:1348-1357. \| Download	September 2014
Michel, E. S., B. K. Strickland, S. Demarais, J. L. Belant, T. M Kautz, J. F. Duquette, D. E. Byer, Jr., M. J. Chamberlain, K. V. Miller, R. M. Shuman, J. C. Kilgo, D. R. Diefenbach, B. D. Wallingford, J. K. Vreeland, S. S. Ditchkoff, C. S. DePerno, C. E. Moorman, M. C. Chitwood, and M. A. Lashley. 2020. Relative reproductive phenology and synchrony affect neonate survival in a nonprecocial ungulate. Functional Ecology 34:2536–2547. https://doi.org/10.1111/1365-2435.13680 \| Download	October 2020
McLaughlin, P., R. Alexander, J. Blomquist, O. Devereux, G. Noe, K. Smalling, and T. Wagner. 2022. Power Analysis for Detecting the Effects of Best Management Practices on Reducing Nitrogen and Phosphorus Fluxes to the Chesapeake Bay Watershed, USA. Ecological Indicators 136:108713. https://doi.org/10.1016/j.ecolind.2022.108713	February 2022
McCullough, I.M., J.A. Brentrup, T. Wagner, J-F. Lapierre, J. Henneck, A.M. Paul, M. Belair, M.A. Mortiz, C.T. Filstrup. 2023. Fire characteristics and hydrologic connectivity influence short-term responses of north temperate lakes to wildfire. Geophysical Research Letters. https://doi.org/10.1029/2023GL103953	August 2023
McCullough, I.M., Hanly, P.J., King, K.B.S., and T. Wagner. 2022. Freshwater corridors in the conterminous US: a coarse-filter approach based on lake-stream networks. Ecosphere e4326. https://doi.org/10.1002/ecs2.4326	December 2022
McClure, C.M., K.L. Smalling, V.S. Blazer, A.J. Sperry, M.K. Schall, D.W. Kolpin, P.J. Phillips, M.L. Hladik, and T. Wagner. 2020. Spatiotemporal variation in occurrence and co-occurrence of pesticides, hormones, and other organic contaminants in rivers in the Chesapeake Bay Watershed, United States. Science of The Total Environment 728:138765.	April 2020
McClintock, B. T., J. M. Hill, L. Fritz, K. Chumbley, K. Luxa, and D. R. Diefenbach. 2013, Mark-resight abundance estimation under incomplete identification ofmarked individuals. Methods in Ecology and Evolutio. doi: 10.1111/2041-210X.12140.	October 2013
Maynard-Bean, E. E. M. Kaye, T. Wagner, E.P. Burkhart. 2020. Citizen scientists record novel leaf phenology of invasive shrubs in eastern U.S. forests. Biological Invasions 22:3325–3337.	August 2020
Mattice, J. A., D. W. Brauning, and D. R. Diefenbach. 2005. Abundance of grassland sparrows on reclaimed surface mines in western Pennnsylvania. Pages (504-510) in C. J. Ralph and T. D. Rich, editors. Pacific Southwest Research Station, U. S. Department of Agriculture, Forest Service General Technical Report PSW-GTR-191.	May 2004
Massie, D.L., Y. Li, and T. Wagner. 2021. A framework for detecting macroscale drivers on fish growth. Canadian Journal of Fisheries and Aquatic Sciences 78:165-172. https://doi.org/10.1139/cjfas-2019-0296	November 2020
Massie, D.L., Hansen, G.J., Li, Y., Sass, G.G. and Wagner, T., 2021. Do lake-specific characteristics mediate the temporal relationship between walleye growth and warming water temperatures? Canadian Journal of Fisheries and Aquatic Sciences 78: 913-923. https://doi.org/10.1139/cjfas-2020-0169	February 2021
Massie, D.L., G.D. Smith, T.F. Bonvechio, A.J. Bunch. D.O. Lucchesi, T. Wagner. 2018. Spatial variability and macroscale drivers of growth for native and introduced Flathead Catfish populations. Transactions of the American Fisheries Society 147:554-565.	May 2018
Marshall, M. R., and D. R. Diefenbach. 2010. Henslow’s sparrow. Pages 159-162 in M. A. Steele, M. C. Brittingham, T. J. Maret, and J. F. Merritt, editors. Terrestrial Vertebrates of Pennsylvania: A Complete Guide to Species of Conservation Concern. Johns Hopkins University Press, Baltimore, Maryland, USA.	October 2010
Marshall, M. R., and D. R. Diefenbach. 2010. Grasshopper sparrow. Pages 316-320 in M. A. Steele, M. C. Brittingham, T. J. Maret, and J. F. Merritt, editors. Terrestrial Vertebrates of Pennsylvania: A Complete Guide to Species of Conservation Concern. Johns Hopkins University Press, Baltimore, Maryland, USA.	October 2010
Marshall, M. R., D. R. Diefenbach, L. A. Wood, and R. J. Cooper. 2004. Annual survival estimation of migratory songbirds confounded by incomplete breeding site-fidelity: study designs that may help. Animal Biodiversity and Conservation 27:59-72.	August 2004
Mahan, C. G. D. R. Diefenbach, and W. Cass. 2007. Evaluating and revising a long-term monitoring program for vascular plants: lessons from Shenandoah National Park. Natural Areas Journal 27:16-24.	January 2007
Lutz, C. L., D. R. Diefenbach, C. S. Rosenberry. 2016. Proximate influences on female dispersal in white-tailed deer. Journal of Wildlife Management 80:1218-1226 DOI: 10.1002/jwmg.21106 \| Download	June 2016
Lutz, C. L., D. R. Diefenbach, C. S. Rosenberry. 2015. Population density influences dispersal in female white-tailed deer. Journal of Mammalogy 96:494-501. \| Download	June 2015
Lottig, N.R., T. Wagner, E.N. Henry, K. Spence Cheruvelil, K.E. Webster, et al. 2014 Long-Term Citizen-Collected Data Reveal Geographical Patterns and Temporal Trends in Lake Water Clarity. PLoS ONE 9(4): e95769. doi:10.1371/journal.pone.0095769. \| Download	April 2014
Lottig, N.R., P.-N. Tan, T. Wagner, K.S. Cheruvelil, P.A. Soranno, E.H. Stanley, C.E. Scott, C.A. Stow, and S. Yuan. 2017. Macroscale patterns of synchrony identify complex relationships among spatial and temporal ecosystem drivers. Ecosphere 8(12).	December 2017
Long, E. S., R. A. Sweitzer, D. R. Diefenbach, and M. Ben-David. 2005. Anthropogenic CO2 alters bone collagen delta-13C of mountain lions: controlling for atmospheric variation in stable isotope studies. Oecologia 146:148-156.	November 2004
Long, E. S., D. R. Diefenbach, C. S. Rosenberry, and B. D. Wallingford. 2008. Multiple proximate and ultimate causes of natal dispersal in white-tailed deer. Behavioral Ecology 19:1235-1242 doi:10. 1093/beheco/arn082. \| Abstract \| Download	August 2008	Proximate and ultimate causes of dispersal in vertebrates vary, and relative importance of these causes is poorly understood. Among populations, inter- and intrasexual social cues for dispersal are thought to reduce inbreeding and local mate competition, respectively, and specific emigration cue may affect dispersal distance, such that inbreeding avoidance dispersal tends to be farther than dispersal to reduce local competition. To investigate potential occurrence of multiple proximate and ultimate causes of dispersal within populations, we radio-marked 363 juvenile male white-tailed deer (Odocoileus virginianus) in 2 study areas in Pennsylvania. Natal dispersal probability and distance were monitored over a 3-year period when large-scale management changes reduced density of adult females and increased density of adult males. Most dispersal (95–97%) occurred during two 12-week periods: spring, when yearling males still closely associate with related females, and prior to fall breeding season, when yearling males closely associate with other breeding-age males. Following changes to sex and age structure that reduced potential for inbreeding and increased potential for mate competition, annual dispersal probability did not change; however, probability of spring dispersal decreased, whereas probability of fall dispersal increased. Spring dispersal distances were greater than fall dispersal distances, suggesting that adaptive inbreeding avoidance dispersal requires greater distance than mate competition dispersal where opposite-sex relatives are philopatric and populations are not patchily distributed. Both inbreeding avoidance and mate competition are important ultimate causes of dispersal of white-tailed deer, but ultimate motivations for dispersal are proximately cued by different social mechanisms and elicit different responses in dispersers.
Long, E. S., D. R. Diefenbach, C. S. Rosenberry, B. D. Wallingford, and M. D. Grund. 2005. Landscape structure influences dispersal distance of white-tailed deer. Journal of Mammalogy 86:623-629.	June 2005
Long, E. S., D. R. Diefenbach, C. L. Lutz, C. S. Rosenberry, B. D. Wallingford. 2021. Risky movements? Natal dispersal does not decrease survival of white-tailed deer. Ecology and Evolution 11:2731–2740. DOI: 10.1002/ece3.7227 \| Download	March 2021
Long, E. S., D. R. Diefenbach, B. D. Wallingford, C. S. Rosenberry. 2010. Influence of Roads, Rivers, and Mountains on Natal Dispersal of White-tailed Deer. Journal of Wildlife Management 74:1242-1249. \| Abstract \| Download	August 2010	Natural and anthropogenic landscape features, such as rivers, mountain ranges, and roads can alter animal dispersal paths and movement patterns. Consequently landscape, through its effects on dispersal, may influence many ecological processes, including disease transmission, invasion dynamics, and gene flow. To investigate influences of landscape features on dispersal patterns of a large mammal, we captured and radiomarked 363 juvenile male white-tailed deer (Odocoileus virginianus), including 212 confirmed dispersers, in 2 topographically dissimilar study areas in Pennsylvania, USA. Dispersal azimuths were uniformly distributed in the western study area (WSA), where there was irregular, hilly topography. Mean dispersal azimuths paralleled ridge direction in the eastern study area, where long parallel ridges were aligned northeast–southwest. Major roads in both areas and a large river in the WSA were semipermeable barriers to dispersal of juvenile males; dispersal paths were less likely to intersect these linear features. Dispersal movements were direct and brief, typically lasting ,12 hours. For all dispersers, we found no evidence for preference or avoidance of establishing adult, postdispersal ranges in proximity to roads; however, deer that encountered roads near the terminus of their dispersal path were more likely to stop on the near side. Further, for deer that established postdispersal home ranges near major roads, these features influenced range placement such that locations were typically clustered on one side of the road. The influence of roads, rivers, and mountains on dispersal paths and postdispersal locations of white-tailed deer suggest that landscape-specific features should be considered in conservation and management of this and possibly other species of large mammals.
Lieb, D. A., and R. F. Carline. 2000. Effects of urban runoff from a detention pond on water quality, temperature and caged Gammarus minus (Say) (Amphipoda) in a headwater stream. Hydrobiologia 441:107-116.	October 2000
Lieb, D. A., and R. F. Carline. 1999. The effects of urban runoff from a detention pond on the macroinvertebrate community of a headwater stream in central Pennsylvania. Journal of the Pennsylvania Academy of Science 73(3):99-105	November 1999
Liang, Z., Y. Xu, Q. Qiu, Y. Liu, W. Lu, and T. Wagner. 2021. Developing Joint Nutrient Criteria Using Quantile Regression for Lake Eutrophication Management. Journal of Hydrology 594:125883. https://doi.org/10.1016/j.jhydrol.2020.125883	January 2021
Liang, Z., Y. Xu, G. Zhao, W. Lu, Z. Fu, S. Wang, and T. Wagner. 2023. Approaching the upper boundary of stressor-response relationships: Identifying factors using a novel framework integrating quantile regression with interpretable machine learning. Frontiers of Environmental Science and Engineering 17:76. https://doi.org/10.1007/s11783-023-1676-2	January 2023
Liang, Z., P.A. Soranno, T. Wagner. 2020. The role of phosphorus and nitrogen on chlorophyll a: evidence from hundreds of lakes. Water Research 185:116236. https://doi.org/10.1016/j.watres.2020.116236	July 2020
Liang, Z., Liu, Y., Xu, Y. and Wagner, T., 2021. Bayesian change point quantile regression approach to enhance the understanding of shifting phytoplankton-dimethyl sulfide relationships in aquatic ecosystems. Water Research, p.117287. https://doi.org/10.1016/j.watres.2021.117287	August 2021
Li, Y., V.S. Blazer, T. Wagner. 2018. Quantifying population-level effects of water temperature, flow and chemical-induced reproduction depression: a simulation study with smallmouth bass. Ecological Modelling 384:63-74. https://doi.org/10.1016/j.ecolmodel.2018.06.015	November 2018
Li, Y., V.S. Blazer, L.R. Iwanowicz, M.K. Schall, K. Smalling, D. Tillitt, and T. Wagner. 2020. Ecological risk assessment of environmental stress and bioactive chemicals to riverine fish populations: an individual-based model of smallmouth bass Micropterus dolomieu. Ecological Modelling 438:109322.	October 2020
Li, Y., T. Wagner, Y. Jiao, R. Lorants, and C.A Murphy. Accepted. Evaluating spatial and temporal variability in growth and mortality for recreational fisheries with limited catch data. Canadian Journal of Fisheries and Aquatic Sciences.	November 2017
Li, Y. and T. Wagner. 2019. Does incorporating gear selectivity during macroscale investigations of fish growth reduce size-selective sampling bias in parameter estimates? Canadian Journal of Fisheries and Aquatic Sciences 76:2089-2101.	February 2019
Levy, O., B.A. Ball, B. Bond-Lamberty, K.S. Cheruvelil, A.O. Finley, N. Lottig, S.W. Punyasena, J. Xiao, J. Zhou, L.B. Buckley, C.T. Filstrup, T. Keitt, J.R. Kellner, A.K. Knapp, A.D. Richardson, D. Tcheng, M. Toomey, R. Vargas, J.W. Voordeckers, T. Wagner, J.W. Williams. 2014. Approaches to advance scientific understanding of macrosystems ecology. Frontiers in Ecology and the Environment 12:15-23. \| Download	February 2014
Lapierre, J-F., S.M. Collins, S.K. Oliver, E.H. Stanley, T. Wagner. 2021. Inconsistent browning of Northeastern US lakes despite increased precipitation and recovery from acidification. Ecosphere 12 e03415.	March 2021
Lapierre JF, Webster KE, Hanks E, Wagner T, Soranno PA, McCullough IM, Reinl KL, Domka M and Lotting NR. Accepted. A continuous classification of the 476,697 lakes of the conterminous US based on geographic archetypes. Limnology and Oceanography. http://doi.org/10.1002/lno.12457	November 2023
Laake, J. L. D. Johnson, D. R. Diefenbach, M. A. Ternent. 2014. Hidden Markov Model for Dependent Tag Loss and Survival Estimation. Journal of Agricultural, Biological, and Environmental Statistics 19:522-540. \| Abstract \| Download	December 2014	Mark-recapture estimators assume no loss of marks to provide unbiased estimates of population parameters. We describe a hidden Markov model (HMM) framework that integrates a mark loss model with a Cormack–Jolly–Seber model for survival estimation. Mark loss can be estimated with single-marked animals as long as a sub-sample of animals has a permanent mark. Double-marking provides an estimate of mark loss assuming independence but dependence can be modeled with a permanently marked sub-sample.We use a log-linear approach to include covariates for mark loss and dependence which is more flexible than existing published methods for integrated models. The HMM approach is demonstrated with a dataset of black bears (Ursus americanus) with two ear tags and a subset of which were permanently marked with tattoos. The data were analyzed with and without the tattoo. Dropping the tattoos resulted in estimates of survival that were reduced by 0.005–0.035 due to tag loss dependence that could not be modeled. We also analyzed the data with and without the tattoo using a single tag. By not using tattoos, survival estimates were reduced by 0.01–0.09 because it was not possible to adjust for tag loss.
Kocovsky, P. M., and R. F. Carline. Stream pH as an abiotic gradient influencing distributions of trout in Pennsylvania streams. Transactions of the American Fisheries Society 134:1299-1312.	September 2005
Kocovsky, P. M., and R. F. Carline. 2006. Influence of landscape-scale factors in limiting brook trout populations in Pennsylvania streams. Transactions of the American Fisheries Society 135:76-88.	February 2006
Kocovsky, P. M., and R. F. Carline. 2001. Influence of extreme temperature on consumption and condition of walleyes in Pymatuning Sanctuary, Pennsylvania. North American Journal of Fisheries Management 21:198-207.	February 2001
Kocovsky, P. M., and R. F. Carline. 2001. Dynamics of the unexploited walleye population of Pymatuning Sanctuary, Pennsylvania, 1997-1998. North American Journal of Fisheries Management 21:178-187.	February 2001
Kocovsky, P. M., and R. F. Carline. 2000. A comparison of methods for estimating ages of unexploited walleyes. North American Journal of Fisheries Management 20:1044-1048.	November 2000
King, D.T., J.W. Fischer, B. Strickland, W.D. Walter, F.L. Cunningham, and G. Wang. 2016. Winter and summer home ranges of American white pelicans (Pelecanus erythrorhynchos) captured at loafing sites in the southeastern United States. Waterbirds 39(3):287–294.	October 2016
Khouri, R.M, D.C. Wagner, and W. D. Walter. 2022. Efficacy of secondary electric fences at preventing direct contact among white-tailed deer. Wildlife Society Bulletin 46:e1350 \| Abstract	September 2022	Although direct contacts at fences separating free-ranging and captive cervid herds are at risk for chronic wasting disease transmission, no study has explored the use of a secondary electric fence to prevent these contacts in white-tailed deer (<i>Odocoileus virginianus</i>). Using a captive herd of white-tailed deer in Pennsylvania, USA, we tested the efficacy of two electric fence designs (one three-strand and one six-strand) constructed along separate primary fence lines (each composed of 20 m of chain link and 20 m of woven wire fencing) dividing paddocks of captive deer. From June to November 2019, we conducted three trials of variable lengths to assess how season, age, and sex impacted behavior and motivation of deer to breach the electric fence. When no electric fence was in place, we observed direct contact through both woven wire and chain link fences. With the electric fences in place, we observed electric fence breaches (some of which led to direct contact between deer) only by weaned fawns (37 breaches, 4 direct contacts) and males in the mid- and late-rut (2 breaches, 1 direct contact). The majority of these breaches occurred across the three-strand-fence. Our results suggest that no style of primary fence alone is sufficient to prevent direct contacts and that the addition of a secondary, properly designed electric fence constructed along the primary fence of captive white-tailed deer facilities could prevent direct contact between captive and free-ranging deer.
Kepler, M.V., T. Wagner, and J.A. Sweka. 2014. Comparative bioenergetics modeling of two Lake Trout morphotypes. Transactions of the American Fisheries Society 143:1592–1604. \| Download	October 2014
Keagy, J., C. Drummond, K. Gilbert, C. Grozinger, J. Hamilton, H. Hines, J. Laske, C. Logan, R. Sawers, and T. Wagner. 2023. Landscape transcriptomics as a tool for addressing global change effects across diverse species. Molecular Ecology Resources. http://doi.org/10.1111/1755-0998.13796	April 2023
Johnson, H.E., J.W. Fischer, M Hammond, P. Dorsey, W. D. Walter, C.W. Anderson, and K.C. VerCauteren. 2014. Evaluation of techniques to reduce deer and elk damage to agricultural crops. Wildlife Society Bulletin 38(2):358–365. \| Abstract	June 2014	Mule deer (Odocoileus hemionus) and Rocky Mountain elk (Cervus elaphus nelsoni) provide important recreational, ecological, and economic benefits, but can also cause substantial damage to agricultural crops. Cervid damage to agriculture generates significant challenges for wildlife agencies responsible for minimizing crop depredation while maintaining healthy deer and elk populations. Sunflower producers in southwestern Colorado have experienced high deer and elk damage in recent years and were interested in temporary methods to reduce damage that were cost-effective for rotational crops. To address this challenge we investigated three temporary, non-lethal exclusion and repellent techniques for reducing deer and elk damage to sunflowers: 1) a polyrope electric fence, 2) the chemical repellent Plantskydd™, and 3) a winged fence. During July through October 2011 and 2012, we used a randomized block design to test the efficacy of these techniques by quantifying cervid damage to sunflowers and the number of deer and elk tracks traversing treatment and control plot boundaries. Using generalized linear mixed models we found that polyrope electric fences significantly reduced deer and elk damage and presence within plots, while the repellent and winged fences did not have significant treatment effects. In areas where wildlife management agencies want to maintain or increase deer and elk populations but reduce seasonal damage by cervids to agriculture, use of an effective exclusion technique like polyrope electric fence could sufficiently protect high-value crops, decrease the need for lethal depredation permits and damage compensation payments, and increase satisfaction among producers and the public.
Jennelle, C.S., W.D. Walter, J. Crawford, C.S. Rosenberry, B.D. Wallingford. 2022. Movement of white-tailed deer in contrasting landscapes influences management of chronic wasting disease. Journal of Wildlife Management 86:e22306. \| Abstract	October 2022	For several decades, chronic wasting disease (CWD) has exhibited an unabated expansion in distribution and intensity across North America. Upon detection, either for the first time in a novel area or in a region with an existing outbreak, wildlife management agencies are tasked with responding to mitigate the disease. This often entails creation or modification of a management zone within which rules and regulations can be modified that support an agency’s disease management plan. To help inform the process of creating an appropriately-sized CWD management zone, assuming that wild deer movements are the primary risk factor for disease spread, we used data from GPS-collared white-tailed deer (<i>Odocoileus virginianus</i>) in southeastern Minnesota and southcentral Pennsylvania to estimate long-distance movements associated with dispersal and migratory behaviors. These contrasting study areas with active CWD outbreaks permit an evaluation of deer movement dynamics in different parts of their range. We quantified the proportion, distribution, timing, and orientation of dispersing and migratory deer. We observed 21% of female and 58% of male yearlings disperse from their apparent natal home range in Minnesota, while in Pennsylvania, 4% of female and 68% of male yearlings dispersed. We also documented 20% of females and 6% of males migrated between seasonal home ranges in Minnesota, while in Pennsylvania, no females and 5% of males migrated. The average distance deer dispersed or migrated in Minnesota was 20 km and 11 km, respectively, while in Pennsylvania deer dispersed or migrated only about 4km. Both sexes in Minnesota tended to disperse in a consisent, westerly direction; however there was no directional preference observed for migratory deer, nor for dispersing deer in Pennsylvania. We found differences in natal and adult home range size for both sexes in Minnesota, but not for males in Pennsylvania. Our results identify the considerable variability in disperal and migration dynamics of white-tailed deer in disparate landscapes, which is important to agencies managing CWD. We summarize the distribution of these long-distance movements and suggest agencies use this information to decide on an optimal management zone size that meets their needs. We encourage the development of formalized assesments of the tradeoffs associated with optimizing decisions about creation of CWD management zones across white-tailed deer populations that exhibit variation in dispersal behavior and caution against an arbitrary size/shape or one-size fits-all approach to creation of disease management zones.
Irwin, B.J., T. Wagner, J.R. Bence, M.V. Kepler, W. Liu, and D.B. Hayes. 2013. Estimating spatial and temporal components of variation for fisheries count data using negative binomial mixed models. Transactions of the American Fisheries Society 142:171-183. \| Download	January 2013
Irwin, B., T Wagner, and J. R. Bence. 2018. Characterization of Spatial and Temporal Variability in Fishes in Response to Climate Change. Project completion report [extended abstract], Northeast Climate Science Center.	January 2018
Hill, J. M., and D. R. Diefenbach. 2013. Occupancy patterns of declining grassland sparrow populations in a fragmented and forested landscape. Conservation Biology 28:735-744. \| Abstract \| Download \| Publisher Website	January 2014	Organisms can be affected by processes in the surrounding landscape outside the boundary of habitat areas and by local vegetation characteristics. There is substantial interest in understanding how these processes affect populations of grassland birds, which have experienced substantial population declines. Much of our knowledge regarding patterns of occupancy and density stem from prairie systems, whereas relatively little is known regarding how occurrence and abundance of grassland birds vary in reclaimed surface mine grasslands. Using distance sampling and single-season occupancy models, we investigated how the occupancy probability of Grasshopper (Ammodramus savannarum) and Henslow's Sparrows (A. henslowii) on 61 surface mine grasslands (1591 ha) in Pennsylvania changed from 2002 through 2011 in response to landscape, grassland, and local vegetation characteristics . A subset (n = 23; 784 ha) of those grasslands were surveyed in 2002, and we estimated changes in sparrow density and vegetation across 10 years. Grasshopper and Henslow's Sparrow populations declined 72% and 49%, respectively from 2002 to 2011, whereas overall woody vegetation density increased 2.6 fold. Henslow's Sparrows avoided grasslands with perimeter–area ratios ≥0.141 km/ha and woody shrub densities ≥0.04 shrubs/m2. Both species occupied grasslands ≤13 ha, but occupancy probability declined with increasing grassland perimeter–area ratio and woody shrub density. Grassland size, proximity to nearest neighboring grassland (inline image = 0.2 km), and surrounding landscape composition at 0.5, 1.5, and 3.0 km were not parsimonious predictors of occupancy probability for either species. Our results suggest that reclaimed surface mine grasslands, without management intervention, are ephemeral habitats for Grasshopper and Henslow's Sparrows. Given the forecasted decline in surface coal production for Pennsylvania, it is likely that both species will continue to decline in our study region for the foreseeable future.
Hill, J. M., and D. R. Diefenbach. 2013. Experimental removal of woody vegetation does not increase nesting success or fledgling production in two grassland sparrows (Ammodramus) in Pennsylvania. Auk 130:764-773. \| Download	October 2013
Hill, J. M., J. F. Egan, G. E. Stauffer, and D. R. Diefenbach. 2014. Habitat availability is a more plausible explanation than insecticide acute toxicity for U.S. grassland bird species declines. PLoS ONE 9(5): e98064. doi:10.1371/journal.pone.0098064 \| Download	May 2014
Henningsen, J.C., A.L. Williams, C.M. Tate, S.A. Kilpatrick, and W.D. Walter. 2012. Distribution and prevalence of Elaeophora schneideri in moose in Wyoming. Alces 48:35-44	June 2012
Hassinger, J. D., C. M. Butchkoski, and D. R. Diefenbach. 2008. Managing surface rock communities for Neotoma magister. Pages 213-246 in J. Wright and J. Peles, editors. The Allegheny Woodrat: Ecology, Conservation, and Management of a Declining Species. Springer-Verlag, New York, USA.	August 2008
Hansen, G.J.A., T.D. Ahrenstorff, B.J. Bethke, J. Dumke, J. Hirsch, K.E. Kovalenko, J.F. LeDuc, R.P. Maki, H. Rantala, and T. Wagner. 2020. Walleye growth declines following zebra mussel and Bythotrephes invasion. Biological Invasions 22:1481–1495.	January 2020
Hansen, G.J.A., S.R. Midway, T. Wagner. 2017. Walleye recruitment is less resilient to warming water temperatures in lakes with abundant largemouth bass populations. Canadian Journal of Fisheries and Aquatic Sciences.	April 2017
Haley, N.J., C. Siepker, W.D. Walter, B.V. Thomsen, J.J. Greenlee, A.D. Lehmkuhl, and J.A. Richt. 2016. Antemortem detection of chronic wasting disease prions in nasal brush collections and rectal biopsies from white-tailed deer by real time quaking-induced conversion. Journal of Clinical Microbiology 54(4): 1108-1116.	March 2016
Haley, N.J., C. Siepker, L.L. Hoon-Hanks, G. Mitchell, W.D. Walter, M. Manca, R.J. Monello, J.G. Powers, M.A. Wild, E.A. Hoover, B. Caughey, and J. Richt. 2016. Seeded amplification of chronic wasting disease prions in nasal brushings and recto-anal mucosal associated lymphoid tissues from elk by real time quaking-induced conversion. Journal of Clinical Microbiology 54(4): 1117-1126.	March 2016
Gundermann, K.P., D. R. Diefenbach, W. D. Walter, A. M. Corondi, J. E. Banfield, B. D. Wallingford, D. P. Stainbrook, C. S. Rosenberry, and F. E. Buderman. 2023. Change-point models for identifying behavioral transitions in wild animals. Movement Ecology 11:65. \| Download	October 2023
Grossman, G.D., R.F. Carline, and T. Wagner. Brown trout (Salmo trutta) in Spruce Creek Pennsylvania: a quarter-century perspective. 2017. Freshwater Biology 62:1143-1154.	April 2017
Gordon, S., T. Wagner, K. Smalling, and O. Devereux. 2023. Estrogenic activity response to best management practice implementation in agricultural watersheds in the Chesapeake Bay Watershed. Journal of Environmental Management 326:116734. https://doi.org/10.1016/j.jenvman.2022.116734	November 2022
Gingery, T. M., D. R. Diefenbach, C. E. Pritchard, D. C. Ensminger, B. D. Wallingford, and C. S. Rosenberry. 2020. Survival is negatively associated with glucocorticoids in a wild ungulate neonate. Integrative Zoology 16:214-225. https://doi.org/10.1111/1749-4877.12499 \| Download	November 2020
Gingery, T. M., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. 2018. Landscape-level patterns in fawn survival across North America. 82:1003-1013 DOI: 10.1002/jwmg.21456. \| Download	June 2018
Gigliotti, L. C., and D. R. Diefenbach. 2018. Risky behavior and its effect on survival: snowshoe hare behavior under varying moonlight conditions. Journal of Zoology 305:27-34. doi:10.1111/jzo.12532 \| Download	January 2018
Gigliotti, L. C., N. D. Berg, R. Boonstra, S. M. Cleveland., D. Diefenbach, E. M. Gese, J. S. Ivan, K. Kielland, C. J. Krebs, A. V. Kumar, L. S. Mills, J. N. Pauli, H B. Underwood, E. C. Wilson, M. J. Sheriff. 2020. Latitudinal variation in snowshoe hare (Lepus americanus) body mass: A test of Bergmann’s Rule. Canadian Journal of Zoology 98:88-95. https://doi.org/10.1139/cjz-2019-0184 \| Download	January 2020
Gigliotti, L. C., D. R. Diefenbach, M. J. Sheriff. 2017. Geographic variation in winter adaptations of snowshoe hares. Canadian Journal of Zoology 95:539-545.	May 2017
Gigliotti, L. C., B. Jones, M. Lovallo, and D. R. Diefenbach. 2018. Snowshoe hare multi-level habitat use in Pennsylvania in relation to prescribed burning. Journal of Wildlife Management 82:435-444 DOI: 10.1002/jwmg.21375. \| Download	February 2018
Gatch, A. Z. Biesinger, E. Bruestly, C. Karboski, K. Lee, T. Wagner, M. Bartron, D. Gorsky. 2021. Discovery of Successful River Spawning by Lake Trout (Salvelinus namaycush) in the Lower Niagara River, Lake Ontario.	January 2021
Ganoe, L.S., M.J. Lovallo, J.D. Brown, and W.D. Walter. 2020. Ecology of an isolated muskrat population during regional population declines. Northeastern Naturalist. 28(1);49-64. DOI: 10.1656/045.028.0104 \| Abstract	February 2021	Evidence indicating a decline in muskrat populations in the United States during the past 40 years has led to speculation in regard to factors influencing muskrat survival. In order to understand population dynamics and survival, it is important to first understand the ecology of local populations. We investigated the dwelling structure use, movements, home range, and survival of radio-tagged muskrats (n = 17) in an urban wetland complex in central Pennsylvania. We used locations collected from intensive radio telemetry monitoring to determine number of lodging structures used, hourly movement, and size and percent area overlap of home ranges. Muskrats shared an average of nine lodging structures and on average 68% of a muskrat’s home range overlapped other muskrat home ranges. We used four home range estimators (Kernel Density Estimator (KDE) <i><sub>href</sub></i>, KDE<i><sub>ad hoc</sub></i>, KDE<i><sub>plug-in</sub></i>, and Local Convex Hull estimator) to assess the ability of each estimator in representing muskrat home ranges. The KDE<i><sub>plug-in</sub></i> that constrained the estimate of home range to habitat boundaries provided the more appropriate home range size for muskrats in a linear-non-linear habitat matrix. We also calculated overwinter survival estimates using known-fate models in Program MARK®. Our top model indicated a positive effect of the average weekly precipitation on survival with an overwinter survival estimate of 0.59 (SE = 0.16). The main cause of muskrat mortality was mink (n = 6). Our model suggests that snowfall may be an important factor in muskrat survival. Our study provides novel data on muskrat ecology in Pennsylvania as well as preliminary evidence for future investigations of climate’s impact on muskrat survival during the winter months.
Ganoe, L.S., J.D. Brown, M.J. Yabsley, M.J. Lovallo, and W.D. Walter. 2020. A review of pathogens, diseases, and contaminants of muskrats (Ondatra zibethicus) in North America. Frontiers in Veterinary Science 7:233. doi: 10.3389/fvets.2020.00233. \| Abstract	May 2020	Over the last 50 years, significant muskrat (<i>Ondatra zibethicus</i>) harvest declines have been observed throughout North America. Several theories for the decline have been proposed, including increased parasite infections and disease within muskrat populations. No existing wholistic review of muskrat exposure to pathogens, contaminants, and diseases exists. To address this knowledge gap, we conducted a thorough review of existing literature on muskrat pathogens, contaminants, and diseases across their natural range. This review is comprised of 129 articles from 1915-2019were and from 27 U.S. states and 9 Canadian provinces. A wide diversity of contaminants, toxins, and pathogens were reported in muskrats, with the most common diseases being cysticercosis, tularemia, Tyzzer’s disease, and biotoxin poisoning from cyanobacteria. This review provides a summary of muskrat pathogens, contaminants, and disease over a century that has observed significant population declines throughout the species’ range in North America. Such data provides baseline data for understanding the potential role of disease in these declines. In addition, these data highlight critical knowledge gaps that warrant future research efforts.
Ganoe, L.S., J.D. Brown, M.J. Lovallo, M.J. Yabsley, K.B. Garrett, A.T. Thompson, R.H. Poppenga, M.G. Ruder, and W.D. Walter. 2021. Surveillance for diseases, pathogens, and toxicants of muskrat (Ondatra zibethicus) in Pennsylvania and surrounding regions. PlosONE 16(12):e0260987. \| Abstract	December 2021	Using diagnostic data and contemporary sampling efforts, we conducted surveillance for a diversity of pathogens, toxicants, and diseases of muskrats (<i>Ondatra zibethicus</i>). Between 1977 and 2019, 26 diagnostic cases were examined from Kansas and throughout the Southeast and Mid-Atlantic, USA. We identified multiple causes of mortality in muskrats, but trauma (8/26), Tyzzer’s disease (5/6), and cysticercosis (5/26) were the most common. We also conducted necropsies, during November 2018 - January 2019 Pennsylvania muskrat trapping season, on 380 trapper-harvested muskrat carcasses after the pelt was removed. Tissue samples and exudate were tested for presence of or exposure to a suite of pathogens and contaminants. Gastrointestinal tracts were examined for helminths. Intestinal helminths were present in 39.2% of necropsied muskrats, with <i>Hymenolepis</i> spp. (62%) and echinostome spp. (44%) being the most common. Molecular testing identified a low prevalence of infection with <i>Clostridium piliforme </i>in the feces and <i>Sarcocystis</i> spp. in the heart. We detected a low seroprevalence to <i>Toxoplasma gondii</i> (1/380)<i>.</i> No muskrats were positive for <i>Francisella tularensis </i>or <i>Babesia </i>spp. Cysticercosis was detected in 20% (5/26) of diagnostic cases and 15% (57/380) of our trapper-harvested muskrats. Toxic concentrations of arsenic, cadmium, lead, or mercury were not detected in tested liver samples. Copper, molybdenum, and zinc concentrations were detected at acceptable levels comparative to previous studies. Parasite intensity and abundance were typical of historic reports; however, younger muskrats had higher intensity of infection than older muskrats which is contradictory to what has been previously reported. A diversity of pathogens and contaminants have been reported from muskrats, but the associated disease impacts are poorly understood. Our data are consistent with historic reports and highlight the wide range of parasites, pathogens and contaminants harbored by muskrats in Pennsylvania. The data collected are a critical component in assessing overall muskrat health and serve as a basis for understanding the impacts of disease on recent muskrat population declines.
Fischer, J.W., W.D. Walter, M.A. Avery. 2013. Brownian bridge movement models to characterize home ranges of avian species. The Condor 115(2): 298-305. \| Abstract	June 2013	A Brownian Bridge movement model (BBMM) is a relatively new concept that estimates the movement path of an animal probabilistically using data collected at frequent time intervals. A BBMM assumes that locations are not independent, whereas the ‘classical’ kernel density estimator (KDE) assumes locations are independent. We estimated BBMM home ranges for 11 Black Vultures (Coragyps atratus) and 7 Turkey Vultures (Cathartes aura) equipped with global positioning system satellite transmitters near Marine Corps Air Station Beaufort, South Carolina from October 2006 to November 2008. For Black Vultures that travelled >100 km from the capture site (n=2), overall 95% BBMM home ranges (95% BBMM) were 833 and 2111 km2. For Black Vultures that did not travel as far (n=9), 95% BBMM ranged from 33 to 778 km2 and averaged (± SE) 243 ± 76 km2. The majority of Turkey Vultures travelled >100 km from the capture site (n=6) with 95% BBMM ranging from 923 to 7058 km2 and averaged (± SE) 3173 ± 1109 km2. We also estimated KDE home ranges using newer satellite technology to compare to previous studies. Overall 95% KDE ranged from 17 to 16066 km2 for Black Vulture and 988 to 36257 km2 for Turkey Vulture. The concept of an animal’s home range has evolved over time, as have home-range estimators. With increasing use of satellite telemetry, application of BBMM can greatly enhance our understanding of home ranges, migratory routes, seasonal movements, and habitat use patterns of wild birds over large and often remote areas.
Fischer, J.W., D. McMurtry, C.R. Blass, W.D. Walter , J. Beringer, and K.C. VerCauteren. 2016. Effects of simulated removal activities on movements and space use of feral swine. European Journal of Wildlife Research 62(3):285–292. \| Abstract	May 2016	The abundance and distribution of feral swine (Sus scrofa) in the United States has increased dramatically during the last 30 years. Effective measures are needed to control and eradicate feral swine populations without displacing animals over wider areas. The objective of this study was to investigate the effects of repeated control activities on feral swine movements and space use. We analyzed location data from 21 feral swine that were captured and fitted with global positioning system harnesses in southern Missouri, USA. Various control activities were applied to eight feral swine before lethal removal, including: trap-n-release, chased with dogs, hunted (but not killed), and chased with helicopter. We found core space use areas were reduced following the first control activity while overall space use areas and diurnal movement rates increased following the second control activity. Space-use center shifts did not differ between pre- and post-periods for either the first or second control activities. Information on feral swine movements and space use precipitated by human control activities, such as hunting, trapping, and chasing with dogs is not available for much of the United States. Effective management strategies are needed to control feral swine populations, while preventing enlarged home ranges and displaced individuals which could lead to increased disease transmission risk and human conflict in adjacent areas.
Fischer, J.W., C.R. Blass, W.D. Walter , C.W. Anderson, M.J. Lavelle, W.H. Hall, and K.C. VerCauteren. 2016. Evaluating a strategy to deliver vaccine to white-tailed deer at a landscape level. Wildlife Society Bulletin 40(2):394–399. \| Abstract	June 2016	Effective delivery of vaccines and other pharmaceuticals to wildlife populations is needed when disease outbreaks pose a risk to public health or have huge economic consequences. We created a grid of experimental bait stations (n=64) on Sandhill Wildlife Management Area, Wisconsin, USA to assess station densities needed to attract and deliver placebo baits to free-ranging white-tailed deer (Odocoileus virginianus) and look for associations between deer density, number of bait stations per deer, and bait consumption. We placed 1L (in volume) of alfalfa cubes at bait stations 652 m apart, and monitored with motion-activated cameras for 5 days to document visitation, consumption, and potential for vaccine delivery to non-target species. Deer discovered only 38% of all bait stations within 37 hours, on average, and the number of bait stations in which deer consumed <50%, 50-99%, or 100% of the bait was proportionally equal (13%; n=8). We documented 94% of all photographs of wildlife at bait stations to be white-tailed deer. We also found no significant relationships between bait consumption and deer density or the number of bait stations per deer. We provide information on use of baits by deer and non-target wildlife with our predetermined baiting density and bait matrix. Altering grid spacing between bait stations, targeting specific areas where deer frequent (e.g. forest edges), and amount of bait per station will enable managers to optimize delivery and consumption of vaccine-laden baits to a large proportion of the deer in similar habitats.
Filstrup, C.T., T. Wagner, S.K. Oliver, C.A. Stow, K.E. Webster, E.H. Stanley, and J.A. Downing. 2018. Evidence for regional nitrogen stress on chlorophyll a in lakes across large landscape and climate gradients. Limnology and Oceanography.	February 2018
Filstrup, C.T., T. Wagner, P.A. Soranno, E.H. Stanley, C.A. Stow, K.E. Webster, and J.A. Downing. 2014. Regional variability among nonlinear chlorophyll-phosphorus relationships in lakes. Limnology and Oceanography 59:1691-1703. \| Abstract \| Download \| Publisher Website	August 2014	The relationship between chlorophyll a and total phosphorus (TP) is a fundamental relationship in lakes that reflects several aspects of ecosystem function and is also used in the regulation and management of inland waters. The exact form of this relationship has substantial impacts on its meaning and its use. We assembled a spatially extensive dataset to examine whether nonlinear models are a better fit for chlorophyll a-TP relationships than traditional log-linear models, whether there were regional differences in the form of the relationships, and if so, which regional factors were related to these differences. We analyzed a dataset from 2,105 temperate lakes across 35 ecoregions by fitting and comparing three different nonlinear models and one log-linear model. The three nonlinear models fit the data better than the log-linear model. In addition, the parameters for the best fitting model varied among regions: the maximum and lower chlorophyll asymptotes were positively and negatively related to percent regional pasture agricultural land use, respectively, and the rate at which chlorophyll increases with TP was negatively related to percent regional wetland cover. Lakes in regions with more pasture agricultural land use had higher maximum chlorophyll concentrations at high TP concentrations, but lower minimum chlorophyll concentrations at low TP concentrations. Lakes in regions with less wetland cover showed a steeper chlorophyll-TP relationship compared to wetland-rich regions. Our findings suggest that interpretation of chlorophyll-TP relationships depends upon regional differences and that theory and management based on a monolithic relationship would be inaccurate.
Fergus, C.E., A.O. Finley, P.A. Soranno, T. Wagner. 2016. Spatial Variation in Nutrient and Water Color Effects on Lake Chlorophyll at Macroscales. PLoS ONE 11(10): e0164592.doi:10.1371/journal.pone.0164592.	October 2016
Fameli, A, J. Edson, J.E. Banfield, C.S. Rosenberry, W.D. Walter. 2022. Variability in prion protein genotypes by spatial unit to inform susceptibility to chronic wasting disease. Prion 16 (1):254–264. \| Abstract	October 2022	Chronic wasting disease (CWD) is a fatal, encephalopathy affecting North American cervids. Certain alleles in host’s prion protein gene are responsible for reduced susceptibility to CWD. We assessed for the first time variability in the prion protein gene of elk (<i>Cervus canadensis</i>) present in Pennsylvania, a reintroduced population for which CWD cases have never been reported. We sequenced the prion protein gene (PRNP) of 565 elk samples collected over seven years (2014-2020), and found two polymorphic sites (codon 21 and codon 132). The allele associated with reduced susceptibility to CWD is present in the population, and there was no evidence of deviations from H-W equilibrium in any of our sampling years (<i>p</i>-values between 0.14 and 1), consistent the lack of selective pressure on the PRNP. The less susceptible genotypes were found in a frequency similar to the ones reported for elk populations of Wyoming and South Dakota before CWD was detected. We calculated the proportion of less susceptible genotypes in each hunt zone in Pennsylvania as a proxy for their vulnerability to the establishment of CWD repeating the process for different hunt zone delineations implemented in previous years. We interpolated these results to obtain a surface representing expected proportion of the less susceptible genotypes across the area. We found significant correlation between the results obtained for different hunt zone delineations (p-value<0.001), showing consistency in the pattern regardless of the hunt zone delineation used. Based on this analysis, hunt zones located in the southern part of our study area have a low proportion of less susceptible genotypes, which is discouraging for elk persistence in Pennsylvania given that these hunt zones were adjacent to the deer Disease Management Area 3, where CWD has been present since 2014.
