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

Vermont Research Activities

Vermont Unit collage of photos including a moose, a research technician, Vermont landscapes, and bobcat.

The Cooperative Research Units Program conducts research on a wide range of disciplines related to fish, wildlife, and natural resource management. The programs offer Federal and State agencies access not only to unit scientists, but also to university expertise and facilities available at each of the 40 cooperating universities. Most research projects are carried out by graduate students participating with and/or under the direction of unit or other university scientists.

The research may be of local, regional, national, or international interest. The research programs conducted by units are approved as directed by the Coordinating Committee overseeing each unit.

Projects

Project	Completion Date
Assessment of Stonecat (Noturus flavus) populations in the Missisquoi and LaPlatte rivers of Vermont	September 2016	Stonecat (Noturus flavus) are known to populate two rivers in Vermont, the Missisquoi and LaPlatte rivers located in the Lake Champlain watershed, and as such is a state listed endangered species and species of greatest conservation need. Little was known about Stonecat populations in Vermont including their abundance and other population parameters in the Missisquoi and LaPlatte rivers, distribution and habitat availability and use, and population viability and persistence. This project assessed Stonecat populations in both rivers resulting in quantifying population parameters necessary to assess risks to populations. The project identified risk assessment models that offer opportunities for further evaluation of the likelihood of sustaining Stonecat populations in Vermont in the face of possible sources of mortality.	Stonecat (Noturus flavus) are known to populate two rivers in Vermont, the Missisquoi and LaPlatte rivers located in the Lake Champlain watershed, and as such is a state listed endangered species and species of greatest conservation need. Little was known about Stonecat populations in Vermont including their abundance and other population parameters in the Missisquoi and LaPlatte rivers, distribution and habitat availability and use, and population viability and persistence. This project assessed Stonecat populations in both rivers resulting in quantifying population parameters necessary to assess risks to populations. The project identified risk assessment models that offer opportunities for further evaluation of the likelihood of sustaining Stonecat populations in Vermont in the face of possible sources of mortality.
Genomic forensics: using bioinformatics to investigate the causes of melanistic lesions in Brown Bullhead	September 2028	Brown Bullhead catfish are scaleless bottom dwellers, which make them ideal indicator species to study the effects of contaminants. Using fish genomics to understand and prevent environmental contamination.	None
Connecticut River Migratory Fish	September 2018	Recently much of the popular science literature has focused on the concept of climate change. Thus far, there have been some very simple predictions on how climate change will affect temperature, especially in more northern latitudes. As ectotherms, fish are affected directly by any changes in temperature, which can range from altering foraging, reproduction, metabolism, migration timing, etc. In the Connecticut River, anadromous fish (e.g., Atlantic salmon (Salmo salar), American shad (Alosa sapidissima), sea lamprey (Petromyzon marinus)) are predicted to change migration patterns in relation to climate change. The life cycle complexity of migratory species introduces several unknowns regarding the transitions from freshwater to marine and back, and from tributary to mainstem in some species. The changing thermal regime will be accompanied by changes in discharge as a component of the altered water cycle. Predictions of changes in shorter-term weather patterns include more severe events; e.g., a tornado occurred in Vermont on May 9, 2009 and Hurricane Irene caused major damage in Vermont tributaries in August 2011. This backdrop provides an opportunity to expand on our previous modeling of Atlantic salmon migration in the Connecticut River. We explored how temperature, discharge, and the indirect effects of dams (by creating delays in migration) were related to survival of Atlantic salmon smolts. We worked in this area for several years using data from previous monitoring and research. The final phase of our efforts was to model juvenile American shad migration in response to changing environmental conditions.	In the Connecticut River, anadromous fish (e.g., Atlantic salmon (Salmo salar), American shad (Alosa sapidissima), sea lamprey (Petromyzon marinus)) are predicted to change migration patterns in relation to climate change. The life cycle complexity of migratory species introduces several unknowns regarding the transitions from freshwater to marine and back. This backdrop provided an opportunity to expand on our previous modeling of Atlantic salmon migration in the Connecticut River. We explored how temperature, discharge, and the indirect effects of dams (by creating delays in migration) were related to survival. In the last phase of this research, we collaborated with Vermont Fish and Wildlife in modeling American shad a mainstem spawner. Our results showed how temperatures and flow regimes can affect juvenile American shad and their success under changing conditions.
Mudpuppies in Vermont: sampling methods and genetics	June 2010	In this study, we focused on developing methods to effectively sample mudpuppies (Necturus maculosus) in the Lamoille River. The sampling area was primarily the 1-km reach immediately below the Peterson Dam. The primary findings were: • Modified minnow traps set between late fall and early spring were the only effective sampling method. Both adult and large juvenile mudpuppies were captured using this technique. Snorkeling, dip netting, and use of coverboards for collecting eggs did not result in any captures. Electrofishing and seining were not used because the Lamoille River is too deep and turbid for those techniques. • From late 2008 until May 2010, we captured a total of 167 individual mudpuppies in 173,712 trap hours (7,238 trap days). Of the 167 mudpuppies, 30 were recaptured at least one time within the same winter. • Capture probability estimates based on modeling were highest when water temperature was between 4 and 6 C. Correspondingly, the highest capture rates occurred in late fall and early spring when water temperature was about 4-6 C. No significant differences were found between mudpuppy capture rates and 1) primary substrate type, 2) secondary substrate type, or 3) water depth. • Capture probability was positively correlated with the presence of a prey animal (minnow or crayfish) in the trap during winter 2009 and fresh bait during winter 2010. Capture probabilities from trapping peaked at about 0.03, which is similar to the capture probability for salamanders in other studies. • Age class distribution of non-target mortalities collected following TFM treatment on 1 October 2009 indicate that all age classes are present in the Lamoille River. • Movement was determined based on time and distance between trap capture events. Mudpuppies moved an average distance of 82 m. The largest movements (>150 m) were in an upstream direction, undertaken by both sexes, and occurred almost entirely in the early spring. • The sex ratio of trapped mudpuppies changed significantly between the two years, from an even ratio in winter 2009 to male-biased in winter 2010. • We used Program MARK to estimate the annual population size and apparent monthly survival of mudpuppies across 2 years in the area of 3 140-m trap arrays set over a 1-km reach. The modeled population size estimate for the trap array area was 335 (154 males, 181 females) during winter 2009 and 132 (117 males, 15 females) during winter 2010. Apparent monthly survival estimates during the 2 years for both sexes were about 0.87. All estimates had large 95% confidence intervals. • Mudpuppy tissue samples (N=600) were collected for genetic analysis from 9 different aquatic systems in the northeast.	In this study, we focused on developing methods to effectively sample mudpuppies (Necturus maculosus) in the Lamoille River. The sampling area was primarily the 1-km reach immediately below the Peterson Dam. The primary findings were: • Modified minnow traps set between late fall and early spring were the only effective sampling method. Both adult and large juvenile mudpuppies were captured using this technique. Snorkeling, dip netting, and use of coverboards for collecting eggs did not result in any captures. Electrofishing and seining were not used because the Lamoille River is too deep and turbid for those techniques. • From late 2008 until May 2010, we captured a total of 167 individual mudpuppies in 173,712 trap hours (7,238 trap days). Of the 167 mudpuppies, 30 were recaptured at least one time within the same winter. • Capture probability estimates based on modeling were highest when water temperature was between 4 and 6 C. Correspondingly, the highest capture rates occurred in late fall and early spring when water temperature was about 4-6 C. No significant differences were found between mudpuppy capture rates and 1) primary substrate type, 2) secondary substrate type, or 3) water depth. • Capture probability was positively correlated with the presence of a prey animal (minnow or crayfish) in the trap during winter 2009 and fresh bait during winter 2010. Capture probabilities from trapping peaked at about 0.03, which is similar to the capture probability for salamanders in other studies. • Age class distribution of non-target mortalities collected following TFM treatment on 1 October 2009 indicate that all age classes are present in the Lamoille River. • Movement was determined based on time and distance between trap capture events. Mudpuppies moved an average distance of 82 m. The largest movements (>150 m) were in an upstream direction, undertaken by both sexes, and occurred almost entirely in the early spring. • The sex ratio of trapped mudpuppies changed significantly between the two years, from an even ratio in winter 2009 to male-biased in winter 2010. • We used Program MARK to estimate the annual population size and apparent monthly survival of mudpuppies across 2 years in the area of 3 140-m trap arrays set over a 1-km reach. The modeled population size estimate for the trap array area was 335 (154 males, 181 females) during winter 2009 and 132 (117 males, 15 females) during winter 2010. Apparent monthly survival estimates during the 2 years for both sexes were about 0.87. All estimates had large 95% confidence intervals. • Mudpuppy tissue samples (N=600) were collected for genetic analysis from 9 different aquatic systems in the northeast.
Rainbow smelt and alewife in Lake Champlain	January 2014	Alewife became established in the 2000s, and are now quite abundant in most basins of Lake Champlain. Previous work on this project studied the distribution of rainbow smelt and alewife in relation to the abiotic environment, and predictive distribution models were created. We used those models, and empirical relationships between distribution and cannibalism, to simulate population and community dynamics for rainbow smelt and alewife. The model was used both to simulate possible future changes in the abiotic environment, and possible management decisions. Our distribution models and data were used to aid fish sampling design, and we compared trawl and acoustic sampling techniques in addition to developing shallow-water sampling methods. We also studied how predators have responded to alewife as new potential prey. Tissue samples were analyzed to determine carbon and nitrogen stable isotope concentrations, and thus trophic positions in the system. Adult rainbow smelt feed at a higher trophic level than adult alewives, and Atlantic salmon consume alewife in addition to rainbow smelt. The basic ecology of mysids (Mysis diluviana) in Lake Champlain was also studied, including trophic relationships, bioenergetics, growth, and abundance. This wass the first such study in this lake.	Alewife became established in the 2000s, and are now quite abundant in most basins of Lake Champlain. Previous work on this project studied the distribution of rainbow smelt and alewife in relation to the abiotic environment, and predictive distribution models were created. We used those models, and empirical relationships between distribution and cannibalism, to simulate population and community dynamics for rainbow smelt and alewife. The model was used both to simulate possible future changes in the abiotic environment, and possible management decisions. Our distribution models and data were used to aid fish sampling design, and we compared trawl and acoustic sampling techniques in addition to developing shallow-water sampling methods. We also studied how predators have responded to alewife as new potential prey. Tissue samples were analyzed to determine carbon and nitrogen stable isotope concentrations, and thus trophic positions in the system. Adult rainbow smelt feed at a higher trophic level than adult alewives, and Atlantic salmon consume alewife in addition to rainbow smelt. The basic ecology of mysids (Mysis diluviana) in Lake Champlain was also studied, including trophic relationships, bioenergetics, growth, and abundance. This wass the first such study in this lake.
Adaptive Management with AMMonitor	August 2025	Adaptive management (AM) is a cyclical process that improves natural resource management and generates knowledge that can inform future decisions. Autonomous monitoring units (AMUs) such as camera traps or recording devices provide opportunities to collect large volumes of species’ occurrence data over long periods of time with relatively low cost. However, the data management requirements of an AMU-based monitoring effort can be immense: processing audio/image data to generate detections can be complicated, and integrating streams of AMU data into species’ distribution models or other analyses may appear unattainable.<br><br>To operationalize AM, the USGS Vermont Cooperative Fish and Wildlife Research Unit created the open-source R package <i>AMMonitor</i>, which simplifies the process of moving from remotely collected data to species’ status, trend analysis, and reports.<br><br>The objectives of this project are to 1) Strengthen and expand the AMMonitor community, and 2) Develop the photographic monitoring capacity of AMMonitor. The Vermont Cooperative Fish and Wildlife Research Unit is working with USGS ScienceBase to facilitate and document monitoring files as a permanent data repository. Further, we are working with USGS Cloud Hosting to develop CNN models to identify species within monitoring files (images, audio) in an automated fashion. The results of this work should streamline data analysis and ultimately permit adaptive management of natural resources in an expedient manner.	Problem statement:<br>Automated monitoring of wildlife with remote camera and recording devices is a cost-effective way to monitor species across vast spaces and time. However, the data management requirements of an AMU-based monitoring effort can be immense: processing audio/image data to generate detections can be complicated, and integrating streams of AMU data into species’ distribution models or other analyses may appear unattainable.<br><br>Why this research matters:<br>Land use change and climate change are dual forces that are shifting the distribution patterns of many wildlife species. Natural resource managers tasked with maintaining viable wildlife populations require in-time data to understand changes in species distribution, and tools that enable them to act<br><br>Collaboration/Partners (1 sentence):<br>The project is a collaboration of researchers across multiple agencies, including USGS ScienceBase, USGS Cloud Computing, and the National Park Service's Natural Sounds and Night Skies Division.<br><br>Research That Informs Decisions:<br><br>AMMonitor is an R package/tool that allows agencies that monitor wildlife remotely to easily manage, archive, and analyze data for their own purposes.
Effects of habitat, density, and climate on moose and winter tick ecology in the northeast US	August 2024	Moose (<i>Alces alces</i>) populations in the northeastern US have declined by over 50% in the past 15 years. Winter tick (<i>Dermacentor albipictus</i>) infestations are a major driver of moose population trends, negatively affecting both survival and reproduction. We will partner with cooperators in Maine, Massachusetts, New Hampshire, New York, and Vermont to measure winter tick and moose distribution and abundance on a large camera trapping array. We will use our data to evaluate moose-tick dynamics across the full distribution of moose in New England. In doing so we can examine the relative importance of climate, habitat, and moose density in driving damaging epizootic conditions.	Moose (<i>Alces alces</i>) populations in the northeastern US have declined by over 50% in the past 15 years. Winter tick (<i>Dermacentor albipictus</i>) infestations are a major driver of moose population trends, negatively affecting both survival and reproduction. We measure winter tick and moose abundance on a large camera array to examine the relative importance of climate, habitat, and moose density in driving damaging epizootic conditions. This regional effort has the full support of partner agencies, who will assist in the collection of data (Vermont Fish and Wildlife Department, New Hampshire Fish and Game, Maine Department of Inland Fisheries and Wildlife, and Massachusetts Division of Fisheries and Wildlife, State College of New York, White Mountain National Forest, and Green Mountain National Forest). Our work will improve the monitoring efforts and provide excellent monitoring data to support management decisions at the regional scale.
Population Dynamics, Foraging Ecology, and Optimal Management of Double-crested Cormorants on Lake Champlain	December 2008	Cormorants are a recent addition to the avifauna of Lake Champlain and have since become a concern to wildlife managers. They first nested on Young Island, Vermont, in 1981; they expanded to Four Brothers Islands, New York, by 1984, and peaked at > 20,000 birds in 1999. Population increases were associated with destruction of vegetation and displacement of other birds from nesting colonies. In 1999, Vermont Department of Fish and Wildlife and U.S.D.A. Wildlife Services began spraying cormorant eggs with corn oil to prevent hatching and limit recruitment on Young Island. By 2001, this colony decreased in size by 58% and the Four Brothers colony increased by 78%, making it the largest colony on Lake Champlain. In other locations, cormorant populations are managed to limit negative effects on fish populations. In 2001, we began studies to 1) determine if oiling eggs increases dispersal away from Young Island, 2) estimate the quantity of fish consumed by cormorants, and 3) develop tools to identify optimal strategies for cormorant management based upon knowledge of their population dynamics. To determine how cormorants respond to egg oiling, we implemented an experiment on Young Island from 2001-2004. The experiment included oiling eggs in some areas of the cormorant colony and allowing cormorants to reproduce in other areas. We individually marked birds and tracked their movements between Young and Four Brothers Islands. We found that oiling eggs increased the proportion of cormorants that dispersed away from Young Island by 0.03. Predation of eggs by gulls, which occurs when eggs are oiled during daytime, increased dispersal by 0.20 when frequent day-time oilings were applied. Cormorant colonies on Lake Champlain interact through dispersal of individuals, and management actions increased dispersal rates. We constructed an energetics model for cormorants from Young and Four Brothers Islands to estimate fish consumption for 2001-2003. The model estimated energy requirements by combining data on duration of time cormorants spent in various activities with energy requirements for these activities. Cormorants from Young Island rested more and traveled shorter distances to foraging locations than cormorants from Four Brothers Islands. We estimated that fish consumption ranged from 320,000 – 416,000 kg of fish for Young Island and 877,000-1,066,000 kg on Four Brothers Islands. Differences in fish consumption were due to differences in energy demands and population sizes between colonies. An unanticipated consequence to management on Young Island was changes in patterns of fish consumption by cormorants across Lake Champlain. We also developed a tool that wildlife managers can use to identify optimal strategies for cormorant management on Lake Champlain. This tool was based on a population model for cormorants, which was parameterized from an analysis of observations of marked cormorants from 2001-2006. We projected population changes expected when individual colonies were managed. These projections were then incorporated into a decision analysis to identify optimal management strategies for a given objective and a set of alternative management actions. Optimal management strategies to reduce sizes of cormorant populations included management at multiple colonies.	None
Grassland Population Viability in the Champlain Valley	December 2009	Over the last 40 years North American grassland bird populations have declined more than any other bird guild. This trend is especially evident in Vermont, where species experiencing precipitous declines include the Savannah Sparrow (Passerculus sandwichensis) and Bobolink (Dolichonyx oryzivorus). These declines are linked to habitat loss due to reforestation and suburbanization, as well as the intensification of grassland management. Modern grassland management includes earlier first-haying dates (late-May) and shorter intervals between haying events (35 days). These management practices have severe repercussions for songbird populations because 1) early-haying results in complete nest failure (99% Savannah Sparrow and 100% Bobolink nests) , 2) the interval between the first and second haying is too short for birds to renest, and 3) intensively managed fields comprise a significant portion of the total available habitat for nesting birds (as much as 40%). In 2002-2006, we examined how hayfield and pasture management affected grassland songbird ecological and evolutionary behavior in the agricultural landscape of the Champlain Valley, Vermont and New York. Our collaborators include Allan Strong and Austin Troy from the University of Vermont, and Neil Buckley from Plattsburg State University. We studied songbirds in four grassland management types: early-hayed fields harvested in late-May or early-June and again in mid-July; middle-hayed fields harvested in late-June or early-July; late-hayed fields harvested after 1 August; rotationally-grazed pastures, a matrix of small paddocks where cows are moved after the grass in a paddock is eaten to a low point. We addressed the following objectives: 1. Determine the annual productivity, survival, and recruitment of Bobolinks and Savannah Sparrows in the four treatment types. 2. Identify the effects of early-haying on the social and genetic mating systems of Savannah Sparrows. 3. Conduct a population viability analysis for Bobolinks and Savannah Sparrows nesting in the Champlain Valley, assessing sensitivities of life-history parameters and identifying effective management alternatives. This study provides information on how agricultural management affects the ecology, evolution, and viability of grassland birds. It will help inform landowners, managers, and law-makers about management practices and habitat requirements needed to sustain populations. Check out our publications by clicking on a link below.	Over the last 40 years North American grassland bird populations have declined more than any other bird guild. This trend is especially evident in Vermont, where species experiencing precipitous declines include the Savannah Sparrow (Passerculus sandwichensis) and Bobolink (Dolichonyx oryzivorus). These declines are linked to habitat loss due to reforestation and suburbanization, as well as the intensification of grassland management. Modern grassland management includes earlier first-haying dates (late-May) and shorter intervals between haying events (35 days). These management practices have severe repercussions for songbird populations because 1) early-haying results in complete nest failure (99% Savannah Sparrow and 100% Bobolink nests), 2) the interval between the first and second haying is too short for birds to renest, and 3) intensively managed fields comprise a significant portion of the total available habitat for nesting birds (as much as 40%). In 2002-2006, we examined how hayfield and pasture management affected grassland songbird ecological and evolutionary behavior in the agricultural landscape of the Champlain Valley, Vermont and New York. Our collaborators include Allan Strong and Austin Troy from the University of Vermont, and Neil Buckley from Plattsburg State University. We studied songbirds in four grassland management types: early-hayed fields harvested in late-May or early-June and again in mid-July; middle-hayed fields harvested in late-June or early-July; late-hayed fields harvested after 1 August; rotationally-grazed pastures, a matrix of small paddocks where cows are moved after the grass in a paddock is eaten to a low point. We addressed the following objectives: 1. Determine the annual productivity, survival, and recruitment of Bobolinks and Savannah Sparrows in the four treatment types. 2. Identify the effects of early-haying on the social and genetic mating systems of Savannah Sparrows. 3. Conduct a population viability analysis for Bobolinks and Savannah Sparrows nesting in the Champlain Valley, assessing sensitivities of life-history parameters and identifying effective management alternatives. This study provides information on how agricultural management affects the ecology, evolution, and viability of grassland birds. It will help inform landowners, managers, and law-makers about management practices and habitat requirements needed to sustain populations.
Acoustical Monitoring of Biodiversity and Phenology: A Pilot Wildlife Monitoring Partnership for Adaptive Management	December 2012	A primary principle guiding the management of the state and federal lands is to conserve and enhance habitats that support a full range of native flora and fauna. Two serious forces threaten the viability of native flora and fauna today: land use change and global climate change. <br /><br />Confronting these resource management challenges requires, first and foremost, robust data to accurately predict how biodiversity will respond to land-use and climate change, and a process that links this information to landuse planning efforts and resource management in a continual way (i.e., adaptive management). The first step in this process, gathering and monitoring biodiversity data, is extremely challenging. First, the sampling area is vast. Second, not all wildlife species can be monitored; many are secretive or rare and are not easily counted by humans (e.g., black bears). Third, even if a few, target species were monitored, field-based monitoring by humans across the entire state of Vermont would be cost prohibitive. <br /><br />One potential solution to these challenges is to establish an acoustical monitoring network, where 1) vocalizations made by indicator wildlife species are recorded continually at sampling stations located throughout the sampling area, 2) recorded sounds are delivered to a central database where computers are used to identify species-specific sounds, and 3) the acoustical data can be accessed and used by natural resource managers in a structured decision making/adaptive management framework. <br /><br />Our goal in this pilot effort is to field test acoustical techniques, database development, computer-automated animal identification, and programmatic methodologies. Through this study, we hope to identify opportunities and constraints for establishing a large-scale acoustic monitoring program. This pilot study is a partnership between the National Park Service, the National Phenology Network, the Vermont Fish and Wildlife Department, and the Vermont Cooperative Fish and Wildlife Research Unit.	None
Structured Decision Making for Land Use Planning in Vermont: Integrating Social and Ecological Objectives	March 2015	The most serious threat to native wildlife species in the Northern Forest is the conversion of natural lands to development. Many wildlife species that live in the Northern Forest require large areas to carry out their life cycle, suggesting a landscape scale approach is needed to ensure long term biological conservation. However, top-down landscape level planning is challenging in the Northern Forest, where the majority of lands are under private ownership, resulting in landscape patterns that are driven from the bottom-up. That is, individual decisions made by local land owners and towns acting in their own interest collectively determine landscape quality for wildlife species, for better or worse. The issue of how to “design” a landscape that meets the needs of multiple interests is inherent in the town planning process. Often, however, wildlife is a silent stakeholder in this process. The goal of this project is to develop a prototype of a Structured Decision Making (SDM) process that will bring wildlife to the table in local town planning efforts. The first phase of the Structured Decision Process is to develop measurable objectives (indicators + standards), such as “Ensure that at least 40% of the town is forested.” To establish indicators and standards for development for 8 Vermont towns, we will develop visual preference surveys that combine CommunityViz software and Google Earth. Residents will be surveyed and asked to respond to visual images of varying levels of development, agriculture and natural lands within their local community. Results of the survey will establish town planning objectives in terms of development, forest, and agriculture for each town. Given individual town objectives, we will use data from previous NSRC efforts to assess the likely ecological consequences of these “norms” for a variety of forest-dependent wildlife species. This process will, for the first time, allow state biologists to evaluate how planning objectives for a collection of local towns acting will likely impact landscape quality for wildlife species. Our goal, ultimately, is to make develop this process so that all communities in Vermont have access to this approach, thus providing state resource managers with an opportunity to determine if state-wide wildlife objectives will likely be met through individual town planning processes.	Problem statement: The most serious threat to native wildlife species in the Northern Forest is the conversion of natural lands to development. So What? Why this research matters: In Vermont, individual decisions made by local land owners and towns acting in their own interest collectively determine landscape quality for wildlife species, for better or worse. The goal of this project is to access how willing Vermonters are to convert natural lands to development, and spatially map those consequences on a town-by-town basis. Collaboration/Partners (1 sentence): The project is a collaboration of researchers in the Vermont Cooperative Fish and Wildlife Research Unit, UVM's Rubenstein School, and Vermont Fish and Wildlife biologists. Research That Informs Decisions (i.e. how the research will be used, 1-2 sentences): This research will allow state biologists to evaluate how planning objectives for a collection of local towns acting will likely impact landscape quality for wildlife species.
Using Relational Databases to Improve Structured Decision Making for Natural Resource Management	September 2012	A major initiative of the USGS Cooperative Research Unit (CRU) Program is teach and apply formal structured decision making approaches to the management of natural resources. Structured decision making, or SDM, is “an organized approach to identifying and evaluating creative options and making choices in complex decision situations.” In the context of natural resource management, SDM is designed to deliver insight to natural resource decision makers about how well their management objectives may be satisfied by potential alternative courses of action. The SDM process generally involves identifying the natural resource management problem, setting management objectives, identifying potential alternative management actions, estimating the likely consequences of each alternative (often through rigorous quantitative modeling), and then weighing each alternative and identifying trade-offs among alternatives. When the same decision problem is tackled on a recurrent basis, new (updated) information is used to provide fresh perspectives on alternatives, their likely outcomes, and trade-offs. “Adaptive management” is the application of SDM approaches when a decision problem is iterative. This project proposes to meld the disciplines of computer science and natural resources management, by investigating and developing efficient ways to identify, collect, serve, and analyze data to support state-based natural resources management problems.	a
Predicting Impacts of Future Human Population Growth and Development on Forest-dependent Wildlife Species	June 2012	Forest loss is perhaps the most important contemporary issue in the Northeast for wildlife species. Given increasing forest loss and fragmentation, the “problem” of how native fauna will respond to eminent land-use change is widespread, and requires tools and methods for understanding population responses as well as management recommendations for conservation. This study will integrate wildlife habitat modeling with GIS models of human population growth to quantify how various forest-dependent wildlife species will respond to projected increases in human population growth (year 2020) for the state of Vermont. The Vermont Cooperative Fish and Wildlife Researcher is collaborating with Dr. David Theobald (Colorado State University) on this work. The study will advance conservation planning by: 1) providing GIS layers on the contemporary distribution (probability of occurrence) for selected forest-dependent species; and 2) providing GIS layers that quantify risk for these same species given future human population growth and development.	None
Minimum Habitat Requirements of the Indiana Bat in the Champlain Valley	December 2006	Indiana bats are medium-sized, brown bats less than 2 inches long that live in the Eastern and Midwestern United States. The Indiana bat was listed as endangered in 1967 under the federal Endangered Species Act of 1973. About 350,000 individuals of this species still exist. Human disturbance, cave commercialization, habitat loss, and pesticides are identified as potential threats to the persistence of this species (USFWS, 1991). The Indiana bat’s natural history is similar to other Myotis species. They hibernate in caves or abandoned mines during the winter. During summer, females roost under the peeling bark of dead and dying trees in groups (maternity colonies) of up to 100 bats or more. Breeding females in the colony give birth to a single pup per year. The mother nurses the young, and young stay with the maternity colony throughout most of their first summer. Migration to the wintering caves usually begins in August, and bats mate in early October before they enter caves for hibernation. Current conservation efforts in Vermont and New York are devoted towards protection of hibernacula. However, a full, well-integrated understanding of the summer needs of individuals has yet to be reached. This lack of knowledge potentially impedes wildlife managers from identifying critical resource needs throughout the annual cycle. Information gaps include 1) information on the identification of roosting and maternity trees in the Champlain Valley, and 2) identification of critical local and landscape habitat features that support roosting, maternity, and feeding behaviors. The Vermont Cooperative Fish and Wildlife Research Unit has partnered with the Susi von Oettingen (USFWS), Scott Darling (Vermont Fish and Wildlife Department), and Al Hicks (New York DEC) to conduct research to fill these key information needs.	None
Vermont Biodiversity Monitoring Project	December 2012	Land use change involves the conversion of one land cover type to another, and often results in the loss and fragmentation of existing wildlife habitat. Although large areas of contiguous habitat still remain in the Northern Forest, increasing development pressures results in the conversion of forests land types to urban, suburban, or exurban land types. In Vermont, for example, the rate of land development is ~ 260% greater than the rate of population growth, where land growth consists primarily of “small urban build up,” i.e., small, unconnected blocks of land that develop within a matrix of less developed land – an effective facilitator of habitat fragmentation for many wildlife species. These trends indicate that research focused on understanding the impacts of land use change on the region’s native flora and fauna is much needed. Because different species are expected to respond to land use and climate change in different ways, these assessments should target both individual species and changes in species richness and biological community composition over time. In 2003-2004, we surveyed plants and animals at over 200 sites across Vermont. The dataset consists of 36,000 bird records, 7,000 amphibian/reptile records, 200 carnivore records, and several thousand invertebrate records and tree records that were collected Sites were separated by ≥ 8 km, and consisted of 4 survey stations that were separated by 500 meters. Survey methods were taxon-specific. Local vegetation was quantified at each station with standard sampling techniques, and landscape pattern surrounding each station was characterized based on 2001 National Landcover. The data for vertebrates are be analyzed as presence-absence on a species-by-species basis with a single-season occupancy-modeling framework with local, landscape, and climatic variables as covariates, which allowed us to generate probability of occurrence maps for multiple taxa across the entire state of Vermont. These maps provide opportunities for a rich variety of ecological investigations, and provide the baseline data upon which future land use change scenarios can be quantitatively assessed.	None
Home Range, Habitat use, and Movements of Bobcats in Vermont	December 2010	The goal of this study is to evaluate habitat use and movements of bobcats (Felis rufus) in northwestern Vermont in order to direct future conservation actions for this species. In northwestern Vermont, rocky ledges, wetlands, and corridors appear to be important habitat, based on trapper surveys and sightings. As with other species in northwestern Vermont, bobcat habitat is threatened by the rapid pace at which agricultural and forest lands are being developed (Vermont Forum on Sprawl, 1999), which results in loss of potential breeding habitat and loss of habitat connectivity. Additionally, increased traffic volume associated with increased development place bobcats at risk. As a result of these potential threats, a standardized study that investigates basic habitat use and movements in response to land pattern and human activity is needed. The data collected and concomitant analyses will aid in developing a targeted conservation plan that attempts to proactively conserve bobcat habitats. This information will be used conservation planning for the bobcat population in Vermont.	The goal of this study is to evaluate habitat use and movements of bobcats (Felis rufus) in northwestern Vermont in order to direct future conservation actions for this species. In northwestern Vermont, rocky ledges, wetlands, and corridors appear to be important habitat, based on trapper surveys and sightings. As with other species in northwestern Vermont, bobcat habitat is threatened by the rapid pace at which agricultural and forest lands are being developed (Vermont Forum on Sprawl, 1999), which results in loss of potential breeding habitat and loss of habitat connectivity. Additionally, increased traffic volume associated with increased development place bobcats at risk. As a result of these potential threats, a standardized study that investigates basic habitat use and movements in response to land pattern and human activity is needed. The data collected and concomitant analyses will aid in developing a targeted conservation plan that attempts to proactively conserve bobcat habitats. This information will be used conservation planning for the bobcat population in Vermont.
Wildlife Monitoring in the U.S. National Parks with Cell Phones	September 2023	The purpose of this pilot research effort is to incorporate adaptive management methodologies into the Indiana Dunes National Lakeshore's Resource Stewardship Strategy (RSS). The primary focus is on monitoring wildlife species that vocalize, including birds and amphibians. This effort is intended to ensure that management actions taken to restore the wetlands and savannas at Indiana Dunes National Lakeshore are effective. This critical research will incorporate cutting-edge technologies and approaches such as machine learning to recognize species. The use of cell phones to collect and transmit acoustic data and imagery automatically is novel and has potential to significantly benefit science, the local community, and recreational and educational opportunities.	The purpose of this pilot research effort is to test a protocol for incorporating wildlife monitoring and analysis into the Indiana Dunes National Lakeshore's Resource Stewardship Strategy (RSS). The Indiana Dunes is a model of active restoration of wetlands and savannas. Monitoring in real time can provide feedback on whether management activities have been successful in achieving the Lakeshore's management objectives. The project is a collaboration of researchers at the Vermont Cooperative Fish and Wildlife Research Unit and the U.S. National Park Service. This pilot study will place the Indiana Dunes National Lakeshore's Resource Stewardship Strategy (RSS) into an adaptive management framework, which will facilitate management decisions in the future.
Population Ecology of Moose in Vermont	June 2024	Concern has risen in Vermont and neighboring states over the past decade regarding high mortality and low recruitment rates of resident moose populations, causing population declines. High winter tick (Dermacentor albipictus) infestations are considered to be a major cause of these trends. The Vermont Fish and Wildlife Department utilizes population models to estimate regional moose numbers and determine appropriate management actions. Model inputs such as age structure, sex ratio, and mortality and recruitment rates are inputs to this model. Management of Vermont’s moose would benefit greatly from more precise estimates of these rates and a population viability assessment. This proposal is to investigate rates of moose mortality, productivity, recruitment, and genetics of moose populations over a three-year period in Wildlife Management Units E1 and E2, which collectively constitute moose management region “E”. This region contains 632 square miles of moose habitat, and hosts the highest moose densities (up to 1.75 moose/sq. mi), highest winter tick loads, and low deer densities. This project is a collaboration between the Vermont Cooperative Fish and Wildlife Research Unit, the University of Vermont, and the Vermont Fish and Wildlife Department. It builds on work done in the neighboring states of New Hampshire, Maine, and New York. The study will contribute to a broader understanding of moose population trends in the Northeast region.	In the past decade, concern has risen in Vermont and neighboring states regarding high mortality and low recruitment rates of resident moose populations. High winter tick (Dermacentor albipictus) infestations are considered to be a major cause of these trends. The rapidly declining moose population may result in the local extinction of this iconic species from Vermont. Information is needed on age-specific survival rates, cause of mortality, and habitat selection in relation to winter tick load. This project is a collaboration between the Vermont Cooperative Fish and Wildlife Research Unit, the University of Vermont, the Vermont Fish and Wildlife Department, and the U.S. Geological Survey. The research will provide estimates of survival and reproductive rates of moose in Vermont, and identify critical habitats and gene flow. More precise estimates of mortality and recruitment rates and the factors that affect these vital rates will provide the Vermont Fish and Wildlife Department information needed to help to reverse this trend.
Development of methods to assess lake sturgeon populations in Lake Champlain	December 2021	Lake sturgeon Acipenser fulvescens are widely distributed in freshwater systems throughout North America, occupying both lake and riverine habitats. Like other members of the sturgeon family, lake sturgeon are long lived, slow to mature, display intermittent spawning, have high fecundity and low natural mortality. Despite their low natural mortality, these life history characteristics make them especially vulnerable to overexploitation. Lake sturgeon populations have declined throughout the range of the species due to factors including habitat loss and overfishing, and are listed as extirpated, endangered, threatened, or of special concern in 12 states. The State of Vermont listed the species as endangered in 1975 due to low abundances in Lake Champlain. In the late 1800s and early 1900s a small commercial fishery for sturgeon existed Lake Champlain, however current numbers are unknown and likely represent a small fraction of the historic population. Since 1998, the Vermont Department of Fish and Wildlife (VTFW) has conducted sampling that has documented adult spawners, eggs, and larvae in the Winooski, Lamoille, and Missisquoi rivers. Spawning adults have not been documented in Otter Creek, a historic spawning tributary of Lake Champlain. Successful reproduction is occurring in multiple rivers in the lake. In this study, we are documenting adult and juvenile movements in the lake and spawning adult movements in the Winooski River and we are working on developing a method to estimate abundance of lake sturgeon in Lake Champlain.	Lake sturgeon Acipenser fulvescens populations have declined throughout its range due to several factors including habitat loss and overfishing, and are listed as extirpated, endangered, threatened, or of special concern in 12 states. The State of Vermont listed the species as endangered in 1975 due to low abundances in Lake Champlain. Since 1998, the Vermont Department of Fish and Wildlife has conducted sampling that documented adult spawners, eggs, and larvae in the Winooski, Lamoille, and Missisquoi rivers. In this study, we are collaborating with Vermont Fish and Wildlife to provide more detailed information that can be used in managing this state endangered fish. Our research determines adult and juvenile movements in the lake and adult spawning movements in the Winooski River. We are using remote technologies in developing methods to estimate the abundance of lake sturgeon in Lake Champlain.
Integrated Forest Ecosystem Assessment to Support Sustainable Management Decisions in a Changing Climate	September 2019	Since the 1970’s, temperatures across the northeastern US have warmed 0.25 degrees Celsius per decade, which has been accompanied by a wide range of biological changes (Hayhoe et al., 2006). Climate change will continue to restructure forests over the coming century, although the details remain uncertain. To refine our understanding of how climate may impact forested ecosystems, this project examines the role of climate in forest ecosystem health and function through a combination of monitoring, experimental and modeling activities. The wildlife component of the project will focus on modeling wildlife distribution of ten key species, including white-tailed deer, American black bear, and moose, under current forest and landscape conditions. Projections of wildlife distribution in the year 2050 will be made in partnership with Harvard Forest's New England Landscape Future's Project -- a community of scientists, business owners, government officials, landowners and non-profit representatives who have developed and analyzed a set of alternative landscape futures (or, “scenarios”) for New England and comparing them to “business as usual.” The resulting maps of current and projected wildlife distribution will be incorporated into a spatial structured decision framework. This framework will allow land managers to compare the probability of management activity success on a pixel by pixel basis, reflecting the complexity of the Northeast’s heterogeneous landscape. This is a large, collaborative effort with many collaborators and graduate students. The wildlife portion of this study is directed by James Murdoch and Therese Donovan, who mentor PhD student Skye Pearman-Gillman.	Since the 1970’s, temperatures across the northeastern US have warmed 0.25 degrees Celsius per decade, which has been accompanied by a wide range of biological changes. Climate change will continue to restructure forests over the coming century, although the details remain uncertain. The wildlife component of the project will focus on ten key species, including high profile species such as white-tailed deer, American black bear, and moose. The resulting maps of current and projected wildlife distribution patterns will be used to assess various management alternatives in a spatial structured decision framework. This is a large, collaborative effort with many collaborators and graduate students. The wildlife portion of this study is directed by Therese Donovan and James Murdoch, who mentor PhD student Skye Pearman-Gillman. Matthew Duveneck (New England Future Scenarios) is a key collaborator. We anticipate the results will inform real world decisions about forest management, land-use planning, green and gray infrastructure investment, and conservation priority-setting.
Advancing Adaptive Management of Harvested Animals with R	June 2019	Wildlife biologists are typically tasked with maintaining viable wildlife populations through time. In its simplest form, a population can gain numbers through the processes of birth or immigration, and can lose numbers through death or emigration. In more complex forms, these numbers are shaped by a myriad of factors. Management of some species includes a regulated harvest season, where hunters are permitted to harvest animals according to set of regulations and thereby contribute to the population's total deaths. When managing a harvested species, a critical challenge is predicting how the wild population will respond to both the harvest and to other environmental factors. If the harvest is too great, the population may decline. And if the harvest is too little, the population may increase to the point of disrupting ecosystem structure and function. Thus, managing the harvest is delicate balancing act. Most state agencies collect data on the age, sex, and number of harvested animals on an annual basis. Fortunately, the data associated with the harvested (dead) animals can provide a glimpse into the status of the living population, making these tasks more tractable. As Gove et al. (2002) suggest, "Intriguingly nested within the age-at-harvest data is information on age and sex composition, survival, and fecundity rates." Because of this, and because of the tremendous effort spent in collecting harvest information across agencies and through time, harvest datasets are among the richest datasets in North America for analyzing the population size, trend, and health of wildlife populations. Agencies are called to implement their harvest programs within an adaptive management (AM) framework. The process generally involves identifying the natural resource management problem, setting management objectives, identifying potential alternative management actions, estimating the likely consequences of each alternative, and then weighing each alternative and identifying trade-offs among alternatives. "Adaptive management" is the application of such approaches when a decision problem is iterative, such that new information can be incorporated into decision making. While a significant amount has been written about the process of adaptive management, in practice it can be difficult to understand how to implement an adaptive management program that seamlessly integrates data collection, models, decision making, analysis, and outputs. To aid this process, the Vermont Cooperative Fish and Wildlife Research Unit is developing a suite of R packages called AMHarvest, AMPop, and AMModels that facilitate adaptive management in practice. R is an open source modeling platform that can be downloaded from the Comprehensive R Network website. The first package, AMModels, has been released on R, and is the linchpin for storing data (inputs) and models (outputs) from an adaptive management program. Work on the AMPop and AMHarvest are ongoing.	Problem statement: Agencies are called to implement their harvest programs within an adaptive management (AM) framework. The process generally involves identifying the natural resource management problem, setting management objectives, identifying potential alternative management actions, estimating the likely consequences of each alternative, and then weighing each alternative and identifying trade-offs among alternatives. "Adaptive management" is the application of such approaches when a decision problem is iterative, such that new information can be incorporated into decision making. So What? Why this research matters (1-2 sentences): While a significant amount has been written about the process of adaptive management, in practice it can be difficult to understand how to implement an adaptive management program that seamlessly integrates data collection, models, decision making, analysis, and outputs. To aid this process, we are developing a suite of R packages called AMHarvest, AMPop, and AMModels that includes a variety of functions for implementing an adaptive management program for harvested species using the open source modeling platform, R (R Core Team, 2013). Collaboration/Partners (1 sentence): The project is a collaboration of the Vermont Cooperative Fish and Wildlife Research Unit, the Vermont Fish and Wildlife Department, and the Maine Department of Inland Fisheries. Research That Informs Decisions (i.e. how the research will be used, 1-2 sentences): The tools developed in this project can aid agencies in organizing their data and metadata, and analyze harvest data in an efficient and repeatable manner.
Advancing Adaptive Management in the Riverside East Solar Energy Zone	January 2020	In a world confronting climate change and rapidly shifting land uses, effective methods for monitoring natural resources are critical to support scientifically-informed management decisions. This study is a pilot study for monitoring the Riverside East Solar Energy Zone (SEZ), a vast area in southern California that may be developed for solar production. The Bureau of Land Management is charged with monitoring wildlife in this area to minimize the effects of the solar production on wildlife species. <br><br>By taking audio recordings of the environment, scientists can acquire presence-absence data to characterize populations of sound-producing wildlife over time and across vast spatial scales. The pilot approach involves the following key elements:<br><br>1. Twenty cell phones are deployed in strategic locations in the SEZ as “prototype” data collection units.<br>2. Each phone is associated with a unique Google account.<br>3. The phones collect audio recordings based on a schedule that is input into Google Calendar, and push the recordings to the cloud on a daily basis.<br>4. Recordings are analyzed for target species.<br><br>Remote acoustic monitoring presents new challenges, however: monitoring programs are often constrained in the total time they can record, automated detection algorithms typically produce a prohibitive number of detection mistakes, and there is no streamlined framework for moving from raw acoustic data to models of wildlife occurrence dynamics. <br><br>In partnership with the U.S Bureau of Land Management’s Riverside East Solar Energy Zone, this study developed a new R software package, AMMonitor, alongside a novel body of work: 1) temporally-adaptive acoustic sampling to maximize the detection probabilities of target species despite recording constraints, 2) statistical learning tools for template-based automated detection of target species, and 3) methods supporting the construction of dynamic species occurrence models from automated acoustic detection data. . Unifying these methods with streamlined data management, the AMMonitor software package supports the tracking of species occurrence, colonization, and extinction patterns through time, introducing the potential to perform adaptive management at landscape scales<br><br>This project is a collaboration of BLM, the Vermont Cooperative Fish and Wildlife Research Unit, and the UVM IGERT SMART program. The primary products are two open-source R packages (AMModels and AMMonitor), coupled with a SQLite database that stores not just recording results but also the full suite of information required to effectively run a wildlife monitoring program. <br>	The Riverside East Solar Energy Zone (SEZ) is vast area in southern California designated for large-scale solar development. The Bureau of Land Management is charged with monitoring wildlife in this area to minimize the effects of the solar production on wildlife species. However, consistent monitoring of wildlife across vast spatial landscapes over time has proven to be a daunting challenge. This study investigates if cell phones can be used as a primary monitoring tool for documenting wildlife occurrence through time and space, and develops data management and software that allow rapid analysis and reporting. The primary product of this effort is the open-source software package, called AMMonitor. This project is a collaboration between scientists at the USGS Vermont Cooperative Fish and Wildlife Research Unit and BLM. In a world confronting climate change and rapidly shifting land uses, cost- and time-effective methods for monitoring natural resources are critical to support scientifically-informed management decisions. By combining remote data collection methods with a streamlined data management and analysis, the AMMonitor software package supports the tracking of species occurrence, colonization, and extinction patterns through time, introducing the potential to place monitoring initiatives within an adaptive management framework.

