Quantitative and Other Methods
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By Forest and Rangeland Ecosystem Science Center
August 22, 2019
Applying quantitative methods to evaluate ecological hypotheses for wild animal populations is inherently challenging due to the complexity of ecological systems and the sampling process that is used to monitor them.
Amphibians can be especially difficult to monitor because they are often cryptic and use different habitats seasonally. Our lab uses occupancy, capture-recapture, and related analyses (using both frequentist and Bayesian approaches) to correct monitoring data for the sampling process (i.e., imperfect detection, sampling designs, etc.) and provide unbiased estimates of system dynamics. Part of this work involves publishing technical reports and peer-reviewed articles on the development and evaluation of new methods accommodating different sources of uncertainty. Examples of field methods used by our lab include environmental DNA (eDNA) sampling, capture-mark-recapture, radio telemetry, skin swabbing for disease and microbiome, water and sediment sampling, and tissue sampling for genetic analyses. We also provide decision support to identify and address the needs of diverse stakeholder groups and wildlife using a structured process.
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If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Filter Total Items: 19
Estimation of metademographic rates and landscape connectivity for a conservation-reliant anuran
ContextAmphibian conservation efforts commonly assume populations are tied to waterbodies that collectively function as a metapopulation. This assumption is rarely evaluated, and there is a need to understand the degree of connectivity among patches to appropriately define, manage, and conserve biological populations.ObjectivesOur objectives were to quantify local persistence, colonization, and re
Authors
Adam Duarte, James Peterson, Christopher Pearl, Jennifer Christine Rowe, Brome McCreary, Stephanie Galvan, Michael J. Adams
Effect of amphibian chytrid fungus (Batrachochytrium dendrobatidis) on apparent survival of frogs and toads in the western USA
Despite increasing interest in determining the population-level effects of emerging infectious diseases on wildlife, estimating effects of disease on survival rates remains difficult. Even for a well-studied disease such as amphibian chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis [Bd]), there are few estimates of how survival of wild hosts is affected. We applied hierarchica
Authors
Robin E. Russell, Brian J. Halstead, Brittany Mosher, Erin L. Muths, Michael J. Adams, Evan H. Campbell Grant, Robert N. Fisher, Patrick M. Kleeman, Adam R. Backlin, Christopher Pearl, R. Ken Honeycutt, Blake R. Hossack
Quantifying climate sensitivity and climate-driven change in North American amphibian communities
Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 8
Authors
David A.W. Miller, Evan H. Campbell Grant, Erin L. Muths, Staci M. Amburgey, M. J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T.J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A.G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers, Thomas A. Gorman, Carola A. Haas, Ward Hughson, David S. Pilliod, Steven J. Price, Andrew M. Ray, Walter Sadinski, Daniel Saenz, William J. Barichivich, Adrianne B. Brand, Cheryl S. Brehme, Rosi Dagit, Katy S. Delaney, Brad M. Glorioso, Lee B. Kats, Patrick M. Kleeman, Christopher Pearl, Carlton J. Rochester, Seth P. D. Riley, Mark F. Roth, Brent Sigafus
By
Ecosystems Mission Area, Water Resources Mission Area, Species Management Research Program, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, John Wesley Powell Center for Analysis and Synthesis, Northern Rocky Mountain Science Center, South Atlantic Water Science Center (SAWSC), Southwest Biological Science Center, Upper Midwest Environmental Sciences Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center
Fitting N-mixture models to count data with unmodeled heterogeneity: Bias, diagnostics, and alternative approaches
Monitoring animal populations is central to wildlife and fisheries management, and the use of N-mixture models toward these efforts has markedly increased in recent years. Nevertheless, relatively little work has evaluated estimator performance when basic assumptions are violated. Moreover, diagnostics to identify when bias in parameter estimates from N-mixture models is likely is largely unexplor
Authors
Adam Duarte, M. J. Adams, James Peterson
A new parameterization for integrated population models to document amphibian reintroductions
Managers are increasingly implementing reintroduction programs as part of a global effort to alleviate amphibian declines. Given uncertainty in factors affecting populations and a need to make recurring decisions to achieve objectives, adaptive management is a useful component of these efforts. A major impediment to the estimation of demographic rates often used to parameterize and refine decision