Evans, T.S., M. Kirchgessner, B. Eyler, C.W. Ryan, and W.D. Walter. 2016. Habitat influences distribution of of chronic wasting disease in white-tailed deer. Journal of Wildlife Management \| Abstract	January 2016	Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in 1967 in a captive research facility in Colorado. In the northeastern United States (Northeast), CWD was first confirmed in 2005 in New York and West Virginia, and has since been found in Maryland, Virginia, and Pennsylvania. Because CWD is a new and emerging disease in populations of white-tailed deer (Odocoileus virginianus) in the central Appalachian region and has yet to be assessed within a Bayesian hierarchical modeling framework, we examined demographic and environmental factors to better understand the spatial epidemiology of CWD in the region. The objectives of our study were to (1) apply Bayesian hierarchical models to harvest location data of white-tailed deer tested for CWD in the central Appalachian region between 2005 and 2012, (2) identify covariates that best described the spatial distribution of CWD, and (3) predict probability of risk for CWD infection in the Northeast. Demographic covariates included sex and age, and environmental covariates included elevation, slope, riparian corridor, percent of clay-sized particles in the soil, and percent of three habitat types (developed, forested, and open). For each deer, environmental covariates were extracted within 6 km2 grid cells as this size reflected estimates of 99% isopleths for home range of white-tailed deer in the region. The model with the most support contained random spatial effects and percent habitat and accounted for 94.4% of the overall weight for the candidate set of hierarchical models. Percent forest cover had the strongest relationship with the distribution of CWD in the region, with increased risk of CWD occurring in areas that had lower amounts of forest cover. Our results will assist resource managers in understanding the spatial distribution of CWD not only within the study area, but also in surrounding areas where CWD has yet to be found. Efficiency of disease surveillance and containment efforts can be improved by allocating resources used for surveillance into areas that are at a greater risk for infection.
Evans, T.S., K.L. Schuler, W.D. Walter. 2014 Surveillance and monitoring of white-tailed deer for chronic wasting disease in the northeastern United States. Journal of Fish and Wildlife Management 5(2):387-393.	December 2014
Ensminger, D.C., C. Pritchard, T. Langkilde, T. Gingery, J.E. Banfield, W.D. Walter. 2020. The influence of hunting pressure and ecological factors on fecal glucocorticoid metabolites in wild elk. Wildlife Biology 2020(2); https://doi.org/10.2981/wlb.00683. \| Abstract	June 2020	Climate change and human population growth have increased anthropogenic threats to biodiversity and habitat fragmentation. Ecologists and conservationists need tools to assess the effect of these ecological and environmental perturbations on organismal fitness. One possibility is glucocorticoids (e.g., cortisol and corticosterone) which integrate various factors such as anthropogenic disturbances, predation, food, or environmental stressors. Here we tested the hypothesis that fecal glucocorticoid metabolite concentrations (GCMs) in wild female elk (<i>Cervus canadensis</i>) increased as the hunting season progressed. We also examined the influence of year, food availability, and elk group size on fecal GCMs. We found that as the hunting season progressed, fecal GCMs tended to decrease. We also found that as the number of cows in a group increased, GCMs decreased, and found a strong effect of year on fecal GCMs, with samples collected in 2016 having lower fecal GCMs than those collected in 2015, 2017, and 2018. However, yearly variation was not driven by availability of hard mast forage. The lack of positive association between hunting pressure and fecal GCMs and identifying what is driving yearly variation in fecal GCMs warrants further study. We highlight the negative influence of group size, possibly due to vigilance, on fecal GCMs and the importance of examining ecologically relevant covariates to accurately identify main treatment effects.
Edson, J., J. Brown, W.L. Miller, and W. D. Walter. 2021. Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses. Scientific Reports 11, 10003. https://doi.org/10.1038/s41598-021-89390-2 \| Abstract	May 2021	Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman FTA cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples other than blood stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer (<i>Odocoileus virginianus</i>). Tissue samples acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions. Also, DNA extractions from nasal swabs provided ample DNA but did not improve extraction time or storage of samples.
Diefenbach, D.R., L.A. Hansen, R.J. Warren, M.J. Conroy, and M.G. Nelms. 2009. Restoration of bobcats to Cumberland Island, Georgia, USA: Lessons learned and evidence for the role of bobcats as keystone predators. Pages 423-435 in A. Vargas, C. Breitenmoser and U. Breitenmoser (editors). Iberian Lynx Ex situ Conservation: An Interdisciplinary Approach. Fundación Biodiversidad, Madrid, Spain. \| Abstract \| Download	October 2009	We translocated 32 bobcats (Lynx rufus; 3.1 bobcats/10 km2) to a coastal barrier island, Cumberland Island, Georgia, USA, during 1988-1989 to restore a native predator. In this paper, we summarize our methods of capturing and handling bobcats and results of post-release monitoring of movements, survival, and reproduction. We use this as an opportunity to (1) identify key lessons we learned that could be useful for future felid reintroductions, (2) demonstrate the importance of post-reintroduction monitoring to learn more about the role of predators in ecosystem functioning, and (3) summarize insights we have gained about bobcat prey selection and social organization in a solitary felid. Also, we present previously unpublished data that provide evidence for bobcats initiating a top-down trophic cascade on the Cumberland Island forested ecosystem. We captured bobcats from the coastal plain of Georgia in the hope that these bobcats would have gene complexes adapted to the environment on Cumberland Island. Captured bobcats were temporarily held in a facility on the mainland so that groups of 4-6 individuals could be translocated and released on the island in fall 1988 and 1989. All reintroduced bobcats were vaccinated for three common feline diseases and fitted with radio-collars. Post-release monitoring included radio-telemetry to monitor movements, spatial organization, and survival, re-capture to assess body condition and replace radio-collars, prey surveys to assess food abundance, and scat collection to assess prey use. We analyzed white-tailed deer (Odocoileus virginianus) harvest data from 1980-1997 to assess changes in the deer population (body weights, age-sex structure, and abundance) because deer were a dominant prey species during our post-release monitoring of 1988-1991. Also, because browsing by deer suppressed oak (Quercus spp.) regeneration prior to the bobcat reintroduction, we investigated whether declines in deer abundance resulted in increased numbers and size of seedlings and root sprouts of these tree species. We reintroduced three males and 11 females in fall 1988 and 12 males and six females in fall 1989. One female released in 1988 returned to the mainland, another died from physical injuries, and one male released in 1989 swam into the Atlantic Ocean and presumably drowned. However, annual survival of adults was 93% (SE = 2.6%) for the first three years and recaptured bobcats exhibited an average weight gain of 0.8 kg (12% increase). We documented reproduction of 10 kittens in 1989 (4 litters), one litter of two kittens in 1990, and one litter of two kittens in 1991. Bobcat prey abundance varied spatially and seasonally, but we detected no effect of season or year on diet composition during 1989-90. Marsh rabbits (Sylvilagus palustris), white-tailed deer, and hispid cotton rats (Sigmodon hispidus) were the only prey species identified in bobcat scats in all seasons and we considered these species principal prey. Only the presence of marsh rabbits and cotton rats in bobcat diets were correlated with abundance, which suggested bobcats exhibited a functional response to these prey species. Diet species diversity and richness were negatively correlated with marsh rabbit abundance, which agrees with predictions of a diet optimization model in which alternate prey species (raccoon [Procyon lotor], feral hogs [Sus scrofa], and cotton deermice [Peromyscus gossypinus]) increased with a decrease in abundance of a preferred prey species. By 1997-1998, prey use changed, in which white-tailed deer and marsh rabbits occurred less frequently in scats and all other species occurred more frequently. Female bobcats reintroduced during the first year of the reintroduction exhibited little change in the location or size of their home range (95% fixed kernel utilization distribution), but failed to exclude newcomers reintroduced in 1989 from either their home range or core areas (50% fixed kernel utilization distribution). No bobcats retained areas of exclusive use from conspecifics of the same sex. We observed increasing intrasexual overlap among females during 1989-91, such that each home range overlap was equivalent to each female sharing her home range with >2 other females. Overlap of core areas was equivalent to each female sharing her core area with nearly one other female. Mean eviscerated body weights of harvested white-tailed deer increased 5.0–7.6 kg for males and 2.0–4.9 kg for females between the pre-reintroduction years (1984-1989) and post-reintroduction years (1990-1997). Eviscerated body weights were 11.0 kg greater in 1997 compared to 1989 (average difference of means by age-sex class). Estimates and indices of deer abundance indicated that following reintroduction of bobcats the population declined and remained low. Population estimates indicated hunter success rates declined following the bobcat reintroduction, even though the number of hunters prior to the reintroduction ( = 270 hunters/year) differed little from after the reintroduction of bobcats ( = 278 hunters/year). On nine plots containing 87 oak trees, where oak regeneration at each tree was measured in 1990, the number of trees with seedlings or root sprouts increased from 52 to 86 and the average number of seedlings per plot increased by 153.5. On plots that contained seedlings and sprouts in both 1990 and 1997, average height increased 4.6 cm (95% CI = 4.0–5.2). We were able to successfully capture and translocate approximately 15 bobcats per year, although we were not able to capture enough bobcats to control the sex ratio of the population of reintroduced bobcats; at the conclusion of the translocations in 1989 the reintroduced population consisted of 14 males and 15 females, although it was female-biased (11females, 3 males) after the translocations in 1988. This introduced potential confounding effects when interpreting results of our post-release monitoring of food habits and spatial organization. We strongly recommend that future reintroduction projects establish a means of conducting ‘soft’ releases of animals whereby animals are held in captivity at the release site and allowed to leave captivity following a waiting period. Even holding bobcats overnight might have prevented the disorientation of the released bobcat that swam into the Atlantic Ocean and presumably drowned. A dramatic population decline in marsh rabbits, caused by above-normal rainfall from a hurricane, allowed us to detect changes in bobcat diets and identify a functional response to prey abundance and evidence for diet optimization. The frequency of occurrence of deer in bobcat diets year-round (23–47%) was greater than reported for other studies in the southeastern United States (0–8%). Although we did not have sufficient data to identify the shape of these functional relationships, bobcat diets in 1997-1998 had lower occurrence of marsh rabbits and deer and a more even distribution of occurrence of all prey species in their diet. Also, there was no evidence the frequent occurrence of deer in the diet was because of a lack of food availability because bobcat survival was high, recaptured bobcats exhibited weight gains, and bobcats maintained normal home range sizes. Results of the analysis of spatial organization of bobcats were consistent with the hypothesis that bobcats maintain home ranges via a system of land tenure established by prior rights. However, we observed significant intrasexual overlap of both home ranges and core areas. Furthermore, we observed declining reproduction with an increase in home range overlap. We believe that successful reproduction in bobcats may be related to access by females to exclusive use areas even under conditions of adequate or good food availability. Under the conditions of this study (moderate bobcat density, adequate food availability, and limited dispersal) bobcats exhibited no evidence of an ability to exclude other adult individuals from their home ranges or core areas. Our observations of bobcat use of deer as a primary prey species following their reintroduction, a decline in deer abundance, and an increase in oak regeneration indicated that bobcats caused a trophic cascade effect on the island. We did not expect to observe such strong trophic level changes on the island ecosystem because deer generally are not considered primary prey for bobcats. However research prior to the restoration of bobcats indicated deer were abundant and deer browsing suppressed tree regeneration, and apparently deer were suitable prey for bobcats because of their abundance and small size. We believe the results of this study provide strong justification for post-release monitoring of a reintroduced species to be able to understand why a reintroduction project succeeds or fails. Moreover, the role of predators in ecosystems in poorly understood, especially vertebrate predators, and restoration projects of predator populations should consider monitoring trophic level characteristics of ecosystems. If such a monitoring program were developed to test theories of community population dynamics, there would be much potential to better understand food webs of terrestrial ecosystems and trophic level inter-relationships.
Diefenbach, D. R., and S. M. Shea. 2011. Managing white-tailed deer: eastern North America. Pages 481-500 in D. G. Hewitt, editor. Biology and Management of White-tailed Deer. CRC Press, Boca Raton, Florida, USA.	July 2011
Diefenbach, D. R., W. M. Knox, and C. S. Rosenberry. 2021. The Future of Managing Ungulate Species: White-tailed Deer as a Case Study. Pages 327-340 in K. Pope and L. Powell, editors. Harvest of fish and wildlife: new paradigms for sustainable management. CRC Press, Boca Raton, Florida, USA. \| Download	June 2021
Diefenbach, D. R., W. C. Vreeland, M.J. Casalena, M. V. Schiavone. 2016. Retention of riveted aluminum leg bands by wild turkeys. Journal of Fish and Wildlife Management. doi: http://dx.doi.org/10.3996/072015-JFWM-064 \| Download	February 2016
Diefenbach, D. R., T. Wagner and G. E. Stauffer. 2014. Setting Objectives for Managing Key Deer. U.S. Department of Interior, Fish and Wildlife Service, Cooperator Science Series FWS/CSS-106-2014,Washington, D.C. \| Download	June 2014
Diefenbach, D. R., S. L. Rathbun, J. K. Vreeland, D. Grove, and W. J. Kanapaux. 2016. Evidence for range contraction of snowshoe hare in Pennsylvania. Northeastern Naturalist 23:229-248. \| Download	June 2016
Diefenbach, D. R., M. R. Marshall, J. A. Mattice, and D. W. Brauning. 2007. Incorporating availability for detection in estimates of bird abundance. Auk 124:96-106.	January 2007
Diefenbach, D. R., M. J. Casalena, M. Schiavone, D. Swanson, M. Reynolds, R. C. Boyd, R. Eriksen, and B. Swift. 2009. Loss of butt-end leg bands on male wild turkeys. Journal of Wildlife Management 73:996-999. \| Abstract	August 2009	We estimated loss of butt-end leg bands on male wild turkeys (Meleagris gallapavo) captured in New York, Ohio, andPennsylvania (USA) during December–March, 2006–2008. We used aluminum rivet leg bands as permanent marks to estimate loss of regular aluminum, enameled aluminum, anodized aluminum, and stainless steel butt-end leg bands placed below the spur. We used band loss information from 887 turkeys recovered between 31 days and 570 days after release (x¯ 5 202 days). Band loss was greater for turkeys banded as adults (.1 yr old) than juveniles and was greater for aluminum than stainless steel bands. We estimated band retention was 79–96%, depending on age at banding and type of band, for turkeys recovered 3 months after release. Band retention was ,50% for all age classes and band types 15 months after banding. We concluded that use of butt-end leg bands on male wild turkeys is inappropriate for use in mark–recapture studies.
Diefenbach, D. R., M. Casalena, M. Schiavone, M. Reynolds, R. Eriksen, W. C. Vreeland, B. Swift, R. C. Boyd. 2012. Variation in Spring Harvest Rates of Male Wild Turkeys in New York, Ohio, and Pennsylvania. Journal of Wildlife Management 76:514-522. \| Abstract	April 2012	Spring harvest rates of male wild turkeys (Meleagris gallapavo) influence the number and proportion of adult males in the population and turkey population models have treated harvest as additive to other sources of mortality. Therefore, hunting regulations and their effect on spring harvest rates have direct implications for hunter satisfaction. We used tag recovery models to estimate survival rates, investigate spatial, temporal, and demographic variability in harvest rates, and assess how harvest rates may be related to management strategies and landscape characteristics. We banded 3,266 male wild turkeys throughout New York, Ohio, and Pennsylvania during 2006–2009. We found little evidence that harvest rates varied by year or management zone. The proportion of the landscape that was forested within 6.5 km of the capture location was negatively related to harvest rates; however, even though the proportion forested ranged from 0.008 to 0.96 across our study area, this corresponded to differences in harvest rates of only 2–5%. Annual survival was approximately twice as high for juveniles as adults. In turn, spring harvest rates for adult turkeys were greater for adults than juveniles . We estimated the population of male turkeys in New York and Pennsylvania ranged from 104,000 to 132,000 in all years and ranged from 63,000 to 75,000 in Ohio. Because of greater harvest rates for adult males, the proportion of adult males in the population was less than in the harvest and ranged from 0.40 to 0.81 among all states and years. The high harvest rates observed for adults may be offset by greater recruitment of juveniles into the adult age class the following year such that these states can sustain high harvest rates yet still maintain a relative high proportion of adult males in the harvest and population.
Diefenbach, D. R., L. Hansen, J. Bohling, and C. Miller-Butterworth. 2015. Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA. Ecology and Evolution 5:4885–4895. doi: 10.1002/ece3.1750. \| Download	January 2015
Diefenbach, D. R., L. A. Hansen, R. J. Warren, and M. J. Conroy. 2006. Spatial organization of a reintroduced population of bobcats. Journal of Mammalogy. 87:394-401.	May 2006
Diefenbach, D. R., L. A. Hansen, C. Miller-Butterworth, J. H. Bohling, R. J. Warren, and M. J. Conroy. 2013. Re-introduction of bobcats to Cumberland Island, Georgia, USA: status and lessons learned after 25 years. Pages 235-240 in P. S. Soorae, editor. Global re-introduction Perspectives: 2013. Further Case Studies from Around the Globe. IUCN/SSC Re-introduction Specialist Group, Gland, Switzerland and Abu Dhabi Environment Agency, UAE. 282pp. \| Download	October 2013
Diefenbach, D. R., J. L. Laake, and G. L. Alt. 2004. Spatio-temporal and demographic variation in the harvest of black bears: implications for population estimation. Journal of Wildlife Management 68:947-959.	December 2004
Diefenbach, D. R., J. A. McQuaide, J. A. Mattice. 2002. Using PDAs to collect geo-referenced data. Bulletin of the Ecological Society of America 83:256-2.	August 2002
Diefenbach, D. R., G. L. Alt, B. D. Wallingford, C. S. Rosenberry, and E. S. Long. 2019. Effect of male age structure on demography and breeding behavior in white-tailed deer. Journal of Wildlife Management 83:1368-1376. DOI: 10.1002/jwmg.21712 \| Download	August 2019
Diefenbach, D. R., E. S. Long, C. S. Rosenberry, B. D. Wallingford, and D. R. Smith. 2008. Modeling the distribution of dispersal distances in male white-tailed deer. Journal of Wildlife Management 72:1296-1303. \| Abstract \| Download	August 2008	Dispersal distances and their distribution pattern are important to understanding such phenomena as disease spread and gene flow, but oftentimes dispersal characteristics are modeled as a fixed trait for a given species. We found that dispersal distributions differ for spring and autumn dispersals of yearling male white-tailed deer (Odocoileus virginianus) but that combined data can be adequately modeled based on a log-normal distribution. We modeled distribution of dispersal distances from 3 distinct populations in Pennsylvania and Maryland, USA, based on the relationship between percent forest cover and mean dispersal distance and the relationship between mean and variance of dispersal distances. Our results suggest distributions of distances for dispersing yearling male white-tailed deer can be modeled by simply measuring a readily obtained landscape metric, percent forest cover, which could be used to create generalized spatially explicit disease or gene flow models.
Diefenbach, D. R., D. W. Brauning, J. A. Mattice. 2003. Variability in Grassland Bird Counts Related to Observer Differences and Species Detection Rates. Auk 120:1168-1179.	October 2003
Diefenbach, D. R., C. S. Rosenberry, and R. C. Boyd. 2004. Efficacy of detecting Chronic Wasting Disease via sampling hunter-killed white-tailed deer. Wildlife Society Bulletin 32:267-272.	April 2004
Diefenbach, D. R., C. O. Kochanny, J. K. Vreeland, and B. D. Wallingford. 2003. Evaluation of an expandable, breakaway radiocollar for white-tailed deer fawns. Wildlife Society Bulletin 31:756-761.	October 2003
Diefenbach, D. R., C. F. Riegner, and T. S. Hardisky. 2001. Harvest and reporting rates of game farm ring-necked pheasants. Wildlife Society Bulletin 29:1050-1059.	March 2001
Diefenbach, D. R., C. B. Swope, J. C. Finley, A. E. Luloff, H. C. Zinn, G. J. San Julian, and R. Stedman. 2005. Bear and Deer Hunter Density and Distribution on Public Land in Pennsylvania. Human Dimensions of Wildlife 10:201-212.	July 2005
Diefenbach, D. R. 2010. Snowshoe hare. Pages 386-389 in M. A. Steele, M. C. Brittingham, T. J. Maret, and J. F. Merritt, editors. Terrestrial Vertebrates of Pennsylvania: A Complete Guide to Species of Conservation Concern. Johns Hopkins University Press, Baltimore, Maryland, USA.	October 2010
Diefenbach, D. R. 2009. Estimating avian population size using Bowden’s estimator. Auk 126:211-217. \| Abstract	January 2009	Avian researchers often uniquely mark birds, and multiple estimators could be used to estimate population sizeusing individually identified birds. However, most estimators of population size require that all sightings of marked birds be uniquelyidentified, and many assume homogeneous detection probabilities. Bowden’s estimator can incorporate sightings of marked birds that are not uniquely identified and relax assumptions required of other estimators. I used computer simulation to evaluate the performance of Bowden’s estimator for situations likely to be encountered in bird studies. When the assumptions of the estimator were met, abundance and variance estimates and confidence-interval coverage were accurate. However, precision was poor for small population sizes (N 50) unless a large percentage of the population was marked (75%) and multiple (8) sighting surveys were conducted. If additional birds are marked after sighting surveys begin, it is important to initially mark a large proportion of the population (pm >0.5 if N >100 or pm 0.1 if N >250) and minimize sightings in which birds are not uniquely identified; otherwise, most population estimates will be overestimated by 10%. Bowden’s estimator can be useful for avian studies because birds can be resighted multiple times during a single survey, not all sightings of marked birds have to uniquely identify individuals, detection probabilities among birds can vary, and the complete study area does not have to be surveyed. I provide computer code for use with pilot data to design mark–resight surveys to meet desired precision for abundance estimates.
Deweber, J.T., Y., Tsang, D.M. Krueger, J.B. Whittier, T. Wagner, D.M. Infante, and G. Whelan. 2014. Importance of understanding landscape biases in USGS gage locations: Implications and solutions for managers. Fisheries 39:155-163. \| Download	April 2014
Deweber, J.T. and T. Wagner. 2014. A regional neural network model for predicting mean daily river water temperature. Journal of Hydrology 517:187-200. \| Download	June 2014
Detar, J., D. Kristine, T. Wagner, and T. Greene. 2014. Evaluation of Catch-and-Release Regulations on Brook Trout in Pennsylvania Streams. North American Journal of Fisheries Management 34:49-56. \| Download	January 2014
DeWeber, J.T. and T. Wagner. 2018. Probabilistic measures of climate change vulnerability, adaptation action benefits, and related uncertainty from maximum temperature metric selection. Global Change Biology.	February 2018
DeWeber, J.T. and T. Wagner. 2015. Translating climate change effects into everyday language: an example of more driving and less angling. Fisheries 40:395-398. \| Download	August 2015
DeWeber, J.T and T. Wagner. 2015. Predicting Brook Trout occurrence in stream reaches throughout their native range in the eastern United States. Transactions of the American Fisheries Society 144:11-24. \| Download	December 2014
DePasquale, C., T. Wagner, G.A. Archard, B. Ferguson, and V.A. Braithwaite. 2014. Learning rate and temperament in a high predation risk environment. Oecologia 176:661-667.	November 2014
Davis, L.A. and T. Wagner. 2016. Scale-dependent seasonal pool habitat use by sympatric wild Brook Trout and Brown Trout populations. Transactions of the American Fisheries Society 145:888-902. \| Download	June 2016
Counahan, D. F., R. F. Carline, and J. W. Reid. 2006. The occurrence of the calanoid copepod Eurytemora affinis (Poppe) in the upper Ohio River. Northeastern Naturalist 12:541-545.	March 2006
Copeland, T., and R. F. Carline. 2004. Relationship of lipid content to size and condition of walleye fingerlings from natural and aquacultural environments. North American Journal of Aquaculture 66: 237-242.	July 2004
Conn, P. B., and D. R. Diefenbach. 2007. Adjusting age and stage distributions for misclassification errors. Ecology 88:1977-1983.	August 2007
Conn, P. B., D. R. Diefenbach, J. L. Laake, M. A. Ternent, and G. C. White. 2008. Bayesian analysis of wildlife age-at-harvest data. Biometrics 64:1170-1177.	November 2007
Collins, S.M., S.K. Oliver, J.F. Lapierre, E.H. Stanley, J.R. Jones, T. Wagner. and P.A. Soranno. 2017. Lake nutrient stoichiometry is less predictable than nutrient concentrations at regional and sub-continental scales. Ecological Applications 27:1529-1540.	July 2017
Collins, S.M., S. Yuan, P-T. Tan, S.K. Oliver, J.F. Lapierre, K.S. Cheruvelil, C.E. Fergus, N.K. Skaff, J.S. Stachelek, T. Wagner, P.A. Soranno. 2019. Winter precipitation and summer temperature predict lake water quality at macroscales . Water Resources Research 55:2708-2721.	March 2019
Cole, M. B., D. E. Arnold, B. J. Watten, and W. F. Krise. 2001. Haematological and physiological responses of brook charr, to untreated and limestone-neutralized acid mine drainage. Journal of Fish Biology 59:79-91.	January 2001
Cheruvelil, S. K., S. Yuan, K.E. Webster, P-N Tan, J.F. Lapierre, S.M. Collins, C.E. Fergus, C.E. Scott, E.N. Henry, P.A. Soranno, C.T. Filstrup, T. Wagner. Creating multi-themed ecological regions for macrosystems ecology: Testing a flexible, repeatable, and accessible clustering method. Ecology and Evolution 7:3046-3058.	August 2017
Cheruvelil, K.S., K. Webster, K. King, A. Poisson, T. Wagner. 2022. Taking a macroscale perspective to improve understanding of shallow lake total phosphorus and chlorophyll a. Hydrobiologia https://doi.org/10.1007/s10750-022-04811-1	March 2022
Casalena, M. J., R. Everett, W. C. Vreeland, I. D. Gregg, and D. R. Diefenbach. 2016. Timing of spring wild turkey hunting in relation to nest incubation. Proceedings of the National Wild Turkey Symposium 11:237-247. \| Download	January 2016
Casalena, M. J., M. A. Lowles, and D. R. Diefenbach. 2005. Factors suppressing a wild turkey population in southcentral Pennsylvania. Proceedings of the Ninth Wild Turkey Symposium 9:135-144.	September 2005
Carrollo, E.M., H.E. Johnson, J.W. Fischer, M. Hammond, P.D. Dorsey, C.W. Anderson, K.C. VerCauteren, and W. David Walter. Influence of precipitation and crop germination on resource selection by mule deer (Odocoileus hemionus) in southwest Colorado. Scientific Reports \| Abstract	November 2017	Mule deer (Odocoileus hemionus) populations in the western United States provide recreational, ecological and economic benefits to local economies; however, they can also cause considerable damage to agriculture. Damage to lucrative crops, particularly sunflower, can be common in agricultural areas of the western US. In some cases entire fields have been decimated by local mule deer populations resulting in a need for investigating resource selection and determining strategies for managing deer damage in these agricultural areas. Limited information exists on movements and resource selection of mule deer in agricultural areas, and no data exists to understand resource selection of mule deer in response to annual variation in crop rotation and climactic conditions. We used Global Positioning System (GPS) collars to monitor 14 mule deer and assess their movement patterns, home range and resource selection in southwestern Colorado, USA. We estimated home ranges for two winter seasons that ranged between 7.68 and 9.88 km2, and for two summer seasons that ranged between 5.51 and 6.24 km2. Mule deer were selecting for areas closer to forest and alfalfa for most periods during 2012, but selected for areas closer to sunflower in a majority of periods during 2013. Considerable annual variation in climate patterns and precipitation levels appeared to influence selection of mule deer due to changes in crop rotation and germination success of sunflower. Our results can assist managers in making informed decisions about crop damage prevention and practices by identifying areas and crops where mule deer damage is expected based on climate conditions and deer presence-absence.
Carline, R. F., and M. C. Walsh. 2004. Responses of streams to riparian restoration in the Spring Creek watershed, central Pennsylvania. Pages 63-64, in Moore, S. E., R. F. Carline, and J. Dillon, eds. Working together to ensure the future of wild trout. Proceedings of Wild Trout VIII Symposium -30th Anniversary, 2004 September 20-22; Yellowstone Park, Wyoming	June 2005
Carline, R. F., and J. F. Machung. 2001. Critical thermal maxima of wild and domestic strains of trout. Transactions of the American Fisheries Society 130:1211-1216.	November 2001
Carline, R. F., and B. J. McCullough. 2003. Effects of floods on brook trout populations in the Monongahela National Forest, West Virginia. Transactions of the American Fisheries Society 132:1014-1020.	September 2003
Carline, R. F., P. M. Barry, and H. G. Ketola. 2004. Dietary uptake of polychlorinated biphenyls (PCBs) by rainbow trout. North American Journal of Aquaculture 66:91-99.	May 2004
Carline, R. F. 2004. Review of 'Electrofishing and its harmful effects on fish'. By D. E. Snyder. U. S. Geological Survey, USGS/BRD/ITR-2003-0002. In Transactions of the American Fisheries Society 133:1539-1540.	November 2005
Carline, R. F. 2001. The "Fisheries in a Changing Climate" Symposium. Fisheries (Bethesda) 26(12):21-22.	December 2001
Carline, R. F. 2001. Effects of high-frequency pulsed-DC electrofishing on a wild brown trout population. North American Journal of Fisheries Management 21:571-579.	August 2001
Buderman, F. E., T. M. Gingery, D. R. Diefenbach, L. C. Gigliotti, D. Begley-Miller, M. E. McDill, B. D. Wallingford, C. S. Rosenberry, and P. J. Drohan. 2021. Caution is warranted when using animal space-use and movement to infer behavioral states . Animal Movement 9:30. https://doi.org/10.1186/s40462-021-00264-8 \| Download	June 2021
Buderman, F. E., D. R. Diefenbach, M. J. Casalena, C. S. Rosenberry, B. D. Wallingford. 2014. Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data. Ecology and Evolution 4:1439-1450. \| Abstract \| Download \| Publisher Website	March 2014	The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50–100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior.
Buderman, F. E., D. R. Diefenbach, C. S. Rosenberry, B. D. Wallingford, and E. S. Long. 2014. Effect of hunter selectivity on harvest rates of radio-collared white-tailed deer in Pennsylvania. Journal of Wildlife Management 78:1456-1465. \| Abstract \| Download \| Publisher Website	October 2014	Radio transmitters are a commonly used tool for monitoring the fates of harvested species, although little research has been devoted to whether a visible radio transmitter changes a hunters' willingness to harvest that animal. We initially surveyed deer hunters to assess their willingness to harvest radio-collared deer and predicted radio collars were unlikely to affect the harvest of antlerless deer, but hunters may be less willing to harvest small-antlered males with radio collars compared to large-antlered males. We fitted white-tailed deer (Odocoileus virginianus) with radio collars that were visible to hunters or with ear-tag transmitters or ear-tags that were difficult to detect visually and estimated if harvest rates differed among marking methods. For females, the best model failed to detect an effect of radio collars on harvest rates. Also, we failed to detect a difference between male deer fitted with radio collars and ear-tag transmitters. When we compared males fitted with radio collars versus ear tags, we found harvest rate patterns were opposite to our predictions, with lower harvest rates for adult males fitted with radio collars and higher harvest rates for yearling males fitted with radio collars. Our study suggests that harvest rate estimates generated from a sample of deer fitted with visible radio collars can be representative of the population of inference.
Brennan, J.C., R.W. Gale, D.A. Alvarez, J.K. Leet, Y. Li, T. Wagner, D.E. Tillitt. 2020. Factors affecting sampling strategies for design of an effects-directed analysis for endocrine-active chemicals. Environmental Toxicology and Chemistry 39:1309-1324. https://doi.org/10.1002/etc.4739	May 2020
Brenden, T. O., T. Wagner, and B.R. Murphy. 2008. Generalized linear mixed modeling as a framework for analyzing proportional size structure index data. North American Journal of Fisheries Management 28:1233-1242. \| Abstract	August 2008	Proportional size distribution (PSD) indices are convenient measures for numerically summarizing size structure of fish populations. Several novel methods for analyzing PSD index data were examined as a means for potentially improving inferences of size structure: generalized linear mixed modeling, calculation of location quotients, and simultaneous construction of 100(1- α)% confidence intervals for PSD indices through multinomial modeling. The methods are demonstrated using simulated and previously published PSD index data. Generalized linear mixed modeling was used to (1) conduct a model selection analysis of PSD index data relative to a change in harvest regulation for walleyes Sander vitreus, (2) partition the variance of PSD index data among spatial, temporal, and environmental attributes, and (3) nonlinearly relate PSD data to adult density for largemouth bass Micropterus salmoides. The location quotient, which is an index for describing relative concentration of proportional data, was used to describe spatial and temporal localization of largemouth bass and walleye PSD index data. Finally, a modified method of constructing simultaneous 100(1 - α)% confidence intervals for multinomial proportions was used to produce 95% confidence intervals for traditional and incremental PSD indices based on length frequency data from muskellunge Esox masquinongy. The approaches described herein can assist fishery biologists in size structure assessments of fish populations and ultimately aid in cost-effective fisheries management.
Bondo, K.J., D. Montecino-Latorre, L. Williams, M. Helwig, K. Duren, M. Hutchinson, W.D. Walter. 2023. Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximations. Ecosphere 14(1): e4346. https://doi.org/10.1002/ecs2.4346 \| Abstract \| Download	January 2023	The abundance of <i>Culex restuans</i> and <i>Culex pipiens</i> in relation to ecological predictors is poorly understood in regions of the United States where their ranges overlap. It is suspected that these species play different roles in spreading West Nile virus in this region, but few studies have used Bayesian hierarchical spatial models to examine the abundance and predict the distribution of these species. Using mosquito surveillance data collected by the Pennsylvania Department of Environmental Protection from 2002–2016, we used Bayesian hierarchical spatial models to predict mosquito abundance and make predictive risk maps of each of these mosquito vectors throughout Pennsylvania in relation to several ecological and land-use variables that have been found to be important predictors of the abundance of these mosquito species. Developed habitat, temperature, and precipitation were important predictor variables for the abundance of <i>Culex restuans</i>, whereas forested habitat, snow water equivalent and normalized water difference index were important predictor variables for the abundance of <i>Culex pipiens</i>. The spatial distribution of each of these species differed from one another, including a negative relationship between the abundance of <i>Culex</i> r<i>estuans </i>and developed habitat, and a negative relationship between the abundance of <i>Culex pipiens </i>and forested habitat. Julian date was modelled as a temporal trend for both species and showed <i>Culex restuans</i> to be more abundant from late April through late June and <i>Culex pipiens </i>to be more abundant from July through September. A seasonal cross-over was observed between these two species, and it occurred in late June. Our results suggest that modelling the spatial abundance of each of these species separately can help gain further insight into understanding the epidemiology of WNV in human and susceptible animal populations in regions where these two mosquito vectors co-exist.
Bhandari, P., R. C. Stedman, A. E. Luloff, J. C. Finley, and D. R. Diefenbach. 2006. Effort versus motivation: factors affecting antlered and antlerless deer harvest success in Pennsylvania. Human Dimensions of Wildlife 11:423-436. \| Download	October 2006
Berentsen, A.R., M.R. Dunbar, C.E. Fitzpatrick, W.D. Walter. 2013. Spatial ecology of urban raccoons in Northeastern Ohio: implications for oral rabies vaccination. Prairie Naturalist 45(1): 39-45. \| Abstract	June 2013	In 1977, rabies was detected in a raccoon (Procyon lotor) in West Virginia, and since the mid 1980’s raccoon variant rabies has spread throughout the eastern United States and moved west as far as the eastern edge of Cleveland, Ohio. The primary tool to combat this spread is the distribution of oral rabies vaccine (ORV) baits. A thorough knowledge of raccoon space use is critical in determining bait placement, particularly in urban areas. We monitored nine raccoons in urban areas of Cleveland, Ohio, calculated home range sizes, monitored raccoon movement with respect to potential movement barriers, and used resource selection functions (RSF) to determine habitat selection within home ranges. Fixed kernel annual home range estimates were 19.2 (±6.7) hectares. Home range estimates were 21.5 (±7.2) and 18.2 (±7.4) hectares for summer and fall, respectively. No seasonal differences in home range estimates were observed (F = 0.16, P = 0.6957). One raccoon crossed an interstate highway and another was located across the Cuyahoga River, suggesting highways and rivers are not impermeable to raccoon movements. Resource selection data indicate that ORV baiting in urban environments should be concentrated in habitat patches and trees adjacent to human-made structures and industrial sites to take advantage of raccoon behavior.
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, and E. H. Just. 2018. Evaluating inter-rater reliability and statistical power of vegetation measures assessing deer impact. Forests 9:669. https://doi.org/10.3390/f9110669 \| Download	October 2018
Begley-Miller, D. B., D. R. Diefenbach, M. McDill, P. Drohan, C. Rosenberry, and E. Just. 2019. Soil Chemistry, not short-term (2 year) deer exclusion, explains occupancy of several understory plant taxa in forests affected by acid deposition. AoB Plants 11:1-15 https://doi.org/10.1093/aobpla/plz044 \| Download	August 2019
Bayuzick, S., D. Guarin, A. Bonhage, F. Hirsch, D. R. Diefenbach, M. McDill, T. Raab, and P. J. Drohan. 2022. Small anthropogenic landforms from past charcoal production control moisture dynamics and fertility in northcentral Appalachian soils. Geomorphology 415:108379. https://doi.org/10.1016/j.geomorph.2022.108379 \| Download	October 2022
Bayuzick, S., D. Guarin, A. Bonhage, F. Hirsch, D. Diefenbach, M. McDill, T. Raab, and P. Drohan. Soil and geomorphic patterns within relict charcoal hearths could represent unique ecosystem niches. Geomorphology 422:108525 https://doi.org/10.1016/j.geomorph.2022.108525	February 2023
Bauder, J.M., C.S. Anderson, H.L. Gibbs, M.J. Tonkovich, and W.D. Walter. 2021. Landscape features fail to explain spatial genetic structure in white-tailed deer across Ohio, USA. Journal of Wildlife Management 85(8):1669-1684. DOI: 10.1002/jwmg.22120 \| Abstract \| Publisher Website	October 2021	Landscape features influence wildlife movements across spatial scales and therefore have the potential to influence the spread of disease. Chronic wasting disease (CWD) is a fatal prion disease affecting members of the family Cervidae, particularly white-tailed deer (<i>Odocoileus virginianus</i>), and the first positive CWD case in a wild Ohio deer was recorded in 2020. While landscape genetics approaches are increasingly utilized to better understand potential pathways for CWD spread in white-tailed deer, little is known about genetic structure of white-tailed deer in Ohio. The objectives of our study were to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. For genetic data we used microsatellite genotypes from 619 individuals from 24 counties across Ohio genotyped at 11 loci and a 547-bp fragment of the mitochondrial DNA Control Region from the same individuals. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data. Non-spatial genetic clustering tests failed to detect spatial genetic structure while spatial genetic clustering tests indicated subtle spatial genetic structure. IBD models consistently outperformed IBR models including land cover, traffic volume, and streams. Our results indicated widespread genetic connectivity of white-tailed deer across Ohio and negligible barrier effects of landscape features. These patterns likely reflect some combination of minimal resistive effects of landscape features on white-tail deer movement in Ohio and the effects of regional recolonization or translocation. We encourage continued CWD surveillance in Ohio, particularly in the proximity of confirmed cases.
Bartley, M.L., E.M. Hanks, E.M. Schliep, P.A. Soranno, and T. Wagner. Identifying and characterizing extrapolation in multivariate response data. PLOSE ONE.	December 2019
Baker, L. A., R. J. Warren, D. R. Diefenbach, W. E. James, and M. J. Conroy. 2001. Prey selection by reintroduced bobcats (Lynx rufus) on Cumberland Island, Georgia. American Midland Naturalist 145:80-93.	March 2001
Argent, D. G., and R. F. Carline. 2004. Fish assemblage changes in relation to watershed landuse disturbance. Aquatic Ecosystem Health Management 7:101-114. .	March 2004
Argent, D. G., R. F. Carline, and J. R. Stauffer, Jr. 2000. A method to identify and conserve rare fishes in Pennsylvania. Journal of the Pennsylvania Academy of Science 74:3-12.	October 2000
Argent, D. G., J. A. Bishop, J. R. Stauffer, Jr., R. F. Carline, and W. L. Myers. 2003. Predicting freshwater fish distributions using landscape-level variables. Fisheries Research 60:17-32.	January 2003
Amor, J.M., R. Newman, W.F. Jensen, B.C. Rundquist, W.D. Walter, and J.R. Boulanger. 2019. Seasonal home ranges and habitat selection of three elk (Cervus elaphus) herds in North Dakota. PlosONE 14(2): e0211650. https://doi.org/ 10.1371/journal.pone.021165	February 2019
Ahrestani, F.S, M.A. Ternent, M.J. Lovallo, and W. David Walter. 2020. Resource use by American black bears in suburbia: a landholder step-selection approach. Human-Wildlife Interactions 14(2): 216-227. \| Abstract	November 2020	The spread of suburbia and the continued conversion of forested lands for people’s needs has meant less land for growing bear populations, resulting in increased human-bear conflict. With a focus to investigate the viability of using hunting as a tool to manage nuisance bears in suburbia, this study investigated the resource selection by bears across Pennsylvania, USA. This study distinguishes itself from earlier studies of recourse selection of bears by incorporating results from a survey of owners of private properties, large enough to accommodate hunting, on whether they support hunting of bears on their lands. This study used the Step Selection Function (SSF) approach, which utilizes consistent location data of short intervals from GPS collars better than older, traditional Resource Selectin Functions. In addition to the data from the survey of private land-owners, the statistical models tested by the SSF approach assessed the influence that housing density, land use type, slope, elevation, and aspect had on movement by the 31 GPS-collared bears monitored in 10-day periods prior to, during, and after the annual bear hunting season in 2010-2012. We analyzed resource selection for each of these three periods by pooling data across study sites and years, and found that the bears selected for: forested lands in all three periods; grasslands in the pre-hunt and hunting periods; east and south facing slopes in the pre-hunt and hunting periods; flatter terrain in the pre-hunt, but steeper terrain the hunting period; and private properties in the post-hunt period that did not permit hunting. Selection of private properties by bears in the post-hunt period suggests that increasing hunting on private properties may be a viable management option. The selection of forest habitats in all three periods is consistent with need for bears to fatten up with fallen mast from trees just before the den for the winter.
Walter, WD,, Kurle, CM, Hopkins III, JB. 2014. Applications of stable isotope analysis in mammalian ecology. Isotopes in Environmental and Health Studies 50(3):287-290. \| Abstract	August 2014	In this editorial we provide a brief introduction and summarize the manuscripts that compose this Special Issue on The application of stable isotope analysis in mammalian ecology. This Special Issue contains 3 methodological manuscripts that document previously unreported discrimination or correction factors for stable isotope analysis. The remaining 6 papers are applied research-style manuscripts that will assist researchers in using stable isotope analysis to address management of various species occupying a variety of landscapes.