Research Publications

Research Publications	Publication Date
Zale, A.V., T.M. Sutton, and D.L. Parrish. 2012. Conducting fisheries investigations. Pages 1-13 in A. V. Zale, D. L. Parrish, and T. M. Sutton, editors. Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland.	January 2013
Zale, A. V., D. L. Parrish, and T. M. Sutton, editors. 2012. Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland.	January 2013
Winter, M., J. A. Shaffer, D. H. Johnson, T. M. Donovan, W. D. Svedarsky, P. W. Jones, and B. R. Euliss. 2005. Habitat and nesting of Le Conte's Sparrows in the northern tallgrass prairie. Journal of Field Ornithology 76:61�71.	April 2005
Winter, M., D. H. Johnson, J. A. Shaffer, T. M. Donovan, and W. D. Svedarsky. 2006. How consistent are the effects of patch size and landscape composition on density and nest success of grassland birds? Journal of Wildlife Management 70:158-172.	June 2006
White, G., J. Claussen, C. Moffitt, B. Norcross, and D. Parrish. 2013. Dr. J Frances Allen: Pioneer of Women in Fisheries 38:103-111. \| Abstract \| Download	March 2013	no abstract for this
Whalen, K. G., and D. L. Parrish. 1999. Nocturnal habitat use of Atlantic salmon parr in winter. Canadian Journal of Fisheries and Aquatic Sciences 56:1543-1550.	September 1999
Whalen, K. G., and D. L. Parrish. 1999. Effect of maturation on parr growth and smolt recruitment of Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences 56:79-86.	January 1999
Whalen, K. G., D. L. Parrish, and S. D. McCormick. 1999. Migration timing of Atlantic salmon smolts relative to environmental and physiological factors. Transactions of the American Fisheries Society 128:289-301.	March 1999
Whalen, K. G., D. L. Parrish, M. E. Mather. 1999. Effect of ice formation on selection of habitats and winter distribution of post-young-of-the-year Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences 56:87-96.	January 1999
Whalen, K. G., D. L. Parrish, M. E. Mather, J. R. McMenemy. 2000. Cross-tributary analysis of parr to smolt recruitment of Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences 57:1607-1616.	January 2000
Watrous, K. S., T. M. Donovan, R. Mickey, S. R. Darling, A. Hicks, and S. Von Oettengen. 2006. Predicting and mapping the minimum habitat requirements of the Indiana Bat in the Champlain Valley. Journal of Wildlife Management 70:1228-1237 \| Download	December 2006
Troy, A., A. M. Strong, S. C. Bosworth, T. M. Donovan, N. J. Buckley. 2005. Attitudes of dairy farmers regarding adoption of management practices for grassland songbirds. Wildlife Society Bulletin 33:528-538. \| Abstract \| Download	October 2005	In the northeastern United States, most populations of grassland songbirds occur on private lands. However, little information exists about the attitudes of farmers toward habitat management for this guild. To address this information gap, we surveyed 131 dairy farmers in Vermont’s Champlain Valley to assess current hayfield management practices and farmers’ willingness to adopt more “bird-friendly” practices. Our results showed a clear trend toward earlier and more frequent hayfield cuts. Farmers indicated they have little flexibility to alter the timing of their cuts on most of their land. However, many farmers (49%) indicated a willingness to adopt alternative management practices on at least a small portion of their land. Combined with the fact that many farmers characterized parts of their land as “wasteland,” or economically unproductive land, this result suggests that some leeway exists for increasing songbird habitat quality on at least portions of dairy farms. Although significant differences existed in the amount of land for which farmers were willing to adopt alternative management based on herd size, acreage, and experience, the directionality of these relationships could not be established except tentatively for herd size, in which case it appeared that farmers with smaller herds were more likely to dedicate a greater percentage of their land to alternative management. The results of this study likely have relevance to dairy farms throughout the northern-tier dairy states. Given the increasing trend for agricultural land to be converted into housing, we recommend that extension and education efforts target farmers with large hayfield acreages, encouraging the maintenance of high-quality habitat for grassland songbirds.
Tierney, G., B. Mitchell;, A. Miller-Rushing, J. Katz, E. Denny, C. Brauer, T. Donovan, A. D. Richardson, M. Toomey, A. Kozlowski, J. Weltzin, K. Gerst, E. Sharron, O. Sonnentag, and F. Dieffenbach. 2013. Phenology monitoring protocol: Northeast Temperate Network. Natural Resource Report. NPS/NETN/NRR—2013/681. National Park Service. Fort Collins, Colorado. Published Report-2197242. \| Abstract \| Download \| Publisher Website	July 2013	Phenology is critical to many aspects of human life and nearly all ecological relationships and processes. As global climate continues to warm and change, widespread shifts in phenological patterns are occurring across the globe, and more change is inevitable. This protocol has been developed to provide standardized methods for monitoring phenology within the National Park Service (NPS) Northeast Temperate Network (NETN), as part of the NPS Inventory and Monitoring Program (I&M). NETN encompasses the Appalachian National Scenic Trail (APPA), Acadia National Park (ACAD), the Boston Harbor Islands National Recreation Area (BOHA), and 10 national historical parks and national historic sites in the Northeastern United States. This protocol was developed in collaboration with and relies upon the procedures and infrastructure of the USA National Phenology Network (USA-NPN), including Nature’s Notebook, USA-NPN’s online plant and animal phenology observation program (www.nn.usanpn.org). Organized in 2007, USA-NPN is a nation-wide partnership among federal agencies, schools and universities, citizen volunteers, and others to monitor and understand the influence of seasonal cycles on the nation’s biological resources. The overall goal of NETN’s phenology monitoring program is to determine trends in the phenology of key species in order to assist park managers with the detection and mitigation of the effects of climate change on park resources. An additional programmatic goal is to interest and educate park visitors and staff, as well as a cadre of volunteer monitors.
Thompson, F. R. III, T. M. Donovan, R. DeGraaf, J. Faaborg, and S. K. Robinson. 2002. A multi-scale perspective of the effects of forest fragmentation on birds in eastern forests. Studies in Avian Biology 25:8-19.	December 2002
Thompson, F. R. III, S. K. Robinson, T. M. Donovan, J. Faaborg, and D. Whitehead. 2000. Biogeographic, landscape, and local factors affecting cowbird abundance and host parasitism levels. Pages 271-279 In Ecology and management of cowbirds (T. Cooke, S. K. Robinson, S. I. Rothstein, S. G. Sealy, J. N. M. Smith, eds. ). University of Texas Press, Austin, TX.	January 2001
Stritzel Thomson, J.L., D.L. Parrish, S.L. Parker-Stetter, L.G. Rudstam, and P.J. Sullivan. 2011. Growth rates of rainbow smelt in Lake Champlain: effects of density and diet. Ecology of Freshwater Fish 20: 503-512.	December 2011
Smith, K. W., W. S. Keeton, T. M. Donovan, and B. Mitchell. 2008. Stand-level forest structure in avian habitat: scale dependencies in predicting occurrences in a heterogeneous forest. Forest Science 54:36-46. \| Abstract \| Download \| Publisher Website	February 2008	We explored the role of stand-level forest structure and spatial extent of forest sampling in models of avian occurrence in northern hardwood-conifer forests for two species: black-throated blue warbler (Dendroica caerulescens) and ovenbird (Seiurus aurocapillus). We estimated site occupancy from point counts at 20 sites and characterized the forest structure at these sites at three spatial extents (0.2, 3.0, and 12.0 ha). Weight of evidence was greatest for habitat models using forest stand structure at the 12.0-ha extent and diminished only slightly at the 3.0-ha extent, a scale that was slightly larger than the average territory size of both species. Habitat models characterized at the 0.2-ha extent had low support, yet are the closest in design to those used in many of the habitat studies we reviewed. These results suggest that the role of stand-level vegetation may have been underestimated in the past, which will be of interest to land managers who use habitat models to assess the suitability of habitat for species of concern.
Simonin, P.W., L.G. Rudstam, P.J. Sullivan, D.L. Parrish, and B. Pientka. 2019. Early mortality and freshwater forage fish recruitment: nonnative alewife and native rainbow smelt interactions in Lake Champlain. Canadian Journal of Fisheries and Aquatic Sciences 76(5): 806-814. doi: 10.1139/cjfas-2017-0571.	July 2018
Simonin, P.W., L.G. Rudstam, D.L. Parrish, B. Pientka, and P.J. Sullivan. 2018. Piscivore diet shifts and trophic level change after Alewife establishment in Lake Champlain. Transactions of the American Fisheries Society 147: 937-947. doi: 10.1002/tafs.10080. \| Abstract	May 2018	Invasions and deliberate introductions of new prey species are likely to affect prey choice and trophic level of resident predators. Rainbow Smelt (Osmerus mordax) and Alewife (Alosa pseudoharengus) are common prey fish species in lakes throughout North America either as native or non-native species. The establishment of Alewife in the 2000s in a lake with a native Rainbow Smelt population (Lake Champlain) presented an opportunity to study changes in the diet and trophic level of fish already established in the system. Using stable isotope analysis, we found that Alewife became a major component of predator diets, in particular of the diets of Atlantic Salmon (Salmo salar) and Walleye (Sander vitreus). Lake Trout (Salvelinus namaycush) consumed relatively few Alewives. For Walleye (the predator with both pre- and post-Alewife isotope ratios available), the δ15N values decreased significantly from the pre-Alewife period of the late 1990s, indicating that Walleye feed at lower trophic levels when Alewife are present. Predation on Alewife was correlated with the amount of spatial overlap of predators and prey. Our results show that the introduction of Alewife has altered the predator-prey linkages in Lake Champlain; alterations that can have major effects on food web structure and trophic cascades.
Simonin, P.W., D.L. Parrish, L.G. Rudstam, P.J. Sullivan, B. Pientka. 2012. Native rainbow smelt and nonnative alewife distribution related to temperature and light gradients in Lake Champlain. Journal of Great Lakes Research 38 (Supplement 1): 115-122.	March 2012
Simonin, P.W., D. L. Parrish, L. G. Rudstam, P. J. Sullivan, and B. Pientka. 2016. Interactions between hatch dates, growth rates, and mortality of age-0 native Rainbow Smelt and nonnative Alewife in Lake Champlain. Transactions of the American Fisheries Society 145: 649-656. doi: 10.1080/00028487.2016.1143401 \| Abstract	April 2016	Timing of hatch in fish populations can be critical for first-year survival and, therefore, year-class strength and subsequent species interactions. We compared hatch timing, growth rates and subsequent mortality of age-0 Rainbow Smelt Osmerus mordax and Alewife Alosa pseudoharengus, two common open-water fish of northern North America. In our study site, Lake Champlain, Rainbow Smelt hatched almost a month earlier than Alewife (hatching began on 26 May for Rainbow Smelt and 20 June for Alewife). Abundance in the sampling area was highest in July for age-0 Rainbow Smelt and August for age-0 Alewife. Later-hatching individuals of both species grew faster than those hatching earlier (0.6 mm/d vs. 0.4 for Rainbow Smelt; 0.7 mm/d vs. 0.6 for Alewife). Mean mortality rate for age-0 Rainbow Smelt was 3.4%/d and for age-0 Alewife was 5.5%/d during the first 45 days of life. Alewife mortality rates did not differ with hatch timing but daily mortality rates of Rainbow Smelt were highest for earlier-hatching fish. Cannibalism is likely the primary mortality source for age-0 Rainbow Smelt in this lake. Therefore, hatching earlier may not be advantageous as the overlap of adult and age-0 Rainbow Smelt is highest earlier in the season. However, Alewife, first documented in Lake Champlain in 2003, may increase the mortality of age-0 Rainbow Smelt in the summer, which should favor selection for earlier hatching.
Shustack, D. P., A. M. Strong, and T. M. Donovan. 2010. Habitat use patterns of Bobolinks and Savannah Sparrows in the northeastern United States. Avian Conservation and Ecology 5(2): 11. [online] URL: http://www.ace-eco.org/vol5/iss2/art11/ \| Abstract \| Download \| Publisher Website	December 2010	In the northeastern United States, grassland birds regularly use agricultural fields as nesting habitat. However, birds that nest in these fields regularly experience nest failure as a result of agricultural practices, such as mowing and grazing. Therefore, information on both spatial and temporal patterns of habitat use is needed to effectively manage these species. We addressed these complex habitat use patterns by conducting point counts during three time intervals between May 21, 2002 and July 2, 2002 in agricultural fields across the Champlain Valley in Vermont and New York. Early in the breeding season, Bobolinks (Dolichonyx oryzivorus) used fields in which the landscape within 2500 m was dominated by open habitats. As mowing began, suitable habitat within 500 m became more important. Savannah Sparrows (Passerculus sandwichensis) initially used fields that contained a high proportion of suitable habitat within 500 m. After mowing, features of the field (i.e., size and amount of woody edge) became more important. Each species responded differently to mowing: Savannah Sparrows were equally abundant in mowed and uncut fields, whereas Bobolinks were more abundant in uncut fields. In agricultural areas in the Northeast, large areas (2000 ha) that are mostly nonforested and undeveloped should be targeted for conservation. Within large open areas, smaller patches (80 ha) should be maintained as high-quality, late-cut grassland habitat.
Shi, Y., Dick, C.M., Karpan, K., Baetscher, D., Henderson, M.J., Sethi, S.A., McPhee, M.V., Larson, W.A. Towards absolute abundance for conservation applications: estimating the number of contributors via microhaplotype genotyping of mixed-DNA samples. submitted to Molecular Ecology Resources. \| Abstract	May 2023	Molecular methods including metabarcoding and qPCR have shown promises for estimating species abundance by quantifying the concentration of genetic material in field samples. However, the relationship between specimen abundance and detectable concentrations of genetic material is often variable in practice. DNA mixture analysis represents an alternative approach to quantify specimen abundance based on the identity of unique alleles in a sample. The DNA mixture approach provides novel opportunities to inform ecology and conservation by estimating the absolute abundance of target taxa through molecular methods; yet, challenges with genotyping many highly variable markers in mixed-DNA samples have prevented its widespread use. To advance molecular approaches for abundance estimation we explored the utility of microhaplotypes for DNA mixture analysis by applying a 125-marker panel to 1,179 Chinook salmon (<i>Oncorhynchus tshawytscha</i>) smolts from the Sacramento-San Joaquin Delta. We assessed the accuracy of DNA mixture analysis through a combination of mock mixtures containing DNA from up to 20 smolts and a trophic ecological application enumerating smolts in predator diets. Mock DNA mixtures of up to 10 smolts could reliably be resolved using microhaplotypes and increasing the panel size would likely facilitate identification of more individuals. However, while analysis of predator gastrointestinal tract contents indicated DNA mixture analysis could discern the presence of multiple prey items, poor DNA quality prevented accurate genotyping and abundance estimation. Our results indicate that DNA mixture analysis can perform well with high-quality DNA, but methodological improvements in genotyping degraded DNA are necessary before this approach can be used on marginal quality samples.
Schwenk, W. S., and T. M. Donovan. 2011. A multi-species framework for landscape conservation planning. Conservation Biology 25:1010-1021. \| Abstract \| Download	October 2011	Rapidly changing landscapes have spurred the need for quantitative methods for conservation assessment and planning that encompass large spatial extents. We devised and tested a multispecies framework for conservation planning to complement single-species assessments and ecosystem-level approaches. Our framework consisted of 4 elements: sampling to effectively estimate population parameters, measuring how human activity affects landscapes at multiple scales, analyzing the relation between landscape characteristics and individual species occurrences, and evaluating and comparing the responses of multiple species to landscape modification. We applied the approach to a community of terrestrial birds across 25,000 km2 with a range of intensities of human development. Human modification of land cover, road density, and other elements of the landscape, measured at multiple spatial extents, had large effects on occupancy of the 67 species studied. Forest composition within 1 km of points had a strong effect on occupancy of many species and a range of negative, intermediate, and positive associations. Road density within 1 km of points, percent evergreen forest within 300 m, and distance from patch edge were also strongly associated with occupancy for many species. We used the occupancy results to group species into 11 guilds that shared patterns of association with landscape characteristics. Our multispecies approach to conservation planning allowed us to quantify the trade-offs of different scenarios of land-cover change in terms of species occupancy.
Schwenk, W. S., T. M. Donovan, W. S. Keeton, and J. S. Nunery. 2012. Carbon storage, timber production, and biodiversity: comparing ecosystem services with multi-criteria decision analysis. Ecological Applications 22:1612-1627. \| Abstract \| Download	July 2012	Increasingly, land managers seek ways to manage forests for multiple ecosystem services and functions, yet considerable challenges exist in comparing disparate services and balancing trade-offs among them. We applied multi-criteria decision analysis (MCDA) and forest simulation models to simultaneously consider three objectives: (1) storing carbon, (2)producing timber and wood products, and (3) sustaining biodiversity. We used the Forest Vegetation Simulator (FVS) applied to 42 northern hardwood sites to simulate forest development over 100 years and to estimate carbon storage and timber production. We estimated biodiversity implications with occupancy models for 51 terrestrial bird species that were linked to FVS outputs. We simulated four alternative management prescriptions that spanned a range of harvesting intensities and forest structure retention. We found that silvicultural approaches emphasizing less frequent harvesting and greater structural retention could be expected to achieve the greatest net carbon storage but also produce less timber. More intensive prescriptions would enhance biodiversity because positive responses of early successional species exceeded negative responses of late successional species within the heavily forested study area. The combinations of weights assigned to objectives had a large inﬂuence on which prescriptions were scored as optimal. Overall, we found that a diversity of silvicultural approaches is likely to be preferable to any single approach, emphasizing the need for landscape-scale management to provide a full range of ecosystem goods and services. Our analytical framework that combined MCDA with forest simulation modeling was a powerful tool in understanding trade-offs among management objectives and how they can be simultaneously accommodated.
Rudstam, L. G., S. L. Parker, Einhouse, D. W., L. D. Witzel, D. M. Warner, J. L. Stritzel, D. L. Parrish, P. J. Sullivan. 2003. Application of in situ target strength estimations in lakes--examples from rainbow smelt surveys in Lakes Erie and Champlain. ICES Journal of Marine Science 60: 500-507.	June 2003
Rosenblatt, E., R. Mickey, S. Creel, K. Gieder, J. Murdoch, and T. Donovan. 2023. Advances in wildlife abundance estimation using pedigree reconstruction. Ecology and Evolution 13(10):e10650. \| Abstract \| Download \| Publisher Website	October 2023	The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density measures. Traditional methods of estimating abundance and related metrics represent trade-offs in effort and precision of estimates. Pedigree reconstruction is an emerging, attractive alternate approach because its use of one-time, noninvasive sampling of individuals to infer the existence of unsampled individuals. However, advances in pedigree reconstruction could improve its utility, including forming a measure of precision for the method, establishing required spatial sampling effort for accurate estimates, ascertaining the spatial extent of abundance estimates derived from pedigree reconstruction, and assessing how population density affects the estimator's performance. Using established relationships for a stochastic, spatially explicit simulated moose (<i>Alces americanus</i>) population, pedigree reconstruction provided accurate estimates of the adult moose population size and trend. Novel bootstrapped confidence intervals performed as expected with intensive sampling but underperformed with moderate sampling efforts that could produce abundance estimates with low bias. Adult population estimates more closely reflected the total number of adults in the extant population, rather than number of adults inhabiting the area where sampling occurred. Increasing sampling effort, measured as the proportion of individuals sampled and as the proportion of a hypothetical study area, yielded similar asymptotic patterns over time. Simulations indicated a positive relationship between animal density and sampling effort required for unbiased estimates. These results indicate that pedigree reconstruction can produce accurate abundance estimates and may be particularly valuable for surveying smaller areas and low-density populations.
Rosenblatt, E., K. Gieder, T. Donovan, J. Murdoch, T. Smith, M. Heaton, T. Kalbfleisch, B. Murdoch, S. Bhattarai, E. Pacht, E. Verbist, V. Basnayake, and S. McKay. 2023. Genetic diversity and connectivity of moose (Alces alces americana) in eastern North America. Conservation Genetics 24:235-248. \| Download \| Publisher Website	January 2023
Rosenblatt, E., J. DeBow, J. Blouin, T. Donovan, J. Murdoch, S. Creel, W. Rogers, K. Gieder, N. Forti, and C. Alexander. Juvenile moose (Alces alces) stress and nutrition dynamics relate to landscape characteristics, climate-mediated factors, and survival. Conservation Physiology 9:coab048. \| Abstract \| Download	July 2021	Moose populations in the northeastern United States have declined over the past 15 years, primarily due to the impacts of winter ticks. Research efforts have focused on the effects of winter tick infestation on moose survival and reproduction, but stress and nutritional responses to ticks and other stressors remain understudied. We examined the influence of several environmental factors on moose calf stress hormone metabolite concentrations and nutritional restriction in Vermont, USA. We collected 407 fecal and 461 snow urine samples from 84 radio-collared moose calves in the winters of 2017–2019 (January–April) to measure fecal glucocorticoid metabolites (fGCM) concentrations and urea nitrogen:creatinine (UN:C) ratios. We used generalized mixed-effects models to evaluate the influence of individual condition, winter ticks, habitat, climate and human development on stress and nutrition in calf moose. We then used these physiological data to build generalized linear models to predict calf winter survival. Calf fGCM concentrations increased with nutritional restriction and snow depth during adult winter tick engorgement. Calf UN:C ratios increased in calves with lighter weights and higher tick loads in early winter. Calf UN:C ratios also increased in individuals with home ranges composed of little deciduous forests during adult winter tick engorgement. Our predictive models estimated that winter survival was negatively related to UN:C ratios and positively related to fGCM concentrations, particularly in early winter. By late March, as winter ticks are having their greatest toll and endogenous resources become depleted, we estimated a curvilinear relationship between fGCM concentrations and survival. Our results provide novel evidence linking moose calf stress and nutrition, a problematic parasite and challenging environment and winter survival. Our findings provide a baseline to support the development of non-invasive physiological monitoring for assessing environmental impacts on moose populations.
Rinehart, K., T. Donovan, B. Mitchell, R. Long. 2009. Factors influencing occupancy patterns of Eastern Newts across Vermont. Journal of Herpetology 43(3):521-531. \| Abstract \| Download \| Publisher Website	September 2009	Of the threats facing amphibian populations today, habitat transformation due to land-use is among the most pressing. Although conservation of pond-breeding salamanders clearly requires protection of breeding ponds and their surrounding habitat, little is known about the effects of land use and other factors on the occurrence of salamanders in the dispersal/terrestrial phase of their life cycle. To determine these effects, we surveyed populations of Eastern Newts (Notophthalmus viridescens) at 551 stations across Vermont, and modeled salamander distribution as a function of environmental variables hypothesized to influence site occupancy. We developed a set of 12 models based on seven a priori hypotheses of site occupancy. We hypothesized that occupancy was influenced by 1) amounts of available habitat types, 2) arrangement of these habitat types, 3) geographic position, 4) housing density, 5) road density, 6) short term changes in habitat distribution, or 7) habitat structure at the stand-level. We used a single-season occupancy model to rank and compare the 12 models. 232 Eastern Newts were detected at 82 of 551 stations. Of the 12 models, amount of habitat within 0.5 km of the survey station best represented the field data. Strong effects were indicated for developed land (-), open water (+), and forest (+) cover. Given a survey station with average forest and open water characteristics, stations with > 5% developed land classes within a 0.5 km buffer had a very low probability of occupancy. Further research is needed to determine the direct role of development on occupancy patterns.
Raffenberg, M. J., and D. L. Parrish. 2003. Interactions of Atlantic salmon (Salmo salar) and trout (Salvelinus fontinalis and Oncorhynchus mykiss) in Vermont tributaries of the Connecticut River. Canadian Journal of Fisheries and Aquatic Sciences 60: 279-285.	March 2003
Puchala, E.A., D.L. Parrish, and T.M. Donovan. 2016. Predicting the stability of endangered Stonecats (Noturus flavus) in the LaPlatte River, Vermont. Transactions of the American Fisheries Society 145: 903-912. \| Abstract	June 2016	Stonecats (Noturus flavus, Rafinesque 1818) in Vermont fit into a rare distribution pattern, as designated by Rabinowitz, because their known distribution is limited to two systems, the LaPlatte and Missisquoi rivers. Here we focus on Stonecats in the LaPlatte River to predict the stability of the population. In 2012, 2013, and 2014 we captured, PIT tagged (> 90 mm total length), and VIE marked all Stonecats collected using backpack electrofishing. A total of 1671 Stonecats was captured, and of those, 1252 were PIT tagged. Only 12% (N=156) of the PIT tagged fish were recaptured and only 22 were recaptured more than one time. We used the Pradel model in Program MARK to estimate the survival and seniority of Stonecats and these values were used to derive lambda (λ), the population rate of change. We ran a total of 64 models in our candidate set with the following covariates: total length, maximum temperature, season, maximum discharge, and area sampled. Model results estimated that survival was highest in the spring, and increased with increasing total length of individuals. We also estimated increases in capture probability with increasing area sampled. We derived an annual λ of 0.9826, which indicates a slightly decreasing population. With only three years of data and a low recapture rate, our estimate has some uncertainty. Although the population could be declining at a slow rate, we have provided insight into population parameters that were otherwise unknown.
Puchala, E.A., D. L. Parrish, and D. H. Ogle. 2018. Size and age of Lake Champlain Stonecats; estimating growth at the margin of their range. North American Journal of Fisheries Management 38:1316–1323. DOI:10.1002/nafm.10230 \| Abstract	October 2018	Little is known about Stonecat (Noturus flavus) populations, especially in the Northeastern United States, where these madtoms are at the edge of their range. In Lake Champlain tributaries, Stonecats are listed as endangered in Vermont, but not in New York. Here we describe the growth of Stonecats in two tributaries to Lake Champlain, one in Vermont and one in New York. We also compared the growth of Stonecats in these waters to results from other locations near the middle of their distribution. Stonecats in the Great Chazy River, NY were larger at ages 1-3, but smaller at age 5, than Stonecats from the LaPlatte River, VT. Stonecats in Lake Champlain tributaries were generally larger at age than those from the middle of their range, except for those from Lake Erie. Lake Champlain Stonecats appear to reach maturity by age 3, though future research that directly estimates age at maturity would be more informative. These results expand the literature that lacks information about growth of this species while also providing specific information needed to manage this and other fishes in Lake Champlain tributaries.
Pientka, B., and D. L. Parrish. 2002. Habitat selection of predator and prey: Atlantic salmon and rainbow smelt overlap, based on temperature and dissolved oxygen. Transactions of the American Fisheries Society 131: 1180-1193.	November 2002
Perlut, N., C. Freeman-Gallant, A. M. Strong, T. M. Donovan, C. W. Kilpatrick, and N. J. Zalik. 2008. Agricultural management affects evolutionary processes in a migratory songbird. Molecular Ecology 17:1248-1255. \| Abstract \| Download \| Publisher Website	February 2008	Hay harvests have detrimental ecological effects on breeding songbirds, as harvesting results in nest failure. Importantly, whether harvesting also affects evolutionary processes is not known. We explored how hay harvest affected social and genetic mating patterns, and thus, the overall opportunity for sexual selection and evolutionary processes for a ground-nesting songbird, the Savannah sparrow (Passerculus sandwichensis). On an unharvested field, 55% of females were in polygynous associations, and social polygyny was associated with greater rates of extra-pair paternity (EPP). In this treatment, synchrony explained variation in EPP rates, as broods by more synchronous females had more EPP than broods by asynchronous females. In contrast, on a harvested field, simultaneous nest failure caused by haying dramatically decreased the overall incidence of EPP by increasing the occurrence of social monogamy and, apparently, the ability of polygynous males to maintain paternity in their own nests. Despite increased social and genetic monogamy, these haying-mediated changes in mating systems resulted in greater than twofold increase in the opportunity for sexual selection. This effect arose, in part, from a 30% increase in the variance associated with within-pair fertilization success, relative to the unharvested field. This effect was caused by a notable increase (+110%) in variance associated with the quality of social mates following simultaneous nest failure. Because up to 40% of regional habitat is harvested by early June, these data may demonstrate a strong population-level effect on mating systems, sexual selection, and consequently, evolutionary processes.
Perlut, N., A. Strong, T. M. Donovan, and N. Buckley. 2006. Grassland songbirds in a dynamic management landscape: behavioral responses and management strategies. Ecological Applications 16:2235-2247. \| Download	December 2006
Perlut, N. G., A. M. Strong, T. M. Donovan, and N. J. Buckley. 2008. Regional population viability of grassland songbirds: effects of agricultural management. Biological Conservation 141:3139-3151. \| Abstract \| Download \| Publisher Website	December 2008	Although population declines of grassland songbirds in North America and Europe are well-documented, the effect of local processes on regional population persistence is unclear. To assess population viability of grassland songbirds at a regional scale (not, vert, similar150,000 ha), we quantified Savannah Sparrow Passerculus sandwichensis and Bobolink Dolichonyx oryzivorus annual productivity, adult apparent survival, habitat selection, and density in the four most (regionally) common grassland treatments. We applied these data to a female-based, stochastic, pre-breeding population model to examine whether current grassland management practices can sustain viable populations of breeding songbirds. Additionally, we evaluated six conservation strategies to determine which would most effectively increase population trends. Given baseline conditions, over 10 years, simulations showed a slightly declining or stable Savannah Sparrow population (mean bootstrap λ = 0.99; 95% CI = 1.00–0.989) and severely declining Bobolink population (mean bootstrap λ = 0.75; 95% CI = 0.753–0.747). Savannah Sparrow populations were sensitive to increases in all demographic parameters, particularly adult survival. However for Bobolinks, increasing adult apparent survival, juvenile apparent survival, or preference by changing habitat selection cues for late-hayed fields (highest quality) only slightly decreased the rate of decline. For both species, increasing the amount of high-quality habitat (late- and middle-hayed) marginally slowed population declines; increasing the amount of low-quality habitat (early-hayed and grazed) marginally increased population declines. Both species were most sensitive to low productivity and survival on early-hayed fields, despite the fact that this habitat comprised only 18% of the landscape. Management plans for all agricultural regions should increase quality on both low- and high-quality fields by balancing habitat needs, nesting phenology, and species’ response to management.
Perlut, N. G., A. M. Strong, T. M. Donovan, and N. J. Buckley. 2008. Grassland songbird survival and recruitment in heterogeneous agricultural landscapes: implications for source-sink demography. Ecology 89:1941-1952. \| Abstract \| Download \| Publisher Website	July 2008	Population growth and decline are particularly sensitive to changes in three key life-history parameters: annual productivity, juvenile survival, and adult survival. However, for many species these parameters remain unknown. For example, although grassland songbirds are imperiled throughout North America, for this guild, only a small number of studies have assessed these parameters. From 2002 to 2006, in the agricultural landscape of the Champlain Valley of Vermont and New York, USA, we studied Savannah Sparrow (Passerculus sandwichensis) and Bobolink (Dolichonyx oryzivorus) demography on four grassland treatments: (1) early-hayed fields cut before 11 June and again in early- to mid-July; (2) middle-hayed fields cut once between 21 June and 10 July; (3) late-hayed fields cut after 1 August; and (4) rotationally grazed pastures. We assessed whether these treatments affected adult apparent survival (phi) and recruitment (f), how sensitive these parameters were to the presence of nonbreeders and local dispersal, and the populations' ability to persist in these four habitats. On average, birds using late-hayed fields had >25% higher apparent survival than those on the more intensively managed early-hayed, middle-hayed, and grazed fields. Overall male phi was 35% higher than female phi, and Savannah Sparrow phi was 44% higher than Bobolink phi. Across all analyses and treatments, apparent survival estimates were 0.58–0.85 for male and 0.48–0.71 for female Savannah Sparrows, and 0.52–0.70 for male and 0.19–0.55 for female Bobolinks. For males of both species, potential nonbreeders decreased the precision of and lowered apparent survival estimates by 25%; female estimates showed little variation with the inclusion of nonbreeders. Inclusion of local dispersal observations increased apparent survival estimates and, in many cases, increased precision, though the effect was stronger for Savannah Sparrows than for Bobolinks, and also stronger for males than for females. High Savannah Sparrow apparent survival rates resulted in stable or near stable populations (λ ≈ 1), particularly in late-hayed and grazed fields, while low Bobolink apparent survival rates resulted in strongly declining populations (λ < 1) in all treatments.