Authors
Adam Duarte, Christopher Pearl, M. J. Adams, James Peterson
Quantitative evidence for the effects of multiple drivers on continental-scale amphibian declines
Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early search for a “smoking gun” was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extin
Authors
Evan H. Campbell Grant, David A. W. Miller, Benedikt R. Schmidt, M. J. Adams, Staci M. Amburgey, Thierry A. Chambert, Sam S. Cruickshank, Robert N. Fisher, David M. Green, Blake R. Hossack, Pieter T.J. Johnson, Maxwell B. Joseph, Tracy A. G. Rittenhouse, Maureen E. Ryan, J. Hardin Waddle, Susan C. Walls, Larissa L. Bailey, Gary M. Fellers, Thomas A. Gorman, Andrew M. Ray, David S. Pilliod, Steven J. Price, Daniel Saenz, Walt Sadinski, Erin L. Muths
Spatial variation in risk and consequence of Batrachochytrium salamandrivorans introduction in the USA
A newly identified fungal pathogen, Batrachochytrium salamandrivorans (Bsal), is responsible for mass mortality events and severe population declines in European salamanders. The eastern USA has the highest diversity of salamanders in the world and the introduction of this pathogen is likely to be devastating. Although data are inevitably limited for new pathogens, disease-risk assessments use bes
Authors
Katherine L. D. Richgels, Robin E. Russell, M. J. Adams, C. LeAnn White, Evan H. Campbell Grant
Salamander chytrid fungus (Batrachochytrium salamandrivorans) in the United States—Developing research, monitoring, and management strategies
The recently (2013) identified pathogenic chytrid fungus, Batrachochytrium salamandrivorans (Bsal), poses a severe threat to the distribution and abundance of salamanders within the United States and Europe. Development of a response strategy for the potential, and likely, invasion of Bsal into the United States is crucial to protect global salamander biodiversity. A formal working group, led by A
Authors
Evan H. Campbell Grant, Erin L. Muths, Rachel A. Katz, Stefano Canessa, M. J. Adams, Jennifer R. Ballard, Lee Berger, Cheryl J. Briggs, Jeremy T. H. Coleman, Matthew J. Gray, M. Camille Harris, Reid N. Harris, Blake R. Hossack, Kathryn P. Huyvaert, Jonathan E. Kolby, Karen R. Lips, Robert E. Lovich, Hamish I. McCallum, Joseph R. Mendelson, Priya Nanjappa, Deanna H. Olson, Jenny G. Powers, Katherine L. D. Richgels, Robin E. Russell, Benedikt R. Schmidt, Annemarieke Spitzen-van der Sluijs, Mary Kay Watry, Douglas C. Woodhams, C. LeAnn White
Using occupancy models to accommodate uncertainty in the interpretation of aerial photograph data: status of beaver in Central Oregon, USA
Beavers (Castor canadensis) influence habitat for many species and pose challenges in developed landscapes. They are increasingly viewed as a cost-efficient means of riparian habitat restoration and water storage. Still, information on their status is rare, particularly in western North America. We used aerial photography to evaluate changes in beaver occupancy between 1942–1968 and 2009 in upper
Authors
Christopher A. Pearl, M. J. Adams, Patricia K. Haggerty, Leslie Urban
Amphibians in the climate vise: loss and restoration of resilience of montane wetland ecosystems in the western US
Wetlands in the remote mountains of the western US have undergone two massive ecological “experiments” spanning the 20th century. Beginning in the late 1800s and expanding after World War II, fish and wildlife managers intentionally introduced millions of predatory trout (primarily Oncorhynchus spp) into fishless mountain ponds and lakes across the western states. These new top predators, which no
Authors
Maureen E. Ryan, Wendy J. Palen, M. J. Adams, Regina M. Rochefort
Trends in amphibian occupancy in the United States
Though a third of amphibian species worldwide are thought to be imperiled, existing assessments simply categorize extinction risk, providing little information on the rate of population losses. We conducted the first analysis of the rate of change in the probability that amphibians occupy ponds and other comparable habitat features across the United States. We found that overall occupancy by amphi
Authors
M. J. Adams, David A.W. Miller, Erin Muths, Paul Stephen Corn, Evan H. Campbell Grant, Larissa L. Bailey, Gary M. Fellers, Robert N. Fisher, Walter J. Sadinski, Hardin Waddle, Susan C. Walls
Using multilevel spatial models to understand salamander site occupancy patterns after wildfire
Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of va
Authors
Nathan Chelgren, M. J. Adams, Larissa L. Bailey, R. Bruce Bury
Applying quantitative methods to evaluate ecological hypotheses for wild animal populations is inherently challenging due to the complexity of ecological systems and the sampling process that is used to monitor them.