Presentations

Presentations	Presentation Date
Zak, A. L., D. R. Diefenbach, E. S. Boyd. Current Snowshoe Hare Occupancy in Northern Pennsylvania and Drivers of Range Contractions. 8 March 2024, Annual Conference of the Pennsylvania Chapter of The Wildlife Society, State College, PA, USA.	March 2024	In Pennsylvania, climate change has been identified as a key driver of this range shift based on changes in the distribution of hunter harvest and that the spatial variation in snow cover explained snowshoe hare site occupancy. We aim to examine current snowshoe hare occupancy in northern Pennsylvania and determine whether range contraction has continued as predicted based on occupancy data collected in 2004.
Zak, A. L., D. R. Diefenbach, E. S. Boyd. Current Snowshoe Hare Occupancy in Northern Pennsylvania and Drivers of Range Contractions. 6-9 November 2023, Annual Conference of The Wildlife Society, Louisville, KY, USA.	November 2023	In Pennsylvania, climate change has been identified as a key driver of this range shift based on changes in the distribution of hunter harvest and that the spatial variation in snow cover explained snowshoe hare site occupancy. We aim to examine current snowshoe hare occupancy in northern Pennsylvania and determine whether range contraction has continued as predicted based on occupancy data collected in 2004.
Winter, V., F. Buderman, D. Diefenbach, K. Lamp, K. Duren, M. J. Casalena, and A. Mowen. Modeling Population Demographics in a Game Species: A Case Study for Wild Turkey inPennsylvania, 6 November 2023, Annual Conference of The Wildlife Society, Louisville, KY, USA.	November 2023	Integrating multiple data sources can provide more accurate estimates of populationsize and other demographic parameters, as well as insights into the factors that may affectpopulation dynamics. We examined turkey population dynamics using a Bayesianmodel that propagates uncertainty across data sources and demographic processes.
Winter, V., F. Buderman, D. Diefenbach, K. Lamp, K. Duren, M. J. Casalena, and A. Mowen. Modeling Population Demographics in a Game Species: A Case Study for Wild Turkey in Pennsylvania, 8 March 2024, Annual Conference of the Pennsylvania Chapter of The Wildlife Society, State College, PA, USA.	March 2024	Integrating multiple data sources can provide more accurate estimates of populationsize and other demographic parameters, as well as insights into the factors that may affectpopulation dynamics. We examined turkey population dynamics using a Bayesianmodel that propagates uncertainty across data sources and demographic processes.
Winter, V. A., K. J. Lamp, M. J. Casalena, K. Duren, D. R. Diefenbach, and F. E Buderman. Identifying wild turkey nest initiation from location and activity data. 30 April 2023, Annual Conference of the Northeast Fish and Wildlife Agencies, Hershey, PA, USA.	April 2023	To understand the reproductive ecology of wild turkey (<i>Meleagris gallopavo</i>) it is important to quantify reproductive success, because variation in nest success has a large effect on population growth rates. By utilizing location data in conjunction with activity data, we were able to gain a more accurate estimate of nesting attempts, which can be used to inform both field data collection, such as initiating counts for poults, and estimates of nesting propensity.
Williamson, L. T., S. R. Klinger, D. R. Diefenbach, W. D. Walter. 2017. Density Estimation and Habitat Modeling for Pheasant Population Restoration in Pennsylvania. The Wildlife Society Annual Meeting, Albuquerque, NM.	September 2017	Ring-necked pheasants (Phasianus colchicus) reached peak abundance in Pennsylvania in the 1970s and declined most likely due to a lack of suitable habitat. From 2007 to 2014, the Pennsylvania Game Commission translocated 2,328 pheasants from North Dakota and Montana to 10 areas in Pennsylvania closed to pheasant hunting. We investigated habitat use of pheasants and estimated whether population densities met the agency’s goal of 3.86 hen pheasants/km2 during 2013–2016.
Williamson, L. T., D. R. Diefenbach, W. D. Walter. 2016. Modeling potential habitat for pheasant population restoration in Pennsylvania. The Wildlife Society Annual Meeting, Raleigh, NC.	October 2016	This project will take a closer look at the habitat needs of pheasants to restore population sizes and reach a population goal of 10 hen pheasants per square mile set by the Pennsylvania Game Commission.
Williamson, L. T., D. R. Diefenbach, W. D. Walter. 2016. Modeling potential habitat for pheasant population restoration in Pennsylvania. The Pennsylvania Chapter of The Wildlife Society Annual Meeting, Raystown Lake, PA.	April 2017	This project will take a closer look at the habitat needs of pheasants to restore population sizes and reach a population goal of 10 hen pheasants per square mile set by the Pennsylvania Game Commission.
Williamson, L. T., D. R. Diefenbach, W. D. Walter. 2016. Modeling potential habitat for pheasant population restoration in Pennsylvania. Pennsylvania Chapter of The Wildlife Society Annual Meeting, State College, PA.	April 2016	This project will take a closer look at the habitat needs of pheasants to restore population sizes and reach a population goal of 10 hen pheasants per square mile set by the Pennsylvania Game Commission.
White, S.L., W.L. Miller, S.A. Dowell, M.L. Bartron, and T. Wagner. 2018. Limited hatchery introgression into wild brook trout populations despite reoccurring stocking. Annual Meeting of The American Fisheries Society, Atlantic City, New Jersey.	August 2018	One of first studies to examine introgression in actively stocked brook trout populations.
White, S.L., E.M. Hanks, and T. Wagner. 2019. A novel quantitative framework for riverscape genetics highlights the importance of mainstem channels for brook trout population connectivity. Annual Meeting of the American Fisheries Society.	September 2019	We present a novel modeling frameowork for riverscape genetics.
White, S.L., C. Gowan, T. Wagner, V.A. Braithwaite. 2015. Boldness impairs spatial learning ability in brook trout. American Fisheries Society Annual Meeting, Portland, Oregon.	August 2015	We investigated how boldness influences learning and decision making in brook trout.
White, S.L. and T. Wagner. 2018. With Connectivity Comes Challenges: Brook Trout Metapopulation Dynamics Reveal Unique Management Challenges. Society for Freshwater Science, Detroit MI.	May 2018	This talk summarizes genetic and brook trout movement research in the context of large-scale conservation efforts.
White, S., W. Miller, S. Dowell, M. Bartron, and T. Wagner. 2018. Limited hatchery introgression in wild brook trout populations in a northcentral Pennsylvania watershed. The Pennsylvania Chapter of the American Fisheries Society.	February 2018	This research is one of the first to examine introgression in wild brook trout populations.
White, S., S. Dowell, M. Bartron, and T. Wagner. 2017. Where do all the fish go? Combining multiple measures of fish movement to gain insights into brook trout population connectivity. Wild Trout Symposium, West Yellowstone, MT.	September 2017	Detailed study of wild trout movements.
White, S., S. Dowell, M. Bartron, and T. Wagner. 2017. Where do all the fish go? Combining multiple measures of fish movement to gain insights into brook trout population connectivity. The Annual Meeting of the American Fisheries Society, Tampa FL.	August 2017	Detailed study of wild trout movements.
White, S., L. Iwanowicz, T. Wagner. 2016. Stream temperature and stress protein regulation in Brook Trout. Susquehanna River Symposium, Bucknell University.	November 2016	Some of the first work to look at stress protein regulation in wild brook trout populations, over time, in response to changing water temperatures.
White, S. and T. Wagner. Movers and Stayers: Can We Predict Movement Behavior in Brook Trout? Joint meeting between the West Virginia and Pennsylvania Chapters of the American Fisheries Society, California State University of Pennsylvania.	February 2017	We integrate animal behavior with information about individual movement to asses the role of personality in brook trout movement dynamics.
Weber, R. J., and R. Carline. October 2000. Effects of electrofishing on growth and survival of wild brown trout (Salmo trutta) from central Pennsylvania streams. Wild Trout VII. Yellowstone National Park, Wyoming.	October 2000
Ward, A.I, G.C. Smith, M.D.F. Shirley, A.C. Mill, W.D. Walter, and P.A. Robertson. 2017. Consequences of chronic wasting disease beyond the individual. Prion Conference, Edinburgh, Scotland.	May 2017	The emergence of chronic wasting disease in cervids in North America and now Europe has understandably triggered much activity in the fields of human and livestock health. Here we discuss the keystone role of cervids in regulating ecosystem structure and function and forecast some possible outcomes of population reduction if CWD spreads across Eurasia and the environmental and socio-economic impacts that could be experienced.
Waraniak, J., M.S. Eackles, J. Keagy, G.D. Smith, M. Schall, S. Stark, S.L. White, D.C. Kazyak, and T. Wagner. 2024. Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US mid-Atlantic rivers. Society for Freshwater Science. Philadelphia, PA.	June 2024	Flathead catfish are a prolific invasive species with high fecundity, long-distance dispersal, and piscivorous feeding habits that can lead to declines of native fish populations. In this study, we analyze the genetics of invasive flathead catfish (<i>Pylodictus olivaris</i>) in the mid-Atlantic region to assess their connectivity and attempt to reconstruct the history of introduced populations.
Waraniak, J., J. Keagy, and T. Wagner. 2024. Landscape transcriptomics of wild brook trout populations (Salvelinus fontinalis) to successive heatwaves. Annual Meeting of the American Fisheries Society, Honolulu, HI.	August 2024	This study shows the utility of landscape transcriptomic approaches to identify important biological processes governing organismal responses to short-term stressors in wild brook trout populations. The results of this study can guide future investigations to identify phenotypic and genetic diversity that contribute to adaptive variation and improve predictions of how populations will respond to climate change.
Walters, T.S., K.C. VerCauteren, and W.D. Walter. 2024. American crow movement and resource selection in an area endemic for chronic wasting disease. Joint Meeting of The Pennsylvania Chapter of Wildlife Society and the Pennsylvania Biological Survey, State College, PA, 22-23 March 2024.	March 2024	CWD is not known to cause disease in crows despite the fact they may encounter it through consuming the meat of infected deer, sharing food sources with infected deer, or prions persisting in the environment. In response to this finding a study was developed in Pennsylvania to sample wild crows for the presence of infectious prions and model crow movement.
Walters, T.S., K.C. VerCauteren, and W.D. Walter. 2023. American crow movement and resource selection in an area endemic for chronic wasting disease. The 30th Annual Conference of the Wildlife Society, Louisville, KY, 5-9 November 2023.	November 2023	CWD is not known to cause disease in crows despite the fact they may encounter it through consuming the meat of infected deer, sharing food sources with infected deer, or prions persisting in the environment. In response to this finding a study was developed in Pennsylvania to sample wild crows for the presence of infectious prions and model crow movement.
Walters, T.S., K.C. VerCauteren, and W.D. Walter. 2022. Infectious prion movement potential of American crows. 6- 10 November 2022, The Wildlife Society Annual Meeting, Spokane, WA.	November 2022	CWD is not known to cause disease in crows despite the fact they may encounter it through consuming the meat of infected deer, sharing food sources with infected deer, or prions persisting in the environment. In response to this finding a study was developed in Pennsylvania to sample wild crows for the presence of infectious prions and model crow movement.
Walter, W.D., and T.S. Evans. 2015. Influence of habitat and demographic components on exposure to chronic wasting disease in white-tailed deer in the eastern United States. Prion Conference	May 2015	Chronic wasting disease is a a transmissible spongiform encephalopathy that affects captive and free-ranging cervids and little is known of its distribution in the Northeast. Efficiency of disease surveillance and containment efforts can be improved by allocating resources used for surveillance into areas that are at a greater risk for infection.
Walter, W.D., J.W. Fischer, and A. Church. Online storage infrastructures and applied interface with program R for analysis of GPS datasets. The 20th Annual Conference of the Wildlife Society, 7 October, 2013.	October 2013	Online storage infrastructures provide a storage facility in the cloud that can serve as a backup for your data or a transfer portal to share data among colleagues or interested researchers. Use of online storage infrastructures with subsequent analysis in R enables data handling and analysis all in a single platform to streamline the scientific process.
Walter, W.D., G. Bastille-Rousseau, M. Craft, P. Cross, M. Diuk-Wasser, R.B. Gagne, J. Hewitt, K. Manlove, L.D. Plimpton, M. Van Acker, K. C. VercCauteren, M. Wilber, G. Wilson-Henjum, G. Wittemyer, and K.M. Pepin. 2023. A national-scale distributed surveillance design for SARS-CoV-2 in a potential wildlife reservoir host. 71st Annual International Conference of the Wildlife Disease Association, Athens, GA, 4 August 2023.	August 2023	Emergence of zoonotic diseases in new wildlife host species continues to occur globally and poses major health or conservation risks for the hosts involved. Here, we describe the design, operationalization, and preliminary findings from a novel distributed surveillance project of SARS-CoV-2 in deer supported through USDA-APHIS and the American Rescue Plan Act that aims to understand establishment and reservoir dynamics of SARS-CoV-2 in deer.
Walter, W.D., F.S. Ahrestani, and W.L. Miller. 2019. Synergy of genetics and diffusion dynamics in white-tailed deer to understand epidemiology of chronic wasting disease. 68th Annual International Conference of the Wildlife Disease Association, Tahoe City, CA.	August 2019	Subpopulation structuring for a species determined by assessing microsatellite variation across a large geographic area can provide valuable information on assessing transmission dynamics of a disease. Combined with knowledge of environmental variables driving diffusion dynamics of a disease across a landscape, understanding disease epidemiology at broad spatial scales is possible.
Walter, W.D., D.P. Onorato, and J.W. Fischer. 2016. Estimators of home range using GPS datasets: a new vision. The 23rd Annual Conference of The Wildlife Society, Raleigh, NC.	October 2016	Global positioning system (GPS) technology for monitoring home range and movements of wildlife has resulted in prohibitively large samples of locations for traditional estimators. Third-generation estimators that interpolate time and space between locations or animal-specific data appear to fit the movement trajectory better than traditional location-based or polygon-derived estimators.
Walter, W.D., C.S. Rosenberry, A. Fameli, and J. Edson. 2022. Associations of white-tailed deer with and without chronic wasting disease. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022	July 2022	Chronic wasting disease (CWD) was first detected in white-tailed deer (<i>Odocoileus virginianus</i>) in Pennsylvania in 2012 and has spread within this initial area with prevalence exceeding 5%. Most studies that characterize the contact rates of white-tailed deer infected with CWD use diseased-free deer that were not monitored with an area that had CWD.
Walter, W.D., C.S. Rosenberry, A. Fameli, and J. Edson. 2022. Associations of white-tailed deer with and without chronic wasting disease. 6- 10 November 2022, The Wildlife Society Annual Meeting, Spokane, WA.	November 2022	Chronic wasting disease (CWD) was first detected in white-tailed deer (<i>Odocoileus virginianus</i>) in Pennsylvania in 2012 and has spread within this initial area with prevalence exceeding 5%. Most studies that characterize the contact rates of white-tailed deer infected with CWD use diseased-free deer that were not monitored with an area that had CWD.
Walter, W.D., C. Lue, and J. Bartz. 2022. Strain types for chronic wasting disease and efforts towards a virtual tissue repository. Prion 2022, Gottingen, Germany, 13 September 2022.	September 2022	Monitoring, characterizing, and tracking progression of CWD across the US has not been possible because identification of distinct strains of CWD has been lacking. Although understanding of the biology of prions has been well studied, prion researchers have been unable to study prion strains in multiple regions of the US because of the lack of availability and information available for samples positive for CWD.
Walsh, M. C., and R. F. Carline. 2002. Responses to riparian restoration in a central Pennsylvania watershed. Riparian and Wetland Stewardship, Chesapeake Bay, Watershed Restoration Conference. Baltimore, Maryland, September 24-26, 2002.	September 2002
Walsh, M. C., and R. F. Carline. 2002. Responses to riparian restoration in a central Pennsylvania watershed. Northeast Fish and Wildlife Conference, Portland, Maine, April 21-24, 2002.	April 2002
Wagner, T., McLaughlin, P., Smalling, K., Breitmeyer, S., Gordon, S., and Noe, G.B., 2022. The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed, USA. Chesapeake Bay Water Quality Goal Implementation Team, Toxic Contaminants Workgroup.	January 2022	I provided an overview of research related to detecting temporal trends in river contaminant concentrations to the Chesapeake Bay Water Quality Goal Implementation Team, Toxic Contaminants Workgroup.
Wagner, T., Jones, M. L., Ebener, M. P., Arts, M. P., Brenden, T. O., Honeyfield, D. C., Wright, G. M., Faisal, M. 2008. Spatial and temporal dynamics of lake whitefish health indicators: linking individual-based indicators to a management-relevant endpoint. 69th Midwest Fisheries and Wildlife Conference, Dec. 14-17, Columbus OH.	December 2008
Wagner, T., J.T. Deweber, J. Detar, D. Kristine, and J.A. Sweka. 2013. Spatial and Temporal Dynamics in Brook Trout Density: Implications for Population Monitoring. American Fisheries Society Pennsylvania Chapter Fall Technical Meeting.	October 2013	This work quantifies the regional dynamics of an ecologically important fish species in an effort to provide guidance for management and conservation at the landscape-scale.
Wagner, T., E. Schliep, G. Hansen, B. Bethke, and P. Jacobson. 2018. C’mon, everyone’s doing it: joint distribution models for studying spatiotemporal dynamics of fish communities and their habitat . Annual Meeting of the American Fisheries Society, Atlantic City, NJ.	August 2018	We discuss the advantages of joint distribution models for fisheries research and management.
Wagner, T., C. Custer, J. North, E. Schliep M. Verhoven, GJA Hansen. 2024. Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model. Annual Meeting of the American Fisheries Society, Honolulu, HI.	August 2024	Here, we present a joint species, spatially dependent physiologically guided abundance (jsPGA) model for predicting multispecies responses to climate warming. The jsPGA model uses a basis function approach to capture both species and spatial dependencies. We apply the jsPGA model to predict the response of eight fish species to projected climate warming in thousands of lakes in Minnesota, USA.
Wagner, T., B.J. Irwin, J.R. Bence, W. Lui, D.B. Hayes. 2012. Developing Expectations for Detecting Temporal Change in Freshwater Fisheries Surveys. 68th Annual Northeast Fish and Wildlife Conference. April 15 - 17, 2012, Charleston, West Virginia.	April 2012
Wagner, T., B.J. Irwin, J.R. Bence, W. Liu, and D.B. Hayes. 2011. The Role of Variance Components and Survey Design in Detecting Trends in Recreational Fisheries Monitoring Data. 6th World Recreational Fishing Conference, Berlin, Germany, August 1 - 4.	August 2011
Wagner, T. Y. Li, V.S. Blazer, L.R. Iwanowicz, M.K. Schall, K. Smalling, D. Tillitt. 2021. Ecological risk assessment of environmental stress and bioactive chemicals to riverine fish populations: an individual-based model of smallmouth bass Micropterus dolomieu. Annual Meeting of the American Fisheries Society.	November 2021	We provide a flexible framework for performing environmental risk assessment for riverine fishes.
Wagner, T. K. Spence Cheruvelil, P.A. Soranno, K.E. Webster. A hierarchical Bayesian approach to modeling regional variation in total phosphorus – chlorophyll a relationships. North American Lake Management Society. October 2009.	October 2009
Wagner, T. 2021. Ecological Risk Assessment of Environmental Stress and Bioactive Chemicals to Riverine Fish Populations: An Individual-Based Model of Smallmouth Bass. Invited presentation. Quantitative Fisheries Center, Michigan State University.	February 2021	I discussed ongoing work examining the risk assessment of environmental stress to riverine fish populations.
Wagner, T. 2017. "Movers" and "Stayers": understanding brook trout movement for conservation and management. Pennsylvania Wild Trout Summit. The Future of Wild Trout in Pennsylvania.	August 2017	This talk summarizes three telemetry studies performed on brook trout movement.
Wagner, T. 2016. Risk assessment of contaminants to fish and wildlife populations in the Chesapeake Bay Watershed: a simulation study with smallmouth bass. PA Department of Environmental Protection, Statewide Annual Biologist Meeting.	October 2016	Presenting results of a smallmouth bass population dynamics model and risk assessment for the Susquehanna River Basin, PA.
Wagner T., Soranno P. A., Bremigan M. T., Spence Cheruvelil K., Webster K. E., Stow C. A. Freshwater Ecosystem Classification for Landscape-scale Management. 65th Northeastern Fish and Wildlife Conference, April 26 – 28, Lancaster, PA.	April 2009
Vreeland, W., D. Diefenbach, M. Ternent. Using capture-recovery data to infer dispersal for Pennsylvania black bear, 1980-2008. The Wildlife Society's 18th Annual Conference, Waikoloa, Hawaii, 5-10 November 2011.	November 2011
Vreeland, W. C., D. R. Diefenbach, M. Ternent. Dispersal Timing, Distance, and Rate of Pennsylvania Black Bear. Annual Conference of The Wildlife Society, Pittsburgh, Pennsylvania. 23 October 2014.	October 2014	In Pennsylvania, the black bear (Ursus americanus) population has expanded its range since bear abundance began increasing in the early 1980s. We investigated if dispersal timing, distance, and rates had changed and if those changes corresponded with range expansion and increasing abundance.
Vreeland, J. K., W. L. Palmer, and D. R. Diefenbach. Twenty-five years of ruffed grouse response to intensive habitat management and hunting closure in a mixed-oak forest in central Pennsylvania. 59th Annual Northeast Fish and Wildlife Conference, 13-16 April 2003, Newport, Rhode Island.	April 2003
Vreeland, J. K., D. R. Diefenbach, and B. D. Wallingford. 9/2001. White-tailed deer fawn survival in northcentral Pennsylvania. Annual Conference of The Wildlife Society, Reno, NV.	September 2001
Vreeland, J. K., D. R. Diefenbach, and B. D. Wallingford. 2001. White-tailed deer fawn survival in northcentral Pennsylvania.	March 2001
Vreeland, J. K., D. R. Diefenbach, B. D. Wallingford. White-tailed deer fawn survival in northcentral Pennsylvania. Annual Meeting of Pennsylvania Chapter of The Wildlife Society, 1-3 March 2002, Myerstown, PA.	March 2002
Vreeland, J. K., D. R. Diefenbach, B. D. Wallingford. Survival rates and cause-specific mortality of white-tailed deer fawns in northcentral Pennsylvania. 58th Annual Northeast Fish and Wildlife Conference, 21-24 April 2002, Portland, ME.	April 2002
Vidal, T., C. Jansch, B. J. Irwin, T. Wagner, J. R. Bence, J. R. Jackson, L. G. Rudstam, and W. W. Fetzer. 2014. Using variance structure as statistical indicators of large scale ecological change. Annual meeting of the American Fisheries Society, Québec City, Québec, Canada.	August 2014	Variability, which is sometimes viewed as an impediment to understanding population response, may reveal important signals regarding critical thresholds, beyond which a system could transition into an alternate, perhaps less desirable, state.
Vidal, T., B. J. Irwin, T. Wagner, L. G. Rudstam, J. R. Bence, and J. R. Jackson. Using variance structure to quantify perturbation induced ecological reorganization. Warnell Graduate Student Symposium, University of Georgia, Athens, GA.	February 2015	We analyzed long term fishery-independent survey data, from Oneida Lake, NY, using a mixed modeling approach to partition total variability into spatial and temporal components. We show that the variance structure associated with the time series of count data produced by the survey was responsive to these perturbations, and suggest that these shifts could provide fine-scale information about how the fish community is reorganizing in adaptation to the altered ecosystem.
Van Buskirk, A., C. S. Rosenberry, B. D. Wallingford, E. J. Domoto, M. E. McDill, P. Drohan, D. R. Diefenbach. 2021. Modeling how to achieve localized areas of reduced deer density. Southeast Deer Study Group Meeting, 23 February 2021.	February 2021	We developed a spatially explicit, agent-based model to investigate the intensity of deer removal required to locally reduce deer density depending on surrounding deer density, dispersal behavior, and size and shape of the removal area. Localized reduction was successful for scenarios in which the surrounding deer density was ≤30 deer/mi², antlerless harvest rates were ≥30% and the removal area was ≥5 mi².
Trowbridge, J., D. R. Diefenbach, T. A. Marques, T. M. McConnell, A. Van Buskirk, C. S. Rosenberry, W. D. Walter, and K. Lamp. Accounting for animal density gradients in distance sampling surveys. Southeast Deer Study Group Meeting, February 2024, Shepherdstown, WV.	February 2024	When roads are used as transects the distance sampling estimator likely will be biased because (1) deer are not distributed uniformly with respect to distance from a road and (2) roads are not distributed randomly on the landscape. We use auxiliary data on the density gradient of deer relative to transects and a generalized form of the distance sampling estimator to eliminate the assumption that objects must be uniformly distributed relative to the transect.
Trowbridge, J., D. R. Diefenbach, T. A. Marques, T. M. McConnell, A. Van Buskirk, C. S. Rosenberry, W. D. Walter, and K. Lamp. Accounting for animal density gradients in distance sampling surveys. Pennsylvania Chapter of The Wildlife Society, March 2024, State College, PA	March 2024	When roads are used as transects the distance sampling estimator likely will be biased because (1) deer are not distributed uniformly with respect to distance from a road and (2) roads are not distributed randomly on the landscape. We use auxiliary data on the density gradient of deer relative to transects and a generalized form of the distance sampling estimator to eliminate the assumption that objects must be uniformly distributed relative to the transect.
Thompson, T.J., V. Blazer, A. Sperry, M. Briggs, and T. Wagner. 2018. Groundwater as a source of emerging contaminants to streams of the Chesapeake Bay Watershed. . Society for Freshwater Science, Detroit MI.	May 2018	Some of the first research on groundwater fluxes of EDCs into surface waters.
Thompson, T.J., T. Wagner, V.S. Blazer, P. Phillips, M. Briggs, and A. Sperry. 2017. Groundwater as a source of emerging contaminants in the Chesapeake Bay. U.S. Geological Survey Chesapeake Bay Meeting, Aug 23-25.	August 2017	We present initial findings for groundwater as a potential sources of contaminants for streams in the Chesapeake Bay Watershed.
Thompson, T., T. Wagner, V. Blazer, A. Sperry, and M.A. Briggs. 2017. Groundwater as a source of emerging contaminants. Susquehanna River Symposium, Bucknell University.	November 2017	We present one of the first studies to examine emerging contaminants in groundwater entering streams and its role as a potential exposure pathway to smallmouth bass.
Thompson, T., M. Schall, T. Wagner, V. Blazer, A. Sperry and J. Niles. An investigation into the role of groundwater as a point source of emerging contaminants to smallmouth bass in the Susquehanna River basin. 2016 Chesapeake Bay Workshop, Aug 30-Sept 1.	August 2016	We present the first accounts of groundwater as a potential source of endocrine disrupting compounds for smallmouth bass in the Susquehanna River basin.
Thompson, T., M. Schall, T. Wagner, V. Blazer, A. Sperry and J. Niles. 2016. An investigation into the role of groundwater as a point source of emerging contaminants to smallmouth bass in the Susquehanna River basin. Joint meeting between the West Virginia and Pennsylvania Chapters of the American Fisheries Society, California State University of Pennsylvania.	February 2017	We present the first accounts of groundwater as a potential source of endocrine disrupting compounds for smallmouth bass in the Susquehanna River basin.
Thomas, N.A., M.K. Schall, G.D. Smith, S. Stark. and T. Wagner. 2002. Using stable isotope analysis to investigate trophic positioning of flathead catfish in the Susquehanna River Basin, PA. 17th Annual River Symposium. Bucknell University, Lewsiburg, PA.	November 2022	We provide initial assessment of the trophic position of invasive flathead catfish in the Susquehanna River, PA.
Thomas, N.A., M.K. Schall, G.D. Smith, S. Stark, and T. Wagner. Piloting the use of stable isotope analysis to understand trophic dynamics of invasive Flathead Catfish Pylodictis olivaris.PA Chapter of the American Fisheries Society, Spring Technical Meeting. Lock Have, PA.	February 2023	We present a pilot study examining the trophic position of invasive flathead catfish in the Susquehanna River, PA.
Sweka, J.A., Wagner, T., Detar, J. 2011. Determination of a Representative Reach to Estimate Brook Trout Biomass in Pennsylvania Streams. American Fisheries Society 141st Annual Meeting. Seattle, WA, September 4 – 8.	September 2011
Sweka, J.A., L. Davis, and T. Wagner. 2016. Survival of Brook and Brown Trout through the Spawning Season in a North Central Pennsylvania Watershed. 146th AFS Annual Meeting in Kansas City, Missouri, August 21-25.	August 2016	This is one of the first research projects to estimate survival for brook and brown trout at a fine temporal scale. This has implications for brook trout conservation and management.
Sweka, J.A. and Wagner, T. Evaluation of hypotheses for explaining temporal trends in Atlantic salmon parr densities in Northeast U.S. Rivers. Annual Meeting of the American Fisheries Society. September 12 – 16.	September 2010
Sweka, J.A. and T. Wagner. Effects of stream discharge on young-of-year brook trout density in North Central Pennsylvania. Annual Meeting of the American Fisheries Society, Atlantic City, NJ.	August 2018	We evaluate flow-density relationship for several brook trout populations.
Sweka, J., Wagner, T., and Detar, J. 2011. Determination of a Representative Sample Reach for Estimation of Native Brook Trout Biomass in Pennsylvania Streams. 67th Annual Northeast Fish and Wildlife Conference, Manchester, New Hampshire, April 17 – 19.	April 2011
Sweka, J. and T. Wagner. 2011. Evaluation of hypotheses for describing temporal trends in Atlantic salmon parr densities in Northeast U.S. Rivers. The Connecticut River Research Forum.	February 2011
Stum, M., M. Marshall, C. Tzilowski, F. Buderman, and T. Wagner. 2023. Spatiotemporal Trends of Stream Fish Community Occupancy in an Appalachian US National Park. American Fisheries Society Annual Meeting, Grand Rapids, MI.	August 2023	We present a preliminary assessment of stream fish occupancy in National Park units in the eastern US.
Stum, M. M. Marshall, C. Tzilkowski, F. Buderman, and T. Wagner. 2023. Documenting Spatiotemporal Trends in Fish Communities of the National Park Service Eastern Rivers and Mountains Network. Northeast Association of Fish & Wildlife Agencies, Hershey, PA.	May 2023	We compare fish assemblages in National Park Units in the eastern US.
Stedman, R., D. R. Diefenbach, C. B. Swope, J. C. Finley, A. E. Luloff, H. C. Zinn, and G. J. San Julian. Integrating wildlife and human dimensions research methods to study deer hunters. Southeast Deer Study Group Meeting, 21-24 February 2005, Shepherdstown, West Virginia.	February 2005
Stauffer, G. E., D. R. Diefenbach, and M. R. Marshall. Site Fidelity and Inter-annual Movements of Grasshopper Sparrows on Reclaimed Surface Mines. Annual Conference of the Pennsylvania Chapter of the Wildlife Society. 22 March 2008.	March 2008
Stauffer, G. E., D. R. Diefenbach, and M. R. Marshall. Reproductive success and site fidelity of male and female grasshopper sparrows on reclaimed surface mines. Annual Conference of The Wildlife Society, Miami, Florida, 8-12 November 2008	November 2008
Stauffer, G. E., D. R. Diefenbach, M. R. Marshall. Apparent Survival and Nesting Success of Grassland Sparrows on Reclaimed Surface Mines. Annual Conference of the Pennsylvania Chapter of the Wildlife Society, State College, Pennsylvania, 17 March 2007.	March 2007
Stauffer, G. E. and D. R. Diefenbach. Site Fidelity and Nesting Success of Grassland Sparrows on Reclaimed Surface Mines in Pennsylvania Northeast Association of Fish and Wildlife Agencies Annual Conference, Groton, Connecticut, 22-24 April 2007.	April 2007
Stark, S.k., M.K. Schall, J.D. Avery, G.D. Smith, and T. Wagner. 2021. Evaluating sampling techniques of Flathead Catfish, Plyodictis olivaris, in the Susquehanna River Basin for dietary analysis. Pennsylvania Chapter of the American Fisheries Society Spring Technical Meeting. February 11-12, 2021.	February 2021	We evaluate gear types for sampling flathead catfish for diet analysis, which is critical for understanding potential effects of this species as it continues to spread throughout the Pennsylvania river systems.
Stark, S.K., Schall, M.K., Smith, G.D., Avery, J.D., Wagner, T. 2022. Preliminary diet analysis of the invasive Flathead Catfish in the Susquehanna River Basin. Keystone Coldwater Conference & PA Chapter of the American Fisheries Society. February 25-26, 2022.	February 2022	We present preliminary information on the diet of invasive flathead catfish in the Susquehanna River, PA.
Stark, S.K., M.K. Schall, J.D. Avery, G.D. Smith, and T. Wagner. 2021. Preliminary Diet Analysis of the invasive Flathead Catfish (Pylodictis olivaris) in the Susquehanna River Basin, PA. The Annual Meeting of the American Fisheries Society.	November 2021	This is the first study to evaluate the diet of the invasive flathead catfish in the Susquehanna River, PA.