Pearman-Gillman, S., M. Duveneck, J. Murdoch, and T. M. Donovan. 2020. Species distribution changes under alternative landscape futures: Using a scenario framework to identify drivers and consequences of landscape change on wildlife in New England. Frontiers in Ecology and Evolution 8:164. doi: 10.3389/fevo.2020.00164. \| Abstract \| Download \| Publisher Website	June 2020	In an era of rapid climate and land transformation, it is increasingly important to understand how future changes impact natural systems. Scenario studies can offer the structure and perspective needed to understand the impacts of change and help inform management and conservation decisions. We implemented a scenario-based approach to assess how two high impact drivers of landscape change influence the distributions of managed wildlife species (<i>n</i> = 10) in the New England region of the northeastern United States. We used expert derived species distribution models (SDMs) and scenarios developed by the New England Landscape Futures Project (NELFP) to estimate how species distributions change under various trajectories (<i>n</i> = 5) of landscape change. The NELFP scenarios were built around two primary drivers – Socio-Economic Connectedness (SEC) and Natural Resource Planning and Innovation (NRPI) – and provide plausible alternatives for how the New England region may change over 50 years (2010–2060). Our models generally resulted in species occurrence and richness declines by 2060. The majority of species (7 of 10) experienced declines in regional occurrence for all NELFP scenarios, and one species experienced a projected increase in mean regional occurrence for all scenarios. Our results indicate that the NRPI and SEC drivers strongly influenced projected distribution changes compared to baseline projections. NRPI had a greater impact on distribution change for five species (coyote, moose, striped skunk, white-tailed deer, and wild turkey), while SEC had a greater impact on four species (American black bear, bobcat, raccoon, and red fox); one species (gray fox) was equally influenced by both NRPI and SEC. These results emphasize the importance of integrating both natural resource planning and socio-economic factors when addressing issues of distribution change and offer insights that can inform proactive management and conservation planning.
Pearman-Gillman, S., M. Duveneck, J. Murdoch, and T. Donovan. 2020. Wildlife resistence and protection in a changing New England landscape. PLOS ONE 15(9): e0239525. https://doi.org/10.1371/journal.pone.0239525 \| Abstract \| Publisher Website	September 2020	Rapid changes in climate and land use threaten the persistence of wildlife species. Understanding where species are likely to occur now and in the future can help identify areas that are resistant to change over time and guide conservation planning. We estimated changes in species distribution patterns and spatial resistance in five future scenarios for the New England region of the northeastern United States. We present scenario-specific distribution change maps for nine harvested wildlife species, identifying regions of increasing, decreasing, or stable habitat suitability within each scenario. Next, we isolated areas where species occurrence probability is high (p > 0.7) and resistant to change across all future scenarios. Resistance was also evaluated relative to current land protection to identify patterns in and out of Protected Areas (PAs). Generally, species distributions declined in area over the 50-year assessment period (2010–2060), with the greatest average declines occurring for moose (-40.9%) and wild turkey (-22.1%). Species resistance varied considerably across the region, with coyote demonstrating the highest average regional resistance (91.81% of the region) and moose demonstrating the lowest (0.76% of the region). At the state level, average focal species resistance was highest in Maine (the largest state) and lowest in Massachusetts. Many of the focal species showed high overlap in resistance and land protection. Coyote, white-tailed deer, and black bear had the highest probability of resistance, given protection, while moose and wild turkey had the highest probability of protection, given resistance. Overall, relatively small portions of New England—ranging between 0.25% and 21.12%–were both protected and resistant for the focal species. Our results provide estimates of resistance that can inform conservation planning for commonly harvested species that are important ecologically, economically, and culturally to the region. Expanding protected area coverage to include resistant areas may provide longer term benefits to these species.
Pearman-Gillman, S, J. E. Katz, R. Mickey, J. Murdoch, and T. Donovan. 2020. Predicting wildlife distribution patterns in New England USA with expert elicitation techniques. Global Ecology and Conservation 21:e00853. \| Abstract \| Download \| Publisher Website	March 2020	Understanding the impacts of landscape change on species distributions can help inform decision-making and conservation planning. Unfortunately, empirical data that span large spatial extents across multiple taxa are limited. In this study, we used expert elicitation techniques to develop species distribution models (SDMs) for harvested wildlife species (n = 10) in the New England region of the northeastern United States. We administered an online survey that elicited opinions from wildlife experts on the probability of species occurrence throughout the study region. We collected 3396 probability of occurrence estimates from 46 experts, and used linear mixed-effects methods and landcover variables at multiple spatial extents to develop SDMs. The models were in general agreement with the literature and provided effect sizes for variables that shape species occurrence. With the exception of gray fox, models performed well when validated against crowdsourced empirical data. We applied models to rasters (30 × 30 m cells) of the New England region to map each species’ distribution. Average regional occurrence probability was highest for coyote (0.92) and white-tailed deer (0.89) and lowest for gray fox (0.42) and moose (0.52). We then stacked distribution maps of each species to estimate and map focal species richness. Species richness (<i>s</i>) varied across New England, with highest average richness in the least developed states of Vermont (<i>s</i> = 7.47) and Maine (s = 7.32), and lowest average richness in the most developed states of Rhode Island (s = 6.13) and Massachusetts (s = 6.61). Our expert-based approach provided relatively inexpensive, comprehensive information that would have otherwise been difficult to obtain given the spatial extent and range of species being assessed. The results provide valuable information about the current distribution of wildlife species and offer a means of exploring how climate and land-use change may impact wildlife in the future.
Parrish, D. L., and F. J. Margraf. 1994. Spatial and temporal patterns of food use by white perch and yellow perch in Lake Erie. Journal of Freshwater Ecology 9(1):29-35.	September 1994
Parrish, D. L., R. J. Behnke, S. R. Gephard, S. D. McCormick, and G. H. Reeves. 1998. Why aren't there more Atlantic salmon (Salmo salar)? Canadian Journal of Fisheries and Aquatic Sciences 55 (Supple. 1):281-287.	December 1998
Parrish, D. L., M. E. Mather, and R. A. Stein. 1995. Problem-solving research for management: a perspective. Fisheries 20(10):6-12.	October 1995
Parrish, D. L., E. J. Hawes, and K. G. Whalen. 2004. Winter growth and survival of juvenile Atlantic salmon in experimental raceways. Canadian Journal of Fisheries and Aquatic Sciences 61: 2350-2357.	February 2005
Parrish, D. L., B. Vondracek, and W. J. Eckmayer. 1994. Accuracy and precision of daily age estimates of walleye from Ohio hatcheries and Lake Erie. Transactions of the American Fisheries Society 123:601-605.	July 1994
Parker Stetter, S. L., L. G. Rudstam, J. L. Stritzel Thomson, D. L. Parrish, and P. J. Sullivan. 2006. Hydroacoustic separation of rainbow smelt (Osmerus mordax) age groups in Lake Champlain. Fisheries Research 82:176-185.	December 2006
Parker Stetter, S. L., J. L. Stritzel Thomson, L. G. Rudstam, D. L. Parrish, and P. J. Sullivan. 2007. Analysis of cannibalism in Lake Champlain. Transactions of the American Fisheries Society 136:227-237.	February 2007
Overman, N. C., and D. L. Parrish. 2001. Stable isotope composition of walleye: 15N accumulation with age and area-specific differences in 13C. Canadian Journal of Fisheries and Aquatic Sciences 58: 1253-1260.	June 2001
Noa, L., D. H. Hirth, T. M. Donovan, and D. Cimprich. 2007. Demographic differences of black-capped vireos in two habitat types in central Texas. Journal of Wildlife Management 71:1042-1049. \| Abstract \| Download \| Publisher Website	June 2007	To understand the effects of habitat selection, we analyzed differences in abundance, age structure, and nesting success of black-capped vireos (Vireo atricapilla) in 2 early successional habitat types found on Fort Hood, a 87,890-ha Military Reservation in central Texas, USA. These habitats were 1) large areas of continuously shrubby vegetation (both natural and mechanically made), referred to as shrubland habitat, and 2) anthropogenically created small patches of shrubby vegetation centered on one or several large trees, known locally as donut habitat. The objectives of our study were to determine whether there were differences in abundance, age structure, and daily nest survival in these 2 habitat types and to determine whether donut habitat is high- or low-quality habitat. Donut habitat had a lower abundance of vireos (half as many as shrubland/point count) and a higher percentage of second-year males, suggesting donut habitat was lower-quality habitat than shrubland. Analyses of daily nest survival indicated that habitat, nest height, and year were all important variables. Nests initiated in 2004, located in shrubland habitats, and higher from the ground were more likely to succeed. Our study provided evidence that habitat is a limiting factor for this federally endangered species. Because habitat is limiting, wildlife biologists at Fort Hood should focus on managing higher quality, contiguous shrubland habitat. Wildlife biologists should also continue to monitor areas of donut habitat to determine whether they represent potential population sinks.
Nislow, K. H., C. L. Folt, and D. L. Parrish. 2000. A spatially-explicit bioenergetic analysis of habitat quality for age-0 Atlantic salmon. Transactions of the American Fisheries Society 129:1067-1081.	January 2000
Nislow, K. H., C. L. Folt, and D. L. Parrish. 1999. Favorable foraging locations for young Atlantic salmon: application to the restoration of populations and habitats. Ecological Applications 9:1085-1099.	August 1999
Murdoch, J., H. Davie, M. Galbadrah, T. Donovan, and R. Reading. 2013. Do Siberian marmots influence toad-headed agama occupancy? Examining the influence of marmot colonies and three steppe habitats in Mongolia. Journal of Arid Environments 92:76-80. \| Download	January 2013
Mitro, M. G., and D. L. Parrish. 1997. Temporal and spatial abundances of larval walleyes in two tributaries of Lake Champlain. Transactions of the American Fisheries Society 126:273-287.	March 1997
Mitchell, B. R., and T. M. Donovan. Mob mentality: the effect of a mobbing tape on detections during point count surveys. Open Ornithology Journal 1:8-19. \| Abstract \| Download \| Publisher Website	July 2008	The probability of detecting an individual or species is an important parameter in studies using mark-recapture and occupancy models to estimate population sizes and occurrence. Because low detection probabilities result in biased estimators and decreased precision, biologists seek methods that maximize detection probability. We evaluated whether we could increase detections of bird species by playing a tape of Black-capped Chickadee (Poecile atricapillus) mobbing calls during point counts. We conducted trios of 10-minute counts (two pre-playback and a playback) at 684 stations throughout Vermont, in forested, agricultural/grassland, and developed habitats. For each of 73 species detected during the surveys, we used occupancy modeling and information-theoretic model selection and averaging methods to evaluate whether detection probabilities varied due to playback or habitat type. Models containing a playback effect accounted for over 90% of the Akaike weights for 41 species. With 15 of these species, habitat effects also accounted for over 90% of the Akaike weights. The playback increased estimated detection probability in all habitats for 14 species, decreased estimated detection probability for 20 species, and had an estimated effect that varied by habitat for 7 species (many species with habitat effects simply had differing magnitudes of the effect dependent on habitat). Smaller resident species were detected more often during tape playbacks, but responses were highly variable for most species and the responses did not appear to follow a taxonomic pattern. We encourage researchers to evaluate their list of target species carefully before deciding to use mobbing playbacks to enhance response rates; in many situations mobbing tapes will not enhance detections and may complicate the interpretation of model parameters.
McKenny, H., W. S. Keeton, and T. M. Donovan. 2006. The effects of structure-based forestry on red-backed salamander (Plethodon cinereus) populations in northern hardwood forests. Forest Ecology and Management 230:186-196.	April 2006
Mather, M. E., D. L. Parrish. C. A. Campbell, J. R. McMenemy, and J. M. Smith. 2008. Summer temperature variation and implications for juvenile Atlantic salmon. Hydrobiologia 603:183-196	March 2008
Mather, M. E., D. L. Parrish, and J. M. Dettmers. 2012. Now That You Have Great Results, Where Should You Submit Your Manuscript? In Scientific Communication for Natural Resources Professionals. Editors C. Jennings,T. Lauer, B. Vondracek. PAGES 121-133. American Fisheries Society, Bethesda, MD.	August 2012
Mather, M. E., D. L. Parrish, and J. M. Dettmers. 2009. The extensive and complex landscape of fish-related journals authors’ response. Fisheries 34:144-145.	March 2009
Mather, M. E., D. L. Parrish, R. A. Stein, and R. M. Muth. 1995. Management issues and their relative priority with state fisheries agencies. Fisheries 20(10):14-21.	October 1997
Mather, M. E., D. L. Parrish, J. M. Dettmers. 2008. Mapping the changing landscape of fish-related journals: setting a course for successful communication of scientific information. Fisheries 33(9): 444-453.	September 2008
Mather, M. E., D. L. Parrish, C. L. Folt, and R. M. DeGraaf. 1998. Integrating across scales: effectively applying science for the successful conservation of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 55 (Supple. 1):1-8.	December 1998
Marschall, E.A., M.E. Mather, D.L. Parrish, G. Allison, and J. McMenemy. Migration delays caused by anthropogenic barriers: modeling dams, temperature, and success of migrating salmon smolts. Ecological Applications 21: 3014-3031.	December 2011
Marschall, E.A., D.C. Glover, M.E. Mather, and D.L. Parrish. 2021. Modeling larval American Shad recruitment in a large river. North American Journal of Fisheries Management 41: 939-954. https://doi.org/10.1002/nafm.10460 \| Abstract	May 2020	We used an bioenergetics-based modeling approach to track American Shad Alosa sapidissima offspring within a template of spatial and temporal habitat conditions defined by a combination of abiotic conditions and prey availability models. We simulated spawning at each river kilometer (RKM 138-280) on each day (1 April-31 August) to understand how spawning date and location drive larval recruitment differentially across years and decades. For both temperature and flow, inter-annual variation was large in comparison to interdecadal differences. Variation in simulated recruitment was best explained by a combination of season-specific temperature and location in along the course of the river. Greatest potential recruitment occurred in years in which June temperatures were relatively high. In years when June and July were warmer than average, maximum recruitment resulted from spawning taking place at the upstream portion of the modeled reach. Model scenarios (stationary or passive-drift larvae and dams or no dams) had predictable effects. When dams were present, but offspring were stationary, the area directly above the dams resulted in poor recruitment, due to the habitat being inappropriate for eggs. When offspring exhibited passive drift, they traveled far downstream. If dams were present, they frequently ended their movement at the dams. When larvae moved downstream but their movement was not limited by dams, spatial differences in expected recruitment relative to spawning sites were reduced. Our results demonstrate the importance of spatiotemporal environmental heterogeneity for producing positive recruitment over the longterm. In addition, our results suggest the importance of successful passage of spawners to historical spawning sites upstream of Vernon Dam in the Connecticut River, especially as conditions shift with climate change.
M. McClure, M.A. Haltuch, E. Willis-Norton, D.D. Huff, E.L. Hazen, L.G. Crozier, M.G. Jacox, M.W. Nelson, K.S. Andrews, L.A.K. Barnett, A.M. Berger, S. Beyer, J. Bizzarro, D. Boughton, J.M. Cope, M. Carr, H. Dewar, E. Dick, E. Dorval, J. Dunham, V. Gertseva, C. Greene, R.G. Gustafson, O.S. Hamel, C.J. Harvey, M.J. Henderson, C.E. Jordan, I.C. Kaplan, S.T. Lindley, N.J. Mantua, S.E. Matson, M.H. Monk, P. Moyle, C. Nicol, J. Pohl, R.R. Rykaczewski, J.F. Samhouri, S. Sogard, N. Tolimieri, J. Wallace, C. Wetzel, S.J. Bograd. 2023. Vulnerability to climate change of managed stocks in the California Curret large marine ecosystem. Frontiers in Marine Science. 10, 1103767. \| Abstract	February 2023	Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. This study applies the NOAA Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information will inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially important to protect or restore.
Long, R. A., T. M. Donovan, P. MacKay, W. J. Zielinski, and J. S. Buzas. 2007. Effectiveness of scat detection dogs for detecting forest carnivores. Journal of Wildlife Management 71:2007-2017. \| Abstract \| Download \| Publisher Website	August 2007	We assessed the detection and accuracy rates of detection dogs trained to locate scats from free-ranging black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus). During the summers of 2003–2004, 5 detection teams located 1,565 scats (747 putative black bear, 665 putative fisher, and 153 putative bobcat) at 168 survey sites throughout Vermont, USA. Of 347 scats genetically analyzed for species identification, 179 (51.6%) yielded a positive identification, 131 (37.8%) failed to yield DNA information, and 37 (10.7%) yielded DNA but provided no species confirmation. For 70 survey sites where confirmation of a putative target species' scat was not possible, we assessed the probability that ≥1 of the scats collected at the site was deposited by the target species (probability of correct identification; PID). Based on species confirmations or PID values, we detected bears at 57.1% (96) of sites, fishers at 61.3% (103) of sites, and bobcats at 12.5% (21) of sites. We estimated that the mean probability of detecting the target species (when present) during a single visit to a site was 0.86 for black bears, 0.95 for fishers, and 0.40 for bobcats. The probability of detecting black bears was largely unaffected by site- or visit-specific covariates, but the probability of detecting fishers varied by detection team. We found little or no effect of topographic ruggedness, vegetation density, or local weather (e.g., temp, humidity) on detection probability for fishers or black bears (data were insufficient for bobcat analyses). Detection dogs were highly effective at locating scats from forest carnivores and provided an efficient and accurate method for collecting detection–nondetection data on multiple species.
Long, R. A., T. M. Donovan, P. MacKay, W. J. Zielinski, and J. S. Buzas. 2007. Comparing scat detection dogs, cameras, and hair snares for surveying carnivores. Journal of Wildlife Management 71:2018-2025. \| Abstract \| Download \| Publisher Website	August 2007	Carnivores typically require large areas of habitat, exist at low natural densities, and exhibit elusive behavior—characteristics that render them difficult to study. Noninvasive survey methods increasingly provide means to collect extensive data on carnivore occupancy, distribution, and abundance. During the summers of 2003–2004, we compared the abilities of scat detection dogs, remote cameras, and hair snares to detect black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus) at 168 sites throughout Vermont. All 3 methods detected black bears; neither fishers nor bobcats were detected by hair snares. Scat detection dogs yielded the highest raw detection rate and probability of detection (given presence) for each of the target species, as well as the greatest number of unique detections (i.e., occasions when only one method detected the target species). We estimated that the mean probability of detecting the target species during a single visit to a site with a detection dog was 0.87 for black bears, 0.84 for fishers, and 0.27 for bobcats. Although the cost of surveying with detection dogs was higher than that of remote cameras or hair snares, the efficiency of this method rendered it the most cost-effective survey method.
Long, R. A., T. M. Donovan, P. MacKay, J. S. Buzas, and W. J. Zielinski. Predicting carnivore occurrence using data collected with multiple, noninvasive methods.Landscape Ecology 26:327-340. \| Abstract \| Download	October 2010	Terrestrial carnivores typically require large areas of habitat and exist at low densities. As “top level” consumers, carnivores affect the biological structure and composition of ecosystems. We employed multiple, noninvasive survey methods—scat detection dogs, remote cameras, and hair snares—to collect detection-nondetection data for American black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus) throughout Vermont. We analyzed these data using an occupancy modeling approach that explicitly incorporated detectability as well as habitat and landscape variables. Model results were then used to predict occurrence for each species across the study area. Receiver operating characteristic (ROC) analyses of our models for species with high detectability suggest that the results of such surveys and modeling efforts may be useful for those striving to conserve or manage species at the regional or landscape scale. The noninvasive methods used for this project enabled us to collect important detection-nondetection information from low density, secretive, and wide-ranging species, without the need to capture or interact with the study subjects directly.
Katz, J., S. Hafner, and T. Donovan. 2016. Tools for automated acoustic monitoring within the R package monitoR. Bioacoustics. DOI:10.1080/09524622.2016.1138415 \| Abstract \| Publisher Website	January 2016	The R package monitoR contains tools for managing an acoustic-monitoring program including survey metadata, template creation and manipulation, automated detection and results management. These tools are scalable for use with small projects as well as larger long-term projects and those with expansive spatial extents. Here, we describe typical workflow when using the tools in monitoR. Typical workflow utilizes a generic sequence of functions, with the option for either binary point matching or spectrogram cross-correlation detectors.
Katz, J., S. Hafner, and T. Donovan. 2016. Assessment of Error Rates in Acoustic Monitoring with the R package monitoR. Bioacoustics. DOI:10.1080/09524622.2015.1133320 \| Abstract \| Publisher Website	January 2016	Detecting population-scale reactions to climate change and land-use change may require monitoring many sites for many years, a process that is suited for an automated system. We developed and tested monitoR, an R package for long-term, multi-taxa acoustic monitoring programs. We tested monitoR with two northeastern songbird species: black-throated green warbler (Setophaga virens) and ovenbird (Seiurus aurocapilla). We compared detection results from monitoR in 52 10-minute surveys recorded at 10 sites in Vermont and New York, USA to a subset of songs identified by a human that were of a single song type and had visually identifiable spectrograms (e.g. a signal:noise ratio of at least 10 dB: 166 out of 439 total songs for black-throated green warbler, 502 out of 990 total songs for ovenbird). monitoR’s automated detection process uses a ‘score cutoff’, which is the minimum match needed for an unknown event to be considered a detection and results in a true positive, true negative, false positive or false negative detection. At the chosen score cut-offs, monitoR correctly identified presence for black-throated green warbler and ovenbird in 64% and 72% of the 52 surveys using binary point matching, respectively, and 73% and 72% of the 52 surveys using spectrogram cross-correlation, respectively. Of individual songs, 72% of black-throated green warbler songs and 62% of ovenbird songs were identified by binary point matching. Spectrogram cross-correlation identified 83% of black-throated green warbler songs and 66% of ovenbird songs. False positive rates were for song event detection.
Katz, J. and T. M. Donovan. 2017. AMModels: Adaptive Management Model Manager. R package version 0.1.2.	February 2016
Jackson, J. R., T. J. Kwak, and D. L. Parrish. 2009. Members of the AFS Education Section response. Fisheries 34:85-86.	February 2009
Izzo, L.K., D.L. Parrish, and G.B. Zydlewski. 2021. Multi-run migratory behavior of adult male lake sturgeon in a short river. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2021.06.012 \| Abstract	July 2021	Lake sturgeon (<i>Acipenser fulvescens</i>) can migrate long distances to spawn, but many populations currently spawn in systems where the length of accessible riverine migratory habitat has been greatly reduced by dam construction. With the increased prevalence of shortened rivers, focusing on migratory dynamics in short rivers (<30 km) is beneficial to understanding the migratory needs of lake sturgeon populations. Here we document male lake sturgeon movements during the spawning period in the Winooski River, Vermont, USA; a river with only 17 km to the first natural upstream barrier. Male lake sturgeon were acoustically tagged (n = 25, 1215–1470 mm TL) and tracked using five to nine stationary receivers from 2017 to 2019. River discharge, temperature, the lagged effect of temperature (3-day), and time of day were significant factors describing upstream movements of tagged fish. Migrating male lake sturgeon (n = 10 in 2017, n = 18 in 2018, and n = 17 in 2019) displayed general movement patterns during the spawning period that included a single run upstream to the spawning site (60%), upstream and downstream movements throughout the river during the season (20%), or multiple runs made up the entire length of the spawning tributary to the spawning site (20%). No multi-run males were observed during 2018 when discharge was less flashy (i.e., fewer steep increases and declines in discharge) than in 2017 and 2019. These results suggest that the prevalence of multi-run spawning behavior of male lake sturgeon is related to flow conditions.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and R. Koenigs. 2021. Second fin ray shows promise for estimating ages of juvenile but not adult Lake Sturgeon. North American Journal of Fisheries Management 41: 217-228. doi: 10.1002/nafm.10561. \| Abstract	February 2021	The first marginal pectoral fin ray (fin spine) is the most common structure used for estimating the age of sturgeons, including listed Lake Sturgeon <i>Acipenser fulvescens </i>populations. However, conflicting results on the effects of fin spine removal have made some managers hesitant about the practice. We investigate if the second pectoral fin ray, which can be removed in a less invasive procedure, could be used for estimating ages of Lake Sturgeon. Ages estimated from fin spine and second fin ray samples were compared for 53 wild (470 to 1981 mm total length, TL) and 16 stocked, known-age (ages 8 – 18) Lake Sturgeon. Mean coefficient of variation (CV) for all samples was 12.4% for the fin spine and 17.5% for the second fin ray. In known-age fish, 17% of estimated ages for the fin spine and the second fin ray matched true age. For the remaining estimates, the difference between the second fin ray and true age was greater than the difference between the fin spine and true age (<i>P </i>< 0.05, Wilcoxon signed rank test). In juvenile fish (n = 24), 75% of ages estimated from fin spines and second fin rays were within ± 4 annuli, which was similar to differences in reader agreement for the same fin spine. Age estimates for adult Lake Sturgeon (n = 45) were less when using the second fin ray relative to the fin spine (up to -34 years). Additionally, poor annulus clarity was observed in > 70% of the second fin rays sampled from adult fish. Our results suggest that the second fin ray does not provide reliable age estimates for adult Lake Sturgeon but may have some utility for estimating age of juvenile Lake Sturgeon. Additional research with a larger sample size would be required to provide more conclusive results.
Irwin, E. R., F. J. Rahel, D. L. Parrish, D. H. Wahl. 1998. Enhancing professionalism: awards and grants for student members of the American Fisheries Society. Fisheries 23(8):20-23.	January 1998
Hyrcik, A.E., P.W. Simonin, L.G. Rudstam, D.L. Parrish, B. Pientka, and T.B. Michuc. 2015. Mysis zooplanktivory in Lake Champlain: a bioenergetics analysis. Journal of Great Lakes Research 41: 492-501. doi:10.1016/j.jglr.2015.03.011 \| Abstract \| Publisher Website	April 2015	Mysid shrimp are important as both predators on zooplankton and as prey for a variety of fish species across most of the Laurentian Great Lakes. In Lake Champlain, where little is known about mysids, this may also be true. We evaluated the role of Mysis diluviana as a planktivore in Lake Champlain using hydroacoustics, gut content analysis, stable isotopes, cohort analysis, and bioenergetics models to estimate Mysis density, diets, growth rates, and prey consumption rates. Density of Mysis in the water column of the deeper Main Lake was lower in July-August of 2008-2011 (38, 38, 21, and 74 Mysis /m2, respectively) than historical values from the 1970s. Mysis selectively foraged for cladocerans, but also consumed cyclopoid and calanoid copepods in 2011. Stable isotope data suggest a mostly carnivorous diet, although agreement between isotope mixing models and observed diets varied. Cohort analyses revealed growth rates ranging from 2.7 mm/month in late spring to 1.3 mm/month in late summer. In contrast to the offshore areas of Lake Ontario and Lake Huron, zooplankton consumption by the Mysis population was low relative to zooplankton density and production indicating that Mysis are not currently a major zooplanktivore in Lake Champlain.
Howell, C. A., S. C. Latta, T. M. Donovan, P. A. Porneluzi, and J. Faaborg. 2000. Landscape effects mediate breeding bird abundance in midwestern forests. Landscape Ecology 15:547-563.	January 2001
Howe, E., J. E. Marsden, T. M. Donovan, and R. Lamberson. 2012. A life cycle approach to modeling sea lamprey population dynamics in the Lake Champlain basin to evaluate alternative control strategies. Journal of Great Lakes Research 38:101-114. \| Abstract \| Download \| Publisher Website	December 2011	Sea lamprey (Petromyzon marinus) is a nuisance species in the Laurentian Great Lakes and Lake Champlain that has devastated native ﬁ sh populations and hampered sport ﬁ sheries development. We developed a modified stage-based life history matrix for sea lamprey to analyze the effects of various management efforts to suppress sea lamprey population growth in Lake Champlain. These efforts targeted different life stages of the sea lamprey life cycle. A beta distribution was used to distribute stochastic larval populations among twenty sea lamprey-bearing tributaries and ﬁve deltas to Lake Champlain, from which sea lamprey that survive through larval metamorphosis were then pooled into a lake-wide parasitic-phase population. Parasitic-phase survival to the spawning stage was evaluated based on proximity to the natal tributary and on the size of the resident larval population in each tributary. Potential control strategies were modeled at egg to emergence, larval, and spawning stages to reduce vital rates at each stage, with the goal of suppressing parasitic-phase production. Simulations indicate that control of the larval stage was essential to achieving this goal, and with supplemental effort to reduce the vital rates at early life stages and at the spawning stage, the parasitic-phase population can be further suppressed. Sensitivity simulations indicate that the life history model was sensitive to egg deposition rate, abundance of parasitic-phase sea lamprey from unknown, uncontrolled sources, and the method in which parasitic-phase sea lamprey select tributaries for spawning. Results from this model can guide management agencies to optimize future management programs.
Henderson, M.J., Loomis, C., Michel, C., Smith, J., Iglesias, I., Lehman, B., Huff, D. Estimates of predator densities using mobile DIDSON surveys: implications for survival of Central Valley Chinook salmon. North American Journal of Fisheries Management 43: 628-645. \| Abstract	June 2023	The Sacramento-San Joaquin Delta (the Delta) is one of the most invaded estuaries in the world, and non-native predators may be a major factor in the observed decline of Central Valley Chinook salmon over recent decades. In order for managers to take actions that might reduce predation related mortality for these ecologically, culturally, and economically valuable salmon, it’s important to understand the factors influencing the distribution and abundance of piscivores in the Delta. In this study, we use a multibeam imaging sonar (i.e., DIDSON) to conduct mobile surveys and quantify the abundances of piscivores in the Delta. We then used these data to identify the habitat features that are correlated with the abundance of piscivores. Prior to conducting the surveys, we used DIDSON data from captured fish to develop an algorithm to distinguish piscivores from non-piscivores with high confidence (98% accuracy). Results from the surveys indicated that predator abundances were most associated with areas of increased submerged aquatic vegetation (SAV) patches, sites that are straighter, and sites with increased bathymetric complexity. When applied to the entire survey area, this model was successfully able to predict known areas of high predator densities. These results indicate that one approach to reduce predator densities along these migration corridors, and improve juvenile salmon outmigration survival, is to reduce the extent of invasive SAV. Because experimental predator removals have been largely ineffective in the Delta, efforts to manipulate habitat to discourage non-native predator recruitment and favor native species recruitment may be more effective.
Hawes, E. J., and D. L. Parrish. 2003. Factors affecting the expansion of white perch in Lake Champlain. Journal of Great Lakes Research 29:268-279.	April 2003
Hartman, K. J., B. Vondracek, D. L. Parrish, and K. M. Muth. 1992. Diets of emerald and spottail shiner and potential interactions with other western Lake Erie prey fishes. Journal of Great Lakes Research 18:43-50.	January 1992
Hall, C. A. S., P. W. Jones, T. M. Donovan, and J. P. Gibbs. 2000. Neoclassical economics and its effects on wildlife and wildlife management. The Wildlife Society Bulletin 28:16-25.	January 2001
Gries, G., K. G. Whalen, F. Juanes, and D. L. Parrish. 1997. Nocturnal activity of juvenile Atlantic salmon in late summer: evidence of diel activity partitioning. Canadian Journal of Fisheries and Aquatic Sciences 54:1408-1413.	July 1997
Greenwald, K., A. Stedman, D. Mifsud, M. Stapleton, K. Larson, I. Chellman, D. L. Parrish, and C. W. Kilpatrick. 2020. Phylogeographic analysis of Mudpuppies (Necturus maculosus). Journal of Herpetology 54: 78-86. doi: 10.1670/19-070 \| Abstract	March 2020	The geology of the Pleistocene, and particularly the Last Glacial Maximum approximately 26.5 ka, is a critical driver of species’ present-day distributions and levels of genetic diversity in northern regions. Using mitochondrial DNA sequence data, we tested several predictions relating to the postglacial recolonization of the northern United States and southern Canada by Mudpuppies (Necturus maculosus). Our analyses revealed a significant split between western and eastern lineages, with the divide corresponding to the location of the Mississippi River. Our data support the presence of one or more Mississippian glacial refugia, with subsequent expansion and diversification of a western clade into the upper Midwest, and an eastern cluster into the eastern Great Lakes and New England. As predicted in cases of postglacial colonization, each of these clades contains a single widespread and common haplotype, along with numerous low-frequency, closely related haplotypes. Given recent conservation concerns about amphibians in general, and Mudpuppies specifically, we discuss our results in light of species conservation. Knowledge of a species’ genetic diversity allows for informed management and facilitates decisions that preserve local adaptation and evolutionary potential.