Amphibians can be especially difficult to monitor because they are often cryptic and use different habitats seasonally. Our lab uses occupancy, capture-recapture, and related analyses (using both frequentist and Bayesian approaches) to correct monitoring data for the sampling process (i.e., imperfect detection, sampling designs, etc.) and provide unbiased estimates of system dynamics. Part of this work involves publishing technical reports and peer-reviewed articles on the development and evaluation of new methods accommodating different sources of uncertainty. Examples of field methods used by our lab include environmental DNA (eDNA) sampling, capture-mark-recapture, radio telemetry, skin swabbing for disease and microbiome, water and sediment sampling, and tissue sampling for genetic analyses. We also provide decision support to identify and address the needs of diverse stakeholder groups and wildlife using a structured process.
Sources/Usage: Some content may have restrictions. View Media Details
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Filter Total Items: 19
Estimation of metademographic rates and landscape connectivity for a conservation-reliant anuran
ContextAmphibian conservation efforts commonly assume populations are tied to waterbodies that collectively function as a metapopulation. This assumption is rarely evaluated, and there is a need to understand the degree of connectivity among patches to appropriately define, manage, and conserve biological populations.ObjectivesOur objectives were to quantify local persistence, colonization, and re
Authors
Adam Duarte, James Peterson, Christopher Pearl, Jennifer Christine Rowe, Brome McCreary, Stephanie Galvan, Michael J. Adams
Effect of amphibian chytrid fungus (Batrachochytrium dendrobatidis) on apparent survival of frogs and toads in the western USA
Despite increasing interest in determining the population-level effects of emerging infectious diseases on wildlife, estimating effects of disease on survival rates remains difficult. Even for a well-studied disease such as amphibian chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis [Bd]), there are few estimates of how survival of wild hosts is affected. We applied hierarchica
Authors
Robin E. Russell, Brian J. Halstead, Brittany Mosher, Erin L. Muths, Michael J. Adams, Evan H. Campbell Grant, Robert N. Fisher, Patrick M. Kleeman, Adam R. Backlin, Christopher Pearl, R. Ken Honeycutt, Blake R. Hossack
Quantifying climate sensitivity and climate-driven change in North American amphibian communities
Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 8
Authors
David A.W. Miller, Evan H. Campbell Grant, Erin L. Muths, Staci M. Amburgey, M. J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T.J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A.G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers, Thomas A. Gorman, Carola A. Haas, Ward Hughson, David S. Pilliod, Steven J. Price, Andrew M. Ray, Walter Sadinski, Daniel Saenz, William J. Barichivich, Adrianne B. Brand, Cheryl S. Brehme, Rosi Dagit, Katy S. Delaney, Brad M. Glorioso, Lee B. Kats, Patrick M. Kleeman, Christopher Pearl, Carlton J. Rochester, Seth P. D. Riley, Mark F. Roth, Brent Sigafus
By
Ecosystems Mission Area, Water Resources Mission Area, Species Management Research Program, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, John Wesley Powell Center for Analysis and Synthesis, Northern Rocky Mountain Science Center, South Atlantic Water Science Center (SAWSC), Southwest Biological Science Center, Upper Midwest Environmental Sciences Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center
Fitting N-mixture models to count data with unmodeled heterogeneity: Bias, diagnostics, and alternative approaches
Monitoring animal populations is central to wildlife and fisheries management, and the use of N-mixture models toward these efforts has markedly increased in recent years. Nevertheless, relatively little work has evaluated estimator performance when basic assumptions are violated. Moreover, diagnostics to identify when bias in parameter estimates from N-mixture models is likely is largely unexplor
Authors
Adam Duarte, M. J. Adams, James Peterson
A new parameterization for integrated population models to document amphibian reintroductions
Managers are increasingly implementing reintroduction programs as part of a global effort to alleviate amphibian declines. Given uncertainty in factors affecting populations and a need to make recurring decisions to achieve objectives, adaptive management is a useful component of these efforts. A major impediment to the estimation of demographic rates often used to parameterize and refine decision