Stark, S.K., M.K. Schall, G.D. Smith, and T. Wagner. 2023. Trophic Impacts by the Invasive Flathead Catfish (Pylodictis olivaris) in the Susquehanna River, PA. American Fisheries Society Annual Meeting, Grand Rapids, MI.	August 2023	We present a preliminary assessment of the trophic impacts of an invasive fish species in the Susquehanna River, PA.
Stark, S.K., M.K. Schall, G.D. Smith, J.D. Avery, and T. Wagner. 2022. Comparison of collection methods for diet studies of invasive flathead catfish. Northeast Fish & Wildlife Conference.	April 2022	We evaluate the efficacy of different gear types for making inferences about the diet of invasive flathead catfish.
Stark, S.K., M.K. Schall, G.D. Smith, J.D. Avery, and T. Wagner. 2021. Let’s eat! A look at the diet of the invasive Flathead Catfish (Pylodictis olivaris) in the Susquehanna River Basin, PA. Southern Division of the American Fisheries Society.	April 2021	We present preliminary results of diet content for the invasive flathead catfish in the Susquehanna River, PA.<br><br>Introductions of nonnative fishes often alter food web structure and trophic interactions in aquatic ecosystems. In such cases, it is important to understand such alterations in order to effectively manage native and naturalized fisheries of recreational and conservation importance. The Flathead Catfish is a large bodied piscivore that can disrupt river systems through direct pr
Stark, S., M. Schall, G. Smith, J. Avery, and T. Wagner. 2023. Investigating community level impacts and trophic positioning of invasive Flathead Catfish, Pylodictis olivaris, in the Susquehanna River. Northeast Association of Fish & Wildlife Agencies, Hershey, PA.	May 2023	We present preliminary findings of the food web effects of flathead catfish invasion in the Susquehanna River, PA.
Stark, S., M. Schall, G. Smith, J. Avery, and T. Wagner. 2023. Diet Analysis of Invasive Flathead Catfish in the Susquehanna River Basin. PA Chapter of the American Fisheries Society, Spring Technical Meeting. Lock Have, PA.	February 2023	We present the first assessment of the diet of invasive flathead catfish in the Susquehanna River Basin, PA.
Stainbrook, D. P., and D. R. Diefenbach. Modeling resource selection of deer to account for non-random sampling with distance sampling. Southeast Deer Study Group Meeting, Oklahoma City, Oklahoma, February 20-23, 2011.	February 2011
Stainbrook, D. P., and D. R. Diefenbach. Methods of Estimating Deer Abundance at Gettysburg National Military Park and Eisenhower National Historic Site: Testing Assumptions of Distance Sampling. Northeast Association of Fish and Wildlife Agencies Annual Conference, Manchester, NH, 17-19 April 2011.	April 2011
Stachelek, J., C.C. Carey, K.M. Cobourn, S.M. Collins, A.R. Kemanian, T. Wagner, K.C. Weathers, W. Weng, and P.A. Soranno. 2019. Analysis of 500 lake catchments reveals the relationship between crop type, fertilizer and manure inputs and lake nutrient concentrations. 2019. Ecological Society of America Annual Meeting.	August 2019	Our work examines how finer-scaled measurements of agricultural land use activity is related to lake water quality.
Spencer, S., S. Talbott, D. R. Diefenbach, M. Runge. Surveying northeastern grassland birds in winter: Can just anyone do it? Annual Meeting of the Virginia Society of Ornithology, 7 May 2005, Norfolk, Virginia.	May 2005
Soranno, PA., P. Hanly, KE Webster, KS Cheruvelil, NR Lottig, IM McCullough, A. McDonald, KL Reinl, EM Schliep, A Shuvo, P-N Tan, and T. Wagner. 2023. ABRUPT CHANGES IN THE PRODUCTIVITY OF 25,000 LAKES IN THE CONTINENTAL US RELATED TO CLIMATE CHANGE AND LAND USE INTENSIFICATION. ASLO Aquatic Sciences Meeting.	June 2023	We examine annual CHL time series from 1984-2018 in 25,000 lakes in the continental U.S. along with climate and ecological drivers of lake CHL at multiple spatial and temporal scales.
Soranno, P.A., T. Wagner, S.M. Collins, J-F. Lapierre, N.R. Lottig, S.K. Oliver. 2018. Spatial variation exceeds temporal variation in lake ecosystem properties at macroscales. Association for the Sciences of Limnology and Oceanography, Summer Meeting, Victoria, BC, Canada.	June 2018	First work to partition and model variation of lake ecosystem properties at macroscales.
Soranno, P.A., K.S. Cheruvelil, E. Bissell, M.T. Bremigan, J.A. Downing, C.E. Fergus, C.T. Filstrup, N.R. Lottig, E. Norton Henry, E.H. Stanley, C. Stow, P-N. Tan, T. Wagner and K. Webster. 2013. A conceptual framework for understanding multi-scaled cause-effect relationships between terrestrial and aquatic ecosystems. Ecological Society of America, 98th Annual Meeting, August 4-9, Minneapolis, MN.	August 2013	The ground-breaking research provides a conceptual framework and case-studies to examining landscape-scale cross-scale interactions.
Soranno P.A., Spence Cheruvelil K., Webster K.E., Bremigan M.T., and Wagner T. 2008. The effect of land use on lake chemistry: The role of spatial scale and landscape position	August 2008
Smith, L. and T. Wagner. 2013. Seasonal movement patterns and habitat use of the Eastern Brook Trout in North-central Pennsylvania. Annual Meeting of the American Fisheries Society, September 2013.	September 2013	This work quantifies movement and habitat use of wild eastern brook trout. This information is essential for the conservation and management of this species.
Smith, L. and T. Wagner. 2013. Seasonal movement patterns and habitat use of the Eastern Brook Trout (Salvelinus fontinalis) and Brown Trout (Salmo trutta) in North Central Pennsylvania. American Fisheries Society Pennsylvania Chapter Fall Technical Meeting.	October 2013	This work models movement and habitat use of both native brook trout and naturalized brown trout.
Smith, G.D., M.K. Schall, V.S. Blazer, H.L. Walsh, and T. Wagner. 2019. The role of disease in altering the population structure of Smallmouth Bass in the Susquehanna River Basin. International Association for Great Lakes Research (IAGLR).	June 2019	Overview of smallmouth bass fish health and effects on population structure.
Smith, A., R. F. Carline, C. Gill, and K. Patten. 2002. The effects of sediment loading from road and bridge construction on Spring Creek, Pennsylvania. Northeast Fish and Wildlife Conference, Portland, Maine, April 21-24, 2002.	April 2002
Sievert, N., W. Daniel, Y. Tang, C. Paukert, D. Infante, J. Whittier, K. Herreman, J. Stewart, T. Wagner. An Assessment of Potential Changes in Habitat Classes Due to Climate Change in the Northeast Climate Science Center Region. Midwest Fish and Wildlife Conference, Grand Rapids, MI	January 2016	This work summarizes how climate change may affect fish habitat for species in the Northeast US.
Siepker C., N. Haley, W. Walter, L. Hoon-Hanks, R. Monello, J. Powers, B. Thomsen, J. Greenlee, A. Lehmkuhl, G. Mitchell, T. Nichols, E. Hoover, J. Richt. 2015. Clinical Stage of Infection is Critical in the Antemortem Diagnosis of Chronic Wasting Disease in Deer and Elk. Prion Conference, Fort Collins, CO	May 2015	Chronic wasting disease (CWD) is an efficiently transmitted spongiform encephalopathy of cervids (e.g. deer, elk, and moose), and is the only known prion disease affecting both free-ranging wildlife and captive animals. Our findings further demonstrate the potential and limitations of antemortem sample analyses by RT-QuIC in the identification and management of prion diseases.
Scott, C.E., C.E. Fergus, S.M. Collins, J-F. Lapierre, N.R. Lottig, C.T. Filstrup, N. Skaff, E.H. Stanley, P-N. Tan, T. Wagner, P.A. Soranno, and K.S. Cheruvelil. Understanding the response of lake water quality at macroscales to measures of regional and global climate. The 2015 Ecological Society of America Annual Meeting, August 9 – 15.	August 2015	This work is the first to quantify lake responses to climate at macroscales.
Scott, C.E., C.E. Fergus, N.R. Lottig, C.T. Filstrup, T. Wagner, E.H. Stanley, and P.A. Soranno. 2014. Which global and regional climate metrics at macroscales best describe lake water quality responses to climate change? Joint Aquatic Sciences Meeting, Portland, OR, USA	May 2014	Regional modeling to elucidate potential effects of climate change on lake water quality.
Schwabenlander, M.D., J.C. Bartz, M. Carstensen, A. Fameli, L. Glaser, R.J. Larsen, M. Li, L.L. Lindsey, J.D. Oliver, R. Shoemaker, G. Rowden, S. Stone, W.D. Walter, T.M. Wolf, P.A. Larsen. 2023. Prion Forensics: a multidisciplinary approach to investigate chronic wasting disease at a deer carcass disposal site. 4th International Chronic Wasting Disease Symposium 31 May-2 June 2023.	May 2023	Although its geographic origin is speculative, much of the spread of chronic wasting disease (CWD) worldwide is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD.
Schwabenlander, M.D., J.C. Bartz, M. Carstensen, A. Fameli, L. Glaser, R.J. Larsen, M. Li, L.L. Lindsey, J.D. Oliver, R. Shoemaker, G. Rowden, S. Stone, W.D. Walter, T.M. Wolf, P.A. Larsen. 2022. Implementing a veterinary forensics approach to investigate chronic wasting disease at a deer carcass disposal site. Southeast Deer Study Group, Baton Rouge, LA, 26-28 February 2023.	December 2022	Although its geographic origin is speculative, much of the spread of chronic wasting disease (CWD) worldwide is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD.
Schwabenlander, M.D., G. Rowden, S. Stone, R. Shoemaker, L.L. Lindsey, J.D. Oliver, L. Glaser, M. Carstensen, J.C. Bartz, W.D. Walter, R.J. Larsen, T.M. Wolf, P.A. Larsen. 2022. Implementing a veterinary forensics approach to investigate chronic wasting disease at a deer carcass disposal site. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022.	July 2022	Although its geographic origin is speculative, much of the spread of chronic wasting disease (CWD) worldwide is attributed to human activities that include the movement of live animals and animal carcasses. Given the potential for CWD-causing prions to remain infectious within the environment, the disposal of CWD-positive animal remains, whether from free-ranging or captive sources, can play an important role in the transmission of CWD.
Schuler, K., B. Hanley, N. Hollingshead, R. Abbott, C. Them, S. Ahmed, W.D. Walter, D. Walsh, S. Christensen, and P. Adams. 2023. What Can the Surveillance Optimization Project for Chronic Wasting Disease (SOP4CWD) Do For You? 4th International Chronic Wasting Disease Symposium, Denver, CO, 31 May-2 June, 2023	May 2023	A group of wildlife biologists, administrators, veterinarians, disease ecologists, and statisticians gathered to talk about chronic wasting disease surveillance (CWD) to determine if surveillance could be made more efficient and effective. Born out of that question, the Surveillance Optimization Project became a regional effort to share data, have better information for decision making, and provide a framework for a disease so every agency doesn’t have to “recreate the wheel.”
Schneider, A.L., A.T. Gilbert, W.D. Walter, G.S. Vandeberg, and J.R. Boulanger. 2019. Spatial Ecology of Urban Striped Skunks (Mephitis mephitis) in the Northern Great Plains. International Urban Wildlife Conference, Portland, OR.	June 2019	Few studies have investigated the ecology of urban striped skunks (Mephitis mephitis) despite their ability to thrive in these landscapes. Information on spatial ecology of striped skunks is important for rabies mitigation efforts via oral rabies vaccine (ORV) baits.
Schall, MK., M.L. Bartron, T. Wertz, J. Niles, V.S. Blazer, T. Wagner. Investigating movement dynamics and population genetics of smallmouth bass in the Susquehanna River Basin. 2016 Chesapeake Bay Workshop, Aug 30-Sept 1.	August 2016	We present the first accounts of movement and populations genetics work for smallmouth bass in the Susquehanna River, and discuss the implications for fish health and disease management.
Schall, M.K., V.S. Blazer, T. Wagner, T. Wertz, and G. Smith. 2015. Investigation of contaminants and disease characteristics of young of the year Smallmouth Bass in the Susquehanna River basin, PA. AFS-Fish Health Section Annual Meeting, Ithaca, NY. July 13-15.	July 2015	This work is one of the first reports of contaminants in fish and the environment in the Susquehanna River, PA, and reports on implications for fish health.
Schall, M.K., V.S. Blazer, H.L. Walsh, G.D. Smith, T. Wertz, and T. Wagner. 2022. Investigating Spatiotemporal Variability in Visual Health Assessments for Adult Smallmouth Bass. Chesapeake Community Research Symposium. Annapolis, MD.	June 2022	We evaluate factors affecting fish pathogens in riverine smallmouth bass populations.
Schall, M.K., V.S. Blazer, H.L. Walsh, G.D. Smith, T. Wertz, and T. Wager. 2021. Where do we go from here?: Quantifying spatiotemporal variability in fish health observations from Smallmouth Bass Micropterus dolomieu after disease and population declines. The Annual Meeting of the American Fisheries Society.	November 2021	This study evaluates disease occurrence and co-occurrence in smallmouth bass populations in the Susquehanna River, PA. Smallmouth Bass <i>Micropterus dolomieu </i>are a popular recreational sport fish that are sensitive to environmental disturbances, disease, and contaminant exposure (e.g., endocrine disrupting chemicals). Smallmouth Bass populations in the Susquehanna River Basin, Pennsylvania, have been threatened by disease, mortality, and population declines over the past fifteen years. Rec
Schall, M.K., V.S. Blazer, H.L. Walsh, G. Smith, T. Wertz, and T. Wagner. 2019. Quantifying spatial variability in young of year smallmouth bass disease infections in the Chesapeake Bay Watershed. International Association for Great Lakes Research (IAGLR), Brockport, NY, June 10 – 14.	June 2019	This work is some of the first to examine coinfection rates in smallmouth bass in the Susquehanna River basin and to quantifying potential underlying factors for coinfection in YOY smallmouth bass. This work provides insight on risk for future disease outbreaks and prioritization of potential management areas.
Schall, M.K., V.S. Blazer, H.L. Walsh, G. Smith, T. Wertz, and T. Wagner. 2017. EVALUATING DIFFERENCES IN FIELD OBSERVATIONS AND HISTOLOGICAL PREVALENCE OF MYXOZOAN PARASITES IN YOUNG-OF-THE-YEAR SMALLMOUTH BASS (MICROPTERUS DOLOMIEU) IN THE SUSQUEHANNA RIVER BASIN, PA. AFS FHS Annual Meeting.	April 2017	Fist comparison of field and lab-based diagnostics for a myxozoan parasite in smallmouth bass.
Schall, M.K., V.S. Blazer, H. Walsh, T. Wertz, G. Smith, and T. Wagner. 2017. Investigating myxozoan parasite prevalence in young of the year smallmouth bass in the Susquehanna River basin, 2013-2016. U.S. Geological Survey Chesapeake Bay Meeting, Aug 23-25.	August 2017	We present initial findings of myxozoan parasite prevalence in young of the year smallmouth bass in the Susquehanna River basin.
Schall, M.K., T. Wagner, V. Blazer, and T. Wertz. Movement dynamics of Smallmouth Bass in the Susquehanna River basin. Pennsylvania-Ohio 2015 Joint American Fisheries Society Annual Meeting, 25–27 February 2015.	February 2015	First study to examine movement of smallmouth bass in the Susquehanna River basin and attempt to link movements with fish health and contaminant exposure.
Schall, M.K., T. Wagner, R.M. Lorantas, G.D. Smith, and V.S Blazer. Investigating trends in riverine smallmouth bass catch per effort data in Pennsylvania. Joint meeting between the West Virginia and Pennsylvania Chapters of the American Fisheries Society, California State University of Pennsylvania.	February 2017	We evaluate temporal dynamics of smallmouth bass in PA rivers within the context of trends in fish health.
Schall, M.K., G.D. Smith, J.D. Avery, and T. Wagner. 2021. Comparing the use of multiple molecular techniques for identification of prey items in invasive Flathead Catfish (Pylodictis olivaris) diets. Southern Division of the American Fisheries Society.	April 2021	We compare two molecular techniques for determining diet of invasive flathead catfish.<br><br>Flathead Catfish are a piscivorous invasive fish species introduced throughout the United States. It is important to understand how Flathead Catfish introductions alter ecosystem function and disrupt community structure through predation. Flathead Catfish are commonly collected with empty stomachs or degraded prey items in stomach contents making it difficult to identify prey using meristic or morphome
Schall, M., T. Wagner, M. Bartron, V.S. Blazer and J. Niles. 2016. Movement dynamics and population genetics of smallmouth bass in the Susquehanna River Basin. Susquehanna River Symposium, Bucknell University.	November 2016	We present the first information on the movement dynamics and genetic structure of smallmouth bass in the Susquehanna River Basin, PA.
Salvesen, K., M. Bartron, T. Wagner. 2012. Genetic Assessment of the Klondike Lake Trout Strain: Comparison of Wild and Hatchery Strains. American Fisheries Society Annual Meeting. Twin Cities, MN. 19 – 23 August.	August 2012
Sabo, A. E., P. Jones, P. Drohan, D. R. Diefenbach, M. E. McDill. Competing vegetation treatments provide little short-term benefit in northcentral Appalachian forests. Presented at annual conference of the Society of American Foresters, Baltimore, MD, 20-24 September 2022.	September 2022	Competing vegetation treatments are typically applied to 1) lower the abundance of undesirable vegetation that casts thick shade and/or creates a dense mat of roots or rhizomes on the forest floor, and 2) increase the abundance and/or size of tree seedlings. Over the short-term (up to four years later), treatments do not appear beneficial for the understory community, prompting questions about other factors that may be limiting regeneration as well as alternative silvicultural interventions.
Russo-Petrick, K, A. Fameli, C.S. Rosenberry, K.L. Schuler, M.J. Tonkovich, J.E. Edson, and W.D. Walter. 2023. Large-scale assessment of spatial genetic structure to assess risk of white-tailed deer populations to chronic wasting disease. 4th International Chronic Wasting Disease Symposium, Denver, CO, 31 May-2 June, 2023.	May 2023	Chronic wasting disease can be spread by direct and indirect transmission, but identifying subpopulations of deer across regions allows delineation of focal areas to target for effective intervention. Genetic assignment tests provided further understanding of subpopulation structuring depending on the analysis used and whether location-specific details were included for each genetic sample.
Rosenberry, C. S., J. Fleegle, B. Wallingford, M. Lovallo, M. Ternent, and D. R. Diefenbach. Under attack? Impacts of predation on white-tailed deer recruitment and populations in Pennsylvania. Annual meeting of the Northeast Association of Fish and Wildlife Agencies, 7-10 April 2013, Saratoga Springs, New York.	April 2013	An evaluation of population dynamics of white-tailed deer and predators in Pennsylvania indicate that predators are unlikely to be limiting deer populations.
Robinson, K., A. Fuller, M. Schiavone, D. Diefenbach, and W. Siemer. A structured decision making approach to addressing wild turkey population declines. Informs Annual Meeting, 22-23 October 2019, Seattle, Washington, USA.	October 2019	Turkey (Meleagris gallapavo) populations in New York have been declining in recent years. Reducing harvest of females during fall hunting season could potentially reduce the population decline but requires consideration of biological and social concerns. We used structured decision making to incorporate the multiple objectives associated with turkey hunting, stakeholder desires, and region-specific ecological and environmental factors that could influence fall harvest.
Rhodes, S., S. White, T. Wagner, J. Niles. 2016.Movers and Stayers: What Factors Influence Brook Trout Movement Behavior? Susquehanna River Symposium, Bucknell University.	November 2016	We present information on linking brook trout movement to individual behavior.
Rhoads, S., S. White, T. Wagner, and J. Niles. Movers and stayers: what factors influence brook trout movement? Susquehanna River Symposium, Bucknell University.	November 2016	We presented a poster on factors affecting brook trout movement.
Responses of streams to riparian restoration in the Spring Creek watershed, central Pennsylvania	September 2004
Rennie, M. D., M.P. Ebener, and T. Wagner. 2010. Can migration mitigate the effects of ecosystem change? Patterns of dispersal, energy acquisition and allocation in Great Lakes lake whitefish (Coregonus clupeaformis). International Association for Great Lakes Research. May 17-21, Toronto, Canada.	May 2010
Regmi, A., M. M. Kreye, D. R. Diefenbach, J. K. Kreye, M. E. McDill, P. J. Drohan, A. Sabo, E. Domoto, C. S. Rosenberry, B. Wallingford, and D. Stainbrook. Perspectives of hunters who purchase antlerless permits for us on state forest lands. 30 April 2023, Annual Conference of the Northeast Fish and Wildlife Agencies, Hershey, PA, USA.	April 2023	The Deer Management Assistance Program (DMAP) in Pennsylvania provides landowners with permits for hunters to harvest antlerless deer in a specific land area. Despite our study population being hunters who purchased DMAP permits to harvest antlerless deer, most wanted higher deer densities.
Peoples, B., W. Annis, G. Hansen, S. Midway, J. Olden, L. Thompson, T. Wagner, and M. Zink. 2022. FishScales: A contemporary stream fish community database for the conterminous United States. Joint Aquatic Sciences Meeting, Grand Rapids, MI.	May 2022	We describe the development of a contemporary large-scale stream fish database.
Peoples, B., W. Annis, G. Hansen, S. Midway, J. Olden, L. Thompson, T. Wagner, and M. Zink. 2022. FishScales: A contemporary stream fish community database for the conterminous United States. American Fisheries Society Annual Meeting, Spokane, WA.	April 2022	We describe the development of a contemporary large-scale stream fish database.
Patten, K. A., R. F. Carline, C. J. Gill, and Smith, A. M. March 2001. Effects of bridge and road construction on Spring Creek: Route 26 Transporation Improvements Project. Riparian buffers: how wide and why. 2001 Annual Meeting of the Pennsylvania Chapters of the American Fisheries Society and The Wildlife Society, Milesburg, PA.	April 2001
Onorato, D, W.D. Walter, J.W. Fischer, J. Downs, M. Criffield, M. Lotz. Pick your poison: applying multiple home range estimators to large GPS datasets from Florida panthers. The 19th Annual Meeting of the Wildlife Society, Portland, OR.	October 2012
Oliver, S.K., S.M. Collins, P.A. Soranno, T. Wagner, E.H. Stanley, J.R. Jones, C.A. Stow, and N.R. Lottig. 2018. Long-term changes in lake nutrient concentrations across the upper Midwest and northeast United States: how does Wisconsin stack up? Wisconsin Lakes Partnership Convention, Stevens Point, WI.	April 2018	This work discusses temporal changes in lake nutrient concentrations, regionally and in the state of WI.
Oliver, S.K., S. Collins, K.S. Cheruvelil, P.A. Soranno, E.H. Stanley, J-F. Lapierre, N. Lottig, and T. Wagner. 2016. Long-term change in lake nutrient concentrations: where are we now? Association for the Sciences of Limnology and Oceanography.	June 2016	This work quantifies long-term trends in water quality across much of the U.S.
Oliver SK, Stanley EH, Cheruvelil KS, Downing J, Fergus CE, Soranno PA, Wagner T, Webster K, Winslow L. 2014. Prediction and patterns of lake depth across a 17-state region in the U.S. Joint Aquatic Sciences Meeting. Portland, OR.	May 2014	This work develops a regional model for predicting lake depth, an important property that drives pysiochemical lake processes.
O'Connell, T. J., M. L. Lanzone, R. S. Mulvihill, D. W. Brauning, and D. R. Diefenbach. How well do removal models applied to count data estimate known densities from territory mapping? Annual Meeting of the Association of Field Ornithologists and the Wilson Ornithological Society, 22-24 April 2004, Ithaca, New York.	April 2004
Norton, A., and D. Diefenbach, C. Rosenberry, B. Wallingford. Evaluation of the Pennsylvania Sex-Age-Kill (SAK) Model for White-tailed Deer. Presented at the Southeast Deer Study Group Meeting in Roanoke, Virginia on February 24, 2009.	February 2009
Noring, A.M., G.G. Sass, S.R. Midway, J.A. VanDeHey, J.K. Raabe, D.A. Isermann, J.M. Kampa, T.P. Parks, J. Lyons, M.J. Jennings, G.J.A. Hansen, and T. Wagner. 2017. Effects of Cisco on Walleye Growth Trajectories in Northern Wisconsin Lakes. 13th International Coregonid Symposium.	September 2017	This work examines the presence/absence of Cisco on growth of walleye.
Nelms, M. G., L. A. Hansen, R. J. Warren, J. J. Brooks, and D. R. Diefenbach. Bobcat restoration, deer herd trends, and oak regeneration on Cumberland Island, Georgia, USA. Society for Conservation Biology Annual Meeting, 14-19 July, 2002, Canterbury, England, United Kingdom.	July 2002
Navarro, N., P. J. Drohan, M. McDill, and D. R. Diefenbach. Analysis of White-Tailed Deer (Odocoileus virginianus) Forage Nutrient Content across Northern Appalachian USDA Ecological Sites. Soil Science Society of America annual meeting, 22-25 October 2017, Tampa, FL, USA.	October 2017	USDA Ecological Sites (ES) delineations can be used as a framework to interpret the dynamics between vegetation and animals. The purpose of this project is to determine differences in palatable forage nutrient quality, specifically Medeola virginiana (Indian cucumber) and Maianthemum canadense (Canada mayflower), across soil chemical gradients between, and within, ESs of northern Appalachian forests.
Murphy, A., D. Miller, and D. R. Diefenbach. Examining habitat partitioning between pennsylvania’s apex carnivores and a common prey species (white-tailed deer fawns). The Wildlife Society Annual Conference, 7-11 October 2018, Cleveland, OH, USA.	October 2018	We examined white-tailed deer (Odocoileus virginianus) fawn, black bear (Ursus americanus), coyote (Canis latrans), and bobcat (Lynx rufus) habitat use to determine whether there was overlap and how that might relate to which predators cause the most fawn mortality. We found that coyotes were 24 times more likely to occupy camera points in hemlock-mixed hardwood palustrine forest compared to mixed oak-mixed hardwood forest, and that, despite black bears and coyotes being the two major predators
Murphy, A. U., D. Miller, and D. R. Diefenbach. Examining Habitat Partitioning between Pennsylvania’s Apex Carnivores and a Common Prey Species (White-tailed Deer Fawns; Odocoileus virginianus). North American Congress for Conservation Biology, 21-26 July 2018, Toronto, Canada.	July 2018	We examined white-tailed deer fawn, black bear (Ursus americanus), coyote (Canis latrans), and bobcat (Lynx rufus) habitat use to determine whether there was overlap and how that might relate to which predators cause the most fawn mortality. We found that coyotes were 24 times more likely to occupy camera points in hemlock-mixed hardwood palustrine forest compared to mixed oak-mixed hardwood forest, and that, despite black bears and coyotes being the two major predators of fawns, black bear, co
Mollenhauer, R., Sweka, J., Kepler, M. and Wagner, T. 2011. Seasonal movement and habitat use of wild brook trout in central Pennsylvania. Pennsylvania Chapter of AFS Spring Technical Meeting, April 22.	April 2011
Mollenhauer, R., Sweka, J., Kepler, M. and Wagner, T. 2011. Habitat use of wild brook trout in central Pennsylvania. 67th Annual Northeast Fish and Wildlife Conference, Manchester, New Hampshire, April 17 – 19.	April 2011
Miller-Butterworth, C., L. Hansen, D. Hoffman, A. Russell, J. Edson, and D. R. Diefenbach. Population genetics of two contrasting island populations of bobcats. The Wildlife Society Annual Meeting, 7-11 October 2018, Cleveland, OH, USA>	October 2018	Habitat isolation and population fragmentation increasingly threaten many wildlife species, particularly carnivores, which are keystone species and may require interventions such as translocation to maintain genetic diversity. This study compared the population genetics of a naturally-maintained island population of bobcats (Lynx rufus) to a similar one that was reintroduced. Observed heterozygosity (Hobs) levels in the founder CUIS bobcats was relatively high but has declined in the 20+ years
Miller-Butterworth, C., J. Bohling, L. Hansen, D. Hoffman, J. Jordan, D. R. Diefenbach. Population genetics of a reintroduced population of bobcats on Cumberland Island, Georgia: relevance for felid management in Pennsylvania. Pennsylvania Chapter of The Wildlife Society annual meeting, 1 April 2017, Raystown Lake, PA.	April 2017	Effective management of isolated populations is particularly important for carnivores, which are keystone species and which may require management interventions such as translocation to maintain genetic diversity. This talk will discuss a case study of a reintroduced population of bobcats (Lynx rufus) on Cumberland Island (CUIS), GA, and implications for the use of translocation as a management tool for re-establishing felid populations.
Miller, W.L., and W.D. Walter. 2015. Landscape genetics of white-tailed deer to assess population structure for surveillance of chronic wasting disease. The Wildlife Society Annual Meeting, Winnipeg, Manitoba, CN.	October 2015	Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that has recently been identified in captive and free-ranging white-tailed deer populations (Odocoileus virginianus) in parts of West Virginia, Virginia, Maryland, and Pennsylvania. Predictive models that incorporate population connectivity (e.g. dispersal) and environmental factors (e.g. topology, land cover) would allow managers to identify potential routes of white-tailed deer and subsequently mitigate the potential
Miller, W.L., W. D. Walter. 2017. Evaluating the risk of chronic wasting disease infection in Mid-Atlantic cervid populations. The Pennsylvania Chapter of the Wildlife Society, Raystown Lake, PA.	April 2017	Uncommon polymorphisms within the prion gene of many cervids have been linked to reductions in perceived susceptibility to chronic wasting disease (CWD). Understanding the underlying frequency and distribution of susceptible prion genotypes in areas of recent CWD infection, such as the eastern United States (USA) and Scandinavia, can provide insights into future epidemiology and infection intensity.
Miller, W.L., J. Brown, W. D. Walter. 2017. Genetic susceptibility of free-ranging cervids to chronic wasting disease in a recently infected region of the United States. Prion Conference, Edinburgh, Scotland.	May 2017	Uncommon polymorphisms within the prion gene of many cervids have been linked to reductions in perceived susceptibility to chronic wasting disease (CWD). Understanding the underlying frequency and distribution of susceptible prion genotypes in areas of recent CWD infection, such as the eastern United States (USA) and Scandinavia, can provide insights into future epidemiology and infection intensity.
Miller, W.L., D.R. Diefenbach, C. Miller-Butterworth, J. Brown, W. D. Walter. 2016. Landscape barriers influence genetic connectivity among white-tailed deer in an area affected by chronic wasting disease. Wildlife Disease Association Meeting, Ithaca NY	August 2016	Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy, which can affect white-tailed deer (Odocoileus virginianus). Transmission of CWD is facilitated by proximal contact between infected and susceptible individuals, therefore, movement of infected individuals, both within and among populations, may be important in driving the geographic spread of CWD.
Miller, W.L., D.R. Diefenbach, C. Miller-Butterworth, J. Brown, W. D. Walter. 2016. Landscape barriers influence genetic connectivity among white-tailed deer in an area affected by chronic wasting disease. 23rd Annual Meeting of The Wildlife Society, Raleigh NC	October 2016	Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy, which can affect white-tailed deer (Odocoileus virginianus). Transmission of CWD is facilitated by proximal contact between infected and susceptible individuals, therefore, movement of infected individuals, both within and among populations, may be important in driving the geographic spread of CWD.
Miller, W.L. and W. D. Walter. 2018. Genetic assignment tests provide insight into the epidemiology of chronic wasting disease in Pennsylvania. The Pennsylvania Chapter of The Wildlife Society, State College, PA	March 2018	Identifying the sources of ongoing and novel disease outbreaks is critical for understanding the geographic diffusion of epizootic diseases. Genetic assignment procedures show great promise for assessing transmission dynamics in situations where it is otherwise impossible to differentiate between putative infection sources.
Miller, W.L. and W. D. Walter. 2017. Genetic susceptibility of eastern cervid populations to chronic wasting disease. The Wildlife Society Annual Meeting, Albuquerque, NM.	September 2017	Genetic variation within the prion gene of many cervids has been linked to reductions in perceived susceptibility to chronic wasting disease (CWD). This may affect the long-term sustainability of cervid populations considering they influence future demography, population genetics, and disease susceptibility.
Midway, S.R., B. Peoples, J.T. DeWeber, and T. Wagner. Native congener richness, not abiotic factors, predicts cyprinid introductions. ANNUAL MEETING 146th AFS Annual Meeting in Kansas City, Missouri, August 21-25, 2016.	August 2016	This work is a regional analysis of factors regulating cyprinid distribution.
Midway, S. M., Wagner, T. and Tracy, B. 2014. Conserving data-poor stream species: A hierarchical approach. Southern Division of the American Fisheries Society Spring Meeting, January 22-26.	January 2014	We used a hierarchical Bayesian multispecies model to develop occupancy probabilities for 126 stream fish. The partial pooling property of the model made it possible to develop occurrence predictions for data-poor species, many of which need information for conservation efforts.
Midway, S. M., S. Wayne, G. Hogue, Wagner, T. and Tracy, B. 2014. Evaluating changes in stream fish species richness over a 50-year time period within a landscape context. Southern Division of the American Fisheries Society Spring Meeting, January 22-26.	January 2014	Worldwide, streams and rivers are facing a suite of pressures that change water quality and degrade physical habitat, both of which can lead to changes in the composition and richness of fish populations. These potential changes are of particular importance in the southeast USA, home to one of the richest stream fish assemblages in North America. Using data from 83 sites sampled in the 1960's and the previous 20 years, we used hierarchical Bayesian models to evaluate relationships between speci