Farrell, L. E. D M. Levy, T. Donovan, R. Mickey, A. Howard, J. Vashon, M. Freeman, K. Royar, and C. W. Kilpatrick. 2018. Landscape connectivity for bobcat (Lynx rufus) and lynx (Lynx canadensis) in the northeastern Northeastern United States. PLoS ONE 13(3): e0194243. https://doi.org/10.1371/journal.pone.0194243 \| Abstract \| Download \| Publisher Website	March 2018	Landscape connectivity is integral to the persistence of metapopulations of wide ranging carnivores and other terrestrial species. The objectives of this research were to investigate the landscape characteristics essential to use of areas by lynx and bobcats in northern New England, map a habitat availability model for each species, and explore onnectivity across areas of the region likely to experience future development pressure. A Mahalanobis distance analysis was conducted on location data collected between 2005 and 2010 from 16 bobcats in western Vermont and 31 lynx in northern Maine to determine which variables were most consistent across all locations for each species using three scales based on average 1) local (15 minute) movement, 2) linear distance between daily locations, and 3) female home range size. The bobcat model providing the widest separation between used locations and random study area locations suggests that they cue into landscape features such as edge, availability of cover, and evelopment density at different scales. The lynx model with the widest separation between random and used locations contained five variables including natural habitat, cover, and levation—all at different scales. Shrub scrub habitat—where lynx’s preferred prey is most abundant—was represented at the daily distance moved scale. Cross validation indicated that outliers had little effect on models for either species. A habitat suitability value was calculated for each 30 m2 pixel across Vermont, New Hampshire, and Maine for each species and used to map connectivity between conserved lands within selected areas across the region. Projections of future landscape change illustrated potential impacts of anthropogenic development on areas lynx and bobcat may use, and indicated where connectivity for bobcats and lynx may be lost. These projections provided a guide for conservation of landscape permeability for lynx, bobcat, and species relying on similar habitats in the region.
Fabrizio, M.C., Henderson, M.J., Rose, K., Petitgas, P. Editorial: Habitat and Distribution Models of Marine and Estuarine Species: Advances for a Sustainable Future. Submitted to Frontiers in Marine Science. \| Abstract	October 2022	The physical and biological characterization of suitable habitats and species-specific models to estimate the extent of available suitable habitats are valuable for conservation and fisheries management. As exploited species and habitats face challenges from anthropogenic influences, such as fishing and climate change, the identification and protection of habitats becomes increasingly important. Most of the papers within this special topic issue used some form of species distribution model (SDM) to identify habitats used by fishes (Asch et al. 2022, Crear et al. 2020, Fabrizio et al. 2021, Freidland et al. 2021, Zydlewski et al. 2021), marine mammals (Astarloa et al. 2021), nearshore invertebrates (Cristiani et al. 2021, Behan et al. 2021), or deep-sea communities (Bowden et al. 2021, Saunders et al. 2021). A few papers focused on developing methods to better describe habitats (Griffin et al. 2021, Henderson et al. 2020, Cecino et al. 2021), while others investigated model performance and incorporation of new statistical methods to improve model accuracy (Asch et al. 2022, Behan et al. 2021, Bowden et al. 2021). Below we provide a synthesis of these papers and examine data sources used for analyses, statistical methods, stationarity and model performance, connectivity, and management implications; we conclude with a consideration of opportunities for advancing this field of study.
Espenshade, J., J. D. Murdoch, T. M. Donovan, R. E. Manning, and C. A. Bettigole. 2018. Public acceptability of development in the Northern Forest of Vermont, USA – the influence of wildlife information, recreation involvement, and demographic characteristics. PLoS ONE 13(12):e0203515. \| Abstract \| Download \| Publisher Website	December 2018	Increasing development such as roads and houses will alter future landscapes and result in biological, social, and economic trade-offs. Managing development requires information on the public’s acceptability of development and understanding which factors shape acceptability. In this study, we examined three questions: 1) What is the public’s acceptability of development? 2) Is acceptability of development influenced by wildlife information? and 3) Is the maximum amount of acceptable development influenced by views about wildlife, involvement in outdoor recreation, and demographic factors? We conducted a visual-preference survey of 9,000 households in Vermont, USA that asked about acceptable levels of development, acceptability of wildlife, involvement in recreation, and individual and town demographics. The survey response rate was 44%. Maximum acceptable condition (MAC) for development was 41 houses/km2 and not meaningfully influenced by broader consequences of development on seven common wildlife species. MAC was influenced by views on individual species, including bear and coyote, but not by other species such as deer, fox, and bobcat. Respondents with a positive attitude toward bear favored less development, whereas the opposite relationship existed for coyote. Similarly, MAC was negatively influenced by involvement in birding and hunting, but not by other common recreational activities. Among demographic factors, respondents that were younger and not born in Vermont were more accepting of development. Population density also positively influenced development acceptability. Results provide measures of the public’s acceptability of development that can help guide decision-making about development, wildlife, and recreation management.
Eisenhower, M. D., and D. L. Parrish. 2009. Double-crested cormorant and fish interactions in a shallow basin of Lake Champlain. Waterbirds 32:388-399.	September 2009
Duerr, A., D. E. Capen, and T. M. Donovan. 2007. Wildlife management increases breeding dispersal in double-crested cormorants. Journal of Wildlife Management 71:2565-2574. \| Abstract \| Download \| Publisher Website	November 2007	We studied breeding dispersal of double-crested cormorants {Phalacrocorax auritus) associated with management practices that suppressed their reproduction on Lake Champlain in the northeastern United States. We implemented an experiment on one colony by spraying corn oil on cormorant eggs in portions of the colony and leaving other portions untreated. Gulls (Larus spp.) consumed cormorant eggs during the oiling process, but we reduced and then eliminated predation levels after the first year of the study. We used mark-recapture techniques within the experimental framework to measure rates of breeding dispersal for cormorants from the experimental colony and an unmanaged colony in Lake Champlain. Egg oiling increased the movement rate to the unmanaged colony by 3% during the year with no egg predation by gulls. When gulls depredated cormorant eggs at high rates during egg oiling, movement to the unmanaged colony increased by 20%. When cormorants are managed to reduce population sizes, methods that limit dispersal away from the managed colony may be most effective. Such methods would mitigate effects to nontarget populations and allow for a greater portion of the metapopulation to be managed.
Duerr, A., D. E. Capen, and T. M. Donovan. 2012. Energetic considerations for managing double-crested cormorants on Lake Champlain. Journal of Great Lakes Research 38:131-140. \| Abstract \| Download \| Publisher Website	December 2011	We studied foraging distribution, activity budgets, ﬁ sh consumption, and energetics of double-crested cormorants (Phalacrocorax auritus) at two breeding colonies on Lake Champlain. Our objective was to determine if ﬁ sh consumption and distribution of predation changed with movements of cormorants associated with efforts to reduce numbers of cormorants on one of the colonies. Wildlife managers reduced populations of cormorants on Young Island, Vermont by oiling their eggs, which resulted in dispersal of breeding cormorants 35 km south to Four Brothers Islands, New York. We found that as cormorants shifted from Young Island to the colony on Four Brothers Islands, energy demands, foraging distribution, and total ﬁ sh consumption increased. Birds on Four Brothers Islands foraged a greater distance from the colony compared to birds on Young Island. Additionally, consumption of yellow perch (Perca ﬂavescens) shifted to rainbow smelt (Osmerus mordax) when more birds bred on Four Brothers Islands. The dispersal of cormorants from Young Island to Four Brothers Islands reduced predation on yellow perch but increased overall ﬁsh consumption. Our estimates of ﬁsh consumption ranged from 322,000–425,000 kg of ﬁ sh per year at Young Island to 899,000–1,086,000 kg of ﬁsh per year at Four Brothers Islands. Results from this study demonstrate secondary impacts of management on Young Island to unmanaged areas.
Driscoll, M. L., and T. M. Donovan. 2004. Landscape context moderates edge effects: Nesting success of Wood Thrushes in central New York. Conservation Biology 18:1330-1338. \| Download	October 2004
Driscoll, M. L., T. M. Donovan, R. Mickey, A. Howard, and K. Fleming. 2005. Determinants of Wood Thrush nesting success: a multi-scale, model selection approach. Journal of Wildlife Management 69:699-708. \| Download	May 2004
Donovan. T. M., C. Balantic, J. Katz, M. Massar, R. Knutson, K. Duh, P. W. Jones, K. Epstein, J. Lacasse-Roger, and J. Dias. 2021. Remote Ecological Monitoring with Smartphones and Tasker. Journal of Fish and Wildlife Management 12:163–173. \| Abstract \| Download \| Publisher Website	June 2021	Researchers have increasingly used autonomous monitoring units to record animal sounds, track phenology with timed photographs, and snap images when triggered by motion. We piloted the use of smartphones to monitor wildlife in the Riverside East Solar Energy Zone (California) and at Indiana Dunes National Park (Indiana). For both efforts, we established remote autonomous monitoring stations in which we housed an Android smartphone in a weather-proof box mounted to a pole and powered by solar panels. We connected each smartphone to a Google account, and the smartphone received its recording/photo schedule daily via a Google Calendar connection when in data transmission mode. Phones were automated by Tasker, an Android application for automating cell phone tasks. We describe a simple approach that could be adopted by others who wish to use nonproprietary methods of data collection and analysis.
Donovan, T.M., and R. M. Mickey. 2019. Bayesian Statistics for Beginners. Oxford University Press, Oxford, UK.	May 2019
Donovan, T.M., M.D. Freeman, A. Howard, K. Royar, H. Abouelezz, and R. Mickey. 2011. Quantifying home range habitat requirements for bobcats (Lynx rufus) in Vermont. Biological Conservation 144:2799-2809. \| Abstract \| Download \| Publisher Website	October 2011	We demonstrate how home range and habitat use analysis can inform landscape-scale conservation planning for the bobcat, Lynx rufus, in Vermont USA. From 2005 to 2008, we outfitted fourteen bobcats with GPS collars that collected spatially explicit locations from individuals every 4 h for 3–4 months. Kernel home range techniques were used to estimate home range size and boundaries, and to quantify the utilization distribution (UD), which is a spatially explicit, topographic mapping of how different areas within the home range are used. We then used GIS methods to quantify both biotic (e.g. habitat types, stream density) and abiotic (e.g. slope) resources within each bobcat’s home range. Across bobcats, upper 20th UD percentiles (core areas) had 18% less agriculture, 42% less development, 26% more bobcat habitat (shrub, deciduous, coniferous forest, and wetland cover types), and 33% lower road density than lower UD percentiles (UD valleys). For each bobcat, we used Akaike’s Information Criterion (AIC) to evaluate and compare 24 alternative Resource Utilization Functions (hypotheses) that could explain the topology of the individual’s UD. A model-averaged population-level Resource Utilization Function suggested positive responses to shrub, deciduous, coniferous forest, and wetland cover types within 1 km of a location, and negative responses to roads and mixed forest cover types within 1 km of a location. Applying this model-averaged function to each pixel in the study area revealed habitat suitability for bobcats across the entire study area, with suitability scores ranging between −1.69 and 1.44, where higher values were assumed to represent higher quality habitat. The southern Champlain Valley, which contained ample wetland and shrub habitat, was a concentrated area of highly suitable habitat, while areas at higher elevation areas were less suitable. Female bobcat home ranges, on average, had an average habitat suitability score of near 0, indicating that home ranges consisted of both beneficial and detrimental habitat types. We discuss the application of habitat suitability mapping and home range requirements for bobcat conservation and landscape scale management.
Donovan, T.M. and J. E Katz. 2018. AMModels: An R package for storing models, data, and metadata to facilitate adaptive management. PLoS ONE 13(2): e0188966. https://doi.org/10.1371/journal.pone.0188966 \| Abstract \| Download \| Publisher Website	January 2018	Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an. RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and using knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date.
Donovan, T., and J. Hines. 2007. Exercises in occupancy modeling and estimation. Electronic book. \| Publisher Website	December 2007
Donovan, T., J. Hines, and D. MacKenzie. 2024. occupancyTuts: Occupancy Modeling Tutorials with RPresence. Methods in Ecology and Evolution. 10.1111/2041-210X.14285 \| Abstract \| Download \| Publisher Website	January 2024	Abstract<br><br>1. The occupancy modelling framework offers tremendous flexibility in estimating species abundance and distribution patterns while accounting for imperfect detection, and has seen rapid growth and adoption since its introduction at the beginning of the century.<br><br>2. At the same time, in an era of big data, there are increasing demands on developing quantitative skills and proficiency in young ecologists, many of whom lack the quantitative training needed to conduct research professionally.<br><br>3. We introduce <i>occupancyTuts</i>, an R package that features 28 <i>learnr </i>tutorials that teach the statistical underpinnings of several occupancy models. The tutorials include written content, instructional videos, R exercises, and quiz elements, covering a range of topics including statistical underpinnings, single- and dynamic-occupancy models, study design and several of the ‘spin-off’ models that extend the basic framework.<br><br>4. We plan for development of new tutorials that use <i>RPresence</i> as the analysis engine, and welcome new tutorial contributions that use other R packages as the analysis engine as well.
Donovan, T., Brown, M., & Katz, J. 2015. Vermont Cooperative Fish and Wildlife Research Unit R Projects: R for Fledglings. Retrieved from https://www.uvm.edu/rsenr/vtcfwru/R/?Page=fledglings/fledglings.htm	January 2015
Donovan, T. M., and C. Welden. 2002. Spreadsheet exercises in ecology and evolution. Sinauer Associates, Inc. Sunderland, MA. 556 pages. \| Publisher Website	January 2002
Donovan, T. M., and C. Welden. 2002. Spreadsheet exercises in conservation biology and landscape ecology. Sinauer Associates, Inc. Sunderland, MA. 464 pages. \| Publisher Website	January 2002
Donovan, T. M., and C. Flather. 2002. Relationships among North American songbird trends, habitat fragmentation, and landscape occupancy. Ecological Applications. 12:364-374. \| Download	September 2001
Donovan, T. M., and A. M. Strong. 2002. Linkages between landscape theory and population dynamics: a review of empirical evidence. Pages 35-54 In: J. Bissonnette and I. Storch, editors. Landscape ecology and resource management: linking theory with practice. Island Press.	December 2002
Donovan, T. M., J. Buzas, P. W. Jones, H. L. Gibbs. 2006. Tracking dispersal in birds: assessing the potential of elemental markers. Auk 123:1-12.	April 2006
Donovan, T. M., G. S. Warrington, W. S. Schwenk, and J. H. Dinitz. 2012. Estimating landscape carrying capacity through maximum clique analysis. Ecological Applications 22:2265-2276. \| Abstract \| Download	December 2012	Habitat suitability (HS) maps are widely used tools in wildlife science and establish a link between wildlife populations and landscape pattern. Although HS maps spatially depict the distribution of optimal resources for a species, they do not reveal the population size a landscape is capable of supporting – information that is often crucial for decision makers and managers. We used a new approach, maximum clique analysis, to demonstrate how HS maps for territorial species can be used to estimate the carrying capacity, Nk, of a given landscape. We estimated Nk of ovenbirds (Seiurus aurocapillus) and bobcats (Lynx rufus) in an 1,153 km2 study area in Vermont, USA. These two species were selected to highlight different approaches in building an HS map as well as computational challenges that can arise in a maximum clique analysis. We derived 30 m2 HS maps for each species via occupancy modeling (ovenbird) and by resource utilization modeling (bobcats). For each species, we then identified all pixel locations on the map (points) that had sufficient resources in the surrounding area to maintain a home range (termed a pseudo home range). These locations were converted to a mathematical graph, where any two points were linked if two pseudo home ranges could exist on the landscape without violating territory boundaries. We used the program, Cliquer, to find the maximum clique of each graph. The resulting estimates of Nk = 236 ovenbirds and Nk = 42 female bobcats were sensitive to different assumptions and model inputs. Estimates of Nk via alternative, ad-hoc methods were 1.4 to > 30 times greater than the maximum clique estimate, suggesting that the alternative results may be upwardly biased. The maximum clique analysis was computationally intensive but could handle problems with <1,500 total pseudo home ranges (points). Given present computational constraints, it is best suited for species that occur in clustered distributions (where the problem can be broken into several, smaller problems), or for species with large home ranges relative to grid scale where resampling the points to a coarser resolution can reduce the problem to manageable proportions.
Donovan, T. M., F. R. Thompson III, and J. Faaborg. 2000. Cowbird distribution at different scales of fragmentation: Tradeoffs between breeding and feeding opportunities. Pages 255-264 In Ecology and management of cowbirds (T. Cooke, S. K. Robinson, S. I. Rothstein, S. G. Sealy, J. N. M. Smith, eds. ). University of Texas Press, Austin, TX. \| Download	January 2001
Donovan, T. M., C. Danforth, D. Shustack. 2008. Predicting annual fecundity from nest success. Open Ornithology Journal 1:20-28. \| Abstract \| Download \| Publisher Website	July 2008	Nest success, the probability that a nest will fledge offspring, is a widely measured parameter in ornithological studies, and is usually estimated by monitoring the fates of nests throughout a breeding season. Because nest success estimates are commonly reported in the avian literature, a key question in population studies is how to derive annual fecundity rates, F (a vital parameter in population biology), from nest success data when breeding individuals are not marked. In this manuscript, we describe a simple, recursive model that generates an estimate of the frequency distribution of annual fecundity rates that can be achieved for a species, given precise and unbiased estimates of nest success, the average number of young that fledge per successful nest, and three life history parameters: the maximum number of possible successful broods per breeding season (J), the maximum number of possible nesting attempts per breeding season (K), and the maximum brood size (B). We illustrate the model for 3 hypothetical species in which the average young that fledge per successful nest is 2 offspring: (1) a single-brooded species in which J =1, K = 3, B = 3; (2) a double-brooded species in which J = 2, K = 3, B = 3, and (3) a triple-brooded species in which J =3, K = 3, B = 3. In general, the frequency distributions of acceptable fecundity solutions for single-, double-, and triple-brooded species are all approximately symmetric, and are defined by Fave (the average acceptable solution), Fmin (the minimum acceptable solution), and Fmax (the maximum acceptable solution). The “breadth” of these distributions, or the difference between Fmin and Fmax, appears to be controlled largely by solutions where an unequal number of young fledge across attempts. However, when examining relationships between annual fecundity and nest success across the full spectrum of nest success values, we find that, more often than not, non-linear relationships characterized the association between nest success, Fmax, Fmin, and Fave. The only case where nest success predicts annual fecundity in a linear fashion occurred when J = K. Thus, the assumption that nest success is an adequate indicator of annual fecundity should be viewed with caution.
Donovan, T. M., C. Beardmore, D. Bonter, J. Brawn, J. A. Fitzgerald, R. Ford, S. Geautreax, L. George, C. Hunter, T. E. Martin, J. Price, K. Rosenberg, P. Vickery, and T. Bentley Wigley. (The Partners in Flight Research Working Group). 2002. Priority research needs for conservation of Neotropical migrants. Journal of Field Ornithology 73:329-338. \| Download	September 2001
Dick, C., Larson, W.A., Karpan, K., Baetscher, D.S., Shi, Y., Sethi, S., Fangue, N.A., Henderson, M.J. Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding. Submitted to Molecular Ecology Resources. \| Abstract	August 2023	Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two different rations of Chinook salmon (<i>Oncorhynchus tshawytscha</i>) to two piscivorous fish species (striped bass [<i>Morone saxatilis</i>] and channel catfish [<i>Ictalurus punctatus</i>]) held at two different temperatures (15.5°C and 18.5°C) and sacrificed at regular intervals up to 120 hours from the time of ingestion to quantify digestive tract contents. We found that ration size had the largest influence on digestion rate followed by prey species and temperature. DNA based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~6 hours for visual analysis versus ~72 hours for molecular analyses). Notably, metabarcoding results had substantially less variance than qPCR results and produced better quantitative estimates of evacuation rates that could be more confidently integrated into modeling efforts. Our study provides evidence that modeling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.
DeBow, J., J. Blouin, E. Rosenblatt, K. Gieder, W. Cottrell, J. Murdoch, and T. Donovan. 2021. Effects of winter ticks and internal parasites on moose survival in Vermont, USA. Journal of Wildlife Management. DOI: 10.1002/jwmg.22101 \| Abstract \| Download \| Publisher Website	August 2021	Moose (<i>Alces alces</i>) have experienced considerable declines along the periphery of their range in the northeastern United States. In Vermont, the population declined 45% from 2010 to 2017 despite minimal hunter harvest and adequate habitat. Similarly, nearby populations recently experienced epizootics characterized by >50% mortality. Declines have largely been associated with the effects of winter ticks (<i>Dermacentor albipictus</i>), but uncertainty exists about the effects of environmental and other parasite-related conditions on moose survival. We examined patterns of moose survival among a radio-collared population (<i>n</i> = 127) in Vermont from 2017 to 2019. Our objectives were to estimate causes of mortality and model survival probability as a function of individual and landscape variables for calves (<1 yr) and adults (≥1 yr). Observed adult survival was 90% in 2017, 84% in 2018, and 86% in 2019, and winter calf survival was 60% in 2017, 50% in 2018, and 37% in 2019. Winter tick infestation was the primary cause of mortality (91% of calves, 25% of adults), and 32% of all mortalities had evidence of meningeal worm (<i>Parelaphostrongylus tenuis</i>). Other sources of mortality such as vehicles, harvest, predation, deep snow, and other parasitic infections were negligible. The best supported calf model included sex differences and negative effects of tick engorgement (%/week) and parasite level (roundworm and lungworm). The best supported adult model included the effect of cumulative tick engorgement (cumulative %/week), which negatively affected survival. Our results indicate that winter tick engorgement strongly affects survival, and is probably compounded by the presence of meningeal worm and other parasites. Reduced tick effects may be achieved by decreasing moose density through harvest and managing late winter habitat to minimize tick density. Management of white-tailed deer (<i>Odocoileus virginianus</i>) density may also affect the transmission of meningeal worm.
DeBow, J., J. Blouin, E. Rosenblatt, K. Gieder, J. Murdoch, and T. Donovan. 2023. Birth Rates and Calf Survival in a Parasite Rich Moose Herd in Vermont, USA. Alces 58: 51–73. \| Abstract \| Download \| Publisher Website	February 2023	Moose (<i>Alces alces</i>) populations have recently declined across the southern portion of their geographic range in North America. In Vermont and other northeastern U.S. states, declines have been attributed to low survival rates driven primarily by winter tick (<i>Dermacentor albipictus</i>), which may also affect birth rate and survival of new calves. We radio-collared and monitored 75 female moose (38 calves and 37 adults) in Vermont from 2017 to 2020 and examined the effects of physiological conditions and spatial and temporal factors on adult birth rates. Physiological measures included fecal glucocorticoid metabolites concentrations (fGCM), which reflect stress, and urine urea nitrogen:creatinine ratio (UN:C), which proxies nutritional state. The pregnancy rate at capture across years was 0.67 (95% CI = 0.50 – 0.80), and negatively influenced by the presence of lungworm (<i>Dictyocaulus </i>spp.). Birth rates, calculated as the average number of offspring delivered per adult female, were < 1.0 overall, did not differ among years (2017-2020, LCI = 0.22, UCI = 0.86), but differed by adult age class, where rates increased with age. We further evaluated daily calf survival rates to age 60 days, the point at which calves become independent of direct care. Logistic exposure models indicated that daily calf survival increased as Julian birth date and days since birth increased (log odds = 0.0819, SE = 0.0215). The per capita independence rate (the rate at which adult females add independent calves to the population) was negatively influenced by average UN:C ratios and positively influenced by fGCM levels. Further, this rate was related to the habitat conditions in home ranges of adult females during the fall, when ticks attach to moose. Specifically, female adults whose fall home ranges were characterized by high levels of mature (canopy) evergreen forests and wetland habitats, and low levels of mixed forests and elevation, had a higher, average binomial success rate in adding an independent calf into the population than those whose home ranges consisted of high levels of mixed forest at high elevation. Our results suggest that winter ticks negatively affect fecundity, and that efforts to reduce parasite loads on individual moose (e.g., directly by reducing moose density or indirectly through habitat alteration) may improve productivity and recruitment.
Cunjak, R. A., T. D. Prowse, and D. L. Parrish. 1998. Atlantic salmon (Salmo salar) in winter: the season of parr discontent. Canadian Journal of Fisheries and Aquatic Sciences 55(Supple. 1):161-180.	December 1998
Cornell, K., and T. Donovan. 2010. Effects of spatial habitat heterogeneity on habitat selection and annual fecundity for a forest songbird. Landscape Ecology 25:109-122. \| Abstract \| Download \| Publisher Website	January 2010	Understanding how spatial habitat patterns influence abundance and dynamics of animal populations is a primary goal in landscape ecology. We used an information-theoretic approach to investigate the association between habitat patterns at multiple spatial scales and demographic patterns for black-throated blue warblers (Dendroica caerulescens) at 20 study sites in west-central Vermont, USA from 2002 to 2005. Sites were characterized by: (1) territory-scale shrub density, (2) patch-scale shrub density occurring within 25 ha of territories, and (3) landscape-scale habitat patterns occurring within 5 km radius extents of territories. We considered multiple population parameters including abundance, age ratios, and annual fecundity. Territory-scale shrub density was most important for determining abundance and age ratios, but landscape-scale habitat structure strongly influenced reproductive output. Sites with higher territory-scale shrub density had higher abundance, and were more likely to be occupied by older, more experienced individuals compared to sites with lower shrub density. However, annual fecundity was higher on sites located in contiguously forested landscapes where shrub density was lower than the fragmented sites. Further, effects of habitat pattern at one spatial scale depended on habitat conditions at different scales. For example, abundance increased with increasing territory-scale shrub density, but this effect was much stronger in fragmented landscapes than in contiguously forested landscapes. These results suggest that habitat pattern at different spatial scales affect demographic parameters in different ways, and that effects of habitat patterns at one spatial scale depends on habitat conditions at other scales.
Cornell, K. L, and T. M. Donovan. 2010. Scale-dependent mechanisms of habitat selection for a migratory passerine: An experimental approach. Auk 127:899-908. \| Abstract \| Download	November 2010	Habitat selection theory predicts that individuals choose breeding habitats that maximize fitness returns on the basis of indirect environmental cues at multiple spatial scales. We performed a 3-year field experiment to evaluate five alternative hypotheses regarding whether individuals choose breeding territories in heterogeneous landscapes on the basis of (1) shrub cover within a site, (2) forest land-cover pattern surrounding a site, (3) conspecific song cues during prebreeding settlement periods, (4) a combination of these factors, and (5) interactions among these factors. We tested hypotheses with playbacks of conspecific song across a gradient of landscape pattern and shrub density and evaluated changes in territory occupancy patterns in a forest-nesting passerine, the Black-throated Blue Warbler (Dendroica caerulescens). Our results support the hypothesis that vegetation structure plays a primary role during presettlement periods in determining occupancy patterns in this species. Further, both occupancy rates and territory turnover were affected by an interaction between local shrub density and amount of forest in the surrounding landscape, but not by interactions between habitat cues and social cues. Although previous studies of this species in unfragmented landscapes found that social postbreeding song cues played a key role in determining territory settlement, our prebreeding playbacks were not associated with territory occupancy or turnover. Our results suggest that in heterogeneous landscapes during spring settlement, vegetation structure may be a more reliable signal of reproductive performance than the physical location of other individuals.
Clarfeld, L., A. Sirén, B. Mulhall, T. Wilson, E. Bernier, J. Farrell, G. Lunde, N. Hardy, K. Gieder, R. Abrams, S. Staats, S. McLellan, and T. Donovan. 2023. Evaluating a tandem human-machine approach to labelling of wildlife in remote camera monitoring. Ecological Informatics 77:e102257 https://doi.org/10.1016/j.ecoinf.2023.102257. \| Abstract \| Download \| Publisher Website	August 2023	Remote cameras (“trail cameras”) are a popular tool for non-invasive, continuous wildlife monitoring, and as they become more prevalent in wildlife research, machine learning (ML) is increasingly used to automate or accelerate the labor-intensive process of labelling (i.e., tagging) photos. Human-machine hybrid tagging approaches have been shown to greatly increase tagging efficiency (i.e., time to tag a single image). However, those potential increases hinge on the extent to which an ML model makes correct vs. incorrect predictions. We performed an experiment using a ML model that produces bounding boxes around animals, people, and vehicles in remote camera imagery (MegaDetector) to consider the impact of a ML model's performance on its ability to accelerate human labeling. Six participants tagged trail camera images collected from 12 sites in Vermont and Maine, USA (January–September 2022) using three tagging methods (one with ML bounding box assistance and two without assistance). We used a generalized linear mixed model to examine the influence of ML model performance and tagging method on tagging efficiency. We found that ML bounding boxes offer significant improvement in tagging efficiency when labelling data compared to unassisted tagging. Additionally, the time taken to label with bounding boxes was not statistically different from an unassisted tagging approach. However, we found that gains in efficiency are contingent on the ML algorithm's performance and that incorrect ML predictions, particularly the 4.2% false positive and 3.6% false negative predictions, can slow the tagging process compared to a non-hybrid approach. These findings indicate that although practitioners usually forgo the production of bounding boxes when selecting a data labelling process due to the increased effort, ML bounding box-assisted tagging can offer an efficient method for labeling. More broadly, ML-assisted data labelling offers an opportunity to accelerate the analysis of trail camera imagery, but an assessment of the ML model's performance can illuminate whether the hybrid-tagging approach is ultimately a help or hinderance.
Cherukuri, A, A. Strong, and T. M. Donovan. 2018. Developing a monitoring protocol for least bitterns (Ixobrychis exilis) in New England: Detection probability and occupancy modeling. Northeastern Naturalist 25:56-71. https://doi.org/10.1656/045.025.0104 \| Abstract \| Publisher Website	January 2018	Ixobrychus exillis (Least Bittern) is listed as a species of high concern in the North American Waterbird Conservation Plan and is a US Fish and Wildlife Service migratory bird species of conservation concern in the Northeast. Little is known about the population of Least Bitterns in the Northeast because of their low population density, tendency to nest in dense wetland vegetation, and secretive behavior. Urban and agricultural development is expected to encroach on and degrade suitable wetland habitat; however, we cannot predict the effects on Least Bittern populations without more accurate information on their abundance and distribution. We conducted surveys of wetlands in Vermont to assess the efficacy of a monitoring protocol and to establish baseline Least Bittern abundance and distribution data at a sample of 29 wetland sites. Surveys yielded detections of 31 individuals at 15 of 29 sites across 3 biophysical regions and at 5 sites where occupancy had not been previously reported. Probability of occupancy was positively related to wetland size and number of patches, though the relationships were not strong enough to conclude if these were true determinants of occupancy. Call—response broadcast surveys yielded 30 detections, while passive surveys yielded 13. Call—response broadcasts (P = 0.897) increased the rate of detection by 55% compared to passive surveys (P = 0.577). Our results suggest that call—response broadcast surveys are an effective means of assessing Least Bittern occupancy and may reduce bias in long-term monitoring programs.
Chellman, I.C., D.L. Parrish, and T.M. Donovan. 2017. Estimating population demographic parameters for the mudpuppy (Necturus maculosus) in Vermont. Herpetological Conservation and Biology 12(2):422-434. \| Abstract	August 2017	The Mudpuppy (Necturus maculosus) is classified as a Species of Greatest Conservation Need by the state of Vermont. There is concern regarding status of populations in the Lake Champlain basin because of habitat alteration and potential effects of 3-trifluromethyl-4-nitrophenol (TFM), a chemical used to control Sea Lamprey (Petromyzon marinus). The purpose of our research was to assess Mudpuppy capture methods and abundance in the Lamoille River, Vermont, USA. We sampled Mudpuppies under a mark-recapture framework, using modified, baited minnow traps set during two winter-spring periods. We marked each Mudpuppy with a passive integrated transponder (PIT) tag and released individuals after collecting morphological measurements. We collected 80 individuals during 2,581 trap days in 2008–2009 (year 1), and 81 individuals during 3,072 trap days in 2009–2010 (year 2). We estimated abundance from spring trapping periods in 2009 and 2010, during which capture rates were sufficient for analysis. Capture probability was low (< 0.04), but highest following precipitation events in spring, during periods of higher river flow, when water temperatures were approximately 3 to 6° C. During October 2009, management agencies treated the Lamoille River with TFM. Surveyors recovered more than 500 dead Mudpuppies during the post-treatment assessment. Overall, Mudpuppy captures did not change between sampling periods; however, we captured fewer females during year 1 compared to year 2, and the sex ratio changed from 0.79:1 (M:F) during year 1 to 3:1 (M:F) during year 2. Our data may help wildlife managers assess population status of Mudpuppies in conjunction with fisheries management techniques.