Authors
Adam Duarte, Christopher Pearl, M. J. Adams, James Peterson
Quantitative evidence for the effects of multiple drivers on continental-scale amphibian declines
Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early search for a “smoking gun” was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extin
Authors
Evan H. Campbell Grant, David A. W. Miller, Benedikt R. Schmidt, M. J. Adams, Staci M. Amburgey, Thierry A. Chambert, Sam S. Cruickshank, Robert N. Fisher, David M. Green, Blake R. Hossack, Pieter T.J. Johnson, Maxwell B. Joseph, Tracy A. G. Rittenhouse, Maureen E. Ryan, J. Hardin Waddle, Susan C. Walls, Larissa L. Bailey, Gary M. Fellers, Thomas A. Gorman, Andrew M. Ray, David S. Pilliod, Steven J. Price, Daniel Saenz, Walt Sadinski, Erin L. Muths
Spatial variation in risk and consequence of Batrachochytrium salamandrivorans introduction in the USA
A newly identified fungal pathogen, Batrachochytrium salamandrivorans (Bsal), is responsible for mass mortality events and severe population declines in European salamanders. The eastern USA has the highest diversity of salamanders in the world and the introduction of this pathogen is likely to be devastating. Although data are inevitably limited for new pathogens, disease-risk assessments use bes
Authors
Katherine L. D. Richgels, Robin E. Russell, M. J. Adams, C. LeAnn White, Evan H. Campbell Grant
Salamander chytrid fungus (Batrachochytrium salamandrivorans) in the United States—Developing research, monitoring, and management strategies
The recently (2013) identified pathogenic chytrid fungus, Batrachochytrium salamandrivorans (Bsal), poses a severe threat to the distribution and abundance of salamanders within the United States and Europe. Development of a response strategy for the potential, and likely, invasion of Bsal into the United States is crucial to protect global salamander biodiversity. A formal working group, led by A
Authors
Evan H. Campbell Grant, Erin L. Muths, Rachel A. Katz, Stefano Canessa, M. J. Adams, Jennifer R. Ballard, Lee Berger, Cheryl J. Briggs, Jeremy T. H. Coleman, Matthew J. Gray, M. Camille Harris, Reid N. Harris, Blake R. Hossack, Kathryn P. Huyvaert, Jonathan E. Kolby, Karen R. Lips, Robert E. Lovich, Hamish I. McCallum, Joseph R. Mendelson, Priya Nanjappa, Deanna H. Olson, Jenny G. Powers, Katherine L. D. Richgels, Robin E. Russell, Benedikt R. Schmidt, Annemarieke Spitzen-van der Sluijs, Mary Kay Watry, Douglas C. Woodhams, C. LeAnn White
Using occupancy models to accommodate uncertainty in the interpretation of aerial photograph data: status of beaver in Central Oregon, USA
Beavers (Castor canadensis) influence habitat for many species and pose challenges in developed landscapes. They are increasingly viewed as a cost-efficient means of riparian habitat restoration and water storage. Still, information on their status is rare, particularly in western North America. We used aerial photography to evaluate changes in beaver occupancy between 1942–1968 and 2009 in upper
Authors
Christopher A. Pearl, M. J. Adams, Patricia K. Haggerty, Leslie Urban
Amphibians in the climate vise: loss and restoration of resilience of montane wetland ecosystems in the western US
Wetlands in the remote mountains of the western US have undergone two massive ecological “experiments” spanning the 20th century. Beginning in the late 1800s and expanding after World War II, fish and wildlife managers intentionally introduced millions of predatory trout (primarily Oncorhynchus spp) into fishless mountain ponds and lakes across the western states. These new top predators, which no
Authors
Maureen E. Ryan, Wendy J. Palen, M. J. Adams, Regina M. Rochefort
Trends in amphibian occupancy in the United States
Though a third of amphibian species worldwide are thought to be imperiled, existing assessments simply categorize extinction risk, providing little information on the rate of population losses. We conducted the first analysis of the rate of change in the probability that amphibians occupy ponds and other comparable habitat features across the United States. We found that overall occupancy by amphi
Authors
M. J. Adams, David A.W. Miller, Erin Muths, Paul Stephen Corn, Evan H. Campbell Grant, Larissa L. Bailey, Gary M. Fellers, Robert N. Fisher, Walter J. Sadinski, Hardin Waddle, Susan C. Walls
Using multilevel spatial models to understand salamander site occupancy patterns after wildfire
Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of va
Authors
Nathan Chelgren, M. J. Adams, Larissa L. Bailey, R. Bruce Bury