Megan K. Schall, Vicki S. Blazer, Heather L. Walsh, Geoffrey Smith, Robert Lorantas, Timothy Wertz, and Tyler Wagner. 2018. Investigating occurrence of disease characteristics and trends in smallmouth bass abundance in rivers within the Chesapeake Bay Watershed. Chesapeake Research & Modeling Symposium, June 12 - 14, Annapolis, MD.	June 2018	We examine trends in occurrence of disease in smallmouth bass populations that have declined in abundance over the past several years.
McLaughlin, P., R. Alexander, J. Blomquist, O. Devereux, G. Noe, K. Smalling, and T. Wagner. 2022. Power analysis for detecting the effects of BMPs on nutrient flux reductions in the Chesapeake Bay Watershed. USGS Chesapeake Bay Workshop. June 27-30^th. National Conservation Training Center.	June 2022	We provide an analytical approach to quantifying the ability to detect nutrient reductions due to BMP implementation in the Chesapeake Bay Watershed.
McLaughlin, P., K.P. Krause, K.O. Maloney, T. Woods, and T. Wagner, T. 2023. Evaluating the effectiveness of joint species distribution modeling for fish communities in the Chesapeake Bay Watershed, USA. Northeaster Division and Southern New England Chapter Joint Meeting. American Fisheries Society.	January 2023	We evaluate the efficacy of joint species distribution models for modeling stream fishes in the Chesapeake Bay Watershed.
McLaughlin, P., Alexander, R., Blomquist, J., Devereux, O., Noe, G., Smalling, K., and Wagner, T., 2022. Keystone Coldwater Conference & PA Chapter of the American Fisheries Society. February 25-26, 2022.	February 2022	This work evaluates the statistical power to detect temporal changes in river nutrient loads.
McGarvey, D. and R. Carline. 2002. Biological assessment of a riparian restoration project in central Pennsylvania using a multimetric index. Poster presented at the North American Benthological Society Annual meeting, Pittsburgh, Pennsylvania, May 28 - June 1, 2002.	May 2002
McDonald, A. and 13 coauthors. 2022. The lake is greener on the other side: A continental-scale study of the nonlinearities and heterogeneity in lake productivity response to climate change. American Geophysical Union Fall Meeting. Chicago, Il.	December 2022	We examine how climate affects lake productivity (estimates of lake chlorophyll a) for 25,000 lakes in the conterminous United States from 1985-2018.
McCullough, I.M., K.B.S. King, P.J. Hanly, and T.Wagner. 2021. Cool, calm, and connected: freshwater connectivity and protected areas in the conterminous US. ESA Annual Meeting, Long Beach, California.	August 2021	We describe structural connectivity of freshwater networks within the conterminous US, their sensitivity to potential disruptions, and the protection status of highly connected lakes within freshwater networks.
McClure, C., K. Smalling, V.Blazer, and T. Wagner. 2020. Maternal sourcing of contaminants from ovary to juvenile Smallmouth Bass in the Chesapeake Bay Watershed. Pennsylvania Chapter of the American Fisheries Society.	February 2020	This is one of the first studies to investigate the potential for maternal sourcing of contaminants to offspring in a socioeconomically important fish species.
McClure, C. K. Smalling, V. Blazer, and T. Wagner. 2019. The spatiotemporal dynamics of contaminants in streams of the Chesapeake Bay Watershed. Annual Meeting of the American Fisheries Society.	September 2019	We describe the spatiotemporal dynamics of emerging contaminants in surface waters of the Chesapeake Bay Watershed.
Mattice, J. A., M. R. Marshall, D. R. Diefenbach, D. W. Brauning. Abundance and detectability of grassland sparrows on reclaimed surface mines in western Pennsylvania. Wilson Ornithological Society Annual Meeting, 22 March 2003, Delaware, Ohio.	March 2003
Mattice, J. A., D. R. Diefenbach, and D. W. Brauning. Grassland songbird density and habitat area on reclaimed surface mines in western Pennsylvania. Annual Meeting of Pennsylvania Chapter of The Wildlife Society, 1-3 March 2002, Myerstown, PA.	March 2002
Mattice, J. A., D. R. Diefenbach, and D. W. Brauning. Grassland songbird density and habitat area on reclaimed surface mines in western Pennsylvania. 58th Annual Northeast Fish and Wildlife Conference, 21-24 April 2002, Portland, ME.	April 2002
Massie, D.L., Hansen, G., Li. Y., and T. Wagner. 2020. Do lake-specific characteristics mediate the temporal relationship between Walleye growth and warming water temperatures? Pennsylvania Chapter of the American Fisheries Society.	February 2020	We investigate temporal patterns in fish growth and whether lake characteristics mediate the effects of warming water temperatures on temperature-growth relationships.
Massie, D.L., G. Hansen, Y. Li. and T. Wagner. 2019. Do lake-specific characteristics mediate the temporal relationship between Walleye growth and warming water temperature? Annual Meeting of the American Fisheries Society.	September 2019	We examine temporal dynamics in walleye growth, it if is related to water temperature, and how lake characteristics may mediate the effect of temperature on growth.
Massie, D., G. Smith, T. Wagner. 2016. Comparing relative abundance and population characteristics of Flathead Catfish across a range of establishment levels at the Susquehanna River.Joint meeting between the West Virginia and Pennsylvania Chapters of the American Fisheries Society, California State University of Pennsylvania.	February 2017	We present the first accounts of flathead catfish abundance and growth in the Susquehanna River, PA.
Massie, D., G. Smith, T. Wagner. 2016. Comparing relative abundance and population characteristics of Flathead Catfish across a range of establishment levels at the Susquehanna River. Susquehanna River Symposium, Bucknell University.	November 2016	We present the first accounts of flathead catfish abundance and growth in the Susquehanna River, PA.
Marshall, M. R., D. R. Diefenbach, L. A. Wood, and R. J. Cooper. Breeding-site fidelity of a migratory songbird: implications for annual survival estimation. Annual Meeting of Pennsylvania Chapter of The Wildlife Society, 1-3 March 2002, Myerstown, PA.	March 2002
Marshall, M. R., D. R. Diefenbach, L. A. Wood, and R. J. Cooper. Breeding site-fidelity of a migratory songbird: implications for annual survival estimation. Third North American Ornithological Conference, 24-28 September 2002, New Orleans, Lousiana.	September 2002
Marshall, M. R., D. R. Diefenbach, L. A. Wood, and R. J. Cooper. Annual survival estimation confounded by incomplete breeding site fidelity: study designs that may help. Third North American Ornithological Conference, 24-28 September 2002, New Orleans, Louisiana.	September 2002
Manlove, K., G. Bastille-Rousseau, M. Craft, P. Cross, M. Diuk-Wasser, J. Hewitt, M. Van Acker, W.D. Walter, K. C. VercCauteren, M. Wilber, G. Wilson-Henjum, G. Wittemyer, and K.M. Pepin. 2023. A national-scale distributed surveillance design for SARS-CoV-2 in a potential wildlife reservoir host. Ecological Society of America Annual Meeting, 6-11 August 2023.	August 2023	Emergence of zoonotic diseases in new wildlife host species continues to occur globally and poses major health or conservation risks for the hosts involved. Here, we describe the design, operationalization, and preliminary findings from a novel distributed surveillance project of SARS-CoV-2 in deer supported through USDA-APHIS and the American Rescue Plan Act that aims to understand establishment and reservoir dynamics of SARS-CoV-2 in deer.
M. Bremigan, P. Soranno, M. Gonzalez, B. Bunnell, K. Arend, W. Renwick, R. Stein, and M. Vanni, K.S. Cheruvelil, K. Webster, C. Stow, and T. Wagner. Linking Foodweb and Landscape Models: Hydrogeomorphic Mediation of Land-use Effects on Reservoirs. Invited talk: 69th Midwest Fisheries and Wildlife Conference, Dec. 14-17, Columbus OH.	December 2008
Lutz, C. L., Diefenbach, D.R., Rosenberry, C. S., and Wallingford, B. D. Dispersal Patterns in Female White-tailed Deer. Pennsylvania Chapter of The Wildlife Society, State College, PA, 17 March 2012.	March 2012
Lutz, C. L., D. R. Diefenbach, C0 .S. Rosenberry, and B. D. Wallingford. Dispersal patterns in female white-tailed deer. The Wildlife Society 18th Annual Conference, 5-10 November 2011. Waikoloa, Hawaii.	November 2011
Luloff, A. E., J. C. Finley, R. Stedman, D. R. Diefenbach, H. C. Zinn, and G. J. San Julian. A multi-method framework in the design of human dimensions research. 11th International Symposium on Society and Resource Management, 16-19 June 2005, Ostersund, Sweden.	June 2005
Lue, C., J. Bartz, M. Hopkins, and W.D. Walter. 2023. SAGOTR, a strain and genetics online repository for chronic wasting disease. 4th International Chronic Wasting Disease Symposium, Denver, CO, 31 May-2 June, 2023.	May 2023	The ability to build our knowledge of chronic wasting disease regarding genetics, biochemistry, host ranges, and disease properties is contingent on available research materials.<b> </b>However, the knowledge about CWD strains is still fragmented, and one of the main obstacles is lack of a centralized collection of CWD-infected tissues so we established the Strain and Genetics Online Tissue Repository (SAGOTR) in attempts to overcome this obstacle.
Lue, C. and W.D. Walter. 2022. Strain types for chronic wasting disease and the need for a National Tissue Repository. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022	July 2022	Monitoring, characterizing, and tracking progression of CWD across the US has not been possible because identification of distinct strains of CWD has been lacking. Although understanding of the biology of prions has been well studied, prion researchers have been unable to study prion strains in multiple regions of the US because of the lack of availability and information available for samples positive for CWD.
Lue, C. and W.D. Walter. 2022. Strain types for chronic wasting disease and the need for a National Tissue Repository. 6- 10 November 2022, The Wildlife Society Annual Meeting, Spokane, WA.	November 2022	Monitoring, characterizing, and tracking progression of CWD across the US has not been possible because identification of distinct strains of CWD has been lacking. Although understanding of the biology of prions has been well studied, prion researchers have been unable to study prion strains in multiple regions of the US because of the lack of availability and information available for samples positive for CWD.
Lowles, M. A., D. R. Diefenbach, M. Casalena, D. Little, M. Niebauer, and L. Humberg. 2001. Reproduction and survival in a suppressed population of wild turkeys.	March 2001
Lottig, N.R., Tan, P-N, K.S. Cheruvelil, C.E. Scott, P.A. Soranno, C.A. Stow, S. Yuan, T. Wagner. 2014. TAXONOMY OF CHANGE: USING CLUSTER ANALYSIS TO IDENTIFY TEMPORAL- PATTERNS IN LIMNOLOGICAL DATA. Joint Aquatic Sciences Meeting, Portland, OR, USA	May 2014	Application of novel data mining methods to investigating temporal dynamics in lake water clarity across a large spatial extent.
Lottig, N.R., P-N. Tan, K.S. Cheruvelil, C.E. Scott, E.H. Stanley, P.A. Soranno, C.A. Stow, T. Wagner, S. Yuan. 2016. Long-term patterns and drivers of water quality at sub-continental spatial scales. Association for the Sciences of Limnology and Oceanography.	June 2016	This paper employs novel methods to examine long-term trends in lake water clarity.
Lottig, N., Wagner, T., Norton, E., Spence Cheruvelil, K., Stow, C.A., Downing, J.A., and Webster, K.E. 2012. Non-monotonic Trends in Citizen-based Regional Lake Water Clarity. North American Lake Management Society 32nd International Symposium, November 7 - 9, 2012 • Madison, Wisconsin.	November 2012
Lottig, N., Stanley, E., Hanson, P., and Wagner, T. 2012. Long-Term Changes in Lake Chemistry Related to Sulfate Deposition and Climate. North American Lake Management Society 32nd International Symposium, November 7 - 9, 2012 • Madison, Wisconsin.	November 2012
Lorantas, R.M., Wagner, T., Miko, D.A., Arnold, D.A., Detar, J., Kaufman, M.L., Kuhn, K., Lorson, R., and Wnuk, R.T. 2010. Evaluation of riverine smallmouth bass recruitment indices on Pennsylvania Rivers. Annual Meeting of the American Fisheries Society. September 12 – 16.	September 2010
Lorantas, R., T. Wagner, D. Arnold, J. Detar, M. Kaufmann, K. Kuhn, R. Lorson, R. Wnuk, and A. Woomer 2015. Characterizing survival of Smallmouth Bass from Age 0 to Age 1 in Pennsylvania river sections using electrofishing survey gear catch rate and regression residuals. The Annual Northeast Fish & Wildlife Conference.	April 2015	This study provides insight into survival of early life stages of Smallmouth Bass on Pennsylvania rivers, an ecologically and socioeconomically important species.
Long, E., D. Diefenbach, B. Wallingford, and C. Rosenberry. Effects of demographic manipulation on dispersal and breeding ecology of white-tailed deer in PA. PA Chapter of The Wildlife Society Annual Conference. April 2003, State College, Pennsylvania.	April 2003
Long, E. S., D. R. Diefenbach, C. S. Rosenberry, and B. D. Wallingfor. Landscape influences on dispersal of white-tailed deer: pathways, directionality, and barriers. Annual Conference of The Wildlife Society, Miami, Florida, 8-12 November 2008.	November 2008
Long, E. S., D. R. Diefenbach, C. S. Rosenberry, B. D. Wallingford, and D. R. Smith. Landscape and demographic effects on dispersal of juvenile male white-tailed deer. Annual Conference of The Wildlife Society, 25-29 September 2005, Madison, Wisconsin.	September 2005
Long, E. S., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. Survival and dispersal of male white-tailed deer in Pennsylvania. Annual Meeting of the Pennsylvania Chapter of The Wildlife Society, 17-18 March 2006, State College, Pennsylvania.	March 2006
Long, E. S., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. Population structure and landscape influences on dispersal of juvenile male white-tailed deer in Pennsylvania. Southeast Deer Study Group Meeting, 21-24 February 2005, Sheperdstown, West Virginia.	February 2005
Long, E. S., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. Landscape effects on dispersal of juvenile male white-tailed deer. 88th ESA Annual Meeting, 8 August 2003, Savannah, Georgia.	August 2003
Long, E. S., D. R. Diefenbach, B. D. Wallingford, C. S. Rosenberry, G. L. Alt, and M. D. Grund. Survival and dispersal of yearling male white-tailed deer in Pennsylvania under antler restriction regulations. 60th Annual Northeast Fish and Wildlife Conference, Ocean City, MD. April 25-28, 2004.	April 2004
Lieb, D. A., V. M. Mengel, and R. F. Carline. 2005. Conservation status and habitat associations of Valley Creek's crayfish fauna. Northeast Fish and Wildlife Conference, Virginia Beach, VA, April 19, 2005.	April 2005
Li, Y., T. Wagner, Y. Jiao, V. Blazer, D. Tillit, P. Phillips, and D. Kolpin. Risk assessment of endocrine disrupting compounds on fish and wildlife populations in Chesapeake Bay watershed: a simulation study with smallmouth bass. 2016 Chesapeake Bay Workshop, Aug 30-Sept 1.	August 2016	We present an integrated analysis that incorporated the Von Bertalanffy growth model, the Ricker spawner-recuritment model, and the fishing processes into the catch-at-length analysis framework to model smallmouth bass population dynamics in the context of EDC risk assessment.
Li, Y. and T. Wagner. 2019. Ecological risk assessment of environmental stress and bioactive chemicals to riverine fish populations: an individual-based model of smallmouth bass. American Geophysical Union Annual Conference.	December 2019	We developed an individual based model for evaluating ecological stressors, including exposure to chemical contaminants, on a socioeconomically important fish species.
Li, Y. and T. Wagner. 2016. Assessing the impacts of endocrine disrupting compounds on fish population dynamics: a case study of smallmouth bass in Pennsylvania, USA. National Conference on Ecosystem Restoration.	April 2016	This work links population-level outcomes to EDCs in an ecologically and economically important fish species.
Lapierre, J-F., S.M. Collins, D. Seekell, P.A. Soranno, K.S. Cheruvelil, P-N. Tan, C.E. Fergus, N. Skaff, T. Wagner, M.T. Bremigan. 2016. Aligning spatial scales improves understanding of biogeochemical relationships between climate, landscape, and limnological properties. Association for the Sciences of Limnology and Oceanography.	June 2016	We demonstrate how aligning spatial scales improves biochemical relationships between climate, land use, and limnological properties.
Lapierre, J-F., S.M. Collins, C. Scott, K.S. Cheruvelil, P-N. Tan, M.T. Bremigan, T. Wagner, and P.A. Soranno. The role of spatial structure in determining the strength of the relationships among climate, landscape and limnological properties. The 2015 Ecological Society of America Annual Meeting, August 9 – 15.	August 2015	This work investigates the role of spatial structure in determining the strength of the relationships among climate, landscape and limnological properties. It is one of the first to examine lakes over a large spatial extent.
Lapierre, J-F, T. Wagner, and 29 coauthors. 2022. Classification of US lakes as continuous mixtures of geographic archetypes. Joint Aquatic Sciences Meeting, Grand Rapids, MI.	May 2022	We describe an approach to classify US lakes as a continuous mixture of geographic archetypes.
Kundel, H., T. Wagner, and G.J.A. Hansen. 2022. Historical Data and Novel Invaders: Impacts of Zebra Mussels on Walleye Recruitment in MN Lakes. Joint Aquatic Sciences Meeting, Grand Rapids, MI.	May 2022	This study quantifies the impact of the invasive zebra mussel on walleye recruitment in Minnesota lakes.
Kristine, D., J. Detar, R. Lorantas, R. Lorson, T. Wagner, D. DeMario. 2012. Assessment of experimental panfish regulations on select Pennsylvania impoundments. American Fisheries Society Annual Meeting. Twin Cities, MN. 19 – 23 August.	August 2012
Krause, K.P., K.O. Maloney, and T. Wagner. 2021. Leveraging an inter-organizational dataset and joint species distribution modeling to understand inland fish communities within the Chesapeake Bay Watershed. (Virtual) presentation at the Association of Mid-Atlantic Aquatic Biologists Meeting, 31 March 2021.	March 2021	We presented information on utilizing joint species distribution models to understand drivers of inland fish communities within the Chesapeake Bay Watershed, USA.
Krause, K., K. Maloney, T. Wagner. 2020. Analyzing stream fish communities of the Chesapeake Bay watershed: A joint species distribution modeling approach. Annual Meeting of the American Fisheries Society.	September 2020	We discuss the use of joint species distribution models for modeling fish community distributions in the Chesapeake Bay Watershed, USA.
Kocovsky, P. M., R. F. Carline. 2005. Stream pH as an abiotic gradient affecting distributions of trout in Pennsylvania. Annual Meeting of the American Fisheries Society, September 11-15, 2005, Anchorage, AK.	September 2005
Knox, W. M., and D. R. Diefenbach. Rearranging the deck chairs on the Titanic. Midwest Deer and Wild Turkey Study Group and Southeast Cervid and Wild Turkey Working Groups, August 15-18, 2022, Junction City, KS	August 2022	Deer hunter demographics (<u>></u> 90% male, 97% white, 55% rural) have changed little over the past 30 years despite more people living in urban environments and an increasing non-white population. Deer hunter numbers continue to decline steadily across most states within the range of white-tailed deer in the United States. Recreational deer hunting will continue to have a role in deer management, but it may transition from the primary method to one of many alternatives.
Kline, B., S.L. White, N. Hitt, and T. Wagner. Resource use by brook trout (Salvelinus fontinalis) in a thermally complex environment. Annual Meeting of The American Fisheries Society, Atlantic City, New Jersey.	August 2018	We present work on thermal refuge use by brook trout.
Kline, B. S. White, N. Hitt, and T. Wagner. 2017. Personality predicts success at using thermal refugia in brook trout (Salvelinus fontinalis). Susquehanna River Symposium, Bucknell University.	November 2017	We discuss the influence of personality on finding and using thermal refugia in brook trout.
King, K., T. Wagner, M.T. Bremigan, D. Infante, and K. Cheruvelil. 2021. Crossing ecosystem boundaries to better understand macroscale fish diversity in lakes and streams. Society for Freshwater Scientists Annual Meeting.	May 2021	We examined 1) the relationship between connectivity and fish species diversity for lakes versus streams and 2) how these relationships change in response to regional anthropogenic drivers.
Kepler, M.V., Wagner, T., Irwin, B.J., Bence, J.R., Hayes, D.B., and Lester, N.P. 2010. Spatial and Temporal Variation in Great Lakes Percid Catch-Per-Effort Data. Annual Meeting of the American Fisheries Society. September 12 – 16.	September 2010
Kepler, M.V., V. Blazer, T. Wagner, H. Walsh, G. Smith. 2014. Evaluation of potential disease causing agents in young of the year smallmouth bass in the Chesapeake Bay Watershed. International Symposium on Aquatic Animal Health. Portland, OR. August 31 – 5 September.	September 2014	This work provides a regional evaluation of disease and contaminants in smallmouth bass helping to understand various risk factors associated with disease and mortality.
Kepler, M.V., T. Wagner, J. A. Sweka. 2013. Comparative bioenergetics modeling of two representative strains of lean and humper lake trout (Salvenlinus namaycush) morphotypes. 69th Annual Northeast Fish & Wildlife Conference, April 7-9, Saratoga Springs, New York.	April 2013	This research is the first to examine bioenergetics of multiple lake trout morphotypes in the Laurentian Great Lakes. In addition, we use Bayesian modeling to account for various sources of uncertainty during the modeling and prediction processes.
Kehler, T., J. Sweka, P. R. Farrell, and R. F. Carline. 2005. Year-class composition of juvenile Atlantic sturgeon in the lower Hudson River. Northeast Fish and Wildlife Conference, Virginia Beach, VA, April 19, 2005.	April 2005
Keenan, M. T., D. R. Diefenbach, C. S. Rosenberry, and B. D. Wallingford. Antlerless deer harvest rate and hunter distribution. Annual Conference of the Pennsylvania Chapter of The Wildlife Society, State College, Pennsylvania, 17 March 2007.	March 2007
Keenan, M. T., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. Antlerless deer harvest rate and hunter distribution. Annual Meeting of the Pennsylvania Chapter of The Wildlife Society, 17-18 March 2006, State College, Pennsylvania.	March 2006
Keating, M., S. Cunningham, D. Diefenbach, J. Frair, J. Jordan, R. Mateo, T. Rainwater, E. Saldo, G. Yarrow, and D. Jachowski. Anticoagulant Rodenticide Exposure in Wild Mammalian Carnivores – An Underappreciated Threatto Eastern Species. 6 November 2023, Annual Conference of The Wildlife Society, Louisville, KY, USA.	November 2023	Reports of carnivores being exposed to anticoagulantrodenticides (ARs) have increased globally since the mid-1990s, with some evidence of ARs having individual and population-level effects. Of the 11 AR compounds reported in these studies, brodifacoumand bromadiolone, two highly potent compounds, were most frequently reported and weredocumented in over 66% of studies, in over 80% of study species, and in over 81% of studylocations.
Keagy, J. and T. Wagner. 2023. A Landscape Transcriptomics Approach to Evaluating Thermal Stress in Wild Brook Trout Populations. Northeast Association of Fish & Wildlife Agencies, Hershey, PA.	May 2023	We utilized a whole-genome approach called landscape transcriptomics to identify genes whose expression are related to current and/or past habitat conditions in of wild brook trout populations.
Keagy, J. J. Waraniak, and T. Wagner. A Landscape Transcriptomics Approach to Evaluating and Predicting Organismal Response to Extreme Heat Events. Evolution.	July 2024	Predicting organismal response to heat waves, understanding the mechanistic basis for this response, and identifying which populations and species are under threat represent key challenges in organismal biology and conservation ecology. In wild trout, we identified candidate genes known to be associated with heat stress, but also suggested several molecular pathways that have not been studied previously with respect to thermal stress response.
Kanapaux, W., G. Kiker, M. McDill, and D. R. Diefenbach. The use of agent-based simulation models for decision support in adaptive resource management: two contrasting examples. Annual meeting of the Resource Modeling Assocation, 18-21 June 2013, Cornell University, Ithaca, New York, USA	June 2013	Agent-based simulation models can provide useful decision support for adaptively managing ecological systems that have a high level of uncertainty. This presentation discusses two simulation models, one in its second generation of development and the other in its initial stages, that are designed to provide decision support for situations at opposite ends of the resource management spectrum in terms of available data and spatial and temporal scales.
Kaeser, A. J., W. E. Sharpe, and R. F. Carline. 2004. Linking Tubifex tubifex ecology and whirling disease in Pennsylvania: an explanation for regional differences in epidemiology. Northeast Fish and Wildlife Conference, April 25-28, 2004, Ocean City, Maryland.	April 2004
K.S. Cheruvelil, P.A. Soranno, K.E. Webster, M.T. Bremigan, T.Wagner, C.A. Stow. 2010. Landscape limnology: Integrating freshwater, terrestrial, and human landscapes for ecological understanding, natural resource management and conservation. ASLO/NABS Summer Meeting, June 6 – 11, Santa Fe, New Mexico.	June 2010
Just, E. M., D. R. Diefenbach, T. Crandall, S. Lehman, C. Nicholas, and J. Brodnicki. A Decision Model for Managing White-Tailed Deer on Pennsylvania State Forests. Annual Conference of The Wildlife Society, 23 October 2014, Pittsburgh, Pennsylvania.	October 2014	The Pennsylvania Department of Conservation and Natural Resources has enrolled portions of state forest lands in DMAP where deer browsing was believed to be adversely affecting forest vegetation. However, no monitoring program was linked to specific objectives for making decisions and monitoring and decision-making was not consistent among state forests. We used Structured Decision Making (SDM) to identify management objectives and develop a decision model and vegetation monitoring program to a
Just, E. H., D. R. Diefenbach, P. A. Roth, T. Crandall, and S. Lehman. A decision model for managing white-tailed deer on Pennsylvania state forests. Annual conference of the Northeast Association of Fish and Wildlife Agencies, 7 April 2013, Saratoga Springs, New York, USA.	April 2013	We have developed a decision model for making deer management decisions by linking forest vegetation conditions with deer management considerations.
Irwin, B.J., Wagner, T., Liu, W., Bence, J.R., and Hayes. D.B. 2011. Developing Negative Binomial Mixed Models to Partition Variance in Fishery-Independent Survey Data. American Fisheries Society 141st Annual Meeting. Seattle, WA, September 4 – 8.	September 2011
Irwin, B. J., and T. Wagner. 2013. Using mixed models to quantify variability in fish populations. GA Chapter of the American Fisheries Society, Jekyll Island, GA	January 2013	Mixed models can provide useful information about the spatio-temporal-dynamics of wild populations.
Irwin, B. J., and T. Wagner. 2013. Shifting variance structure as a potential indicator of fish-population responses to large-scale perturbation. Southern Division of the American Fisheries Society Annual Meeting.	February 2013	We expect that the structure of variation (i.e., variance components themselves), not just the total variance, will be responsive to severe large-scale perturbation, and that this change in variance structure will have implications for how we conduct population monitoring.
Irwin, B. J., T. Vidal, T. Wagner, J. R. Bence, J. R. Jackson, L. G. Rudstam, and W. W. Fetzer. 2014. Shifting variance structure as an indicator of large-scale ecological change. Annual meeting of the Ecological Society of America, Sacramento, CA.	August 2014	The variance structure of monitored indicators, which has traditional been viewed as "noise", may serve as a signal.
Ikis, D., E. Post, and T. Wagner. 2015. Bird Occupancy Dynamics in Alaskan Wetlands: Why different size ponds matter? Ecological Society of America Annual Meeting.	August 2015	This work is some of the first to examine bird occupancy dynamics in small arctic ponds.
Hill, J.M., and D.R. Diefenbach. Does woody vegetation removal positively influence grassland sparrow abundance and fitness? Wildlife Society Annual Conference, Waikoloa, Hawaii 5-10 November 2011.	November 2011
Hill, J. M., and D. R. Diefenbach. Does woody vegetation removal positively influence grassland bird abundance and fitness? Northeast Association of Fish and Wildlife Agencies Annual Conference, Manchester, NH, 17-19 April 2011.	April 2011
Hill, J. M., and D. R. Diefenbach. 2014. Occupancy Patterns of Regionally Declining Grassland Sparrow Populations in a Forested Pennsylvania Landscape. Northeast Association of Fish and Wildlife Agencies Annual Conference	April 2014	Much of our knowledge regarding patterns of occupancy and density stem from prairie systems, while relatively little is known regarding how occurrence and abundance of grassland birds vary in reclaimed surface mine grasslands.Our results suggest that reclaimed surface mine grasslands, without management intervention, are ephemeral habitats for Grasshopper and Henslow's Sparrows. Given the forecasted decline in surface coal production for Pennsylvania, it is likely that both species will continu
Hill, J. M., and D. R. Diefenbach. 2012. Enhancing grassland sparrow populations on reclaimed mine grasslands: A large-scale experiment of woody vegetation removal. The Wildlife Society Annual Conference, 15 October 2012, Portland, Oregon, USA.	October 2012	Grassland bird species are declining and reclaimed surface mines are thought to be critical habitat. We investigated the effect of removing woody vegetation from reclaimed surface mine grasslands and found minimal population response by these species.
Hill, J. M., J. F. Egan, G. E. Stauffer, and D. R. Diefenbach. Habitat availability is a more plausible explanation than insecticide acute toxicity for U.S. grassland bird species declines. Annual Conference of The Wildlife Society, 23 October 2014, Pittsburgh, Pennsylvania.	October 2014	A recent analysis of North American Breeding Bird Survey (BBS) "grassland breeding" bird trends reported the surprising conclusion that insecticide acute toxicity was a better correlate of grassland bird declines in North America from 1980 – 2003 (the insecticide-acute-toxicity hypothesis) than was habitat loss through agricultural intensification. In this paper we reached the opposite conclusion by using an alternative statistical approach with additional habitat covariates to analyze the same
Hansen, JAG, C. Custer, H. Kundel, JKR Nelson, J. North, L. Platt, JS Read, E. Schliep, M. Verhoven, and T. Wagner. 2023. NOBODY SAID IT WAS EASY, NO ONE EVER SAID IT WOULD BE THIS HARD: QUANTIFYING FISH RESPONSES TO CLIMATE CHANGE IN LAKES OF THE MIDWESTERN UNITED STATES. ASLO Aquatic Sciences Meeting.	June 2023	We discuss novel approaches to predicting the effects of climate change on lake fish abundance.
Hansen, JA., Custer, C., Kundel, H., North, J., Read, J.S., Schliep, E., and T. Wagner. 2022. The importance of water temperature in governing lake fish abundance across a landscape of diverse lakes. Midwest Fish and Wildlife Conference.	February 2022	We assess the importance of lake water temperature in driving fish communities, within the context of climate change.
Hansen, G.J.A., E.M. Schliep, J. North, C. Custer, J. Nelson, H. Kundel, and T. Wagner. 2023. Predicting climate change impacts on poikilotherms using physiologically guided species abundance models. Species on the Move Conference.	May 2023	We present a novel model for predicting the effects of climate change on poikilothermic animals.
Hansen, G., B. Bethke, J. Dumke, J. Hirsch, K. Kovalenko, J. leDuc, R. Maki, H. Rantala, and T. Wagner. 2021. Impacts of invasive spiny water fleas and zebra mussels on first-year growth of walleye and yellow perch in Minnesota’s large lakes. Rainy-Lake of the Woods Watershed 2021 Forum. March 10-11, 2021.	March 2021	We document the effects of invasive invertebrates on the growth of walleye and yellow perch in Minnesota lakes.
Gunderman, K. P., D. R. Diefenbach, W. D. Walter, and F. E. Buderman. 2021. Efficacy of positional and behavioral change-point models to determine ungulate parturition events. 31 May - 11 June 2021, EURING Technical Meeting, Quebec City, Quebec, Canada.	June 2021	There is a rapidly expanding volume of innovative modelling methods that allow researchers to make inference about unobserved animal behaviors from movement data. In the movement literature, hidden Markov models fit to step-lengths and turning angles have become one of the primary ways that researchers identify behavioral states from movement data. However, we can frame behavioral state identification in a number of ways, and the optimal framework will depend on the ecology of the species in qu
Gunderman, K. P., D. R. Diefenbach, W. D. Walter, A.M. Corondi, J. Banfield, C. Rosenberry, and F. E. Buderman. 2021. Efficacy of positional and behavioral change-point models to determine ungulate parturition events. 1 - 5 November 2021, The Wildlife Society Annual Meeting, Baltimore, MD.	October 2021	There is a rapidly expanding volume of innovative modelling methods that allow researchers to make inference about unobserved animal behaviors from movement data. In the movement literature, hidden Markov models fit to step-lengths and turning angles have become one of the primary ways that researchers identify behavioral states from movement data. However, we can frame behavioral state identification in a number of ways, and the optimal framework will depend on the ecology of the species in qu
Gingery, T.M., and Diefenbach, D.R. 2022. Fawn Survival Patterns: looking beyond predators.7-11 November 2022, The Wildlife Society Annual Meeting, Spokane, WA.	November 2022	We present a commentary on the state of white-tailed deer fawn research. We suggest additional research focusing solely on predation will lead to limited novel insights.
Gingery, T. M., D. R. Diefenbach, C. S. Rosenberry, B. D. Wallingford. Landscape-level Patterns in White-tailed deer Fawn Survival in North America. Southeast Deer Study Group Meeting, 21 February 2018, Nashville, TN.	February 2018	We conducted a meta-analysis of white-tailed deer (Odocoileus virginianus) fawn survival and cause-specific mortality across North America to identify large-scale patterns in these population parameters. Given that neonate survival is the most variable demographic parameter for white-tailed deer, harvest management decisions may need to consider that fawn survival rates likely will be lower in forested landscapes.