Butryn, R.S., D.L. Parrish, and D.M. Rizzo. 2013. Summer stream temperature metrics for predicting brook trout (Salvelinus fontinalis) distribution in streams. Hydrobiologia 703:47-57.	January 2013
Brown, M., C. D. Canham, L. Murphy, and T. M. Donovan. 2018. Timber harvest as the predominant disturbance regime in northeastern U.S. forests: effects of harvest intensification. Ecosphere 9:1-19. DOI:10.1002/ecs2.2062 \| Abstract \| Download \| Publisher Website	April 2018	Harvesting is the leading cause of adult tree mortality in forests of the northeastern United States. While current rates of timber harvest are generally sustainable, there is considerable pressure to increase the contribution of forest biomass to meet renewable energy goals. We estimated current harvest regimes for different forest types and regions across the U.S. states of New York, Vermont, New Hampshire, and Maine using data from the U.S. Forest Inventory and Analysis Program. We implemented the harvest regimes in SORTIE-ND, an individual-based model of forest dynamics, and simulated the effects of current harvest regimes and five additional harvest scenarios that varied by harvest frequency and intensity over 150 yr. The best statistical model for the harvest regime described the annual probability of harvest as a function of forest type/region, total plot basal area, and distance to the nearest improved road.Forests were predicted to increase in adult above ground biomass in all harvest scenarios in all forest type and region combinations. The magnitude of the increase, however, varied dramatically—increasing from 3% to 120% above current landscape averages as harvest frequency and intensity decreased. The variation can be largely explained by the disproportionately high harvest rates estimated for Maine as compared with the rest of the region. Despite steady biomass accumulation across the landscape, stands that exhibited old-growth characteristics (defined as≥300 metric tons of biomass/hectare) were rare (8% or less of stands). Intensified harvest regimes had little effect on species composition due to widespread partial harvesting in all scenarios, resulting in dominance by late-successional species over time. Our analyses indicate that forest biomass can represent a sustainable, if small, component of renewable energy portfolios in the region, although there are tradeoffs between carbon sequestration in forest biomass and sustainable feedstock supply. Integrating harvest regimes into a disturbance theory framework is critical to understanding the dynamics of forested landscapes, especially given the predominance of logging as a disturbance agent and the increasing pressure to meet renewable energy needs.
Brown, M., C. Canham, T. Buchholz, J. Gunn, and T. Donovan. 2024. Net carbon sequestration implications of intensified timber harvest in northeastern U.S. forests. Ecosphere 15(2): e4758. https://doi.org/10.1002/ecs2.4758 \| Abstract \| Download \| Publisher Website	February 2024	U.S. forests, particularly in the eastern states, provide an important offset to greenhouse gas (GHG) emissions. Some have proposed that forest-based natural climate solutions can be strengthened via a number of strategies, including increases in the production of forest biomass energy. We used output from a forest dynamics model (SORTIE-ND) in combination with a GHG accounting tool (ForGATE) to estimate the carbon consequences of current and intensified timber harvest regimes in the Northeastern United States. We considered a range of carbon pools including forest ecosystem pools, forest product pools, and waste pools, along with different scenarios of feedstock production for biomass energy. The business-as-usual (BAU) scenario, which represents current harvest practices derived from the analysis of U.S. Forest Service Forest Inventory and Analysis data, sequestered more net CO<sub>2</sub> equivalents than any of the intensified harvest and feedstock utilization scenarios over the next decade, the most important time period for combatting climate change. Increasing the intensity of timber harvest increased total emissions and reduced landscape average forest carbon stocks, resulting in reduced net carbon sequestration relative to current harvest regimes. Net carbon sequestration “parity points,” where the regional cumulative net carbon sequestration from alternate intensified harvest scenarios converge with and then exceed the BAU baseline, ranged from 12 to 40 years. A “no harvest” scenario provides an estimate of an upper bound on forest carbon sequestration in the region given the expected successional dynamics of the region's forests but ignores leakage. Regional net carbon sequestration is primarily influenced by (1) the harvest regime and amount of forest biomass removal, (2) the degree to which bioenergy displaces fossil fuel use, and (3) the proportion of biomass diverted to energy feedstocks versus wood products.
Brown, M. L., T. M. Donovan, W. S. Schwenk, and D. M. Theobald. 2013. Predicting impacts of future human population growth and development on occupancy rates of forest-dependent birds . Biological Conservation. Available online 31 October 2013, ISSN 0006-3207, http://dx.doi.org/10.1016/j.biocon.2013.07.039 \| Abstract \| Download \| Publisher Website	October 2013	Forest loss and fragmentation are among the largest threats to forest-dwelling wildlife species today, and projected increases in human population growth are expected to increase these threats in the next century. We combined spatially-explicit growth models with wildlife distribution models to predict the effects of human development on 5 forest-dependent bird species in Vermont, New Hampshire, and Massachusetts, USA. We used single-species occupancy models to derive the probability of occupancy for each species across the study area in the years 2000 and 2050. Over half a million new housing units were predicted to be added to the landscape. The maximum change in housing density was nearly 30 houses per hectare; however, 30% of the towns in the study area were projected to add less than 1 housing unit per hectare. In the face of predicted human growth, the overall occupancy of each species decreased by as much as 38% (ranging from 19% to 38% declines in the worst-case scenario) in the year 2050. These declines were greater outside of protected areas than within protected lands. Ninety-seven percent of towns experienced some decline in species occupancy within their borders, highlighting the value of spatially-explicit models. The mean decrease in occupancy probability within towns ranged from 3% for hairy woodpecker to 8% for ovenbird and hermit thrush. Reductions in occupancy probability occurred on the perimeters of cities and towns where exurban development is predicted to increase in the study area. This spatial approach to wildlife planning provides data to evaluate trade-offs between development scenarios and forest-dependent wildlife species.
Brown, M. L., T. M. Donovan, R. M. Mickey, G. S. Warrington, W. S. Schwenk, and D. S. Theobald. 2017. Predicting effects of future development on a territorial forest songbird: methodology matters. Landscape Ecology 33:93-108. DOI 10.1007/s10980-017-0586-8 \| Abstract \| Download \| Publisher Website	October 2017	Context Projected increases in human population size are expected to increase forest loss and fragmentation in the next century at the expense of forest-dwelling species. Objectives We estimated landscape carrying capacity (Nk) for Ovenbirds in urban, suburban, exurban, and rural areas for the years 2000 and 2050, and compared changes in Nk with changes in occupancy probability. Methods Maximum clique analysis, a branch of mathematical graph theory, was used to estimate landscape carrying capacity, the maximum potential number of territories a given landscape is capable of supporting (Nk). We used occupancy probability maps as inputs for calculating Ovenbird Nk in the northeastern USA and a spatially explicit growth model to forecast future development patterns in 2050. We compared occupancy probability with estimates of Nk for urban, suburban, exurban, and rural areas for the years 2000 and 2050. Results In response to human population growth and development, Ovenbird Nk was predicted to decrease23% in urban landscapes, 28% in suburban landscapes, 43% in exurban landscapes, and 20% in rural landscapes. These decreases far exceeded decreases in mean occupancy probabilities that ranged between 2 and 5% across the same development categories. Thus, small decreases in occupancy probability between 2000 and 2050 translated to much larger decreases in Nk. Conclusions For the first time, our study compares occupancy probability with a species population metric, Nk, to assess the impact of future development. Maximum clique analysis is a tool that can be used to estimate Nk and inform landscape management and communication with stakeholders.
Brauer, C., T. Donovan, R. Mickey, J. Katz, and B. Mitchell. 2016. A comparison of acoustic montoring methods for common anurans of the northeastern United States. Wildlife Society Bulletin 40:140-149. \| Publisher Website	February 2016
Bonter, D. N., T. M. Donovan, and E. W. Brooks. 2007. Daily changes in energetic condition in landbirds during migration stopover on the south shore of Lake Ontario. Auk 124:122-133 \| Abstract \| Download	January 2007	Assigning conservation priorities to areas used by birds during migration requires information on the relative quality of areas and habitats. The rate at which migratory birds replenish energy reserves during stopover may be used as an indicator of stopover-site quality. We estimated the rate of mass gain of 34 landbird species during stopover at a near-shore terrestrial site on the south shore of Lake Ontario in New York during 12 migration seasons from 1999 to 2004. The average rate of mass gain was estimated by relating a measure of condition to time of capture (hour after sunrise) with linear regression. Data from 25,385 captures were analyzed. Significantly positive rates of mass change were detected for 20 of 30 species during spring migration and 19 of 21 species during autumn migration. No significantly negative trends were detected in either season. Daily rates of mass gain across all species averaged 9.84% of average lean body weight during spring migration and 9.77% during autumn migration. Our regression estimates were significantly greater than estimates from traditional analyses that examine mass changes in recaptured birds. Analyses of mass changes in recaptured birds revealed a mean daily change of -0.68% of average lean mass in spring and 0.13% in autumn. Because of sampling biases inherent in recapture analyses, the regression approach is likely more accurate when the assumptions of the method are met. Similar studies in various habitats, landscapes, and regions are required to prioritize conservation efforts targeting migratory stages of the annual cycle.
Bonter, D. N., T. M. Donovan, E. Brooks. 2008. What are we missing with ground-level mist nets? Using elevated nets at a migration stopover site. Journal of Field Ornithology 79:314-320. \| Abstract \| Download \| Publisher Website	September 2008	Mist nets deployed in a standard ground-level fashion capture birds approximately 0.5–2.6 m above the ground. In habitats where the vegetation extends above this height, standard mist net deployment may inadequately sample the targeted avian community and age- and sex-classes within species. Such sampling biases may raise questions regarding studies based on data from mist-net captures. To determine if birds were equally likely to be captured by mist nets at different heights, we constructed a series of paired ground-level and elevated mist nets (hereafter "net rigs") at a research station in western New York State. Net rigs were operated during 14 migration seasons from 2000 to 2006 (spring and fall each year), and 19,735 birds of 118 species were captured. Capture rates were significantly higher in ground-level nets, but 12 species were only captured in elevated nets. Of 44 species with at least 50 captures, 25 species were more likely to be captured in the ground-level nets and two species in the elevated nets. For four of 18 species, more birds were captured in the elevated nets during fall migration than during spring migration. We conclude that standard ground-level net placement was more efficient in capturing birds in the secondary growth habitats that we sampled. However, ground-level nets may not adequately sample the entire targeted community or all age- or sex-classes within species.
Bonter, D. N., S. A. Gauthreaux, Jr., and T. M. Donovan. 2009. Characteristics of important stopover locations for migrating birds: Remote sensing with radar in the Great Lakes Basin. Conservation Biology 23:440-448. \| Abstract \| Download	April 2009	A preliminary stage in developing comprehensive conservation plans involves identifying areas used by the organisms of interest. The areas used by migratory land birds during temporal breaks in migration (stopover periods) have received relatively little research and conservation attention. Methodologies for identifying stopover sites across large geographic areas have been, until recently, unavailable. Advances in weather-radar technology now allow for evaluation of bird migration patterns at large spatial scales. We analyzed radar data (WSR-88D) recorded during spring migration in 2000 and 2001 at 6 sites in the Great Lakes basin (U.S.A.). Our goal was to link areas of high migrant activity with the land-cover types and landscape contexts corresponding to those areas. To characterize the landscapes surrounding stopover locations, we integrated radar and land-cover data within a geographic information system. We compared landscape metrics within 5 km of areas that consistently hosted large numbers of migrants with landscapes surrounding randomly selected areas that were used by relatively few birds during migration. Concentration areas were characterized by 1.2 times more forest cover and 9.3 times more water cover than areas with little migrant activity. We detected a strong negative relationship between activity of migratory birds and agricultural land uses. Examination of individual migration events confirmed the importance of fragments of forested habitat in highly altered landscapes and highlighted large concentrations of birds departing from near-shore terrestrial areas in the Great Lakes basin. We conclude that conservation efforts can be more effectively targeted through intensive analysis of radar imagery.
Blouin, J., J. DeBow, E. Rosenblatt, J. Hines, C. Alexander, K. Gieder, N. Fortin, J. Murdoch, and T. Donovan. 2021. Moose habitat selection and fitness consequences during two critical winter tick life stages in Vermont, USA. Frontiers in Ecology and Evolution 9:642276. \| Abstract \| Download \| Publisher Website	May 2021	Moose (<i>Alces Alces</i>) are a charismatic species that has been in decline across much of their southern range.<b> </b>In New England, USA, the reduction has been attributed, in part, to winter tick (<i>Dermacentor albipictus</i>) infestations. Winter ticks tend to be fairly immobile throughout all life stages, and therefore their distribution patterns at any given time are shaped largely by the occurrence of moose across the landscape during the peak of two critical time periods; fall questing (when ticks latch onto a moose, which coincides with the rut) and spring drop-off (when engorged female ticks detach from moose and lay their eggs in leaf litter). We used recent land cover and lidar data within a dynamic occupancy modeling framework to estimate first-order habitat selection (use vs non-use) of female moose (n = 74) during the questing and drop-off periods. Patch (1 km<sup>2</sup>) extinction and colonization rates during spring drop-off periods were strongly influenced by habitat and elevation, but these effects were diminished during the questing period when moose were more active across the landscape. In the spring drop-off period, patches where colonization was high and extinction low (highest probability of female moose occupancy) had higher proportions of young (shrub/forage) mixed forest at greater elevations. We evaluated the fitness consequences of individual-based habitat selection (second-order habitat selection) by comparing Resource Selection Functions (RSF) for 5 females that successfully reared a calf with 5 females whose calf perished. Second-order habitat selection analyses showed adult female moose whose offspring perished selected patches during the questing period that matched the first-order selection during the spring drop-off period. In contrast, adult female moose whose offspring survived selected areas with proportions of young deciduous habitats, as well as higher proportions of mature (canopy) evergreen forests and wetlands at lower elevations, i.e., their second-order habitat selection patterns deviated from the overall patterns illuminated by the multi-season occupancy analysis. Our model coefficients and mapped results define “hotspots” that are likely encouraging the deleterious effects of the tick-moose cycle. Knowledge about the composition and structure of these hotspots may influence more direct (i.e. hunter harvest) and indirect (i.e. conservation, modification, or formation of habitats) management decisions.
Blouin, J., J. DeBow, E. Rosenblatt, C. Alexander, K. Gieder, J. Murdoch, and T. Donovan. Modeling moose habitat use by age, sex, and season in Vermont, USA using high-resolution lidar and National Land Cover data. Alces 57:71-98. \| Abstract \| Download \| Publisher Website	September 2021	Moose (<i>Alces alces</i>) populations have experienced unprecedented declines along the southern periphery of their range, including Vermont, USA. Habitat management may be used to improve the status of the population and health of individuals. To date, however, Vermont wildlife managers have been challenged to effectively use this important tool due to the lack of fine-scale information on moose space use and habitat characteristics. To assess habitat use, we combined more than 40,000 moose locations collected from radio-collared individuals (n = 74), recent land cover data, and high resolution, 3-dimensional lidar (light detection and ranging) data to develop Resource Utilization Functions (RUF) by age (mature and young adult), season (dormant and growth), and sex. Each RUF linked home range use to average habitat conditions within 400 m or 1 km of each 30 m2pixel within the home range. Across analyses, the top RUF models included both composition (as measured through the National Land Cover Database) and structure (as measured through lidar) variables, and significantly outperformed models that excluded lidar variables. These findings support the notion that lidar is an effective tool for improving the ability of models to estimate patterns of habitat use, especially for larger bodied mammals. Generally speaking, female moose actively used areas with proportionally more regenerating forest (i.e., forage < 3.0 m) and more mature forest (i.e., canopy structure > 6.0 m), while males actively used more high elevation, mixed forest types. Further, moose exhibited important seasonal differences in habitat use that likely reflect temporal changes in energetic and nutritional requirements and behavior across the year. Moose used areas with proportionally more regenerating forest (i.e., forage < 3.0 m) during the growth period and female moose had strong positive associations with lidar-derived canopy structure during the growth (but not the dormant) period. Ultimately, the resultant maps of habitat use provide a means of informing management activities (e.g., the restoration or alteration of habitats to benefit moose) and policies around land use that may contribute to population recovery.
Bettigole, C., T. M. Donovan, R. Manning, and J. Austin. 2013. Normative standards for land use in Vermont: Implications for biodiversity. Biological Conservation. \| Abstract \| Download \| Publisher Website	August 2013	The conversion of natural lands to developed uses poses a great threat to global terrestrial biodiversity. Natural resource managers, tasked with managing wildlife as a public trust, require techniques for predicting how much and where wildlife habitat is likely to be converted in the future. Here, we develop a methodology to estimate the “social carrying capacity for development” –SKd – for 251 towns across the state of Vermont, USA. SKd represents town residents’ minimum acceptable human population size and level of development within town boundaries. To estimate SKd across towns within the state of Vermont (USA), as well as the average state-wide SKd, we administered a visual preference survey (n = 1505 responses) to Vermont residents, and asked respondents to rate alternative landuse scenarios in a fictional Vermont town on a scale of +4 (highly acceptable) to −4 (highly unacceptable). We additionally collected demographic data such as age and income, as well as ancillary information such as participation in town-planning meetings and location of residence. We used model selection and AIC to fit a cubic function to the response data, allowing us to estimate SKd at a town scale based on town demographic characteristics. On average, Vermonters had a SKd of 9.1% development on the landscape; this estimate is 68% higher than year 2000 levels for development (5.4%). Respondents indicated that management action to curb development was appropriate at 9.4% development (roughly the statewide SKd average). Management by local, regional, and state levels were considered acceptable for curbing development while federal level management of development was considered unacceptable. Given a scenario where development levels were at SKd, we predicted a 16,753 km2 reduction in forested land (−11.16%) and a 1038 km2 reduction in farmland (−60.45%). Such changes would dramatically alter biodiversity patterns state-wide. In a companion paper, we estimate how these changes would affect the distribution of wildlife species.
Bettigole, C., T. Donovan, R. Manning, J. Austin, and R. Long. 2013. Acceptability of residential development in a regional landscape: Potential effects on wildlife occupancy patterns. Biological Conservation. \| Abstract \| Download \| Publisher Website	October 2013	The conversion of natural lands to developed uses may pose the single greatest human threat to global terrestrial biodiversity. Continued human growth and development over the next century will further exacerbate these effects of habitat loss and fragmentation. Natural resource managers are tasked with managing wildlife as a public trust, yet often have little say in land use decisions. Generally speaking, decision makers could benefit from an understanding of what different regulations mean in terms of wildlife distribution. In a companion paper (Bettigole et al., 2013), we surveyed town residents throughout Vermont to measure how respondents feel about a range of development levels within their town boundaries. We estimated the “social carrying capacity for development” – or SKd – for 251 towns in Vermont. SKd provides an estimate of the level of developed land cover classes that town residents deem “acceptable” within their town boundaries. In this paper, we design a framework for linking the town-specific SKd estimates with the wildlife distribution patterns for three wide-ranging mammalian species: American black bear (Ursus americanus), fisher (Martes pennanti), and bobcat (Lynx rufus). We simulated landscape conditions at SKd for each town in Vermont, and then used existing occupancy models for the three target species to spatially map and compare occupancy rates in the baseline year 2000 with occupancy rates at SKd. With nearly 90% of Vermont towns willing to increase developed landcover classes within town boundaries compared to baseline levels, significant state-wide changes in occupancy rates were predicted for all three focal species. Average occupancy rates declined by −15.9% and −3.1% for black bear and bobcats, respectively. Average occupancy rates for fisher increased by 9.0%. This study provides a method for linking development standards within a town with wildlife occurrence. Across towns, the methodology spatially identifies areas that may be at risk of future development, as well as identifying areas where wildlife distribution patterns may face future change as a result of increased human population growth and development.
Beauchamp, D. A., D. L. Parrish, and R. A. Whaley. 2009. Salmonids/coldwater species in large standing waters, Chapter 7, Pages 97-117 In S. Bonar, D. Willis, and W. Hubert, editors. Standard Sampling Methods for North American Freshwater Fishes. American Fisheries Society.	August 2009
Balantic, C., and T. M. Donovan. 2019. Temporally-adaptive acoustic sampling to maximize detection across a suite of focal wildlife species. Ecology and Evolution 9(18)10582-10600. DOI: 10.1002/ece3.5579 \| Abstract \| Download \| Publisher Website	August 2019	1. Acoustic recordings of the environment can produce species presence–absence data for characterizing populations of sound‐producing wildlife over multiple spatial scales. If a species is present at a site but does not vocalize during a scheduled audio recording survey, researchers may incorrectly conclude that the species is absent (“false negative”). The risk of false negatives is compounded when audio devices have sampling constraints, do not record continuously, and must be manually scheduled to operate at pre‐selected times of day, particularly when research programs target multiple species with acoustic availability that varies across temporal conditions.<br><br>2. We developed a temporally adaptive acoustic sampling algorithm to maximize detection probabilities for a suite of focal species amid sampling constraints. The algorithm combines user‐supplied species vocalization models with site‐specific weather forecasts to set an optimized sampling schedule for the following day. To test our algorithm, we simulated hourly vocalization probabilities for a suite of focal species in a hypothetical monitoring area for the year 2016. We conducted a factorial experiment that sampled from the 2016 acoustic environment to com ‐pare the probability of acoustic detection by a fixed (stationary) schedule versus a temporally adaptive optimized schedule under several sampling efforts and monitoring durations.<br><br>3. We found that over the course of a study season, the probability of acoustically capturing a focal species (given presence) at least once via automated acoustic monitoring was greater (and acoustic capture occurred earlier in the season) when using the temporally adaptive optimized schedule as compared to a fixed schedule.<br><br>4. The advantages of a temporally adaptive optimized acoustic sampling schedule are magnified when a study duration is short, sampling effort is low, and/or species acoustic availability is minimal. This methodology presents the opportunity to maximize acoustic monitoring sampling efforts amid constraints.
Balantic, C., and T. M. Donovan. 2019. Statistical learning mitigation of false positive detections in automated acoustic wildlife monitoring. Bioacoustics 29(3):296-321. DOI: 10.1080/09524622.2019.1605309 \| Abstract \| Download \| Publisher Website	May 2019	Audio sampling of the environment can provide long-term, landscape-scale presence-absence data to model populations of sound-producing wildlife. Automated detection systems allow researchers to avoid manually searching through large volumes of recordings, but often produce unacceptable false positive rates. We developed methods that allow researchers to improve template-based automated detection using a suite of statistical learning algorithms when false positive rates are problematic. To test our method, we acquired 668 hours of recordings in the Sonoran Desert, California USA between March 2016 and May 2017, and created spectrogram cross-correlation templates for three target avian species. We trained and tested five classification algorithms and four performance-weighted ensemble classifier methods on target signals and false alarms from March 2016, and then selected high-performing ensemble classifiers from the train/test phase to predict the class of new detections thereafter. For three target species, our ensemble classifiers were able to identify 98%, 81%, and 100% of false alarms compared with the baseline template detection system, and comparative positive predictive values improved from 6% to 69%, 87% to 95%, and 2% to 77%. We show that statistical learning approaches can be implemented to mitigate false detections acquired via template-based automated detection in automated acoustic wildlife monitoring.
Balantic, C., and T. M. Donovan. 2019. Dynamic wildlife occupancy models using automated acoustic monitoring data. Ecological Applications 29(3):e01854. \| Abstract \| Download \| Publisher Website	April 2019	Automated acoustic monitoring of wildlife has been used to characterize populations of sound‐producing species across large spatial scales. However, false negatives and false positives produced by automated detection systems can compromise the utility of these data for researchers and land managers, particularly for research programs endeavoring to describe colonization and extinction dynamics that inform land use decision‐making. To investigate the suitability of automated acoustic monitoring for dynamic occurrence models, we simulated underlying occurrence dynamics, calling patterns, and the automated acoustic detection process for a hypothetical species under a range of scenarios. We investigated an automated species detection aggregation method that considered a suite of options for creating encounter histories. From these encounter histories, we generated parameter estimates and computed bias for occurrence, colonization, and extinction rates using a dynamic occupancy modeling framework that accounts for false positives via small amounts of manual confirmation. We were able to achieve relatively unbiased estimates for all three state parameters under all scenarios, even when the automated detection system was simulated to be poor, given particular encounter history aggregation choices. However, some encounter history aggregation choices resulted in unreliable estimates; we provide caveats for avoiding these scenarios. Given specific choices during the detection aggregation process, automated acoustic monitoring data may provide an effective means for tracking species occurrence, colonization, and extinction patterns through time, with the potential to inform adaptive management at multiple spatial scales.
Balantic, C., and T. Donovan. 2020. AMMonitor: Remote monitoring of biodiversity in an adaptive framework with R. Methods in Ecology and Evolution 11:869-877. DOI: 10.1111/2041-210X.13397 \| Abstract \| Download \| Publisher Website	April 2020	1. Ecological research and management programs are increasingly using autonomous monitoring units (AMUs) to collect large volumes of acoustic and/or photo data to address pressing management objectives or research goals. The data management requirements of an AMU-based monitoring effort are often overwhelming, with a considerable amount of processing to translate raw data into models and analyses that have research and management utility. <br><br>2. We created the r package AMMonitor to simplify the process of moving from remotely collected data to analysis and results, using a comprehensive SQLite database for data management that tracks all components of a remote monitoring program. This framework enables the tracking of analyses and research/ management objectives through time. <br><br>3. We illustrate the AMMonitor approach with the example of evaluating an occurrence-based management objective for a target species. First, we provide an overview of the database and data management approach. Next, we illustrate a few available workflows: temporally adaptive sampling, automated detection of species sounds from acoustic recordings and aggregation of automated detections into an encounter history for use in an occupancy analysis, the outcome of which can be analysed with respect to the motivating management objective.<br><br> 4. Without a comprehensive framework for efficiently moving from raw remote monitoring data collection to results and analysis, monitoring programs are limited in their capacity to systematically characterize ecological processes and inform management decisions through time. AMMonitor provides an option for such a framework. Code, comprehensive documentation and step-by-step examples are available online at https://code.usgs.gov/vtcfwru/AMMonitor
Aylward, C. J. D. Murdoch, T. M. Donovan, C. W. Kilpatrick, C. Bernier, and J. Katz. 2018. Estimating distribution and connectivity of recolonizing American marten (Martes americana) in the northeastern United States using expert elicitation techniques. Animal Conservation. doi:10.1111/acv.12417 \| Abstract \| Download \| Publisher Website	June 2018	The American marten, Martes americana, is a species of conservation concern in the northeastern United States due to widespread declines from over-harvesting and habitat loss. Little information exists on current marten distribution and how landscape characteristics shape patterns of occupancy across the region, which could help develop effective recovery strategies. The rarity of marten and lack of historical distribution records are also problematic for region-wide conservation planning. Expert opinion can provide a source of information for estimating species–landscape relationships and is especially useful when empirical data are sparse. We created a survey to elicit expert opinion and build a model that describes marten occupancy in the northeastern United States as a function of landscape conditions. We elicited opinions from 18 marten experts that included wildlife managers, trappers and researchers. Each expert estimated occupancy probability at 30 sites in their geographic region of expertise. We, then, ﬁt the response data with a set of 58 models that incorporated the effects of covariates related to forest characteristics, climate, anthropogenic impacts and competition at two spatial scales (1.5 and 5 km radii), and used model selection techniques to determine the best model in the set. Three top models had strong empirical support, which we model averaged based on AIC weights. The ﬁnal model included effects of ﬁve covariates at the 5-km scale: percent canopy cover (positive), percent spruce-ﬁr land cover (positive), winter temperature (negative), elevation (positive) and road density (negative). A receiver operating characteristic curve indicated that the model performed well based on recent occurrence records. We mapped distribution across the region and used circuit theory to estimate movement corridors between isolated core populations. The results demonstrate the effectiveness of expert-opinion data at modeling occupancy for rare species and provide tools for planning marten recovery in the northeastern United States.
Abouelezz, H. G, T. M. Donovan, J. Murdoch. R. M. Mickey, M. Freeman, and K. Royar. 2018. Landscape composition mediates movement and habitat selection in bobcats (Lynx rufus): Implications for conservation planning. Landscape Ecology 33:1301-1318. https://doi.org/10.1007/s10980-018-0654-8 \| Abstract \| Download \| Publisher Website	August 2018	Context The analysis of individual movement choices can be used to better understand population-level resource selection and inform management. Objectives We investigated movements and habitat selection of 13 bobcats in Vermont, USA, under the assumption individuals makes choices based upon their current location. Results were used to identify “movement-defined” corridors. Methods We used GPS-collars and GIS to estimate bobcat movement paths, and extracted statistics on land cover proportions, topography, fine-scale vegetation, roads, and streams within “used” and “available” space surrounding each movement path. Compositional analyses were used to determine habitat preferences with respect to landcover and topography; ratio tests were used to determine if used versus available ratios for vegetation, roads, and streams differed from 1. Results were used to create travel cost maps, a primary input for corridor analysis. Results Forested and scrub-rock land cover were most preferred for movement, while developed land cover was least preferred. Preference depended on the composition of the “available” landscape: Bobcats moved > 3 times more quickly through forest and scrub-rock habitat when these habitats were surrounded by agriculture or development than when the available buffer was similarly composed. Overall, forest edge, wetland edge and higher stream densities were selected, while deep forest core and high road densities were not selected. Landscape-scale connectivity maps differed depending on whether habitat suitability, preference, or selection informed the travel cost map. Conclusions Both local and landscape scale land cover characteristics affect habitat preferences and travel speed of bobcats, which in turn can inform management and conservation activities.