Gingery, T. M., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. Space Use of White-tailed Deer Neonates Using Micro-GPS Units. The Wildlife Society Annual Conference, 7-11 October 2018, Cleveland, OH, USA.	October 2018	Despite its importance for informing a range of topics including predator-prey interactions and susceptibility to mortality, movements of large herbivore neonates are poorly understood. Fawn home range size increased with age where 1-week home ranges averaged 4.86 ha and 4-week home range size averaged 18.98 ha. Current models that use a single home range size regardless of neonate age may inaccurately portray how habitat features influence survival of large herbivore neonates.
Gingery, T. M., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. Landscape-level patterns in white-tailed deer fawn survival in North America. Annual meeting of The Wildlife Society, 27 September 2017, Albuquerque, NM.	September 2017	We conducted a meta-analysis of white-tailed deer (Odocoileus virginianus) fawn survival and cause-specific mortality across North America to identify broad-scale biotic factors related to this population parameter. Survival to 3–6 months of age was 42.3% in contiguous forest landscapes (no agriculture) and for every 10% increase in agricultural land area fawn survival increased 4.8% (n = 12, SE = 0.12).
Gingery, T. M., D. R. Diefenbach, B. D. Wallingford, and C. S. Rosenberry. 2016. White-tailed deer fawn behavior and survival in Pennsylvania. Annual Meeting of the Pennsylvania Chapter of The Wildlife Society, 16 April 2016, State College, PA.	April 2016	Maternal behaviors can influence fawn survival via predator avoidance, habitat selection, and aggressive defense. We present preliminary results from the first year of a 3-year study of white-tailed deer fawn survival.
Gingery, T. M., D. R. Diefenbach, B. D. Wallingford, C. S. Rosenberry. White-tailed deer fawn survival in North America. Pennsylvania Chapter of The Wildlife Society annual meeting, 1 April 2017, Raystown Lake, PA.	April 2017	We present a meta-analysis of fawn survival from 9 populations in 8 states across North America. Survival from 3-6 months was 51.3% in contiguous forest landscapes (no agriculture), and for every 10% increase in agricultural land area fawn survival increased 3.4% (SE = 0.07). We detected no relationship between fawn survival and deer density.
Gingery, T. M. and D. R. Diefenbach. 2021. Fawn survival patterns: looking beyond predators. Southeast Deer Study Group Meeting, 23 February 2021.	February 2021	White-tailed deer fawn mortality causes, and their frequency, are often used to identify limiting factors to recruitment. Although predation may simply mask ultimate causes of mortality, concerns regarding predation dominate neonate survival literature because it is the primary source of mortality. We suggest that a new paradigm is needed to explain patterns in fawn mortality, and that factors that influence physiological condition of fawns may better explain why fawns exposed to no predators e
Gigliotti, L.C., E. Boyd, and D.R. Diefenbach. 2023. Delayed positive responses of snowshoe hares to prescribed burning in a fire-adapted ecosystem. The Wildlife Society's 30th Annual Conference, Louisville, KY.	November 2023	Prescribed burning can be beneficial to snowshoe hares, but more information is needed of the amount of time it takes for hares to begin using burned areas, and the effects of prescribed burning on snowshoe hare survival.
Gigliotti, L.C., E. Boyd, and D.R. Diefenbach. 2023. Delayed positive responses of snowshoe hares to prescribed burning in a fire-adapted ecosystem. The 78th Annual Northeast Fish & Wildlife Conference, Hershey, PA.	May 2023	Habitat management such as prescribed burning can be beneficial for southern populations of snowshoe hares, but more information is needed on the time scale that hares respond to burning. We found that it takes at least 7 years for hares to begin using burned areas, which can help managers plan prescribed burns.
Ganoe,L.S. and W.D. 2018. Walter.Muskrat (Ondatra zibethicus) movements, survival and disease. The Wildlife Society Annual Meeting, Cleveland, OH.	October 2018	Declines in muskrat (Ondatra zibethicus) harvest has been observed across the United States and in several Canadian provinces, with many states recording larger than 50% decline in muskrat harvest within the past few decades. . Expanding the knowledge of muskrat movements, creating baseline population estimates and survival rates, and understanding the exposure of muskrats to different diseases will increase the knowledge of the muskrat and the potential reasons for their population decline.
Ganoe, L.K., C. Bocetti, J. Larkin, W.D. Walter. 2017. Feasibility of remote mark-recapture methods on fisher (Pekania pennanti) in Clarion County. The Wildlife Society Annual Meeting, Albuquerque, NM.	September 2017	Since reintroduction into Pennsylvania in the 1980s, fisher population has taken hold and is growing significantly. Original population estimates have not been formally investigated so this study was designed to test the feasibility of using remote mark-recapture methods of genetics in hair samples collected on fishers to estimate population size.
Ganoe, L, M. Lovallo, J. Brown, and W.D. Walter. 2019. Muskrat (Ondatra zibethicus) ecology and health. The Pennsylvania Chapter of the Wildlife Society, State College, PA.	February 2019	Declines in muskrat (Ondatra zibethicus) harvest has been observed across the United States and in several Canadian provinces. Harvest rates are historically used as indicators of population status, thus declines in muskrat harvest indicate a decline in the muskrat population.
Ganoe, L, J. Brown, M. Lovallo, Michael Yabsley, Mark Ruder, and W.D. Walter. 2019. Defining Pathogens and Disease of Muskrats (Ondatra zibethicus) in Pennsylvania. 68th Annual International Conference of the Wildlife Disease Association, Tahoe City, CA.	August 2019	Declines in muskrat (Ondatra zibethicus) harvest have been observed throughout their North American range. The exact cause of the declines is unknown, but potential theories include habitat loss or degradation, predation, and disease. Minimal recent data exists on muskrat diseases.
Gagne, R.B., G. Bastille-Rousseau, M. Craft, P. Cross, M. Diuk-Wasser, J. Heale, J. Hewitt, M. Van Acker, K. C. VercCauteren, W.D. Walter, M. Wilber, G. Wilson-Henjum, G. Wittemyer, and K.M. Pepin. 2023. A national-scale distributed surveillance design for SARS-CoV-2 in a potential wildlife reservoir host. The 30th Annual Conference of the Wildlife Society, Louisville, KY, 5-9 November 2023.	November 2023	Emergence of zoonotic diseases in new wildlife host species continues to occur globally and poses major health or conservation risks for the hosts involved. Here, we describe the design, operationalization, and preliminary findings from a novel distributed surveillance project of SARS-CoV-2 in deer supported through USDA-APHIS and the American Rescue Plan Act that aims to understand establishment and reservoir dynamics of SARS-CoV-2 in deer.
Fritsky, R. S., D. R. Diefenbach, R. C. Boyd, and S. R. Klinger. Habitat use, Density, and Survival of Eastern Cottontails on Six CREP Sites in Pennsylvania. Annual Meeting of the Pennsylvania Chapter of The Wildlife Society, 17-18 March 2006, State College, Pennsylvania.	March 2006
Fritsky, R. S., D. R. Diefenbach, R. C. Boyd, and S. R. Klinger. Effects of the Conservation Reserve Enhancement Program on Eastern Cottontail Populations in Pennsylvania. Poster presented at The Wildlife Society 12th Annual Conference, 25-29 September 2005, Madison, Wisconsin.	September 2005
Forman, N.S., T. Hardisky, M. Lovallo, W.D. Walter. 2014. Monitoring river otter populations in northeastern Pennsylvania using non-invasive genetic sampling and spatial capture-recapture models. The 21st Annual Wildlife Society Conference, Pittsburgh, PA.	October 2014	River otter populations in Pennsylvania were nearly extirpated by the 20th century, with a remnant population limited to the the northeastern part of the state. We will use our population estimates from the region to provide the state agency with the first population estimate of river otters since reintroductions were initiated.
Forman, N.F., and W.D. Walter. 2013. Population estimates of river otters in northeastern Pennsylvania using non-invasive genetic sampling. The Wildlife Society Annual Conference, Milwaukee, WI	October 2013	River otter populations in Pennsylvania were nearly extirpated by the 20th century, with a remnant population limited to the the northeastern part of the state. We will use our population estimates from the region to provide the state agency with the first population estimate of river otters since reintroductions were initiated.
Forcey, G., D. W. Brauning, and D. R. Diefenbach. 2000. Grassland bird surveys on reclaimed surface mines of western Pennsylvania. Pennsylvania Chapter of The Wildlife Society Annual Meeting, Titusville, Pennsylvania, April 8-9, 2000,	April 2000
Fischer, J.W., W. D. Walter, and K. C.VerCauteren. What to do when security protocols deny your ability to use online storage infrastructures. The 20th Annual Conference of the Wildlife Society, Milwaukee, WI, 7 October 2013.	October 2013	Wildlife tracking technology is constantly improving, resulting in large amounts of biotelemetry data for numerous species and study designs. Our methods and solutions should be helpful to public and private data providers whom want to publish and share wildlife tracking data.
Finley, J. C., D. R. Diefenbach, A. E. Luloff, R. Stedman, G. J. San Julian, and H. C. Zinn. Monitoring hunter habitat use and movement patterns. 11th International Symposium on Society and Resource Management, 16-19 June 2005, Ostersund, Sweden.	June 2005
Filstrup, C.T., T. Wagner, C.A. Stow, S.K. Oliver, E.H. Stanley, K.E. Webster, J.A. Downing. 2016. Nitrogen stress effects on lake phytoplankton vary by region based on land use. Association for the Sciences of Limnology and Oceanography.	June 2016	This is the first work to quantify and model phytoplankto stress responses to N-enrichment at macroscales.
Filstrup, C.T., Soranno, P.A., Stanley, E.H., Stow, C.A., Wagner, T., Webster, K.E., and Downing, J.A. 2012. Chlorophyll a response to total phosphorus enrichment in lakes differs by spatial scales and among regions: implications for developing water quality criteria at the state level. North American Lake Management Society 32nd International Symposium, November 7 - 9, 2012 • Madison, Wisconsin.	November 2012
Filstrup, C.T., S.K. Oliver, E.H. Stanley, C.A. Stow, T. Wagner, K.E. Webster, and J.A. Downing. 2015. Regional land use influences nitrogen subsidy-stress effects on lake phytoplankton. Association for the Sciences of Limnology and Oceanography 2015 Aquatic Sciences Meeting, February 2015, Granada, Spain.	February 2015	We examine potential subsidy-stress responses of phytoplankton to nitrogen enrichment in lakes across the midwest and northeastern United States.
Filstrup, C.T., S. Oliver, E.H. Stanley, C.A. Stow, T. Wagner, K.E. Webster, J.A. Downing. Subsidy-stress effects of nitrogen on phytoplankton biomass. Joint Aquatic Sciences Meeting, Portland, OR, 2014.	May 2014	One of the first studies to examine the potential for inhibitory effects of nitrogen on phytoplankton in lakes across a large spatial extent.
Filstrup, C.T., J-F. Lapierre, S.K. Oliver, P.A. Soranno, T. Wagner, and J.A. Downing. 2018. Spatiotemporal patterns in extreme lake chlorophyll concentrations at the sub-continental scale. Association for the Sciences of Limnology and Oceanography, Summer Meeting, Victoria, BC, Canada.	June 2018	We look at spatiotemporal patterns in extreme lake chlorophyll concentrations at the sub-continental scale.
Filstrup, C. T., T. Wagner, P.A. Soranno, E.H. Hill, C.A. Stow. 2013. Regional variability in non-linear chlorophyll response to total phosphorus enrichment in lakes. ASLO 2013 Aquatic Sciences Meeting, 17-22 February, New Orleans, LA.	February 2013	This study is the first to explicitly model variation in non-linear model parameters that describe how lake algae response to phosphorus enrichment across large spatial scales.
Fergus, C.E., A.O. Finley, P.A. Soranno, T. Wagner. Examining the nutrient-color paradigm across macroscales: Multivariate spatial relationships among lake phosphorus, water color, and chlorophyll. The 2015 Ecological Society of America Annual Meeting, August 9 – 15.	August 2015	This study is the first spatially explicit and multivariate modeling to examine the nutrient-color paradigm in inland lakes.
Faulk, E. and T. Wagner. 2014. Stream Fish Communities in the Delaware Water Gap National Recreation Area: A Multi-Species Occupancy Approach. American Fisheries Society, 144th Annual Meeting, August 17-12.	August 2014	This work develops an occupancy-based fish sampling program for National Parks in the eastern United States.
Farnsworth, G. L., and D. R. Diefenbach. A new point count bird survey method: Incorporating time to detection and distance from observer to estimate detection probability and density. EURING 2007, Dunedin, New Zealand, 14-20 January 2007.	January 2007
Farnsworth, G. L., D. R. Diefenbach , R. S. Mulvihill, M. J. Lanzone, and D. W. Brauning. Estimating breeding bird abundances with point counts from the 2nd Pennsylvania Breeding Bird Atlas. 4th North American Ornithological Conference, 3-7 October 2006, Veracruz, Mexico.	October 2006
Fameli, A., K. Russo-Petrick, C.S. Rosenberry, K.L. Schuler, M.J. Tonkovich, J.E. Edson, and W.D. Walter. 2023. Large-scale assessment of genetic structure of white-tailed deer: applications to genetic assignment tests. The 30th Annual Conference of the Wildlife Society, Louisville, KY, 5-9 November 2023.	November 2023	Chronic wasting disease can be spread by direct and indirect transmission, but identifying subpopulations of deer across regions allows delineation of focal areas to target for effective intervention. Genetic assignment tests provided further understanding of subpopulation structuring depending on the analysis used and whether location-specific details were included for each genetic sample.
Fameli, A., J. Edson, C. Jennelle, and W.D. Walter. 2022. Relatedness of white-tailed deer from culling efforts within a disease management zone in Minnesota. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022.	July 2022	Direct contact between individuals is likely the main process driving chronic wasting disease (CWD) transmission in recently infected areas. Given that multiple social groups can overlap spatially, white-tailed deer (<i>Odocoileus virginianus</i>) culled in a site over weeks/months may represent a collection of unrelated deer from different social groups, however, this assertion has not been evaluated.
Fameli, A., J. Edson, C. Jennelle, and W.D. Walter. 2022. Relatedness of white-tailed deer from culling efforts within a disease management zone in Minnesota. 6- 10 November 2022, The Wildlife Society Annual Meeting, Spokane, WA.	November 2022	Direct contact between individuals is likely the main process driving chronic wasting disease (CWD) transmission in recently infected areas. Given that multiple social groups can overlap spatially, white-tailed deer (<i>Odocoileus virginianus</i>) culled in a site over weeks/months may represent a collection of unrelated deer from different social groups, however, this assertion has not been evaluated.
Fameli, A., C.S. Rosenberry, K.L. Schuler, M.J. Tonkovich, J.E. Edson, and W.D. Walter. 2024. Large-scale assessment of genetic structure of white-tailed deer: applications to genetic assignment tests. Joint Meeting of The Pennsylvania Chapter of Wildlife Society and the Pennsylvania Biological Survey, State College, PA, 22-23 March 2024.	March 2024	Chronic wasting disease can be spread by direct and indirect transmission, but identifying subpopulations of deer across regions allows delineation of focal areas to target for effective intervention. Genetic assignment tests provided further understanding of subpopulation structuring depending on the analysis used and whether location-specific details were included for each genetic sample.
Evans, T.S., M. Kirchgessner, B. Eyler, C. Ryan, and W.D. Walter. 2014. Bayesian hierarchical modeling of chronic wasting disease in the central Appalachian region. The 21st Annual Wildlife Society Conference, Pittsburgh, PA.	October 2014	Chronic wasting disease is a a transmissible spongiform encephalopathy that affects captive and free-ranging cervids and little is known of its distribution in the Northeast. Efficiency of disease surveillance and containment efforts can be improved by allocating resources used for surveillance into areas that are at a greater risk for infection.
Evans, T.S. and W.D. Walter. Development of a chronic wasting disease surveillance plan and modeling of the potential spread in Pennsylvania. Pennsylvania Chapter of the Wildlife Society, State College, PA, 22-23 March 2013.	March 2013	To develop a CWD surveillance plan for the state of Pennsylvania given surveillance data of free-ranging deer in adjacent states. Also, to model the potential spread of CWD given multiple demographic and environmental covariate factors in Pennsylvania.
Evans, T.S. and W.D. Walter. 2014. Bayesian hierarchical modeling of chronic wasting disease in free-ranging white-tailed deer in the eastern U.S. Prion Conference, Trieste, Italy.	May 2014	Landscape level modeling of chronic wasting disease in white-tailed deer has not been investigated in the northeast regions since its initial discovery in 2005. Our results indicated that the odds of infection for CWD is likely controlled by areas that congregate deer in the region and these areas differ from areas found in the Midwestern U.S. and endemic area in Colorado.
Evans, T.S. and W.D. Walter. 2013. Development of a chronic wasting disease surveillance plan and modeling of the potential spread in Pennsylvania. The Wildlife Society Annual Conference, Milwaukee, WI.	October 2013	To develop a CWD surveillance plan for the state of Pennsylvania given surveillance data of free-ranging deer in adjacent states. Also, to model the potential spread of CWD given multiple demographic and environmental covariate factors in Pennsylvania.
Drohan, P., S. Bayuzick, D. Guarin, R. Raab, A. Bonhage, D. Diefenbach, and M. McDill. USA Appalachian relict charcoal hearths have complex landscapeand pedologic patterns that are unique from surrounding forest ecosystems.	May 2022	Across the United Kingdom,Europe, and recently the northeastern United States, the examination of historic forest changedue to charcoal manufacturing for the firing of iron or lime furnaces is yielding new insightsrelative to landscape stability, anthropogenic vs natural soil genesis, and forest evolution. Results indicated that RCHs arepotentially a unique location of refugia for forest flora and perhaps fauna due to the uniquegeochemistry with higher bases and C and some concentrated metals a
Drohan, P., S. Bayuzal, D. Diefenbach, M. McDill, T. Raab, F. Hirsch, and A. Bonhage. Northern Appalachian, USA relic charcoal hearths and their unique Ecological Fingerprint. Virtual EGU General Assembly 2021, 19-30 April 2021.	April 2021	<sup>Across the United Kingdom, Europe, and recently the northeastern United States, the examination of historic forest change due to charcoal manufacturing for the firing of iron or lime furnaces is yielding new insights relative to landscape stability, anthropogenic vs natural soil genesis, and forest evolution. We present results of a study that strives to evaluate how historic land clearing for the charcoal industry (supporting iron furnaces) affected local soils and may drive surrounding p
Diefenbach, D., Tess Gingery 2021. Glucocorticoid hormones associated with reduced White-tailed deer fawn survival. Friday Findings, USGS Ecosystems Mission Area. Virtual Webinar Series. 1 October, 2021. USGS Friday’s Findings Webinar Approval Form Friday's Findings is a public webinar series hosted by the USGS Ecosystems Mission Area. Our webinars are typically the first Friday of each month at 2 p.m. eastern time. These half hour webinars are meant to provide listeners an overview of the science topic and chance to ask questions. Title: Glucocorticoid hormones associated with reduced White-tailed deer fawn survival USGS Presenter(s): Tess Gingery, PA Cooperative Fish and Wildlife Research Unit, Pennsylvania State University; Duane R. Diefenbach, U.S. Geological Survey, , PA Cooperative Fish and Wildlife Research Unit, Pennsylvania State University	October 2020	Abstract: It is unknown how ungulate physiological responses to environmental perturbations influence overall population demographics. Moreover, neonatal physiological responses remain poorly studied despite the importance of neonatal survival to population growth. Glucocorticoid (GC) hormones potentially facilitate critical physiological and behavioral responses to environmental perturbations. However, elevated GC concentrations over time may compromise body condition and indirectly reduce sur
Diefenbach, D. R., and W. A. Link. Using integrated population models to monitor game species. International Statistical Ecology Conference. 1-4 July 2014, Montpellier, France.	July 2014	Traditional harvest-based estimators of abundance for game species, especially white-tailed deer, lack measures of precision and make strong assumptions about mortality processes or accounting of mortality. We developed an integrated population model in a Bayesian framework that provides measures of precision and incorporates multiple sources of data in a population dynamics model to make inferences about survival, harvest, and reproductive rates, abundance, and population trends.
Diefenbach, D. R., and M. A. Ternent. Monitoring activity patterns and timing of denning in black bears. Annual Conference of The Wildlife Society, 25-29 September 2005, Madison, Wisconsin.	September 2005
Diefenbach, D. R., T. Wagner, S. A. Christensen, A. S. Norton. Using Multilevel Models to Quantify Heterogeneity in Resource Selection. Presented at the Annual Conference of The Wildlife Society, Snowbird, Utah, 2 October 2010.	October 2010
Diefenbach, D. R., T. Wagner, R. D. Brubaker, E. H. Just. Managing white-tailed deer to restore and maintain plant species diversity. Presented at the Annual Conference of The Wildlife Society, 4 October 2010, Snowbird, Utah.	October 2010
Diefenbach, D. R., T. A. Marques, J. L. Laake, T. M. Gingery, A. Van Buskirk, C. S. Rosenberry, W. D. Walter, and K. Lamp. Accounting for animal density gradients in distance sampling surveys. The Wildlife Society Annual Conference, 6-10 November 2022, Spokane, WA	November 2022	Monitoring the abundance of large ungulates via distance sampling has often used roads as transects because these species avoid observers on foot and dense vegetation rules out aerial surveys. We modified the distance sampling estimator to address the problems outlined above by using auxiliary data to model the density gradient of objects as a function of distance from road and habitat type.
Diefenbach, D. R., N. C. Johnson, M. A. Ternent, and H. N. Weiss. Using Fourier and wavelet transforms to analyze activity patterns of female black bears. Northeast Association of Fish and Wildlife Agencies Annual Conference, Groton, Connecticut, 22-24 April 2007	April 2007
Diefenbach, D. R., M. R. Marshall, and G. E. Stauffer. Estimating abundance of songbirds using resightings of marked birds. Annual Meeting of the Pennsylvania Chapter of The Wildlife Society, 17-18 March 2006, State College, Pennsylvania.	March 2006
Diefenbach, D. R., M. R. Marshall, and G. E. Stauffer. Effect of bird singing behavior on time-of-detection methods to estimate abundance. EURING Technical Meeting, Pescara, Italy, September 19-23, 2009	September 2009
Diefenbach, D. R., M. R. Marshall, and G. E. Stauffer. Challenges with Using Mark-Recapture Methods to Estimate Songbird Abundance. Presented at International Statistical Ecology Conference, St. Andrews, Scotland, 8-11 July 2008.	July 2008
Diefenbach, D. R., M. R. Marshall, L. A. Wood, and R. J. Cooper. Breeding site-fidelity of a migratory songbird: Implications for annual survival estimation. The Wildlife Society's 9th Annual Conference, 24-28 September 2002, Bismarck, ND.	September 2002
Diefenbach, D. R., M. R. Marshall, L. A. Wood, and R. J. Cooper. Breeding site-fidelity and survival estimation of a migratory songbird: implications for conservation, life-history and study designs. EURING, 6-11 October 2003, Radolfzell, Germany.	October 2003
Diefenbach, D. R., M. R. Marshall, J. A. Mattice, and D. W. Brauning. Availability of singing male grassland sparrows for detection during abundance estimation. 122nd Meeting of the American Ornithologists' Union, 16-21 August 2004 Quebec City, Quebec, Canada.	August 2004
Diefenbach, D. R., M. J. Lovallo, L. A. Hansen, R. J. Warren, M. J. Conroy. 2000. Changes in spacing patterns with increasing population density of an insular reintroduced bobcat population. The Wildlife Society Annual Meeting, Nashville, Tennessee, September 11-15, 2000	September 2000
Diefenbach, D. R., M. J. Casalena, P. L. Fackler. A Decision Model for Setting Fall Harvest Regulations for Wild Turkey. Annual Conference of the Northeast Association of Fish and Wildlife Agencies. Virtual conference, 26-28 April 2021.	April 2021	Fall hunting of female wild turkeys (<i>Meleagris gallapavo</i>) can limit population growth if harvest rates are too high. The decision model we developed is transparent, scientifically defendable, and can help decision makers evaluate the effects of different fall season lengths on future wild turkey populations.
Diefenbach, D. R., L. M. Hansen, J. H. Bohling, C. Miller-Butterworth, and G. Veron. Impact of Genetic Drift on Island Populations of Mesocarnivores Established on Cumberland Island, Georgia. Annual Meeting of the American Society of Mammalogists, 4 June 2013, Philadelphia, Pennsylvania, USA.	June 2013	Processes such as genetic drift and founder effects are important processes that can govern the success of mammalian reintroduction programs. Understanding the process of drift following a reintroduction effort is important for gauging the population viability of a population. In this study, we examined 2 mesocarnivores on Cumberland Island, Georgia, to quantify the genetic impact of founder effects several decades after population establishment.
Diefenbach, D. R., L. A. Baker, R. J. Warren, M. J. Conroy, and M. G. Nelms. Restoration of bobcats to Cumberland Island, Georgia, USA: lessons learned and evidence for the role of bobcats as keystone predators. Iberian Lynx Ex-Situ Conservation Series, Donana, Spain, 17-18 November 2006.	November 2006
Diefenbach, D. R., J. C. Finley, A. E. Luloff, R. Stedman, C. Swope, H. Zinn, and G. J. San Julian. Using aerial surveys to map hunter distribution. 11th International Symposium on Society and Resource Management, 16-19 June 2005, Ostersund, Sweden.	June 2005
Diefenbach, D. R., J. C. Finley, A. E. Luloff, H. C. Zinn, G. J. San Julian, and C. B. Swope. Deer Hunter Distribution and Implications for Deer Harvest Management. Southeast Deer Study Group Meeting, 21-24 February 2005, Sheperdstown, West Virginia.	February 2005
Diefenbach, D. R., G. L. Alt, B. D. Wallingford, C. S. Rosenberry, and E. S. Long. Effect of male age structure on demography and breeding behavior in white-tailed deer. International Deer Biology Congress, 5-10 August 2018, Estes Park, CO, USA.	August 2018	In 2002, Pennsylvania implemented statewide harvest regulations that increased the survival rate of males by implementing antler point restriction (APR) regulations and reduced the survival rate of females by increasing the allocation of antlerless licenses. Harvest regulations, similar to what were implemented in Pennsylvania, that create an older male age structure and shift the sex ratio towards 1:1 are unlikely to affect the timing of breeding, synchrony of breeding, productivity, and sex r
Diefenbach, D. R., E. S. Long, B. D. Wallingford, C. S. Rosenberry, M. E. Grund, and G. L. Alt. Survival and dispersal of yearling male white-tailed deer in Pennsylvania under new antler restriction regulations. 27th Annual Southeast Deer Study Group Meeting, 22-25 February 2004, Lexington, Kentucky.	February 2004
Diefenbach, D. R., E. H. Just, T. Crandall, and S. Lehman. Using Decision Tools to Develop a Deer and Forest Management Program. The Wildlife Society annual meeting, 12 October 2016, Raleigh, NA.	October 2016	We used structured decision making workshops to develop management objectives and a vegetation monitoring program to assess whether objectives were being met. Also, we developed a decision tool for deciding when and how to apply additional deer harvest to specific state forest lands.
Diefenbach, D. R., D. R. Begley-Miller, M. E. McDill, P. J. Drohan, P. D. Jones, B. D. Wallingford, C. S. Rosenberry, E. H. Domoto, and A. E. Sabo. Effect of deer herbivory, soil conditions, and competing vegetation on understory plant growth in an oak-hickory forest ecosystem. Tenth International Deer Biology Congress, September 4-9, 2022, Osijek, Croatia.	September 2022	White-tailed deer (<i>Odocoileus virginianus</i> [Zimmerman]) at high densities reduce tree regeneration and plant species diversity in forests in eastern North America. However, other factors also influence forest plant communities. Soil acidification over the past 40 years could explain some of the difficulties with tree regeneration in oak-hickory forests. In turn, deer herbivory likely exacerbates tree regeneration on acidified soils.
Diefenbach, D. R., D. R. Begley-Miller, M. E. McDill, P. J. Drohan, P. D. Jones, B. D. Wallingford, C. S. Rosenberry, E. H. Domoto, and A. E. Sabo. Effect of deer herbivory, soil conditions, and competing vegetation on understory plant growth in an oak-hickory forest ecosystem. Southeast Deer Study Group Meeting, February 2024, Shepherdstown, WV.	February 2024	White-tailed deer (<i>Odocoileus virginianus</i> [Zimmerman]) at high densities reduce tree regeneration and plant species diversity in forests in eastern North America. However, other factors also influence forest plant communities. Soil acidification over the past 40 years could explain some of the difficulties with tree regeneration in oak-hickory forests. In turn, deer herbivory likely exacerbates tree regeneration on acidified soils.
Diefenbach, D. R., D. A. Brauning, and J. A. Mattice. August 2001. Effect of differences in observer ability and species detection when estimating abundance of grassland birds. International Conference on Distance Sampling, St. Andrews, Scotland.	August 2001
Diefenbach, D. R., C. G. Mahan, and W. B. Cass. Re-designing a long-term vegetation monitoring program at Shenandoah National Park. Annual Conference of The Wildlife Society, 6-10 September 2004, Calgary, Alberta, Canada.	September 2004
Diefenbach, D. R., Buderman, F. E., and L. C. Gigliotti. Efficiency of joint known-fate and tag-recovery models for estimating harvest rates of large animals. EURING Technical Meeting, 2-7 July 2017, Barcelona, Spain.	July 2017	Estimates of demographic parameters for large animals (e.g., cervids) are usually obtained by fitting individuals with transmitters so that capture probability is 1.0 and fates for every individual can be determined. Depending on research objectives, joint known-fate tag-recovery models have the potential for significant costs savings without loss of precision of harvest rate estimates.
Diefenbach, D. R. Linking research and management to solve complex problems. Pennsylvania Chapter of The Wildlife Society annual meeting, 1 April 2017, Raystown Lake, PA.	April 2017	The wildlife profession is ideally set up for rapid learning of ecological systems because natural resource agencies make management decisions based upon a system of management units (e.g., water bodies or land areas), which readily provides opportunities for replication of treatments and controls. A variety of decision tools (structured decision making, adaptive management, and stochastic dynamic optimization) can effectively link research and management and, if embraced by decision makers, ca
Diefenbach, D. R. Linking research and management to improve decision making. 20 February 2018. Southeast Deer Study Group Meeting, Nashville, TN.	February 2018	Deer management is ideally positioned for rapid learning about the ecological system because natural resource agencies make management decisions based upon a system of management units, which readily provides opportunities for replication of treatments and controls. I provide an overview of the strategies used by state agencies toimprove deer and forest management decision making in Pennsylvania.
Diefenbach, D. R. Linking Research and Management: Why You Should Clearly Define the Problem. The Wildlife Society annual meeting, 12 October 2016, Raleigh, NA. (Invited Oral)	October 2016	The wildlife profession is ideally set up for experimentation because natural resource agencies make management decisions based upon a system of management units (e.g., water bodies or land areas), which readily provides opportunities for replication of treatments and controls. Wildlife management has traditionally been conservative with manipulations of wildlife populations and habitats, especially hunting regulations, but these manipulations can create experiments that can rapidly improve our
Diefenbach, D. R. Integrated Population Models: Taking Advantage of All Available Data. Southeast Deer Study Group Meeting, Oklahoma City, Oklahoma, February 20-22, 2011.	February 2011
Diefenbach, D. R. Estimating abundance of grassland songbirds: lessons from the field. Point Count Workshop, Patuxent Wildlife Research Center, Laurel, Maryland, 7-9 November 2006.	November 2006
Diefenbach, D. R. Coyotes, and Bobcats, and Bears! Oh My! Annual conference of the Northeast Fish and Wildlife Agencies, 7 April 2013, Saratoga Springs, New York, USA. DENIED ATTENDANCE BY USGS.	April 2013	Predation of white-tailed deer has been raised as a potential concern for wildlife managers. If one considers the life history characteristics of deer and predators, however, a number of management options exist that do not require control of non-human predators.
Diefenbach, D. R. 2007. Estimating abundance of songbirds using Bowden's estimator. EURING 2007, Dunedin, New Zealand, 14-20 January 2007.	January 2007
Diefenbach, D. R. Estimating avian population size using Bowden?s estimator. Annual Conference of The Wildlife Society, Miami, Florida, 8-12 November 2008.	November 2008
Deweber, T. and T. Wagner. 2012. Linking Climate and Land Use Projections to Stream Habitat. American Fisheries Society Annual Meeting. Twin Cities, MN. 19 – 23 August.	August 2012
Deweber, J.T. and T. Wagner. 2014. The future of brook trout in changing climate and landscape. 70th Annual Northeast Fish & Wildlife Conference, Portland, Maine, April 13 –15.	April 2014	One of the first region-wide assessment of changes in brook trout habitat under both future climate and land use change scenarios.
Deweber, J.T. and T. Wagner. 2014. A model for predicting daily river water temperature in the Northeast and its utility for management. 70th Annual Northeast Fish & Wildlife Conference, Portland, Maine, April 13 –15.	April 2014	This is the first regional model for the the northeast region to predict daily river water temperatures.
Deweber, J. T. and T. Wagner. 2013. Climate and land use change implications for native brook trout management. American Fisheries Society Pennsylvania Chapter Fall Technical Meeting.	October 2013	One of the few studies to model and forecast both land use and climate change impacts on brook trout.
Deweber, J. T. and T. Wagner. 2011. Predicted Impacts of Climate Change on Stream Habitat and Brook Trout Populations in the Eastern United States. 6th World Recreational Fishing Conference, Berlin, Germany, August 1 -4.	August 2011
Detar, J., Kristine, D., Greene, R.T., Weber, R. and Wagner, T. Evaluation of brook trout enhancement regulations in Northcentral Pennsylvania. Annual Meeting of the American Fisheries Society. September 12 – 16.	September 2010
Detar, J., D. Kristine, T. Greene, and T. Wagner. 2012. Evaluation of Catch and Release Regulations for Wild Brook Trout in Pennsylvania Streams. East Coast Trout Management and Culture Workshop V, Frostburg, MD, June 11 – 13.	June 2012
Dec Peevey, D. W., L.M. Williams, and W. D. Walter. 2019. Characterizing landscape factors of two West Nile virus vectors in Pennsylvania, USA. 68th Annual International Conference of the Wildlife Disease Association, Tahoe City, CA.	August 2019	Zoonotic diseases have increased global concern and increased human ill- nesses with viral outbreaks such as yellow fever, dengue fever, West Nile and Zika virus. Emerging and established zoonotic diseases are being studied by the World Health Organization and the Center for Disease Control with prime ex- amples being West Nile virus (WNV) and diseases spread by mosquito or other insect vectors.
DeWeber, T. and T. Wagner. 2015. Predicting Mean Daily River Water Temperature to Identify Brook Trout Habitat. American Fisheries Society Annual Meeting, Portland, Oregon.	August 2015	This is the first regional stream water temperature model for the northeast United States.
DeWeber, T. and T. Wagner. 2015. Is That the Best Metric for Predicting Climate Change Effects on Brook Trout? American Fisheries Society Annual Meeting, Portland, Oregon.	August 2015	This is the first work to compare multiple metrics for summarizing the effects climate change on river water temperature and its effects on forecasted Brook Trout occurrence patterns.
DeMario, D.A., Iwanowicz, L.R., Wagner, T., Kepler, M.V., and Honeyfield, D. C. 2011. Effects of Dietary Restriction on PCB Congener Dynamics and Their Association with Health in Channel Catfish. American Fisheries Society 141st Annual Meeting. Seattle, WA, September 4 – 8.	September 2011
DeMario, D. Iwanowicz, L., Blazer, V., Honeyfield, D., Kepler, M., and Wagner, T. Effects of dietary restriction on PCB congener dynamics and their association with innate immune function in Channel Catfish. Annual Meeting of the American Fisheries Society. September 12 – 16.	September 2010
DeMario D., Wagner T., Miko D., Lorantas R., Lorson R., Detar J., Kristine D., Weigle J. Evaluation of Panfish Enhancement Regulations in Pennsylvania Lakes. 65th Northeastern Fish and Wildlife Conference, April 26 – 28, Lancaster, PA.	April 2009
Daniel, W., N. Sievert, D. Infante, C. Paukert, J. Stewart, J. Whittier, T. Wagner, K. Herreman, and Y. Tsang. FISHTAIL: A decision support mapper for conserving stream fish habitats of the NE CSC region Midwest Fish and Wildlife Conference, Indianapolis, IN.	February 2015	This work demonstrates a tool managers can use to identify species and stream reaches most vulnerable to climate change.
Custer, CA, EM Schliep, JS North, GJA Hansen, H Kundel, JKR Nelson, T Wagner. 2023. Developing a joint species, spatially dependent physiologically guided abundance model to improve predictions under future climate change scenarios. Southern Division American Fisheries Society Meeting, Norfolk, VA.	February 2023	We present a novel modeling framework for predicting the effects of climate change on the abundance and distribution of fishes.
Custer, CA, EM Schliep, JS North, GJA Hansen, H Kundel, JKR Nelson, T Wagner. 2023. Developing a joint species, spatially dependent physiologically guided abundance model to improve predictions under future climate change scenarios. Northeast Association of Fish & Wildlife Agencies, Hershey, PA.	May 2023	We present a novel modeling framework for predicting the effects of climate change on the abundance and distribution of fishes.
Custer, C. Fischer, D., Henning, A., Hintz, D., Schall, M.K., Shank, M., Smith, G., Wertz, T., and Wagner, T. Quantifying the roles of biotic and abiotic factors structuring stream fish communities. Keystone Coldwater Conference & PA Chapter of the American Fisheries Society. February 25-26, 2022.	February 2022	This research examines modeling fish communities while accounting for both abiotic drivers and biotic interactions.
Crawford, CS and WD Walter. 2013. Spatial analysis of black bear (Ursus americanus) to assess harvest vulnerability in relation to anthropogenic activity in Pennsylvania. The Wildlife Society Annual Conference, Milwaukee, WI	October 2013	This study will examine the harvest vulnerability of black bears in urban/suburban study sites in Pennsylvania. The results will determine the amount of huntable land within the study site to aid in understanding harvest dynamics.
Crawford, C.S., M.A. Ternent, M.J. Lovallo, and W.D.Walter. 2014. Resource selection and harvest vulnerability of black bear near suburban areas of Pennsylvania. The 21st Annual Wildlife Society Conference, Pittsburgh, PA.	October 2014	Black bear population growth and expansion along with anthropogenic disturbance of traditional bear habitat over the past several decades has directly led to increased human-bear interactions and subsequently increased conflicts in Pennsylvania. Our results will assist resource managers in understanding resource selection of black bear near suburban areas where human-bear conflict is a growing concern of state agencies.
Crawford, C.S. and W.D.Walter. Spatial analysis of black bear (Ursus americanus) to assess harvest vulnerability in relation to anthropogenic activity in Pennsylvania. Pennsylvania Chapter of the Wildlife Society, State College, PA, 22-23 March 2013.	March 2013	Expanding black bear populations have directly lead to an increase in human-bear interactions and influenced management decisions for black bear. With more than 85 percent of Pennsylvania lands in private ownership, an understanding of and a collaborative management efforts with private lands is critical to the long-term success of management of black bears in the state.
Craft, M.E., G. Wilson-Henjum, G. Bastille-Rousseau, P. Cross, M. Diuk-Wasser, R.B. Gagne, J. Heale, J. Hewitt, K. Manlove, L.D. Plimpton, M. Van Acker, K. C. Vercauteren, W.D. Walter, M. Wilber, G. Wittemyer, and K.M. Pepin. 2023. A national-scale distributed surveillance design for SARS-CoV-2 in a potential wildlife reservoir host. 20th annual Ecology and Evolution of Infectious Disease Conference, State College, PA, May 22-25 2023.	May 2023	Emergence of zoonotic diseases in new wildlife host species continues to occur globally and poses major health or conservation risks for the hosts involved. Here, we describe the design, operationalization, and preliminary findings from a novel distributed surveillance project of SARS-CoV-2 in deer supported through USDA-APHIS and the American Rescue Plan Act that aims to understand establishment and reservoir dynamics of SARS-CoV-2 in deer.
Corondi, A.M., J.E. Banfield, J.D. Brown, and W.D. Walter. 2023. Reproductive success and calf survival of elk in Pennsylvania. 30 April-2 May, 2023, 78th Annual Northeast Fish and Wildlife Conference, Hershey, PA, USA.	May 2022	Investigating natality and subsequent juvenile survival rates is costly, labor intensive, and difficult to thoroughly assess though understanding reproduction and recruitment of ungulate populations is necessary for creating comprehensive management plans. Through the winters of 2020-2022, 150 vaginal implant transmitters (VITs) paired with global positioning system collars were deployed in pregnant cow elk. Pregnancy was assessed in the field using ultrasound and later confirmed by pregnancy-s
Corondi, A.M., J.E. Banfield, J.D. Brown, and W.D. Walter. 2022. Unexpected findings through the use of vaginal implant transmitters in elk in Pennsylvania. 16-19 May, 2022, 24th Eastern Elk Management Workshop. Bemidji, MN, USA.	May 2022	Investigating natality and subsequent juvenile survival rates is costly, labor intensive, and difficult to thoroughly assess though understanding reproduction and recruitment of ungulate populations is necessary for creating comprehensive management plans. Through the winters of 2020-2022, 150 vaginal implant transmitters (VITs) paired with global positioning system collars were deployed in pregnant cow elk. Pregnancy was assessed in the field using ultrasound and later confirmed by pregnancy-s
Corondi, A.M., J.E. Banfield, J.D. Brown, and W.D. Walter. 2021. G.U.T.-check – GPS, Ultrasound, and Transmitters to properly evaluate reproduction in elk. 1-5 November, 2021, The Wildlife Society Annual Conference, Baltimore, MD.	October 2021	Investigating natality and subsequent juvenile survival rates is costly, labor intensive, and difficult to thoroughly assess though understanding reproduction and recruitment of ungulate populations is necessary for creating comprehensive management plans.
Conn, P. B., J. L. Laake, G. C. White, D. R. Diefenbach, and M. A. Ternent. Joint analysis of mark-recovery and age-at-harvest data: Pennsylvania black bear and beyond. Annual Conference of The Wildlife Society, 25-29 September 2005, Madison, Wisconsin.	September 2005
Conn, P. B., J. L. Laake, G. C. White, D. R. Diefenbach, M. A. Ternent. Demographic analysis of a black bear population using mark-recovery and age-at-harvest data. EURING 2007, Dunedin, New Zealand, 14-20 January 2007.	January 2007
Collins, S.M., S.K. Oliver, J-F. Lapierre, E.H. Stanley, J. Jones, T. Wagner, P.A. Soranno. 2016. What drives lake nutrients at continental scales, and why is it so hard to predict nutrient ratios? Association for the Sciences of Limnology and Oceanography.	June 2016	This work attempts to understand multi-scaled drivers of lake nutrients and nutrient ratios at macroscales.
Collins, S.M., S. Yuan, P.-N. Tan, S.K. Oliver, J.F. Lapierre, K.S. Cheruvelil, E. Fergus, N.K. Skaff, J. Stachelek, T. Wagner, P.A. Soranno. 2018.c. Society for Freshwater Science, Detroit MI.	May 2018	First work to examine climate effects on lakes at macroscales.
Collins, S., K.S. Cheruvelil, E. Fergus, J.F. Lapierre, S. Oliver, J. Skaff, P.A. Soranno, P-N. Tan, T. Wagner, S. Yuan. 2017. Which measures of climate are the best predictors of lake water quality at sub-continental scales? Ecological Society of America Annual Meeting, Portland, OR.	August 2017	First mascroscale study to quantify effects of climate on lake water quality.
Church, A. J.W. Fischer, and W.D. Walter. 2013. Applied use of online storage infrastructures for tracking wildlife species in near real-time. The Wildlife Society Annual Conference, 7 October 2013.	October 2013	Recent technological advancements for monitoring wildlife populations have resulted in concomitant expansion in data storage requirements and more efficient remote download capabilities. Online storage of locations in Movebank enabled passive tracking and monitoring of mortality events that likely is a more efficient and less expensive alternative than traditional methods of monitoring, such as very high frequency telemetry from a vehicle or aircraft.
Christensen, S. and D. R. Diefenbach. Movements and habitat use of sika and white-tailed deer on Assateague Island. Annual Conference of the Pennsylvania Chapter of the Wildlife Society, State College, Pennsylvania, 17 March 2007.	March 2007
Christensen, S. A., D. R. Diefenbach, and M. Sturm. Movements and Habitat Use of Sika and White-Tailed Deer on Assateague Island National Seashore. Northeast Fish and Wildlife Conference, Galloway, New Jersey, 27-30 April 2008	April 2008
Christensen, S. A., D. R. Diefenbach, and M. Sturm. Movements and Habitat Use of Sika and White-Tailed Deer on Assateague Island National Seashore. Annual Conference of the Pennsylvania Chapter of the Wildlife Society. 22 March 2008.	March 2008
Christensen, S. A., D. R. Diefenbach, and M. Sturm. Habitat use of sika and white-tailed deer on Assateague Island National Seashore, Maryland. Southeast deer study group meeting. 25-27 February, 2007, Ocean City, Maryland.	February 2007
Cheruvelil, K.S., T. Wagner, K. Webster, K. King, A. Poisson. 2018. Macroscale patterns and drivers of phosphorus and chlorophyll in shallow lakes. Association for the Sciences of Limnology and Oceanography, Summer Meeting, Victoria, BC, Canada.	June 2018	Macroscale investigation into shallow lakes P and chlorophyll patterns and drivers.
Cheruvelil, K.S., S. Yuan, S. Collins, C.E. Fergus, C. Filstrup, E. Norton Henry, J-F. Lapierre, C. Scott, P. Soranno, P-N. Tan, T. Wagner, K. Webster. Including the freshwater landscape in a multi-themed regionalization system to capture macroscale patterns. The 2015 Ecological Society of America Annual Meeting, August 9 – 15.	August 2015	We develop the first regionalization system based on the freshwater landscape.
Cheruvelil, K.S., P.A. Soranno, K.E. Webster, M.T. Bremigan, T. Wagner, C.A. Stow. Freshwater Ecosystem Classification for Landscape-scale Management. Oral presentation at the 57th Annual Meeting of the North American Benthological Society. Grand Rapids, MI. May, 2009.	May 2009
Cheruvelil, K.S., P.A. Soranno, B. Liu, Q. Wang, P-N. Tan, J. Zhou, K.B.S. King, I.M. McCullough, J. Stachelek, M. Bartley, C.T. Filstrup, E.M. Hanks, J-F. Lapierre, N.R. Lottig, E.M. Schliep, T. Wagner, K.E. Webster. Ecological prediction at macroscales using big data: Does sampling design matter? ASLO-SFS Summer Meeting.	June 2020	We examined how the sampling strategy used to collect data across large spatial extentsinfluences predictive performance.
Changes in Spring Creek's biological resources in response to human activities	October 2003
Casalena, M. J., W. C. Vreeland, R. Everett, I. Gregg, and D. R. Diefenbach. Timing of spring wild turkey hunting in relation to nest incubation. National Wild Turkey Symposium.	January 2016	, opening the spring hunting season after 50% of hens have initiated incubation is thought to balance the risk of disturbance with maximizing hunting opportunities. We have no evidence to suggest that timing of incubation has changed during 1953-2013, or varies spatially. If incubation behavior is controlled primarily by photoperiod (day length) rather than variations in weather or vegetation, the existing guideline of using the Saturday closest to 1 May for the opening day of Pennsylvania's sp
Carrollo, E., H.E. Johnson, J.W. Fischer, M. Hammond, P.D. Dorsey, C. Anderson, K.C. VerCauteren, W.D. Walter. 2014. Mule deer resource selection of agricultural crops in southwestern Colorado. The 21st Annual Wildlife Society Conference, Pittsburgh, PA.	October 2014	Methods to prevent deer damage to the crops can be costly so we wanted to specifically address movement and resource selection on agricultural crops in southwestern Colorado. Identification of annual- and seasonal-specific use of agriculture crops will assist managers in understanding mule deer use of specific crop types and their distribution on the landscape.
Carline, R. F., and R. J. Weber. 2000. Effects of electrofishing on wild brown trout. Third East Coast Trout Management and Culture Workshop, Frostburg, Maryland, June 6-8, 2000.	June 2000
Carline, R. F., and M. C. Walsh. 2003. Sustaining productive fisheries in well managed forests. Forestry's role in integrated water management. Penn State University, University Park, March 25-26, 2003.	March 2003
Carline, R. F., and K. Umphrey. 2000. Riparian restoration in agricultural watersheds: science and sociology. Annual meeting of the Wisconsin Chapter of the American Fisheries Society, Manitowoc, Wisconsin, January 4-6, 2000.	January 2000
Carline, R. F., P. M. Barry, and G. H. Ketola. 2002. Uptake of dietary PCBs by rainbow trout. Annual Meeting American Fisheries Society, Baltimore, Maryland, August 18-22, 2002.	August 2002
Carline, R. F., M. C. Walsh. 2005. Responses of streams to riparian restoration in the Spring Creek watershed, central Pennsylvania. Annual Meeting of the American Fisheries Society, Sept. 11-15, 2005, Anchorage, Alaska.	September 2005
Carline, R. F. October 2000. Effects of annual electrofishing with high-frequency DC on wild brown trout. Wild Trout VII. Yellowstone National Park, Wyoming.	October 2000
Carline, R. F. 2005. Regulation of an unexploited brown trout population in Spruce Creek, Pennsylvania. Northeast Fish and Wildlife Conference, Virginia Beach, VA, April 19, 2005	April 2005
Carline, R. F. 2005. Regulation of an unexploited brown trout population in Spruce Creek, Pennsylvania. Annual Meeting of the American Fisheries Societ, September 11-15, 2005, Anchorage, Alaska.	September 2005
Carline, R. F. 2003. Evolution of a volunteer monitoring project: Spring Creek Watershed. Statewide Summit for Volunteer Watershed Monitoring. Penn State University, University Park, February 21-22, 2003.	February 2003
Carline, R. F. 2001. Effects of acidic runoff episodes on fish communities in Appalachian streams of Pennsylvania. Appalachian Region Science Workshop, U.S. Geological Survey, Gatlinburg, Tennessee, Oct. 22-23, 2001.	October 2001
Carline, R. F. 2000. Spawning habitat of trout in Pennsylvania waters. Keystone Coldwater Conference, Penn State University, University Park, PA, February 19, 2000.	February 2000
Carline, R. F. 2000. Responses of aquatic communities to riparian restoration. A technical training workshop: Enhancing Wildlife Habitat Through the Conservation Reserve Enhancement Program. Dauphin, PA, April 19, 2000.	April 2000
Carline, R. F. 2000. Nature and causes of spinal injuries in brown trout subjected to electrofishing. Pennsylvania Animal Laboratory Technicians Quarterly Meeting, University Park, PA, June 15, 2000.	June 2000
Buderman, F.E. and D.R. Diefenbach, C.S. Rosenberry, and B.D. Wallingford. An integrated population model approach to monitoring response of white-tailed deer populations to regulation changes. Pennsylvania Chapter of The Wildlife Society Annual Conference, State College, Pennsylvania. 17 March 2012.	March 2012
Buderman, F. E., and D. R. Diefenbach. Improve harvest estimates using known-fate data to inform a band-recovery model. Northeast Association of Fish and Wildlife Agencies Annual Conference, Manchester, NH, 17-19 April 2011.	April 2011
Buderman, F. E., and D. R. Diefenbach. Accounting for tagging-harvest mortality in a Brownie dead-recovery model by incorporating radio-telemetry data. EURING Analytical Meeting, 28 April 2013, Athens, Georgia, USA.	April 2013	We developed an estimator that combines tag-recovery and known fate data to improve accuracy and precision of harvest and survival rates.
Buderman, F. E., T. M. Gingery, D. R. Diefenbach, L. C. Gigliotti, D. Begley-Miller, M. E. McDill, B. D. Wallingford, C. S. Rosenberry, and P. D. Drohan. Guidance on inferring behavioral states from animal location data. 31 May - 11 June, 2021, EURING Technical Meeting, Quebec City, Quebec, Canada.	June 2021	With the advent of modern tracking methods, we have also developed a suite of statistical methods that can be used to model metrics that describe space-use and movement. We discuss multiple case studies, centered on ungulates in Pennsylvania, in which various statistical methods for animal space-use and movement can result in erroneous inference on behavioral states.
Buderman, F. E., T. M. Gingery, D. R. Diefenbach, L. C. Gigliotti, D. Begley-Miller, B. D. Wallingford, C. S. Rosenberry. Using animal space-use and movement to infer behavioral states: A cautionary tale. Southeast Deer Study Group Meeting, 23 February 2021.	February 2021	Successfully mating is one of the primary components of an individuals’ lifetime reproductive success and fitness, but the movements that characterize ungulate mating strategies are poorly understood. Caution is warranted when interpreting behavioral insights rendered from statistical models applied to location data, particularly when there is no form of validation data. Unvalidated assumptions about variation in space-use and movement can lead to incorrect inference about behavioral strategies.
Buderman, F. E., D. R. Diefenbach, C. S. Rosenberry, and B. D. Wallingford. An integrated population model approach to monitoring response of white-tailed deer populations to regulation changes. 26-28 February 2012, Southeast Deer Study Group Meeting, Sandestin, Florida.	February 2012
Buderman, F. E, and D. R. Diefenbach. Using auxiliary known-fate data to improve harvest estimates from tag-recovery models. The Wildlife Society Annual Conference, 16 October 2012, Portland, Oregon, USA.	October 2012	We developed an estimator that combines tag-recovery and known fate data to improve accuracy and precision of harvest and survival rates.
Brennan, J.C., S.R. Corsi, R.W. Gale, D.A. Alvarez, J.P. Berninger, J.K. Leet, Y. Li, T. Wagner, and D.E. Tillit. Factors affecting sampling strategies for an effects-directed analysis of EACs and identifying hotspots of concern for EAC contamination in water sources. ASLO-SFS Summer Meeting.	June 2020	This work proposes a conceptual EDA (framework) based on a critical review of EDA literature and concentrations of common EACs in waste and surface waters.
Bremigan, M., Spence Cheruvelil, K., Wagner, T., Soranno, P., Webster, K., and Alger, B. 2008. Landscape scale management for lakes: connecting lake landscapes to water chemistry and fishes	August 2008
Brauning, D. W., and D. R. Diefenbach. 2000. Analysis of distance sampling methodology for grassland bird population studies. Wilson Ornithological Society Annual Meeting, Galveston, Texas, April 28-30, 2000.	April 2000
Brauning, D. W., J. A. Mattice, D. R. Diefenbach. Value of strip-mine habitats for birds. 2nd Ohio Avian Ecology and Conservation Conference, 1 August 2003, Cincinnati, Ohio.	August 2003
Boyd, E., L.C. Gigliotti, D.R. Diefenbach, E. Clees, and P.S. Weiss. 2023. Pennsylvania snowshoe hares (Lepus americanus). 13th International Mammal Congress, Anchorage, AK.	July 2023	Snowshoe hares in Pennsylvania are near the southern extent of their range, so understanding their ecology could be beneficial in planning localized management.
Borsuk, F. A., R. F. Carline. 2005. Effects of paternally-derived polychlorinated biphenyls on the gametes and early life stages of brown trout. Annual Meeting of the American Fisheries Society, September 11-15, 2005, Anchorage, AK.	September 2005
Bondo, K.J., D. Stainbrook, C.S. Rosenberry, and W.D. Walter. 2023. Comparing the spatial risk of chronic wasting disease in roadkill and hunter harvest white-tailed deer using Bayesian hierarchical models. The 30th Annual Conference of the Wildlife Society, Louisville, KY, 5-9 November 2023.	November 2023	One of the most important measures in controlling chronic wasting disease is understanding spatial distribution of risk of disease transmission in relation to deer demographic and environmental variables. Understanding variability in predictions for risk across a landscape between surveillance samples collected and the tools available for modeling and mapping diseases of wildlife in relation to ecological variables will help guide future surveillance efforts for this disease in cervids.
Bondo, K.J., D. Stainbrook, C.S. Rosenberry, and W.D. Walter. 2023. Comparing the spatial risk of chronic wasting disease in roadkill and hunter harvest white-tailed deer using Bayesian hierarchical models. 71st Annual International Conference of the Wildlife Disease Association, Athens, GA, 29 July-4 August 2023.	August 2023	One of the most important measures in controlling chronic wasting disease is understanding spatial distribution of risk of disease transmission in relation to deer demographic and environmental variables. Understanding variability in predictions for risk across a landscape between surveillance samples collected and the tools available for modeling and mapping diseases of wildlife in relation to ecological variables will help guide future surveillance efforts for this disease in cervids.
Bondo, K.J. and W.D Walter. Acquiring large scale spatial data for use in Integrated Nested Laplace Approximation (INLA) models. 6- 10 November 2022, The Wildlife Society Annual Meeting, Spokane, WA.	November 2022	Recently, integrated nested Laplace approximations (INLA) using stochastic partial differential equation (SPDE) solutions were developed to model large spatial datasets because traditional Bayesian methods were unsuitable due to slow computational times. We developed code that streamlines downloading of various sources of statewide spatial data and assigns these data to sampling locations with large extents.
Bondo, K. L. Williams, and W.D. Walter. 2022. Using mosquito surveillance to inform risk of West Nile virus exposure to ruffed grouse populations in Pennsylvania. Wildlife Disease Association Meeting, Madison, WI, 23-29 July 2022.	July 2022	Recent evidence suggests that population declines of ruffed grouse (<i>Bonasa umbellus</i>) throughout their range in the United States have been driven by the loss of optimal habitat and the introduction of West Nile virus (WNV). Determining the risk of WNV exposure to ruffed grouse populations would help inform management decisions for this species.
Blinick, N. S., H. Kundel, T. D. Ahrenstorff, B. J. Bethke, J. Hirsch, D. P. Krabbenhoft, H. M. Rantala, C. Rude, K. Vitense, T. Wagner, G.J.A. Hansen. How do zebra mussels affect walleye recruitment, food webs, and mercury concentrations? Minnesota Aquatic Invasive Species Research Center Research Showcase. September 22, 2021. Virtual Conference.	September 2021	An assessment of invasive mussels on an ecologically and economically important fish species.
Bishop, J., R. Brooks, W. Myers, T. O'Connell, D. Argent, J. Stauffer, and R. Carline. 2001. Systematic analysis of habitat availability for conservation planning in Pennsylvania. Riparian buffers: how wide and why. April 2001 Annual Meeting of the Pennsylvania Chapters of the American Fisheries Society and The Wildlife Society, Milesburg, PA.	April 2001
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, and E. Just. Soil chemistry and interspecific competition influence understory forest composition in central Pennsylvania: Implications for wildlife. 2018 Pennsylvania Chapter of The Wildlife Society Annual Conference, State College, PA.	March 2018	Eastern deciduous forest understories represent mosaics of food and cover for wildlife, supporting a diversity of insects, small mammals, birds, and large herbivores like white-tailed deer. Soil chemistry plays a role in shaping plant community composition, but that the presence of dominant ericaceous vegetation (high cover) does not limit the abundance of some valuable food resources for wildlife.
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, and E. Just. Soil Chemistry and Interspecific competition influence understory forest composition in central Pennsylvania: implications for wildlife. The Wildlife Society Annual Meeting, 7-11 October 2018, Cleveland, OH, USA.	October 2018	Understanding the factors that shape plant diversity and understory composition are crucial for better managing wildlife habitat, especially in the context of food availability. soil chemistry plays a role in shaping plant community composition, but that the presence of dominant ericaceous vegetation (high cover) does not limit the abundance of some valuable food resources for wildlife.
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, and E. Just. Evaluation of Short-term (3 Year) Understory Plant Community Responses to Deer Exclusion, Herbicide, and Lime Application in Central Pennsylvania. Annual Meeting of the Ecological Society of America, 5-10 August 2018, New Orleans, LA, USA.	August 2018	In oak-hickory forests of central Pennsylvania, browsing by white-tailed deer (Odocoileus virginianus), acid deposition, and competition from dominant vegetation are all thought to reduce understory diversity and limit tree regeneration, however, to date no direct experimental manipulation has occurred to evaluate these factors simultaneously. Although results should be considered preliminary due to the short-term nature of the study, plant community responses to single factors were limited, mi
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, and E. Just. 2017. Soil chemistry and its effect on central Pennsylvania's forest wildlife habitat. Annual meeting of The Wildlife Society, 27 September 2017, Albuquerque, NM.	September 2017	Soil acidification is known to change forest soil conditions, reducing Ca and Mg available to plants, while increasing toxic metals (Al, Mn, and Fe). Lower pH (2.5-3.5) was a predictor of increased occupancy () for mountain laurel and huckleberry. High levels of Mn (> 0.2 cmol(+)/kg) reduced occupancy of mountain laurel and Indian cucumber-root, while high levels of Al (> 5.0 cmol(+)/kg) reduced occupancy (Psi) for black birch. Occupancy of red maple was constant between study areas (Psi = 0.3
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, and E. Just. 2016. Greater than the Sum of its Parts: Understanding Forest Habitat in the Context of Deer, Soil Chemistry, and Competing Vegetation. Annual meeting of the Pennsylvania Chapter of The Wildlife Society, 16 April 2016, State College, PA.	April 2016	We used 2 years (2014-2015) of summer (May-August) forest inventory data collected across a range of vegetation treatments (fence, lime, and herbicide) in the Rothrock and Bald Eagle State Forests to assess the relative role of deer, soil chemistry, and competing vegetation (Ericaceae) on forest understory plant community structure and composition.
Begley-Miller, D. R., D. R. Diefenbach, M. E. McDill, C. S. Rosenberry, E. Just. Soil Chemistry and its Effect on the Occupancy of Understory Plant Species. Presented at Pennsylvania Chapter of The Wildlife Society annual meeting, 1 April 2017, Raystown Lake, Pennsylvania.	April 2017	It is well documented that soil acidification changes forest soil conditions, but the specifics of how soil chemistry influences occurrence of many understory plant species is not well understood. To investigate this relationship, we used single-species occupancy models to compare baseline forest inventory data to site-specific soil chemistry (pH, extractable nutrients, effective cation exchange capacity, and toxic metal saturation) for several species.
Bayuzick, S., P. Drohan, T. Raab, F. Hirsch, A. Bonhage, M. McDill, and D. Diefenbach. Relic charcoal hearths geomorphology and hydrology in mid-Appalachian region of Pennsylvania. Virtual EGU General Assembly 2021, 19 April 2021.	April 2021	Relic charcoal hearths (RCHs) across the northcentral Appalachians, USA have been minimally investigated, thus determining where they occur on the landscape, their shape, and their morphologic positions will be useful in discerning their effect on surface hydrology and soil development. Our study focuses on developing a repeatable process for: finding RCHs and quantifying how RCHs may alter surface hydrology.
Batchelor, S., J. Keagy, and T. Wagner. 2022. A Landscape Transcriptomics Approach to Evaluating Thermal Stress in Wild Populations of Salvelinus fontinalis. Wild Trout Symposium.	September 2022	We use a whole-genome approach to understand the thermal stress response in brook trout.
Batchelor, S., J. Avery, M.S. Eackles, D.C. Kazyak, M. Schall, K. Smalling, G. Smith, S.L. White, and T. Wagner. 2022. Understanding the spread and impact of invasive flathead catfish in the Chesapeake Bay Watershed, USA. USGS Chesapeake Bay Workshop. June 27-30^th. National Conservation Training Center.	June 2022	We provided an overview of a research portfolio to understand the spread and impact of invasive flathead catfish in the Chesapeake Bay Watershed.
Bastille-Rousseau, G., Chandler, J., Craft, M., Cross, P., Diuk-Wasser M., Gagne, R., Heale, J., Hewitt, J., Manlove, K., Pleszewski, R., Plimpton, L., Quintanal, C., VanAcker, M., VerCauteren, K., Walter, D., Wilber, M., Wilson-Henjum, G., Wittemyer, G. and Pepin, K. A nationally distributed surveillance design for SARS-CoV-2 in a potential wildlife reservoir host. Scialog – Mitigating Zoonotic Threats, Tucson, AZ.	September 2023	Current knowledge of disease emergence in wildlife reservoirs remains weak because of the challenges with collecting enough appropriate data for a system-level understanding of the drivers of emergence and the relative infrequency that these events occur. Here, we describe the design, operationalization, and preliminary findings from a novel distributed surveillance project of SARS-CoV-2 in deer.
Barry, P., R. Carline, D. Argent, and W. Kimmel. 2004. Movement and habitat use of stocked paddlefish in the Ohio River system, Pennsylvania	August 2004
Barry, P. M., and R. F. Carline. 2003. Movement and habitat use of stocked paddlefish in the Ohio River system. 2003 Joint Meeting of the Pennsylvania Chapters of AFS, SAF, TWS, and SWSC. State College, Pennsylvania, April 10-12, 2003.	April 2003
Arts M.T., Blukacz A., Claramunt R., Ebener M., Faisal M., Fitzsimmons J., Honeyfield D., Hoyle J., Johnson T., Jones M., Kinnunen R.E., Koops M.A., Mezek T., Muir A.M., Richards A., Sutton T.M., Wagner T., and Wright G. 2008. Fatty acid profiles of lake whitefish (Coregonus clupeaformis) in the ever-changing Great Lakes. American Society of Limnology and Oceanography Aquatic Sciences Meeting.	June 2008
Argent, D., W. Kimmel, P. Kocovsky, R. Carline, A. Smith, and G. Huchko. 2002. Fish assemblages in three lock and dam pools on the Ohio River in Pennsylvania and West Virginia. Annual Meeting American Fisheries Society, Baltimore, Maryland, August 18-21, 2002.	August 2002
Argent, D. G., J. A. Bishop, J. R. Stauffer, Jr., W. L. Myers, and R. F. Carline. August 2001. GIS and Fish Conservation in Pennsylvania. California University of Pennsylvania. Southpointe: GIS Conference 2001, Canonsburg, PA.	August 2001