Presentations

Presentations	Presentation Date
Winter, M., D. H. Johnson, T. Donovan, and W. D. Svedarsky. August 2000. BCA evaluation in the northern tallgrass prairie. AOU Annual Meeting, St. John's, Newfoundland.	August 2000
Wilson, TL, APK Sirén, J Berube, L Clarfeld TM Donovan. 2023. Designing camera trap arrays for multi-species monitoring of mammals at large spatial extents. Annual Meeting, International Association for Landscape Ecology- North America, Riverside, California, 19-23 March2023.	March 2023	We demonstrate the importance of sampling design for improving detection and inference in wildlife monitoring. The work can be used to inform biodiversity monitoring terrestrial mammals using remote sensor arrays.
Watrous, K., T. Donovan, S. Darling, and S. Von Oettingen. Maternity roost tree use by Indiana bats in the Champlain Valley. North Eastern Bat Working Group Meeting, Rosendale, NY, 10 December, 2003.	December 2003
Watrous, K. S., T. M. Donovan, S. Darling, A. Hicks, and S. A. Von Oettingen. 2005. Roosting and foraging habitat of the Indiana bat (Myotis sodalist) at multiple scales. The Wildlife Society Annual Meeting, Madison, WI. 25-29 September, 2005.	September 2005
Watrous, K. S., T. M. Donovan, S. Darling, A. Hicks, and S. A. Von Oettingen. 2005. Roosting and foraging habitat of the Indiana bat (Myotis sodalist) at multiple scales. The Ecological Society of America 90th Annual Meeting, Montreal, Quebec, CA. 7-12 August, 2005.	August 2005
Strong, A., T. Donovan, N. Perlut, and N. Buckley. 2006. When good birds select bad habitat: grassland birds in an agricultural landscape. IVth North American Ornithological Conference, Veracruz, Mexico. October 3-7, 2006.	October 2006
Stritzel, J.L., D.L. Parrish, S.L. Parker, L.G. Rudstam, and P.J. Sullivan. Effects of food web composition on rainbow smelt in Lake Champlain. 133rd Annual Meeting of the American Fisheries Society, Quebec City, QC, 10-14 August 2003.	August 2003
Stritzel, J.L., D.L. Parrish, S.J. Parker, L.G. Rudstam, and P.J. Sullivan. Effects of cannibalism on rainbow smelt in Lake Champlain: Do size and density matter? 132nd Annual Meeting of the American Fisheries Society, Baltimore, MD, 18-22 August 2002.	August 2002
Siren, A., L. Clarfeld, C. Balantic, K. Gieder, P. Jensen, T. Wilson, and T. Donovan. Northeast Wildlife Monitoring Network (NEWMN): A Unifying Framework for Regional Collaboration Using Autonomous Monitoring Units. Northeast Natural History Conference, Burlington VT, 21-23 April 2023.	April 2023	Camera traps have become a standard tool for collecting data on wildlife distribution, abundance, and species richness, but present challenges in terms of data storage, tagging, and sharing data across projects. In this talk, we discuss our standardized, bottom-up approach for regional approach and introduce workflow that streamlines data collection and collaboration.
Siren, A., Clarfeld, L, C. Balantic, R. Cliche, M. Feehan, K. Gieder, P. Jensen, H. Jones, L. Kantar, R. Patry, L. Prout, S. Wixsom, T. Wilson, and T. Donovan. Northeast Wildlife Monitoring Network (NEWMN): A unifying framework for regional collaboration using autonomous monitoring units. April 3 - 5, 2022. 77th Annual Northeast Fish and Wildlife Association. Long Branch, New Jersey, USA.	April 2022	This presentation introduces the Northeast Monitoring Network (NEWMN), a collaboration of agencies, universities, and independent groups to monitor wildlife with remotely deployed cameras at large spatial extents.
Simonin, P.W., S. Tideman, B. Pientka, L.G. Rudstam, P.J. Sullivan, and D.L. Parrish. Uncertainty in hydroacoustic-derived fisheries data: an analysis of simulation hydroacoustic-trawl surveys. A Joint Special Workshop of the Acoustical Society of America and the American Fisheries Society. Acoustic Challenges in Aquatic Ecosystem Assessment. 25-27 May 2011. (Poster presentation.)	May 2011
Simonin, P.W., S. Tideman, B. Pientka, L.G. Rudstam, P.J. Sullivan, and D.L. Parrish. Reducing uncertainty in pelagic fish assessments: an analysis of hydroacoustic- and trawl-derived data. 141st Annual Meeting of the American Fisheries Society, Seattle, WA, 4-8 September 2011. (Poster presentation.)	September 2011
Simonin, P.W., M. Riha, L.G. Rudstam, P.J. Sullivan, and D.L. Parrish. Comparing and predicting spatial community ecology of rainbow smelt and alewife in Lake Champlain vs. Lake Ontario. 58th Annual Conference of the International Association, 25-29 May 2015, Burlington, VT.	May 2015	This work is important in understanding the spatial distributions of these pelagic species in large lakes. In addition to the effects of climate change, we need to understand how these cannibalistic species are regulated.
Simonin, P.W., L.G. Rudstam, P.J. Sullivan, D.L. Parrish, and B. Pientka. Spatial community ecology of rainbow smelt and alewife in Lake Champlain. Ecology of Fish in Lakes and Reservoirs 2014, Ceske Budejovice, Czech Republic, 8 September 2014.	September 2014	Illustrates importance of knowing species spatial distributions. Our results provide information useful to management agencies that in stock sportfish in the lake.
Simonin, P.W., L.G. Rudstam, P.J. Sullivan, D.L. Parrish, and B. Pientka. Physical gradients to population dynamics: distribution, cannibalism, and mortality of rainbow smelt in Lake Champlain. 95th Ecological Society of America, Pittsburgh, PA, 1-6 August 2010.	August 2010
Simonin, P.W., L.G. Rudstam, P.J. Sullivan, D. L. Parrish, and B. Pientka. Forecasting native rainbow smelt and nonnative alewife distribution patterns, cannibalism, and long-term community dynamics. Joint Aquatic Sciences Meeting, Portland, OR. 18-23 May 2014.	May 2014	Alewife invaded Lake Champlain several years ago and has changed the pelagic food web. Our results indicate that alewife and rainbow smelt interactions vary throughout the lake in relation to habitat.
Simonin, P.W., L.G. Rudstam, D.L. Parrish, P.J. Sullivan, and B. Pientka. Spatial community ecology, cannibalism, and the resilience of Lake Champlain forage fish. 145th Annual Meeting of the American Fisheries Society, Portland, Oregon, 16-21 August 2015.	August 2015	Understanding the distributions of pelagic prey fish is important to managing the fish harvested in the fishery. This is especially important when dealing with an invasive species.
Simonin, P.W., D.L. Parrish, L.G. Rudstam, P.J. Sullivan and B.Pientka. Survival of early- versus late-hatched rainbow smelt and alewife in Lake Champlain. New York Chapter Meeting of the American Fisheries Society, Lake George, NY, 10-12 February 2010.	February 2010
Simonin, P.W., D.L. Parrish, L.G. Rudstam, B. Pientka, and P.J. Sullivan. Young of year planktivore dynamics: native rainbow smelt and non-native alewife in Lake Champlain. 138th Annual Meeting of the American Fisheries Society, Ottawa, Ontario, Canada, 17-21 August 2008.	August 2008
Simonin, P.W., D.L. Parrish, L.G. Rudstam, B. Pientka, and P.J. Sullivan. Rainbow smelt and alewife in Lake Champlain: abundance dynamics of native and invasive planktivores. 139th Annual Meeting of the American Fisheries Society, Nashville, TN, 31 August- 3 September 2009.	September 2009
Simonin, P.W., D.L. Parrish, L.G. Rudstam, B. Pientka, and P.J. Sullivan. Rainbow smelt and alewife distribution dynamics in relation to temperature and light in Lake Champlain. 52nd Annual Conference on Great Lakes Research, International Association for Great Lakes Research, Toledo, OH, 18-22 May 2009.	May 2009
Schwenk, W. S., and T.M. Donovan. Factors associated with landbird occupancy and species richness across Vermont, USA. Meeting of the American Ornithologists’ Union. 7-11 February 2010. San Diego, CA	February 2010
Rudstam, L., S. Parker, D. Einhouse, L. Witzell, D. Warner, J. Stritzel, D. Parrish, P. Sullivan. June 2002. Application of in situ target strength to abundance estimations in lakes-examples from rainbow smelt surveys in Lakes Erie and Champlain. ICES Symposium: Acoustics in Fisheries and Aquatic Ecology, Montpellier, France.	June 2002
Rosenblatt, E., T. M. Donovan, and J. Murdoch. Novel wildlife population estimates using pedigree reconstruction: exploring applications with moose (Alces alces). April 15-17, 2018. 74th Annual Northeast Fish and Wildlife Conference. April 15-17, 2018. Burlington Vermont	April 2018	Accurate and precise population estimates for wildlife is an important tool in conserving and managing wildlife populations. This presentation will focus on a novel method of population estimation using genetic material to reconstruct a population’s pedigree and infer the existence of individuals that were not sampled.
Rosenblatt, E., J. D. Murdoch, J. Debow, J. Blouin, and T. Donovan. Moose stress dynamics related to landscape characteristics and climate-mediated factors. April 19-21, 2020. 76th Annual Northeast Fish & Wildlife Conference, Long Branch, New Jersey.	April 2020	While research has focused on the effects of winter tick infestation on moose survival and reproduction, the stress response to ticks or any other potential stressor remains understudied. We used repeated fecal sampling of 116 radio-collared moose from 2017 to 2019 to quantify fecal glucocorticoid metabolites (fGCM). Preliminary analysis suggest winter tick load had a strong positive effect on fGCM levels, but snow depth, road density, and conifer forest coverage also positively influenced fGMC
Rosenblatt, E., J. D. Murdoch, J. Debow, J. Blouin, and T. Donovan. Moose stress and nutrition dynamics related to landscape characteristics and climate-mediated factors. Sept 28 - Oct 2, 2020. The 27^thannual conference of The Wildlife Society (virtual conference).	September 2020	Moose (<i>Alces alces americana</i>) in the northeastern United States have experienced substantial population declines over the past 15 years, primarily due to the impacts of winter ticks (<i>Dermacentor albipictus</i>). This study examines stress levels and nutritional responses to ticks and other potential stressors, providing a means of monitoring moose health with non-invasive measures.
Quist, M. C., M. E. Mather, D. L. Parrish, S. R. Chipps, T. J. Kwak, and C. P. Paukert. 2013. The voices of reality: why effective fisheries education is challenging and practical ways to move forward. 143 rd Annual Meeting of the American Fisheries Society, Little Rock, Arkansas, September 11. Platform	September 2013	This work review how academic programs are integrating with thew needs to state and federal agencies
Puchala, E.A., and D.L. Parrish. Modeling the potential effects of intermittent perturbations on endangered stonecats. 144th annual meeting of the American Fisheries Society, Quebec City, Quebec, 17-22 August 2014.	August 2014	Stonecats are endangered in Vermont. We are modeling the populations in two rivers to document whether they should remain listed.
Puchala, E.A., and D.L. Parrish. Endangered stonecats in Vermont: differential mortality effects on the likelihood of sustainability. 143rd Annual Meeting of the American Fisheries Society, Little Rock, AR, 8-12 September 2013.	September 2013	This study is important to Vermont Fish and Wildlife because stonecats are state endangered fish. This study is providing information to the state for managing the population for sustainability.
Puchala, E.A., and D.L. Parrish. Endangered stonecats in Vermont: a risk assessment approach. 145th annual meeting of the American Fisheries Society, Portland, Oregon, 16-21 August 2015.	August 2015	This talk presents an approach to predict the sustainability of the stonecat population in the Missisquoi River, Vermont. These results are important in a river where stonecats sustain intermittent increases in mortality from dewatering and lampricide.
Pientka, B., and D.L. Parrish. August 2000. Using bioenergetics of yellow perch to determine the importance of ontogenetic diet shifts, 130th Annual Meeting of the American Fisheries Society, St. Louis, MO.	August 2000
Perlut, N., C. Freeman-Gallant, A. Strong, T. Donovan, and C. Kilpatrick. 2006. The impacts of hayfield management on a songbirds? social and genetic mating system. 4th North American Ornithological Conference, Veracruz, Mexico. October 3-7, 2006.	October 2006
Perlut, N., A. Strong, T. M. Donovan, and N. Buckley. Sept 2004. Hayfields of the Champlain Valley: An ecological trap for grassland nesting songbirds? The Wildlife Society 11th Annual Conference, Calgary, CA.	September 2004
Perlut, N., A. M. Strong, T. M. Donovan, and N. J. Buckley. Sept 2003. Hayfields in the Champlain Valley: An ecological trap for grassland nesting songbirds? The Wildlife Society 10th Annual Conference, Burlington, VT.	September 2003
Perlut, N., A. M. Strong, T. M. Donovan, and N. J. Buckley. Grassland songbirds in a dynamic management landscape: Behavioral responses and management strategies. The Northeast Fish and Wildlife Annual Conference, Burlington, VT; 23-26 April, 2006.	April 2006
Perlut, N. P., Freeman-Gallant, C. F., Strong, A. M., Donovan, T. M. & W. Kilpatrick. 2008. Habitat management and variable patterns of sexual selection in Savannah sparrows. 12th International Behavioral Ecology Congress, Ithaca, NY; Aug 9-15 2008.	August 2008
Perlut, N. G., T. M. Donovan, and A. M. Strong. The effects of hayfield management on the social mating system of Savannah Sparrows. The American Ornithologists Union 122nd Annual Meeting, Quebec, CA, 16-21 August, 2004.	August 2004
Perlut, N. G., C. R. Freeman-Gallant, A. M. Strong, T. M. Donovan, and C. W. Kilpatrick. 2006. The evolutionary impacts of hayfield management on a songbirds? social and genetic mating system. Animal Behavior Society Annual Meeting, Snowbird, UT. 12-16 August, 2006.	August 2006
Pearman-Gillman, S., T. M. Donovan, J. Murdoch, and J. Katz. 2018. Estimating wildlife distributions using expert elicitation techniques: an assessment of harvested species in the Northeastern United States. April 15-17, 2018. 74th Annual Northeast Fish and Wildlife Conference, Burlington, Vermont.	April 2018	In the Northeastern United States, population expansion, agriculture, industrial development, and urban sprawl pose serious concerns for wildlife and challenges for wildlife managers. Understanding the impacts of landscape change on species' distributions can help inform decision-making for conservation planning. Unfortunately, empirical data on distribution is limited for many species. In this study, we used expert elicitation techniques to develop species distribution models (SDMs) for 22
Pearman-Gillman, S., J. Murdoch, and T. M. Donovan. Wildlife in a future New England landscape: Estimating species distributions under projected climate and landscape change. April 14-16, 2019. 75th Annual Northeast Fish and Wildlife Conference, Groton, Connecticut.	April 2019	In the Northeastern United States, population expansion, agriculture, industrial development, and urban sprawl pose serious concerns for wildlife and challenges for wildlife managers. Understanding the impacts of landscape change on species' distributions can help inform decision-making for conservation planning. We used expert elicitation techniques to develop species distribution models (SDMs) for 22 harvested species in the northeast, and project future changes in distribution patterns as
Parrish, D.L., P.W. Simonin, L.G. Rudstam, P.J. Sullivan, and B. Pientka. Pelagic species interactions in Lake Champlain, USA-Canada. Annual Meeting of the Japanese Society of Fisheries Science, 28-31 March 2015, Shinagawa, Japan.	March 2015	Understanding the spatial distributions of rainbow smelt and alewife populations in Lake Champlain is important to making predictions of foodweb stability. The species are cannibalistic, which adds a level of complexity in making accurate predictions.
Parrish, D.L., E.J. Hawes, and K.G. Whalen. Winter growth and survival of juvenile Atlantic salmon in experimental raceways. 133rd Annual Meeting of the American Fisheries Society, Quebec City, QC, 10-14 August 2003.	August 2003
Parrish, D.L., E.A. Marschall, and Martha E. Mather. Modeling fish migration in the Connecticut River, USA. Japanese Society of Fisheries Science.	March 2016	This work is important because we have modeled a tributary spawner and are modeling a mainstem spawner. These species provide a basis for understanding the effects of climate change on migrating fish with distinctively different life histories.
Parrish, D.L., B. Pientka, and M. Eisenhower. Individual growth and diets of yellow perch in Lake Champlain in relation to cormorant predation. Percis III Symposium, Madison, WI, 20-24 July 2003.	July 2003
Parrish, D.L., B. Pientka, L.G. Rudstam, P.W. Simonin, and P.J. Sullivan. Hydroacoustic surveys of the pelagic fish community in Lake Champlain. 74th annual meeting of the Northeast Fish and Wildlife Conference, Burlington, VT, 15-17 April 2018.	April 2018	This presentation documents the long history of using acoustic technology to determine the abundance of pelagic fish species in Lake Champlain. The more advanced sounders have allowed for more accurate abundance estimates.
Parrish, D.L. October 2001. Global climate change and Atlantic salmon. Vermont Water Resources and Lake Studies Center Annual Meeting	October 2001
Parrish, D.L. Introduction: improving written communications. 135th Annual Meeting of the American Fisheries Society, Anchorage, AK, 11-15 September 2005. (Co-organizer with Katie Bertrand and Martha Mather, presenter, and moderator in a symposium "Written communications: Writing and Reviewing Papers for Fisheries Journals.�?)	September 2005
Parrish, D.L. Atlantic salmon in the Connecticut River. 38th Annual Meeting of the Atlantic International Chapter (American Fisheries Society), Averill, Vermont, 23-25 September 2012. Keynote address.	September 2012
Parrish, D.L. A scientist in the Cooperative Research Units Program. A workshop organized by the AFS Student and Early Career Professionals Subsection--Preparing the future scientists of fisheries: how to become a more a-lure-ing job candidate. Annual Meeting of the American Fisheries Society (virtual), 17 September 2020.	September 2020	Presentation for a workshop for students and early career professionals. My presentation was about being a scientist in the Cooperative Research Units.
Parrish, D. L., Rudstam, L.G., Sullivan, P.J., Parker, S.L., and Stritzel, J.L. Population dynamics of rainbow smelt in Lake Champlain. Vermont Water Resources and Lake Studies Center Annual Meeting, Burlington, VT, 10 October 2003.	October 2003
Parker,S., D. Fitzgerald, L. Rudstam, P. Sullivan, J. Stritzel, D.L. Parrish. Using truss analysis to identify sympatric rainbow smelt races in Lake Champlain. 132nd Annual Meeting of the American Fisheries Society, Baltimore, MD, 18-22 August 2002.	August 2002
Parker, S.L., L.G. Rudstam, J.L. Stritzel, D.L. Parrish, and P.J. Sullivan. Population characteristics of rainbow smelt in Lake Champlain. 133rd Annual Meeting of the American Fisheries Society, Quebec City, QC, 10-14 August 2003.	August 2003
Parker Stetter, S.L., J.L. Stritzel, L.G. Rudstam, D.L. Parrish, P.J. Sullivan. Hydroacoustic assessment of rainbow smelt year class vertical overlap. 134th Annual Meeting of the American Fisheries Society, Madison, WI, 22-26 August 2004.	August 2004
Overman, N.C., and D.L. Parrish. Stable isotope analysis of walleye in Lake Champlain. 57th Northeast Fish and Wildlife Conference, Saratoga Springs, NY, 22-25 April 2001.	April 2001
Omland, K., and D.L. Parrish. A model selection approach to understanding decline of a brown trout population. 133rd Annual Meeting of the American Fisheries Society, Quebec City, QC, 10-14 August 2003.	August 2003
Olsen, J.R., and D.L. Parrish. Factors affecting the growth of age-1 and older Atlantic salmon parr in Vermont tributaries to the Connecticut River. 57th Northeast Fish and Wildlife Conference, Saratoga Springs, NY, 22-25 April 2001.	April 2001
Olsen, J.R., and D.L. Parrish. Factors affecting the growth of age 1 and older Atlantic salmon in Vermont tributaries of the Connecticut River. Connecticut River Atlantic Salmon Commission Research Forum, Hadley, MA, 25 January 2001.	January 2001
Mitchell, B. R., and T. M. Donovan. 2005. Factors influencing the probability of detecting Vermont songbirds during point counts. The Wildlife Society Annual Meeting, Madison, WI. 25-29 September, 2005.	September 2005
Mitchell, B. R., and T. M. Donovan. 2005. Factors influencing the probability of detecting Vermont songbirds during point counts. The Ecological Society of America 90th Annual Meeting, Montreal, Quebec, CA. 7-12 August, 2005.	August 2005
McReynolds, A., Pientka, B., Henderson, M., Jech, M., Rudstam, L., Marsden, E., Stockwell, J. Shifts in rainbow smelt distributions during alewife invasion in Lake Champlain. International Association for Great Lakes Research, May 20-24, 2024. Windsor, ON, CAN.	May 2024	The adaptability of mid-trophic level fishes to changing environments is critical for food web structure and function, including piscivore production. We used acoustic and trawl data from 1990 to 2015 to determine how rainbow smelt responded to alewife in three environmentally distinct basins within Lake Champlain.
McKenny, H. C., W. Keeton, and T. M. Donovan. 2005. Effects of structural complexity enhancement on red-backed salamanders (Plethodon cinereus) in northern hardwood forests. The Ecological Society of America 90th Annual Meeting, Montreal, Quebec, CA. 7-12 August, 2005.	August 2005
Mather, M.E., J. M. Dettmers, R. A. Stein, D. L. Parrish, D. Glover. 2019. A portfolio approach to integrated assessment and research can provide a larger context for the successful evaluation of fisheries harvest regulations. 79th Midwest Fish and Wildlife Meeting, January 27-30, 2019, Cleveland, OH.	January 2019	Harvest regulations are essential tools that fisheries managers use to alter fish populations and achieve angler satisfaction. Evaluation of regulations is essential but evaluating all regulations for all species in all systems across multiple time periods is not logistically feasible. Thus, a strategic plan that identifies what regulations need to be evaluated where, when, and how can assist effective decision-making. Specifically, an integrated framework of assessment and research (i.e., t
Mather, M.E., J. M. Dettmers, D. L. Parrish, R. A Stein. E. A. Marschall. 2018. A portfolio of integrated monitoring and research can advance successful science-based conservation and fisheries management. Invited Talk in 2018 American Fisheries Society Symposium (Atlantic City, NJ, August 19 - 23, 2018) entitled “From Catastrophe to Recovery: Stories of Fishery Management Success.”	August 2018	Resource agencies manage fisheries and conserve aquatic resources based on sound data and scientific principles. This always-difficult task is ever more challenging as fish species and aquatic systems are assaulted by an increasing diversity of human disturbances. Here we propose a pathway by which resource agencies and their collaborators can advance sustainable science-based fisheries management. Using successful examples from a variety of agencies and fisheries, we illustrate this multi-ste
Mather, M.E., J. Dettmers, and D.L. Parrish. Navigating the changing landscape of fisheries publications: setting a course, avoiding the rocks, and facilitating the rescue. 135th Annual Meeting of the American Fisheries Society, Anchorage, AK, 11-15 September 2005. (Invited symposium presentation.)	September 2005
Mather, M.E., E.A. Marschall, and D.L. Parrish. Predicting interactive effects of climate change and dams on success of downstream-migrating salmon. Fish and Climate Change, The Fisheries Society of the British Isles Annual Symposium, Belfast, UK, 26-30 July 2010. Presenter	July 2010
Mather, M. E., E. A. Marschall, D. L. Parrish, G. Allison, J. McMenemy. 2009 River discharge, temperature, dams, and the timing of downstream migration of Atlantic salmon smolts: a modeling approach. Connecticut River Atlantic Salmon Research Forum, Hadley, MA, February, 2009.	February 2009
Marschall, E.A., M.E. Mather, D.L. Parrish, and G.W. Allison. River discharge, river temperature, dams, and the timing of downstream migration of Atlantic salmon smolts: a modeling approach. 137th Annual Meeting of the American Fisheries Society, San Francisco, CA, 2-6 September 2007. (Invited symposium presentation.)	September 2007
Marschall, E. A., D. C. Glover, M. E. Mather, and D. L. Parrish. Modeling the effects of climate change on larval cohort success in anadromous fish populations in the mainstem of a large river. 4th Mississippi-Yangtze River Symposium, Chongqing, China, 17 October 2018.	October 2018	The success of anadromous fish populations is partly dependent on conditions in the rivers in which they spawn. A key question in understanding how anadromous populations will respond to climate change is how well behaviors adapted for historical conditions will perform under scenarios of climate change.
Manaras, K. W., W. S. Keeton, T. M. Donovan, and B. Mitchell. 2005. Forest structure and avian habitat: scale dependences in occurrence prediction. The Ecological Society of America 90th Annual Meeting, Montreal, Quebec, CA. 7-12 August, 2005.	August 2005
Long, R.A., T.M. Donovan, P. MacKay, W.J. Zielinski, and J.S. Buzas. 2004. Detecting wide-ranging carnivores in the Northeast: A comparison of three noninvasive methods. Defenders of Wildlife's Carnivores 2004: Expanding partnerships in carnivore conservation. Santa Fe, New Mexico. 14-17 November, 2004	November 2004
Long, R.A., T.M. Donovan, P. MacKay, W.J. Zielinski, and J.S. Buzas. 2002. Scat-sniffing dogs as a tool for studying forest carnivores in Vermont. Defenders of Wildlife's Carnivores 2002: From the mountains to the sea. A conference on carnivore biology and consevation. Monterey, California. 17-20 November.	November 2002
Long, R.A., T.M. Donovan, P. MacKay, W.J. Zielinski, and J.S. Buzas. 2006. Predicting carnivore occurrence with data collected via multiple, noninvasive methods. Defenders of Wildlife?s Carnivores 2006: Habitats, challenges, and opportunities. St. Petersburg, FL; 14-17 November, 2006.	November 2006
Long, R.A., T.M. Donovan, P. MacKay, W.J. Zielinski, and J.S. Buzas. 2006. A comparison of noninvasive survey techniques: forest carnivores in Vermont. Annual Conference of the Western Section of the Wildlife Society Pre-conference Symposium: Fisher and Marten in California: Moving Science and Management Forward. Sacramento, California. 8-10 February, 2006.	February 2006
Long, R., T. M. Donovan, P. MacKay, W. J. Zielinski, and J. S. Buzas. Predicting carnivore occurrence with data collected via multiple non-invasive methods. The Northeast Fish and Wildlife Annual Conference, Burlington, VT; 23-26 April, 2006.	April 2006
Long, R. A., T. M. Donovan, P. MacKay, W. J. Zielinski, and J. S. Buzas. 2005. Comparing the effectiveness of scat detector dogs, remote cameras, and hair snares for detecting forest carnivores. The Wildlife Society Annual Meeting, Madison, WI. 25-29 September, 2005.	September 2005
Katz, J. E., S. Hafner, and T. M. Donovan. 2014. Automated acoustic monitoring: reporting survey presence for a northeastern warbler . 70th Annual Northeast Fish and Wildlife Conference, Portland, ME.	April 2014	Most monitoring programs require information on presence-absence of species at a site, yet automated acoustic monitoring methods provide error rates on a song by song basis. Here, we demonstrate how to scale up individuals songs (with false positive rates) to determine the probaiblity that the species occurs on a site.
Katz, J. E., S. Hafner, and T. M. Donovan. 2014. monitor: an R package for automated acoustic monitoring, tested on two northeastern warblers. 70th Annual Northeast Fish and Wildlife Conference, Portland, ME.	April 2014	We introduce an acoustical monitoring framework that integrates monitoring data with automated acoustic detection in the program, R.
Jensen, P., J. Walker, J. Frair, S. McNulty, R. Bakerian, V. Rojas, A. Siren, L. Clarfeld, T. Donovan, T. Wilson, et al. Many hands make light work: establishing a camera trap network to inventory and monitor wildlife populations across broad spatial and temporal scales. April 3 - 5, 2022. 77th Annual Northeast Fish and Wildlife Association. Long Branch, New Jersey, USA.	April 2022	Monitoring wildlife populations has been facilitated and enhanced through technological advances in automated sensors that provide noninvasive sampling data. This presentation introduces the Adirondack Inventory and Monitoring (AIM) Camera Trap Network and its part in the Northeast Monitoring Network.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and J.E. Marsden. Seasonal movements and habitat use of juvenile lake sturgeon in Lake Champlain. Joint meeting of the American Fisheries Society and The Wildlife Society, Reno, Nevada, 30 September-3 October 2019.	October 2019	Little is known regarding juvenile lake sturgeon seasonal movements and habitat use, especially in large lakes. In this study, we characterize the habitat use and movement patterns of juvenile lake sturgeon.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Lake Champlain sturgeon: Characterizing the spawning run using acoustic technology. 147th Annual Meeting of the American Fisheries Society, Tampa, Florida, 20-25 August 2017.	August 2017	This study aims to develop a hydroacoustic sampling program to estimate the number of adult spawners in a Lake Champlain tributary, the Winooski River. Results of this work will provide managers with methods for future assessments and enable the tracking of progress towards recovery targets without the need to handle pre-spawn sturgeon.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Estimating abundance of spawning lake sturgeon in the Winooski River, VT using dual-frequency identification sonar (DIDSON). 74th annual Northeast Fish and Wildlife Conference, Burlington, VT, 15-17 April 2018.	April 2018	Results of this work, which will continue through 2019, will provide managers with an estimate of spawning adult abundance without the need to handle pre-spawn fish. In addition, the methods developed during this study can be used to track progress towards lake sturgeon recovery in Lake Champlain.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Estimating abundance of spawning lake sturgeon in the Winooski River, VT using dual-frequency identification sonar (DIDSON). Lake Champlain Research Conference, Burlington, VT, 8-9 January 2018.	January 2018	Our goal is to use newer technology to provide spawning population estimates of this endangered species. The state agency wants an estimate of sturgeon numbers for the purpose of providing management options.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Estimating abundance of spawning lake sturgeon in the Winooski River, VT using dual-frequency identification sonar (DIDSON). Great Lakes Lake Sturgeon Workshop, Port Huron, MI, 21-22 February 2018.	February 2018	Our goal is to use newer technology to provide spawning population estimates of this endangered species. The state agency wants an estimate of sturgeon numbers for the purpose of providing management options.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Combining dual-frequency identification sonar (DIDSON) and acoustic telemetry to estimate abundance of spawning lake sturgeon. 148th annual meeting of the American Fisheries Society, Atlantic City, NJ, 19-23 August 2018.	August 2018	This is the major focus of our research. We are attempting to quantify spawning lake sturgeon using remote techniques so fish will not have to be physically sampled.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Feasibility of estimating Lake Sturgeon abundance using side-scan SONAR on a river delta in Lake Champlain. Southern New England Chapter Meeting of AFS and Northeastern Division Meeting of AFS, Mystic, CT, 26-28 February 2017.	February 2017	This work is important in being able to determine the numbers of lake sturgeon in Lake Champlain. This research is intended to help Vermont Fish and Wildlife with managing the lake sturgeon population.
Izzo, L.K., D.L. Parrish, G.B. Zydlewski, and C. MacKenzie. Feasibility of estimating Lake Sturgeon abundance using side-scan SONAR on a river delta in Lake Champlain. New York Chapter Meeting of AFS, Buffalo, NY, 1-3 February 2017.	February 2017	This work is important in being able to determine the numbers of lake sturgeon in Lake Champlain. This research is intended to help Vermont Fish and Wildlife with managing the lake sturgeon population.
Izzo, L. K., D. L. Parrish, G. B. Zydlewski, and J. E Marsden. Second fin ray shows promise for aging juvenile but not adult lake sturgeon. Annual Meeting of the North American Sturgeon and Paddlefish Society. (Virtual Meeting 26-29 October 2020.)	October 2020	We show the limitations of using the second fin ray for aging lake sturgeon. This result is important for other researchers and managers attempting to use these structures for aging sturgeon.
Izzo, L. K., D. L. Parrish, G. B. Zydlewski, and J. E Marsden. Seasonal dynamics of spatial overlap between juvenile and adult lake sturgeon in Lake Champlain. 150th Annual Meeting of the American Fisheries Society, Columbus, OH, 30 August- 3 September 2020 (changed to virtual meeting 14 - 25 September 2020).	September 2020	This work relays the differences in juvenile and adult lake sturgeon distributions on a seasonal basis. This information is important in better understanding habitat use by these life stages.