Theses and Dissertations

Theses and Dissertations	Publication Date
Williamson, L. T. 2017. Monitoring wild ring-necked pheasant population restoration in Pennsylvania. M.S. Thesis, Pennsylvania State University, University Park, PA, USA.	December 2017
Wiederholt, R. P. 2010. Effects of environmental variation on ateline primate population dynamics. Dissertation, Pennsylvania State University, University Park, Pennsylvania, USA.	December 2010
Wallingford, B. D. 2012. White-tailed deer antler point restrictions, harvest and survival rates, and hunter support: perception versus reality. Dissertation, The Pennsylvania State University, University Park, PA, USA.	May 2012
Vreeland, W. C. 2015. Dispersal timing, distances, and rates of Pennsylvania black bear. Thesis, Pennsylvania State University, University Park, Pennsylvania, USA.	May 2015
Van Buskirk, A. 2020. Estimating the effecs of changes in harvest management on white-tailed deer (Odocoileus virginianus) populations. Thesis, Pennsylvania State University, University Park, PA, USA.	July 2020
Thompson, T. 2020. Groundwater discharges as a source of phytoestrogens and other agriculturally derived contaminants to streams. The Pennsylvania State University.	September 2020
Stauffer, G. E. 2008. Nesting ecology and site fidelity of grassland sparrows on reclaimed surface mines in Pennsylvania. M.S. Thesis. Pennsylvania State University, University Park, Pennsylvania, USA.	May 2008
Stainbrook, D. P. 2011. Methods of estimating white-tailed deer abundance at Gettysburg National Military Park: Testing Assumptions of Distance Sampling. Thesis, Pennsylvania State University, University Park, PA, USA.	December 2011
Smith, L. Seasonal movement patterns and habitat use of brook trout Salvelinus fontinalis and brown trout Salmo trutta in North Central Pennsylvania. The Pennsylvania State University, University Park, PA.	December 2013
Salvesen, K.E. 2015. Lake Trout restoration in the Great Lakes: From hatchery to natural reproduction. The Pennsylvania State University, University Park, PA	January 2015
Norton, A. S. 2010. An evaluation of the Pennsylvania Sex-Age-kill model for white-tailed deer. Thesis, Pennsylvania State University, University Park, Pennsylvania, USA.	May 2010
Murphy, A. M. 2021. Examining how spatial-temporal interactions between predators influence the distribution, vigilance, and survival of white-tailed deer (Odocoileus virginianus) fawns. Ph.D. dissertation, Pennsylvania State University, University Park, PA, USA.	May 2021
Mollenhauer, R. 2011. Seasonal movement and habitat use of wild brook trout (Salvelinus fontinalis). M.S. Thesis. Pennsylvania State University, University Park, PA.	December 2011
Miller, W.L. 2018. The genetic structure of white-tailed deer to evaluate the potential epizootiology of chronic wasting disease in an area of recent emergence. The Pennsylvania State University, University Park, PA, 212 pp.	December 2018
Lutz, C. L. 2015. Dispersal behavior in female white-tailed deer. M.S. Thesis. The Pennsylvania State University, University Park, PA, USA.	November 2015
Kepler, M. V. 2013. Comparative bioenergetics of two lake trout morphotypes. M.S. Thesis. Pennsylvania State University, University Park, PA.	June 2013
Keenan, M. T. 2010. Hunter distribution and harvest of female white-tailed deer in Pennsylvania. M.S. thesis, Pennsylvania State University, University Park, Pennsylvania, USA.	December 2010
Hill, J. M. 2012. Population ecology of grassland sparrows on reclaimed surface mine grasslands in Pennsylvania. Dissertation, The Pennsylvania State University, University Park, Pennsylvania, USA.	December 2012
Hall, L. Spatial analysis for sea turtle conservation on the Georgia coast. The Pennsylvania State University, University Park, PA.	May 2014
Gingery, T. M. 2018. Spatial and Temporal patterns in white-tailed deer fawn survival and cause-specific mortality. Thesis, Pennsylvania State University, University Park, PA.	May 2018
Gigliotti, L. C. 2016. Ecology, habitat use, and winter thermal dynamics of snowshoe hares in Pennsylvania. M.S. Thesis, The Pennsylvania State University, University Park, Pennsylvania, USA.	May 2016
Ganoe, L.S. 2019. Using a multi-faceted approach to assess ecological components affecting muskrat (Ondatra zibethicus) populations. The Pennsylvania State University, University Park, PA, 137 pp.	December 2019
Forman, N.S. 2015. River otter population monitoring in Northeastern Pennsylvania using non-invasive genetic sampling and spatial capture-recapture models. The Pennsylvania State University, University Park, PA, 77 pp.	December 2015
Faulk, E.A. 2015. Patterns in distributions of stream fishes in the Eastern Rivers and Mountains Network: A multi-species occupancy approach. The Pennsylvania State University, University Park, PA.	March 2015
Evans, T.S. 2014. Chronic wasting disease in the Central Appalachian region of the United States. The Pennsylvania State University, University Park, PA, 81 pp.	May 2015
DeWeber, J.T. Potential climate and land use change effects on brook trout in the eastern United States. The Pennsylvania State University, University Park, PA.	June 2014
DeMario, D. 2012. PCB exposure and channel catfish: An analysis of immune response and PCB dynamics in the presence of food deprivation. M.S. Thesis. Pennsylvania State University, University Park, PA.	November 2012
Christensen, S. A. 2010. Movement and habitat use of sika and white-tailed deer on Assateague Island National Seashore. Thesis, Pennsylvania State University, University Park, Pennsylvania, USA.	May 2010
Carrollo, E.M. 2016. Exploration of methods for analyses of resource selection using location-based data. The Pennsylvania State University, University Park, PA, XX pp.	May 2016
Buderman, F. E. 2012. A joint Kaplan-Meier known-fate and Brownie tag-recovery model to estimate harvest and survival rates. M.S. Thesis, Pennsylvania State University, University Park, Pennsylvania.	December 2012
Begley-Miller, D. 2018. Shaping Pennsylvania's Forests: Effects of white-tailed deer, soil chemistry, and competing vegetation on oak-hickory forest understory plant community composition. Dissertation, Pennsylvania State University, University Park, PA.	May 2018

Technical Publications

Technical Publications	Publication Date
Weber, R. J., and R. Carline. 2000. Effects of electrofishing on survival and growth of wild brown trout (Salmo trutta) from central Pennsylvania streams. pages 215-223, in D. Schill, S. Moore, P. Byroth, and B. Hamre, editors, Wild Trout VII Management in the new millenium: are we ready?	October 2000
Storm, G. L., W. L. Palmer, and D. R. Diefenbach. 2003. Ruffed grouse responses to management of mixed oak and aspen communities in central Pennsylvania. Grouse Research Bulletin No. 1, Pennsylvania Game Commission, Harrisburg, Pennsylvania, USA.	October 2003
Stainbrook, D. P., and D. R. Diefenbach. 2012. Estimating white-tailed deer abundance at Gettysburg National Military Park and Eisenhower National Historic Site. Natural Resource Technical Report NPS/NER/NRTR—2012/626. National Park Service, Fort Collins, Colorado.	August 2012
Myers, W., J. Bishop, R. Brooks, T. O'Connell, D. Argent, G. Storm, J. Stauffer, Jr., and R. Carline. 2000. Pennsylvania Gap Analysis Project. Final Report to USGS Gap Analysis Program.	January 2000
Moore, S. E., R. F. Carline, and J. Dillon. eds. 2004. Working together to ensure the future of wild trout. Proceedings of Wild Trout VIII Symposium - 30th Anniversary, 2004 September 20-22; Yellowstone Park, Wyoming. 398 pages.	October 2004
Lorantas, R., Wagner, T., Arnold, D., Detar, J., Kaufmann, M., Kuhn, K., Lorson, R., Wnuk, R., and Woomer, A. 2010. Smallmouth Bass Electrofishing Catch Rate in Large Pennsylvania Rivers and Examination of Smallmouth Bass Recruitment Indices. Technical Report, Pennsylvania Fish and Boat Commission.	July 2010
Lieb, D. A., R. F. Carline, and M. Mengel. 2005. Discovery of a member of the Cambarus acuminatus complex (Decapoda: Cambaridae) in Pennsylvania with notes on its biology and habitat preferences. Final Report to National Park Service. 20 pp.	May 2005
Lieb, D. A., R. F. Carline, and H. M. Ingram. 2005. Development of a historical database as a first step in assessing changes in the crayfish fauna of Pennsylvania over the past 100 years. Final Report submitted to the Pennsylvania Department of Conservation and Natural Resources, Wild Resources Conservation Program.	September 2005
Lieb, D. A., R. F. Carline, and H. M. Ingram. 2005. Development of a historical database as a first step in assessing changes in crayfish fauna of Pennsylvania over the past 100 years. Final Report submitted to the Pennsylvania Department of Conservation and Natural Resources, Wild Resources Conservation Program. 19 pp.	August 2005
Kristine, D., Detar, J., Lorantas, R., Lorson, R., Wagner, T., and DeMario, D. 2010. Biological Assessment of Experimental Panfish Enhancement Regulations on Select Pennsylvania Impoundments. Technical Report, Pennsylvania Fish and Boat Commission.	January 2010
Irwin, B. J., T. Wagner, M. V. Kepler, W. Liu, J. R. Bence, D. B. Hayes, and N. Lester. 2011. Spatial and temporal components of variation in Great Lake percid populations: implications for conservation and management. Great Lakes Fish and Wildlife Restoration Act, Project Completion Report.	June 2011
Hopkins, M.C., Carlson, C.M., Cross, P.C., Johnson, C.J., Richards, B.J., Russell, R.E., Samuel, M.D., Sargeant, G.A., Walsh, D.P., and Walter, W.D., 2019, Chronic wasting disease—Research by the U.S. Geological Survey and partners: U.S. Geological Survey Open-File Report 2019‒1109, 29 p., https://doi.org/10.3133/ofr20191109.	September 2019
Diefenbach, D., W. Vreeland, and K. M. Heister. 2008. Statistical Analysis of Understory Vegetation Data from Valley Forge National Historical Park, Pennsylvania, 1993–2003. Technical Report NPS/NER/NRTR—2008/118. National Park Service. Philadelphia, PA.	April 2008
Diefenbach, D. R., and S. A. Christensen. 2009. Movement and habitat use of sika and white-tailed deer on Assateague Island National Seashore, Maryland. Natural Resource Technical Report NPS/NER/NRTR—2009/140. National Park Service, Philadelphia, PA.	July 2009
Diefenbach, D. R., B. J. Irwin, and T. Wagner. 2011. Summary of outcomes for the structured decision making workshop for catch and release trout regulations. State College, PA.	March 2011
Carlson, C.M., Hopkins, M.C., Nguyen, N.T., Richards, B.J., Walsh, D.P., and Walter, W.D. 2018, Chronic wasting disease—Status, science, and management support by the U.S. Geological Survey: U.S. Geological Survey Open File Report 2017-1138, 8 p., https://doi.org/10.3133/ofr20171138.	March 2017
Carline, R., P. Barry, D. Counahan, D. Argent, and W. Kimmel. 2004. Assessment of the paddlefish reintroduction program in Pennsylvania. Final Report submitted to the Pennsylvania Fish and Boat Commission.	October 2004
Carline, R. F., and M. C. Walsh. 2004. Responses of streams to riparian restoration in the Spring Creek watershed, central Pennsylvania. Extended abstract, p. 63-64 in Moore, S. E., R. F. Carline, and J. Dillon. eds. 2004. Working together to ensure the future of wild trout. Proceedings of Wild Trout VIII Symposium - 30th Anniversary, 2004 September 20-22; Yellowstone Park, Wyoming.	October 2004
Carline, R. F., P. Barry, and H. G. Ketola. 2001. Accumulation of PCBs in hatchery trout. Final Report submitted to the Pennsylvania Fish and Boat Commission.	January 2002
Carline, R. F., C. Gill, K. Patten, and A. Smith. 2001. Effects of bridge and road construction on Spring Creek: Route 26 transportation improvement project. Progress report submitted to Pennsylvania Department of Transportation and Pennsylvania Fish and Boat Commission.	January 2001
Carline, R. F. 2005. Designing a sampling protocol for freshwater mussels in large, Pennsylvania rivers. Final Report submitted to the Pennsylvania Fish and Boat Commission. 24 pp.	July 2005
Carline, R. F. 2000. Effects of annual electrofishing with high-frequency DC on wild brown trout. pages 227-228, in D. Schill, S. Moore, P. Byroth, and B. Hamre, editors, Wild Trout VII Management in the new millenium: are we ready?	October 2000

Data or Software Releases

Type	Citation	Publication Date
Software Release	White, S., Waraniak, J., Eackles, M., Keagy, J., Smith, G., Schall, M., Stark, S., Kazyak, D., Wagner, T., 2023, Microsatellite genotypes for flathead catfish used for analysis of genetic structuring in Pennsylvania rivers: U.S. Geological Survey data release, https://doi.org/10.5066/P13QEOK3	December 2023
Software Release	Waraniak, J., M.S. Eackles, J. Keagy, G.D. Smith, M. Schall, S. Stark, S.L. White, D.C. Kazyak, and T. Wagner. Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US mid-Atlantic rivers Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P13VRDLF	March 2024
Software Release	Walter, W.D., Hollingshead, N., Kelly, J., Grove, D., Abbot, R., and Schuler, K. 2023. Input for Habitat Risk Software: U.S. Geological Survey data release, https://doi.org/10.5066/P9CMQWRB.	August 2023
Software Release	Walter, W.D., Fameli, A.F., Russo-Petrick, K. and Edson, J.E. 2023. Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA: U.S. Geological Survey data release, https://doi.org/10.5066/P965MK53.	October 2023
Software Release	Walter, W.D. and Pearce, D. 2023. Evaluation of DNA yield from various sources for use in single nucleotide polymorphism panels: U.S. Geological Survey data release, https://doi.org/10.5066/P96VPBSO.	July 2023
Software Release	Wagner, T., P. McLaughlin, K. E. Faunce, S. Austin, and K. Smalling. The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9JMXJ7B	May 2023
Software Release	Wagner, T., McLaughlin, P., Faunce, K., Austin, S., and Smalling, K., 2023, Accumulated wastewater calculations for smallmouth bass sampling sites in the Shenandoah River Watershed, USA: U.S. Geological Survey data release, https://doi.org/10.5066/P9JTAHXZ.	July 2023
Software Release	Wagner, T., E.M. SchliepFolt, J.S. North, H. Kundel, J.K. Ruzich, C.A. Custer, and G.J.A. Hansen. Predicting climate change impacts on poikilotherms using physiologically guided species abundance models. Version 1.1.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9YYGI5R	July 2022
Data Release	Wagner, T., E.M. SchliepFolt, J.S. North, H. Kundel, J.K. Ruzich, C.A. Custer, and G.J.A. Hansen. Predicting climate change impacts on poikilotherms using physiologically guided species abundance models. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9YYGI5R	April 2024
Data Release	Wagner, T., A. McDonald, and P. Hanly. R and Python code for analysis of productivity in thousands of US lakes in response to climate over the last 30 years. https://doi.org/10.5066/P15PMPVG	January 2024
Data Release	Stark, S., Schall, M.K., and Wagner, T. 2024. Feeding Habits and Ecological Implications of the Invasive Flathead Catfish, Pylodictis olivaris in the Susquehanna River Basin, Pennsylvania. U.S. Geological Survey software release; https://doi.org/10.5066/P9GP5TPH.	August 2023
Software Release	Pearce, D.L. and W.D. Walter. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P96QMZUE	February 2023
Software Release	North, J.S., E.M. Schliep, G.J.A. Hansen, J. Kundel, C.A. Custer, P. McLaughlin, and T. Wagner. 2023. Accounting for spatio-temporal variation in catchability in joint species distribution models. U.S. Geological Software release: https://doi.org/10.5066/P9DALGBL	May 2023
Data Release	Mitchell, C., Walter, W. D., Hollingshead, N., & Schuler, K. 2021. Processing of Geospatial Data for the Habitat Risk Software. Version 1.0. U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9MR2N4H.	January 2024
Software Release	McLaughlin, P., Krause, K., Maloney, K., Woods, T., and Wagner, T. 2023. Evaluating the effectiveness of joint species distribution modeling for riverine fish communities: U. S. Geological survey software release, https://doi.org/10.5066/P9AH5MDN	February 2024
Software Release	Kundel, H., T. Wagner, and G.J.A. Hansen. Widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9IL595W	February 2023
Software Release	Kelly L. Smalling, Kristin M. Romanok, Paul M. Bradley, Mathew C. Morriss, James L. Gray, Leslie K. Kanagy, Stephanie E. Gordon, Brianna M. Williams, Sara E. Breitmeyer, Daniel K. Jones, Collin A. Eagles-Smith, and Tyler Wagner. Per- and Polyfluoroalkyl Substances (PFAS) in U.S. Tapwater: Comparison of Public-Supply and Underserved Private-Well Exposures and Associated Health Implications. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9MCYEVS	October 2022
Software Release	Hanley, B.J., Mitchell, C.I., Walter, W.D., Kelly J., Grove, D., Abbott, R.C., Hollingshead, N., and Schuler, K.L. Habitat Risk Software. U.S. Geological Survey software release, https://doi.org/10.5066/P9541B7T.	August 2023
Data Release	Gundermann K.P. and Buderman F.E. Change-point models for identifying behavioral changes in wild animals. Version 1.0.0: Software release. Reston, Va. https://doi.org/10.5066/P9B2HE47	July 2023
Software Release	Fameli, A.F., Edson, J., and Walter, W.D. 2024, White-tailed deer from culling efforts in Minnesota: U.S. Geological Survey data release, https://doi.org/10.5066/P13BGPFC.	November 2023
Data Release	Fameli, A. K. Russo-Petrick, J.E. Edson, and W.D. Walter. Population genetic structure of white-tailed deer using microsatellites across the Mid-Atlantic. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9XBNYCR	August 2023
Software Release	Custer, C., North, J. S., Schliep, E. M., and Wagner, T. 2023. Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model. U.S. Geological Survey software release, https://doi.org/10.5066/P959EMT5	December 2023
Software Release	Bondo, K.J., D. Montecino-Latorre, W.D. Walter. Workflow to acquire and process large spatial data and build complex models. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9ONHXN3	October 2022
Software Release	Bondo, K.J., D. Montecino-Latorre, W.D. Walter. Workflow to acquire and process large spatial data and build complex models. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9ONHXN3	February 2023
Software Release	Bondo, K.J., D. Montecino-Latorre, W.D. Walter. Workflow to acquire and process large spatial data and build complex models. Version 1.0.0: U.S. Geological Survey software release. Reston, Va. https://doi.org/10.5066/P9ONHXN3	April 2024
Software Release	Bondo, K.J., D. Montecino-Latorre, W.D. Walter. Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximations. Version 1.0.0: U.S. Geological Survey software release. Reston, Va.https://doi.org/10.5066/P9QAB3ZZ	April 2022
Data Release	Bondo, K.J. and W.D. Walter. 2023. Comparing datasets by surveillance method using spatial models. Version 1.0.0: U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P9348BA8	October 2023
Software Release	Bondo, K.J. and W.D. Walter. 2023. Comparing datasets by surveillance method using spatial models. Version 1.0.0: U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P9348BA8	February 2023

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

Pennsylvania Research Activities

Links

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

Pennsylvania Research Activities

Links

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