Izzo, L. K., D. L. Parrish, G. B. Zydlewski, and C. MacKenzie. Combining dual-frequency identification sonar (DIDSON) and acoustic telemetry to estimate abundance of spawning lake sturgeon. 44th Annual Meeting of the Atlantic International Chapter of the American Fisheries Society. 23-25 September 2018.	September 2018	This is the major focus of our research. We are attempting to quantify spawning lake sturgeon using remote techniques so fish will not have to be physically sampled.
Izzo, L. K., D. L. Parrish, G. B. Zydlewski, and C. MacKenzie. Using sonar to estimate lake sturgeon abundance in a river and lake delta in the northeastern USA. 4th Mississippi-Yangtze River Basins Symposium, Chongqing, China, 15-20 October 2018. Presenter.	October 2018	A major goal of our work is to develop methods of estimating the abundance of lake sturgeon in which we do not have to physically sample the fish. Lake sturgeon in Lake Champlain are listed by the state as endangered so it is important not do do sampling that could further endanger them.
Howe, E. A., J. E. Marsden, T. M. Donovan, R. H. Lamberson, and T. Tear. Development of a matrix-based population viability model to manage a population for extinction. Poster. World Fisheries Congress, Vancouver, British Columbia, 3 May 2004.	April 2004
Hitchcock, D.J., and D.L. Parrish. Potential strategies for removing adult sea lamprey prior to spawning. 135th Annual Meeting of the American Fisheries Society, Anchorage, AK, 11-15 September 2005. (Poster).	September 2005
Hitchcock, D.J., M. R. Harrington, and D.L. Parrish. Sea lamprey sex pheromone experiments: using males to attract females into traps. 136th Annual Meeting of the American Fisheries Society, Lake Placid, NY, 10-14 September 2006. (Invited symposium presentation.)	September 2006
Herrera-Herrera, J. R. and T. M. Donovan. August 2000. Seasonal importance of wetland and upland habitats to the bird diversity in southeastern Mexico. AOU Annual Meeting, St. John's, Newfoundland.	August 2000
Futia, M., Henderson, M., Fisk, A., Marsden, E. Using acoustic telemetry to understand Lake trout restoration in Lake Champlain. 153rd Meeting of the American Fisheries Society. Grand Rapids, Michigan, August 20-24, 2023	August 2023	We used acoustic telemetry to compare the three-dimensional habitat use of stocked and wild Lake Trout to test the hypothesis that wild fish selected more suitable spawning sites that resulted in more successful recruitment. Our results indicate that sampling efforst to evaluate presence of wild adults may have been misleading due to differences in the behaviors and distribution of the wild and stocked populations, which could bias the population assessments and management efforts.
Frater, B. J., and D.L. Parrish. Habitat selection of juvenile walleye in Malletts Bay, Lake Champlain, Vermont. 57th Northeast Fish and Wildlife Conference, Saratoga Springs, NY, 22-25 April 2001.	April 2001
Eisenhower, M., and D.L. Parrish. Fish availability and changes in forage site fidelity by Double-crested cormorants. 59th Northeast Fish and Wildlife Conference, Newport, RI, 13-16 April 2003.	April 2003
Duerr, A.E., D.E. Capen, and T.M. Donovan. 2005. Use of decision analysis modeling to choose optimal management strategies for double-crested cormorant on Lake Champlain. First Biennial Symposium of the Jack H. Berryman Institute, Logan, Ut.	June 2005
Duerr, A.E., D. E. Capen, T. M. Donovan, and C. Maisonneuve, Decision-analysis modeling to evaluate management options for double-crested cormorants in the Northeast. 14th Annual Wildlife Society Conference, Tuscon, AZ; Sept 22-26 2007.	September 2007
Duerr, A., E., K. Stromborg, C. Weseloh, D. Capen and T. Donovan. Survival of DCCOs and philopatry to natal colonies on Lake Michigan Ontario and Champlain. 50th Annual Conference International Association for Great Lakes Research, University Park, PA; 28 May ? 1 June, 2007.	May 2007
Duerr, A., D. E. Capen, and T. M. Donovan. April 2003. Egg oiling and nest colony fidelity of double-crested cormorants in Lake Champlain. Northeast Fish and Wildlife Annual Conference, Newport, RI.	April 2003
Duerr, A., D. E. Capen, and T. M. Donovan. 2003. Metapopulation dynamics of double-crested cormorants on Lake Champlain: How egg oilings causes corrmorants to avoid management. The Wildlife Society 10th Annual Conference, Burlington, VT. September 2003.	September 2003
Duerr, A., D. Capen, and T. M. Donovan. Decision analysis modeling to evaluate management options for double-crested cormorants on Lake Champlain. The American Ornithologists Union 122nd Annual Meeting, Quebec, CA. 16-21 August, 2004.	August 2004
Duerr, A. E., R. Strickland, D. E. Capen, T. M. Donovan and G. Nohrenberg. Effects of capture, color-banding, and radio transmitters on survival and colony fidelity of double-crested cormorants on Lake Champlain. 50th Annual Conference International Association for Great Lakes Research, University Park, PA; 28 May ? 1 June, 2007.	May 2007
Duerr, A, D. E. Capen, and T. M. Donovan. Diet, foraging, distribution, and energy requirements of cormorants on Lake Champlain. The Northeast Fish and Wildlife Annual Conference, Burlington, VT; 23-26 April, 2006.	April 2006
Driscoll, M., and T. M. Donovan. Predicting Wood Thrush nest success: local habitat versus landscape factors. American Ornithologists Union Annual Meeting, New Orleans, LA.	September 2002
Driscoll, M., and T. M. Donovan. Edge effects, landscape context, and regional population viability of Wood Thrushes. American Ornithologists Union Annual Meeting, New Orleans, LA.	September 2002
Driscoll, M. and T. M. Donovan. August 2000. Landscape and edge effects on the abundance, distribution, and nesting success of Wood Thrushes in central New York. AOU Annual Meeting, St. John's, Newfoundland.	August 2000
Dricoll, M. L., and T. M. Donovan. August 2001. Landscape and edge effects on the distribution, abundance, and nesting success of Wood Thrushes in central New York. American Ornithologists Union Annual Meeting, Seattle, WA.	August 2001
Donovan, T.M. and C. Flather. August 2001. Population trends in North American songbirds: Interactions between habitat fragmentation and landscape occupancy patterns. Ecological Society of America Annual Meeting. 2001. Madison, Wisconsin.	August 2001
Donovan, T., R. Long, A. Troy, A. Vionov, and W. Keeton. Land use change in Northern Forests: Assessments and recommendations for conserving biodiversity. 1st Meeting of the Northeastern States Research Cooperative, Burlington, VT, 13 November 2003.	November 2003
Donovan, T. M., and C. Flather. 2002. Relationships among North American songbird trends, habitat fragmentation, and landscape occupancy. American Ornithologists Union Annual Meeting, New Orleans, LA.	September 2002
Donovan, T. M. An overview of wildlife research at the Vermont Cooperative Fish and Wildlife Research Unit. Lake Champlain Ecosystem Team Meeting.	May 2002
DeBow, J., J. Murdoch, T. M. Donovan, and C. Alexander. 2017. Overview of moose mortality and productivity research in northern Vermont. April 15-17, 2018. 74th Annual Northeast Fish and Wildlife Conference, Burlington, Vermont.	April 2018	Moose (Alces alces) research in Maine and New Hampshire identified three consecutive years (2014-2016) of winter tick (Dermacentor albipictus) epizootics causing >70% annual calf mortality. This presentation provides an overview of a study of cow and calf mortality in Vermont.
DeBow, J., J. Blouin, E. Rosenblatt, J. D. Murdoch, K. Gieder, C. Alexander, and T. Donovan. Effects of winter ticks and other parasites on moose survival in Vermont, USA. April 19-21, 2020. 76th Annual Northeast Fish & Wildlife Conference, Long Branch, New Jersey.	April 2020	Since January of 2017, 126 moose have been radio-marked (90 calves and 36 adult cows) and tracked on a daily basis with GPS technology. Winter ticks (<i>Dermacentor albipictus)</i>, lungworm presence (<i>Dictyocaulus viviparous)</i>, and roundworm presence (<i>Parelaphostrongylus tenuis</i>) were negatively associated with weekly calf survival, and winter tick load and stage in the tick life cycle were important predictors monthly adult survival rates.
DeBow, J., E. Rosenblatt, J. Blouin, C. Alexander, T. Donovan, and J. Murdoch. Parasite induced moose decline in northeastern Vermont: Year three update. June 10-14, 2019. 53rd Annual North American Moose Conference. Carrabassett Valley, Maine.	June 2019	The rapid decline of moose populations in Vermont and other northeastern U.S. states has prompted investigations of annual variation in mortality and productivity rates. Pathology thus far has attributed ~70% of all observed mortalities to clinical signs associated with winter tick (Dermacentor albipictus) and brain worm (Parelaphostrongylus tenuis). Final results will be used to modify key parameters in state population models and better inform future management of moose in Vermont.
DeBow, J., C. Alexander, J. Murdoch, and T. M. Donovan. An Overview of Ongoing Moose Mortality and Productivity Research in Northern Vermont. Forest Ecosystem Monitoring Cooperative Conference, Burlington, VT. 15 December 2017.	December 2017	Current moose (Alces alces) research in Maine and New Hampshire identified 3 consecutive years (2014-2016) of winter tick (Dermacentor albipictus) epizootics causing >70% annual calf mortality (March-April). Tick indices on harvested bull moose in northeastern Vermont have consistently been lower than study areas in New Hampshire and western Maine.
DeBow, J, C. Alexander, J. Murdoch, and T. Donovan. Assessing mortality and productivity of moose in northern Vermont: Year one preliminary data. 51st Annual Moose Conference and Workshop, Ingonish, Cape Breton, Nova Scotia, August 28 - September 01 2017.	August 2017	Current moose (Alces alces) research in Maine and New Hampshire identified 3 consecutive years (2014-2016) of winter tick (Dermacentor albipictus) epizootics causing >70% annual calf mortality (March-April). This study investigates rates of mortality in Vermont; preliminary results are provided. 51st North American Moose Conference. 28 August-01 September. Ingonish, Nova Scotia, Canada.
Cummings, J., and T. Donovan. 2014. The Value of Maps in Natural Resource Management: An Application of Expected Value of Sample Information. 70th Annual Northeast Fish and Wildlife Confernce, Portald, ME.	April 2014	This project outlines how to calculate the value of information stored in a map with respect to natural resource decision making.
Cummings, J. and T. Donovan. Structured Decision Making provides insight when selecting a preferred population monitoring program. The Wildlife Society Annual Meeting. Sept 29 - Oct 3, 2019. Reno, Nevada	September 2019	Population monitoring programs typically aim to meet many objectives, but standard analyses mainly consider a monitoring program's ability to effectively estimating population size and trend. Using structured decision making to identify and score the importance of objectives in addition to estimation effectiveness – management cost, citizen engagement, and disease detection – we found that despite the costs of the necropsy monitoring program it best achieves the state's objectives, a conclusio
Cox, K.M, S.R. Roy, K.S. Omland, and D.L. Parrish. Declining brown trout in the Batten Kill. Wild Trout 8 Symposium, Yellowstone National Park, 19-22 September 2004.	September 2004
Cornell, K., and T. M. Donovan. Landscape-scale patterns of demography in black-throated blue warblers in Vermont. The Northeast Fish and Wildlife Annual Conference, Burlington, VT; 23-26 April, 2006.	April 2006
Cornell, K. L., and T. M. Donovan. Landscape-scale patterns of Black-throated blue warbler abundance and productivity in Vermont. The Wildlife Society Annual Meeting, Madison, WI. 25-29 September, 2005.	September 2005
Cornell, K. L., and T. M. Donovan. Determinants of territory occupancy of a forest songbird in a fragmented landscape: are conspecific cues indicators of quality? IV North American Ornithological Conference, Veracruz, Mexico; October 3-7, 2006.	October 2006
Cole, W., T. M. Donovan, M. Brown, and J. Murdoch. Effects of landscape development on bobcat carrying capacity in Vermont.	December 2014	This work estimates how changes in Vermont's landscape to the year 2050 are expected to change the state's carrying capacity for supporting bobcat populations.
Clarfeld, L., K. Gieder, and T. M. Donovan. 2024. Estimating moose productivity from trail cameras and hunter sightings in Vermont. 78th Annual Northeast Fish and Wildlife Association. Cape Cod, Massachusetts, USA.	April 2024	A key challenge faced by fish and wildlife agencies today is how to monitor an ever-growing list of species with limited resources. Many agencies are turning to remote camera monitoring to supplement hunter-derived monitoring methods. Here, we compare moose productivity rata as estimated from trail camera monitoring with those derived from deer-hunter sightings of cows and calves.
Clarfeld, L., K. Gieder, S. Wixsom, C. Bernier, A. Sirén, J. Peckham, R. Abrams, S. Gifford, S. Staats, L. McNally, and T. Donovan. Forest monitoring for early successional species in the Green Mountains. April 3 - 5, 2022. 2022 Forest Ecosystem Monitoring Cooperative Annual Conference. Burlington, Vermont, USA.	December 2022	In response to lack of information on status and trend of species that rely on early-succession habitat, the Vermont Cooperative Fish & Wildlife Research Unit, Vermont Fish and Wildlife Department, and Green Mountain National Forest began acoustic monitoring of nearly 50 sites in the Green Mountain National Forest. In this talk, we’ll provide an overview of this new research endeavor and an update on preliminary findings.
Clarfeld, L., D. Ignizio, C. Balantic, A. Siren, and T. Donovan. AMMonitor: A remote wildlife monitoring framework. April 3 - 5, 2022. 77th Annual Northeast Fish and Wildlife Association. Long Branch, New Jersey, USA.	April 2022	Remote monitoring of wildlife can yield terabytes of data through the automated collection of images and recordings. This presentation illustrates the AMMonitor approach that links monitoring data with a permanent archive in the USGS ScienceBase system.
Clarfeld, L. C. Balantic, T. Wang, and T. Donovan. Machine learning: Opening the black box. April 3 - 5, 2022. 77th Annual Northeast Fish and Wildlife Association. Long Branch, New Jersey, USA.	April 2022	Remote monitoring of wildlife across large geographic areas inevitably produces large volumes of data in the form of audio recordings or camera trap photos, in which machine learning models can be used to automate the detection of target species and removal of false triggers. In this talk, we introduce core concepts of machine learning, explaining how these models learn and discussing some of the challenges and opportunities they present.
Clarfeld, L, A. Siren, P. Jensen, T. Wilson, C. Balantic, J. Frair, T. Donovan. August 14-19, 2022. Ecological Society of American & Canadian Society for Ecology and Evolution Joint Meeting. Montreal, Quebec, CA.	August 2022	Collecting ecological and environmental data over broad spatial extents is a challenging yet necessary endeavor in the face of ongoing climate and land use change. Remote sensors (e.g., camera traps) are one solution to this problem, providing abundant data to tackle applied and fundamental questions. However, expanding studies beyond local or landscape scales and across jurisdictional boundaries, can be challenging due to myriad logistical and legal factors, including how to collect, manage, t
Chen, Y., and 18 coauthors. 2018. Moving the Mississippi-Yangtze Fisheries Network Forward: Past, Current, and Future. American Fisheries Society Annual Meeting, Atlantic City, NJ.	August 2018	This work summarized an international collaboration network that help managers and decision makers work together on complex riverine problems on river conservation and management.
Chen, E.K., Som, N.A., Deibner-Hanson, J.D., Anderson, D.G., Henderson, M.H., A life cycle model for evaluating estuary residency and restoration potential in Chinook salmon. California Department of Fish and Wildlife Conservation Lecture Series.	August 2022	Understanding the spatial and temporal habitat use of a population is a necessary step for restoration decision making. To evaluate how juvenile life history variation affects a population’s response to potential restoration, we developed a stage-structured model for a Chinook salmon population in a northern California river with a seasonally closed estuary.
Chellman, I.C., and D.L. Parrish. Sampling strategies and population estimation of mudpuppies (Necturus maculosus) in the Lamoille River, Vermont. 66th Annual Meeting of the Northeast Fish and Wildlife Conference, Newton, MA, 25-27 April 2010.	April 2010
Chellman, I.C., and D.L. Parrish. Field sampling and genetic analyses of mudpuppies (Necturus maculosus) in Vermont. Northeast Partners in Amphibian and Reptile Conservation annual meeting, Watkins Glen, NY, 11-13 August 2009.	August 2009
Capen, D.E., A.E. Duerr, and T.M. Donovan. 2005. Management of Double-crested Cormorants on Lake Champlain: an interagency, international, interjurisdictional, interesting challenge. First Biennial Symposium of the Jack H. Berryman Institute, Logan, Ut.	June 2005
Capen, D., E., A. E. Duerr, C. Maisonneuve, T. M. Donovan, and G. Cabana. Research and monitoring of double-crested cormorant populations on Lake Champlain and St. Lawrence River: Lessons for management. 50th Annual Conference International Association for Great Lakes Research, University Park, PA; 28 May ? 1 June, 2007.	May 2007
Butryn, R.S., D.L. Parrish, D.M. Rizzo, and B.C. Wemple. Predicting brook trout distribution with thermal stress events. 139th Annual Meeting of the American Fisheries Society, Nashville, TN, 31 August- 3 September 2009.	September 2009
Butryn, R.S., D.L. Parrish, D.M. Rizzo, and B.C. Wemple. Biological relevance of summer stream temperatures for brook trout in Vermont. 138th Annual Meeting of the American Fisheries Society, Ottawa, Ontario, Canada, 17-21 August 2008.	August 2008
Butryn, R.S., D.L. Parrish, D.M. Rizzo, and B.C. Wemple. Summer temperatures and the distribution of brook trout in Vermont streams. 66th Annual Meeting of the Northeast Fish and Wildlife Conference, Newton, MA, 25-27 April 2010.Presenter	April 2010
Brown, M., T. Donovan, W. S. Schwenk. D. Theobald. 2013. Predicting Impacts of Future Human Population Growth and Development on Occupancy Rates of Forest-Dependent Birds. 70th Annual Northeast Fish and Wildlife Confernce, Portald, ME.	April 2014	This work established a method for measuring the relative contribution protected lands for bird conservation.
Brown, M., T. Donovan, G. Warrington, W. S. Schwenk. D. Theobald. 2014. Predicting Effects of Future Human Population Growth and Development on a Territorial Forest Songbird: Small Declines in Occupancy Equates to Large Declines in Landscape Carrying Capacity. 70th Annual Northeast Fish and Wildlife Confernce, Portald, ME.	April 2014	This work introduces a method for estimating the maximum numbers of territories that a landscape can support. The metric is very informative for land use conservation.
Brown, M., C. Canham, and T. Donovan. 2016. Effects of Forest Biomass Energy Production on Long-Term Northern Forest Structure and Composition. Northeast Natural History Conference	April 2016	This study examined the capacity of the Northern Forest to meet regional bioenergy goals over the next 50 years. Forest biomass can represent a viable component of renewable energy policy in the Northeast, however, tradeoffs between biomass stock and supply must be considered.
Brown, M. L, C. Canham, L. Murphy, and T. M. Donovan. Effects of forest biomass energy production on long-term Northern Forest structure, composition and wildlife. April 15-17, 2018. 74th Annual Northeast Fish and Wildlife Conference, Burlington, Vermont.	April 2018	Federal and state governments in the Northeast U.S. are actively engaged in assessing the potential role of forest biomass in meeting renewable energy goals. Our results suggest that forest biomass can represent a viable component of renewable energy policy in the Northeast, however, tradeoffs between biomass stock, supply, and wildlife distribution must be considered.
Bridegum, J., Kinziger, A., Bandy, G., Poytress, B., and Henderson, M. Comparing eDNA and juvenile salmon trap passage estimates on the Sacramento River. Coastwide salmonid genetic conference, Boise, ID June 27-29, 2023.	June 2023	Monitoring for juveniles salmon on the Sacramento River is critical because these populations have been declining and abundance estimates are necessary to determine the efficacy of management actions. One sampling method that has been proposed to improve salmon monitoring efforts throughout the Sacramento River is Environmental DNA (eDNA). In this study, we found a positive correlation between the quantity of eDNA in the water samples and the abundance of outmigrating juvenile Chinook salmon.
Bridegum, J., Kinziger, A., Bandy, G., Poytress, B., and Henderson, M. Comparing eDNA and Juvenile Salmon trap passage estimates on the Sacramento River. 153rd Meeting of the American Fisheries Society. Grand Rapids, Michigan, August 20-24, 2023	August 2023	We compare the abundance of eDNA to that of juvenile chinook salmon in the Sacramento River. We observed a positive correlation that could be used by biologists and managers to facilitate a better understanding of the timing, survival, abundance, and movement of juvenile Chinook Salmon throughout the entire Sacramento River.
Bouffard, W., J.E. Marsden, and D.L. Parrish. Field trials for the use of sea lamprey migratory pheromone as an attractant within tributary systems. 138th Annual Meeting of the American Fisheries Society, Ottawa, Ontario, Canada, 17-21 August 2008.	August 2008
Bonter, D. N., S. A. Gauthreaux, and T. M. Donovan. 2002. Divergent migration directions in the Great Lakes basin: The result of atmospheric circulation? American Ornithologists Union Annual Meeting, New Orleans, LA.	September 2002
Bonter, D. N. and T. M. Donovan. August 2001. Temporal, spatial, and competition factors influencing migration stopover site quality. American Ornithologists Union Annual Meeting. St. John's, Newfoundland.	August 2001
Bonter, D. N. and T. M. Donovan. August 2000. Migration stopover concentration areas in the northeastern United States. AOU Annual Meeting, St. John's Newfoundland.	August 2000
Blouin, J., J. Debow, E. Rosenblatt, J. Murdoch, C. Alexander, and T. Donovan. Assessing moose habitat suitability in Vermont using GPS radio-collar data and lidar. April 19-21, 2020. 76th Annual Northeast Fish & Wildlife Conference, Long Branch, New Jersey.	April 2020	We present an upgraded HSI model for moose in Vermont based on three new sources of information: GPS radio-collar locations of moose (approx. 50,000 collected to-date), contemporary maps of land cover types (from the newly available 2016 National Land Cover Database), and fine-scale landscape conditions from 2016 LIDAR (<i>light detection and ranging</i>) imagery. We used the model to map suitability throughout Vermont by providing a suitability score at a fine-scale resolution, highlighting di
Blouin, J., J. DeBow, E. Rosenblatt, J. Hines, C. Alexander, K. Gieder, N. Fortin, J. Murdoch, and T. Donovan. Moose habitat selection and fitness consequences during two critical winter tick (Dermacentor albipictus) life stages in Vermont, USA. Dec 17 - 19, 2020. 2020 Forest Ecosystem Monitoring Cooperative Conference. (Virtual conference).	December 2020	In New England, USA, the decline of moose (<i>Alces alces</i>) has been attributed, in part, to winter tick (<i>Dermacentor albipictus</i>) infestations, whose distribution patterns at any given time are shaped largely by the occurrence of moose during the peak of two critical time periods: fall questing (when ticks latch onto a moose, which coincides with the rut) and spring drop-off (when engorged female ticks detach from moose and lay their eggs in leaf litter). We studied habitat selection
Blouin, J., J. DeBow, E. Rosenblatt, J. Hines, C. Alexander, K. Gieder, N. Fortin, J. Murdoch, and T. Donovan. Choices Matter: Fitness Consequences of Habitat Selection by Moose During Two Critical Winter Tick Life Stages in Vermont, USA. April 26 - 28, 2021. 76th Annual Northeast Fish and Wildlife Association (Virtual conference).	April 2021	The moose (<i>Alces alces</i>) is a charismatic species in decline across part of their southern distribution in North America, attributed, in part, to winter tick (<i>Dermacentor albipictus</i>) infestations. This study evaluates habitat selection of moose during the peak of two critical winter tick time periods: fall questing (when ticks latch onto a moose) and spring drop-off (when engorged female ticks detach from moose). Further, we evaluate if habitat selection decisions made by adult fem
Blouin, J., J. DeBow, E. Rosenblatt, C. Alexander, K. Gieder, N. Fortin, J. Murdoch, and T. Donovan. Modeling moose habitat suitability by age, sex, and season in Vermont, USA based on GPS radio-collar data and lidar imagery. Dec 17 - 19, 2020. 2020 Forest Ecosystem Monitoring Cooperative Conference. (Virtual conference).	December 2020	The moose (<i>Alces alces</i>) population has experienced unprecedented declines along the southern periphery, spurring the need to identify habitat conditions that are most used by moose and their distribution in space. We combined more than 41,000 moose locations collected from radio-collared individuals (n = 74), recent land cover data, and high resolution, 3-dimensional lidar data to develop Resource Utilization Functions that link home range use to habitat conditions by age (mature and you
Blouin, J., J. DeBow, E. Rosenblatt, C. Alexander, K. Gieder, N. Fortin, J. Murdoch, and T. Donovan. Assessing Habitat Suitability by Age, Sex, and Season for Moose in Vermont, USA . April 26 - 28, 2021. 76th Annual Northeast Fish and Wildlife Association (Virtual conference).	April 2021	We combined more than 41,000 moose locations collected from radio-collared individuals (n = 74), recent land cover data, and high resolution, 3-dimensional lidar data to develop Resource Utilization Functions that link home range use to habitat conditions by age (mature and young adult), season (dormant and growth), and sex. The resultant maps of habitat suitability provide a means of informing management activities (e.g., the restoration or alteration of habitats to benefit moose) and policies
Blouin, J. DeBow, J., E. Rosenblatt, T. Donovan, J. Murdoch, and C. Alexander. Assessing moose habitat suitability in Vermont using GPS radio-collar data and LIDAR imagery. June 10-14, 2019. 53d Annual North American Moose Conference. Carrabassett Valley, Maine.	June 2019	Understanding the relative suitability of habitats in a landscape provides a foundation for wildlife population management and is especially important for harvested species and those that are declining. An upgraded HSI (habitat suitability index) model for moose in Vermont will be developed based on three new sources of information: GPS radio-collar locations of moose (approx. 35,000 collected to-date), contemporary maps of land cover types (from the newly available 2016 National Land Cover Dat
Berube, J., A. P. K. Sirén, C. Frank, L. Clarfeld, B. Simpson, T.M. Donovan, T. L. Wilson. 2022. Perfecting the Imperfect Detection of Ticks: Winter Tick Epizootics and Moose Populations in the Northeastern U.S. Presentation. The Wildlife Society Annual Conference, Spokane, WA. 6-10 November.	November 2022	Imperfect detection is a general problem of sampling anything. We discuss how imperfect detection has contributed to uncertainty about tick abundance, the challenge it poses for inference, and a potential path forward using improved sampling design.
Berube, J. APK Sirén, CF Sullivan, L Clarfeld, B Simpson, TM Donovan, TL Wilson. 2023. A Big Little Problem: Assessing Winter Tick Epizootics and Moose Populations in the Northeastern U.S. 78^th Annual Fish and Wildlife conference, Northeast Association of Fish and Wildlife Agencies, Hershey Pennsylvania, April 30 – May 2.	May 2023	We describe the approach and present preliminary results from our regional project to evaluate drivers of winter tick epizootics in 5 states. This presentation will serve as an update for cooperators.
Beauchamp, D.A., D.L. Parrish, Roy A. Whaley. Sampling coldwater fish in large lakes. 138th Annual Meeting of the American Fisheries Society, Ottawa, Ontario, Canada, 17-21 August 2008. (Presenter--Invited speed presentation and poster)	August 2008
Balantic, C., T. M. Donovan, J. Katz, and M. Massar. Temporally-adaptive acoustic sampling to maximize detection across a suite of focal wildlife species with the R package AMMonitor. April 15-17, 2018. 74th Annual Northeast Fish and Wildlife Conference, Burlington, Vermont.	April 2018	Acoustic recordings of the environment can produce species presence-absence data for characterizing populations of sound-producing wildlife over vast spatial scales. If a species is present on site but does not vocalize during a scheduled audio recording session, researchers may incorrectly conclude that the species is absent ('false negative'). We present a novel method for reducing false negatives when monitoring a suite of focal species, each with unique calling patterns, with the R package
Balantic, C., T. M. Donovan, J. Katz, and M. Massar. Temporally-adaptive acoustic sampling to maximize detection across a suite of focal wildlife species with the R package AMMonitoR. Northeast Regional Environmental Acoustics Symposium, University of New Hampshire. March 20, 2018. Durham, NH.	March 2018	Acoustic recordings of the environment can produce species presence-absence data for characterizing populations of sound-producing wildlife over vast spatial scales. If a species is present on site but does not vocalize during a scheduled audio recording session, researchers may incorrectly conclude that the species is absent ('false negative'). We present a novel method for reducing false negatives when monitoring a suite of focal species, each with unique calling patterns, with the R package
Balantic, C., T. M. Donovan, J. Katz, and M. Massar. Machine learning mitigation of false positives in automated acoustic wildlife monitoring with the R package AMMonitor. April 15-17, 2018. 74th Annual Northeast Fish and Wildlife Conference, Burlington, Vermont.	April 2018	Audio recordings of the environment can provide long-term, landscape-scale presence-absence data to model populations of sound-producing wildlife. Automated detection algorithms allow researchers to avoid manually searching through terabytes of recordings, but often produce unacceptably high false positive rates, in which an event was detected wherein the target species did not actually vocalize. We present an approach towards reducing false positives with the R pacakge, AMMonitoR.
Balantic, C. and T. M. Donovan. 2019. Landscape-scale monitoring using smartphones and the R package AMMonitor. April 14-16, 2019. 75th Annual Northeast Fish and Wildlife Conference, Groton, Connecticut.	April 2019	In a world confronting climate change and rapidly shifting land uses, effective methods for monitoring natural resources are critical to support scientifically-informed management decisions. We introduce the R package, AMMonitor, as a cost-effective remote monitoring stations that take audio recordings and photos of the environment, scientists can acquire presence-absence data to characterize populations of wildlife over time and across vast spatial scales (in addition to soundscape, phenologi
Aylward, C., J. Murdoch, T. Donovan, and W. Kilpatrick. 2017. Modeling distribution and connectivity of recovering American marten populations in Vermont using expert elicitation techniques. 97th Meeting of the American Society of Mammologists. Moscow, ID. 20 June - 24 June 2017.	June 2017	We developed an occupancy model for American marten (Martes americana) using an expert-opinion approach, then used the model to map connectivity between populations. Maps of connectivity reveal potential pathways of movement that can inform conservation planning for marten recovery in the state.
Lindsey N. Hartzell, Vicki S. Blazer, Heather L. Walsh, Peter Emerson, Matthew Bodnar, Thomas Jones, Jean-Sébastien Messier, Patricia M. Mazik and Mark J. Henderson. Malignant Melanomas of Brown Bullhead Ameiurus nebulosus in Lake Memphremagog. 2023 Joint Meeting of the Northeast Fish Health Committee and the AFS Fish Health Section. Burlington, VT, July 24-27, 2023.	July 2023	Some Brown Bullhead <i>Ameiurus nebulosus</i> individuals from Lake Memphremagog located in Vermont and Quebec develop visible raised and non-raised melanistic lesions on their skin which was first reported by anglers in 2012. Currently, the etiology of the lesions is unknown, thus, our goal is to determine potential risk factors associated with the melanomas.

Theses and Dissertations

Theses and Dissertations	Publication Date
Watrous, K. 2006. Predicting minimum habitat characteristics of the Indiana bat (Myotis sodalis) in the Champlain Valley of Vermont and New York. M.S. Thesis, University of Vermont, Burlington, VT.	December 2005
Simonin, P. W. 2010. Distribution and abundance of native rainbow smelt and nonnative alewife in Lake Champlain. M.S. Thesis. University of Vermont, Burlington.	May 2010
Rosenblatt, E. 2022. Implications of population generics and physiological responses on the conservation of moose (Alces alces americana). Ph.D. Dissertation, University of Vermont, Burlington, VT USA	March 2022
Rinehart, K. 2015. Analytical and decision tools for wildlife population and habitat management. PhD Dissertation. University of Vermont, Burlington, VT USA.	January 2015
Puchala, E.A. 2015. The status of Stonecats (Noturus flavus) in the LaPlatte and Missisquoi rivers, Vermont. M.S. Thesis. University of Vermont, Burlington.	June 2015
Perlut, N. 2007. Effects of hayfield management on grassland songbirds: behavioral responses and population processes. Ph.D. Dissertation, University of Vermont, Burlington, VT.	May 2007
Pearman-Gillman, S. 2020. Predicting wildlife distributions and resilience under alternative futures. PhD Dissertation, University of Vermont, Burlington, VT USA.	May 2020
Long, R. 2006. Developing predictive occurrence models for carnivores in Vermont using data collected with multiple non-invasive methods. Ph.D. Dissertation, University of Vermont, Burlington, VT.	May 2006
Katz, J. E. 2015. monitoR: Automation tools for landscape-scale acoustic monitoring. PhD Dissertation. University of Vermont, Burlington, VT USA.	May 2015
Izzo, L. 2021. Movements, habitat use, and abundance of a remnant population of Lake Sturgeon (Acipenser fulvescens) from the Winooski River, Vermont. PhD Dissertation, University of Vermont, Burlington, VT, USA.	May 2021
Freeman, Mark. 2010. Bobcat (Lynx rufus) habitat and home range analysis for Northwester and Central Vermont. MS Thesis, University of Vermont, Burlington, VT.	January 2010
Duerr, A. 2007. Population dynamics, foraging ecology, and optimal management of Double-crested Cormorants of Lake Champlain. Ph.D. Dissertation, University of Vermont, Burlington, VT.	May 2007
DeBow, J. 2020. Effects of winter ticks and internal parasites on moose survival and fecundity in Vermont, USA. MS Thesis. University of Vermont, Burlington, VT USA.	May 2020
Cummings, J. W. 2014. Decision support for natural resource management. Ph.D. Dissertation, University of Vermont, Burlington, VT USA.	August 2014
Cornell, K. L. 2007. Scale-dependent mechanisms of habitat selection and demography for a forest songbird in a heterogeneous landscape. Ph.D. Dissertation. University of Vermont, Burlington, VT.	May 2007
Chellman, I.C. 2011. Population demographics and genetic diversity of mudpuppies (Necturus maculosus) in Vermont. M.S. Thesis, University of Vermont, Burlington.	January 2011
Butryn, R. 2010. Summer stream temperature as an indicator of coldwater fish distribution. Master's Thesis, University of Vermont, Burlington.	May 2010
Brown, Michelle L. 2012. Predicting impacts of future human population growth and development on forest-dependent birds. MS Thesis, University of Vermont, Burlington Vermont.	June 2012
Brown, M. L. 2023. Forest management tradeoffs: Examining relationships between timber harvest, carbon sequestration and storage, bioenergy, and wildlife. Ph.D. Dissertation, University of Vermont, Burlington, VT, USA.	February 2023
Brauer, Corinne L. 2012. A comparison of acoustic monitoring methods for common anurans of the northeastern United States. MS Thesis, University of Vermont, Burlington VT USA.	June 2012
Bonter, D. N. 2003. Migration and ecology of landbirds during migration in the Great Lakes Basin. Ph.D. Dissertation, University of Vermont, Burlington, VT.	October 2003
Blouin, J. 2021. Assessing moose habitat suitability and fitness consequences of habitat selection during two critical winter tick life stages in Vermont, USA. MS Thesis, University of Vermont, Burlington, VT.	May 2021
Bettigole, Charles A. 2012. Normative standards for land use in Vermont: The effects of social norms on wildlife occupancy . MS Thesis, University of Vermont, Burlington VT USA.	June 2012
Balantic, C. 2018. Tools for landscape-scale automated acoustic monitoring to characterize wildlife occurrence dynamics. PhD Dissertation. University of Vermont, Burlington, VT USA.	February 2018
Abouelezz, Hanem. 2009. Quantifying Bobcat (Lynx rufus) Movement Patterns and Habitat Selection in Northwestern Vermont. MS Thesis, University of Vermont, Burlington, VT.	October 2009

Technical Publications

Technical Publications	Publication Date
Winter, M., D. H. Johnson, J. A. Dechant, T. M. Donovan, and W. D. Svedarsky. 2001. Evaluation of the bird conservation area concept in the northern tallgrass prairie. Annual report. U.S.G.S.	December 2001
Tierney, G., B. Mitchell, A. Miller-Rushing, J. Katz, E. Denny, C. Brauer, T. Donovan, A. Richardson, M. Toomey, A. Kozlowski, J. Weltzin, K. Gerst, E. Sharron, O. Sonnentag, F. Dieffenbach . 2013. Phenology monitoring protocol: Northeast Temperate Network. Natural Resource Report. NPS/NETN/NRR—2013/681. National Park Service. Fort Collins, Colorado. Published Report-2197242.	July 2013
Parrish, D.L., L.G. Rudstam, P.J. Sullivan, S.L. Parker, and J.L. Stritzel. 2004. Dynamics of the rainbow smelt populations in Lake Champlain. Final Report. Lake Champlain Sea Grant.	June 2004
Parrish, D. L., M. E. Mather, and E. A. Marschall. 2009. Population modeling of Atlantic salmon in Vermont tributaries of the Connecticut River. Progress report to NMFS	August 2009
Parrish, D. L., M. E. Mather, and E. A. Marschall. 2008. Population modeling of Atlantic salmon in Vermont tributaries of the Connecticut River. Progress report to NMFS	August 2008
Omland, K.S., and D.L. Parrish. 2007. Population modeling for Batten Kill trout. Final Report. U.S. Forest Service, Green Mountain National Forest, Rutland, VT.	May 2007
Olsen, J.R., and D.L. Parrish. 2002. Effects of spring warming on bioenergetics of juvenile Atlantic salmon. Final Report. National Marine Fisheries Service, NOAA Grant No. NA96FI0255.	June 2002
Olsen, J.R., and D.L. Parrish. 2001. Bioenergetics of age-1 Atlantic salmon in Vermont tributaries. Final Report. National Marine Fisheries Service, NOAA Grant No. NA96FA0256.	September 2001
Olsen, J. R., and D. L. Parrish. 2000. Effects of food on growth rates of age-1 and older Atlantic salmon in Vermont streams. Final Report. National Marine Fisheries Service, NOAA Grant No: NA86FI0388.	January 2000
Olsen, J. R., and D. L. Parrish. 2000. Bioenergetics of age-1 Atlantic salmon in Vermont tributaries. Final Report. National Marine Fisheries Service, NOAA Grant No. NA96FA0256.	January 2000
Hitchcock, D.J., and D.L. Parrish. 2005. Using radio-tagged sea lampreys to investigate potential alternative control methods. Final Report. The Nature Conservancy, West Haven, VT.	April 2005
Frater, B., and D.L. Parrish. 2001. Relating juvenile walleye distributions to the sportfishery of Lake Champlain. Final Report Research Work Order #26. U.S. Geological Survey and Vermont Department of Fish and Wildlife.	February 2001
Donovan, T.M., and K. Watrous. Habitat requirements of the Indiana Bat (Myotis Sodalis) in the Champlain Valley, VT and NY. Final Report. Research Work Order 31. U.S. Geological Survey and U.S. Fish and Wildlife Service.	December 2006
Donovan, T.M., K. Rinehart, and J. Cummings. 2014. Improving Structured Decision Making Processes through Relational Database Development and Analysis. Final Report to the U.S. Geological Survey.	March 2014
Donovan, T.M., J. Katz, C. Brauer, and B. Mitchell. 2014. Acoustical Monitoring of Biodiversity and Phenology: A Pilot Wildlife Monitoring Partnership for Adaptive Management. Final Report to the National Park Service.	September 2014
Donovan, T., and J. Hines. 2007. Exercises in occupancy modeling and estimation. Electronic book.	September 2007
Donovan, T. M., and K. Cornell. 2007. Relationships between forest bird abundance and nesting productivity in Vermont. Final Report. Vermont Fish and Wildlife Department.	July 2007
Donovan, T. M., and A. Duerr. 2007. Influence of egg oiling on the metapopulation dynamics of double-crested cormorants. Final Report. Vermont Fish and Wildlife Department.	July 2007
Donovan, T. M., W. S. Schwenk, and W. Keeton. 2011. The influence of forest attributes on indicators of biodiversity: Establishing guidelines for sustainable forest management. Final Report for the Northeastern States Research Cooperative.	January 2011
Donovan, T. M., C. Brauer, J. Katz, and B. Mitchell. 2013. A pilot test for monitoring phenology with acoustic sensors. Final Report to the National Phenology Network.	December 2013
Donovan, T. M. 2008. How much forest is enough? Effects of forest amount and arrangement on forest bird population viability. McIntire Stennis Final Report.	September 2008
Donovan, T. M. 2006. Identifying the effects of scale on population dynamics in birds: An individually-based approach. Final Report. National Science Foundation Grant No. 0344369.	December 2006
Donovan, T. M. 200 Towards a theory of landscape effects on population dynamics in birds. Final Report. The National Science Foundation Grant No. 0108875.	December 2005
Donovan, T. 2006. Effects of habitat fragmentation on bird species richness in the continental U.S. Final Report Research Work Order 32. NASA.	June 2007
Chellman, I.C., and D.L. Parrish. 2010. Developing methods for sampling mudpuppies in Vermont tributaries of Lake Champlain. Final Report. State Wildlife Grants Program, Vermont Fish and Wildlife, Waterbury.	July 2010
Bonter, D. N., and T. M. Donovan. 2003. An Inventory of Migration Stopover Concentration Areas in the Northeastern United States: Remote Sensing with WSR-88D (NEXRAD) Radar. A final report to the USFWS.	September 2003
Bonter, D. N., and T. M. Donovan. 2002. Near-shore habitat priorities for migratory songbirds (GL99072). Final report to the U.S. Environmental Protection Agency, Great Lakes National Program Office	October 2002
Bonter, D. N., and T. M. Donovan. 2002. Migratory landbird stopover concentration areas in the Great Lakes Basin. Final report to the Nature Conservancy.	July 2002

Data or Software Releases

Type	Citation	Publication Date
Software Release	McKay, S.D., Rosenblatt, E., Donovan, T.M., Gieder, K., Murdoch, J., Smith, T.P.L., Heaton, M.P., Kalbfleisch, T.S., Murdoch, B.M., Bhattarai, S., Pacht, E., Verbist, E., and Basnayake, V., 2023, Population Structure and Genetic Diversity of Eastern North American Moose: U.S. Geological Survey data release, https://doi.org/10.5066/P9B30K2L	September 2022
Data Release	Donovan, T., J. E. Hines, and D. MacKenzie. 2023. occupancyTuts: Tutorials for occupancy modeling with RPresence. Version 1.1.0: U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P9KJ84U5	February 2023
Data Release	Clarfeld, L., Tang, C., and Donovan, T. shinymgr: A framework for building, managing, and stitching shiny modules into reproducible workflows. Version 1.0.0: U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P9UXPOBN	August 2023
Data Release	Clarfeld, L., Tang, C., and Donovan, T. shinymgr: A framework for building, managing, and stitching shiny modules into reproducible workflows. Version 1.0.0: U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P9UXPOBN	April 2024
Software Release	Clarfeld, L., Donovan, T., Siren, A., Mulhall, B., Bernier, E., Farrell, J., Lunde, G., Hardy, N., Abrams, R., Staats, S., and McLellan, S., 2023, Evaluating a tandem human-machine approach to labelling of wildlife in remote camera monitoring: U.S. Geological Survey data release, https://doi.org/10.5066/P9FGUQEZ.	August 2023
Software Release	Balantic, C., and Donovan, T. AMMonitor: Remote monitoring of biodiversity in an adaptive framework. Version 1.0.0: U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P9669095	August 2022

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

Vermont Research Activities

Links

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

Vermont Research Activities

Links

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