Ambystoma californiense - California Tiger Salamander is a A dark brown salamander with yellow spots.
Patrick M Kleeman
Patrick Kleeman is a Supervisory Ecologist at the Western Ecological Research Center.
Patrick Kleeman's research focuses on the ecology and conservation biology of amphibians. Topics of study within these categories include population demography through capture-mark-recapture methods, habitat use by using radiotelemetry, and phenology of breeding as evidenced by vocalizations. His research also examines what role stressors such as environmental contaminants, disease, and climate may have on amphibian populations. In addition to amphibians, he also works with island night lizards (Xantusia riversiana) on San Nicolas Island and Townsend's big-eared bats (Corynorhinus townsendii) at Point Reyes National Seashore.
EDUCATION
- B.A. in Biology, University of Colorado, Boulder, 1988
- M.S. in Wildlife Management, Humboldt State University, 1999
Science and Products
Filter Total Items: 24
Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA
These data were collected to assess the occurrence of foothill yellow-legged frogs (Rana boylii) in 2022, one year after the 2021 Dixie Fire in northeastern California, USA. The data included herein are those required to replicate the occupancy analysis presented in the manuscript, cited in the larger work. Additional site data are included in the manuscript itself.
Captures and Trapping Effort for Deer Mice (Peromyscus sonoriensis) at Point Reyes National Seashore, California, USA from 2021 to 2022
These data represent trapping effort and captures of deer mice at Point Reyes National Seashore, Marin County, California. Deer mice were captured and marked with ear tags to allow identification of individuals. The location of captures can be used in a spatially explicit capture recapture model to estimate density of mice and how mouse density varies by site and habitat type.
Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
Mercury concentrations in amphibian tissues across the United States, 2016-2021
Comma-separated values (.csv) file containing data related to amphibian sampling across the United States between 2016 and 2021. Data files contain mercury concentrations in amphibian and dragonfly tissues, mercury concentrations in sediment, as well as amphibian morphometrics, and habitat and climate characteristics where the samples were collected.
Western Pond Turtle (Emys [Actinemys] marmorata) Observations at Point Reyes National Seashore and Golden Gate National Recreation Area
These data represent incidental observations of western pond turtles (Emys [Actinemys] marmorata) collected by the U.S. Geological Survey, Western Ecological Research Center, at Point Reyes National Seashore and Golden Gate National Recreation Area between 1993 and 2014. These data do not have associated survey effort, and are intended to represent incidental observations, rather than a random, sy
Multi-State Occurrence Data and Predictors for Amphibians in Yosemite National Park (2007-2021)
These data include field-collected observations of the occurrence of adult and larval amphibians at 174 sites in 14 watersheds at Yosemite National Park from 2007 through 2021. Also included in the data are potential variables affecting site occurrence, probability of reproduction, and probability of detection of amphibians, including static site-specific variables like site size and elevation, an
USGS Occupancy Surveys for Dixie Valley Toads, Anaxyrus williamsi, in Churchill County, Nevada from April 2018 to May 2021
Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. The Dixie Valley Toad (Anaxyrus williamsi) is a recently described anuran species endemic to desert spring wetlands in the Dixie Valley, Churchill County, Nevada, USA. Given this species was only recently recognized as distinct from Anaxyrus boreas, little is
Temperature and Relative Conductivity at Sampling Locations in the Dixie Valley, Churchill County, Nevada, 2019-2021
These data provide temperatures and relative conductivity to determine the presence or absence of water at specific locations in Dixie Meadows, Dixie Valley, Churchill County, Nevada, 2019-2021.
Concentrations of pesticides in silicone bands as passive samplers and sediment in Pinnacles National Park and Bureau of Land Management lands in San Benito County, California, 2019-2021
To better understand the potential pesticide exposure, samples were collected from locations along two creeks in Pinnacles National Park and four creeks in nearby Bureau of Land Management (BLM) lands. Silicone bands were used as passive sampling devices (PSD) staked in the creek and above in the air (above the water line). Sampling was conducted in the summer from 2019 to 2021. PSDs were deployed
Western Spadefoot Survey Data in Northern and Central California (2019)
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas la
Amphibian chytrid swab data from Mendocino County, California (2016 - 2020)
This dataset includes results from external skin swabbing of Rana boylii and Dicamptodon tenebrosus to test for the fungus Batrachochytrium dendrobatidis from Fox Creek in Mendocino County, California, in 2016-2020. Morphological measurements of swabbed animals were recorded, and Rana boylii had a unique identifier (pit tag) inserted beneath their skin for identification in future capture events.
Northwestern Pond Turtle Survey Data in Northern California Forest Streams (2021)
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander is a A dark brown salamander with yellow spots.
Pacific Chorus Frog
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Point Reyes National Seashore.
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Point Reyes National Seashore.
Pacific Chorus Frog
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Lassen Volcanic National Park.
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Lassen Volcanic National Park.
Filter Total Items: 40
From eDNA to decisions using a multi-method approach to restoration planning in streams
Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted
Authors
Andrea J. Adams, C. Kamoroff, Daniel R. Norton, R. L. Grasso, Brian J. Halstead, Patrick M. Kleeman, C. Mengelt, K. Powelson, T. Seaborn, C.S. Goldberg
Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California
Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles (Actinemys marmorata) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand the distrib
Authors
Brian J. Halstead, Patrick M. Kleeman, Caren S. Goldberg, Jonathan P. Rose
Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog
Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd
Authors
A.M. Belasen, R.A. Peek, A.J. Adams, I.D. Russell, M.E. De León, Michael J. Adams, J. Bettaso, K.G.H. Breedveld, A. Catenazzi, C.P. Dillingham, Daniel A. Grear, Brian J. Halstead, P.G. Johnson, Patrick M. Kleeman, M.S. Koo, C.W. Koppl, J.D. Lauder, G. Padgett-Flohr, J. Piovia-Scott, K.L. Pope, V. Vredenburg, M. Westphal, K. Wiseman, S.J. Kupferberg
Broad-scale assessment of methylmercury in adult amphibians
Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scal
Authors
Brian J. Tornabene, Blake R. Hossack, Brian J. Halstead, Collin A. Eagles-Smith, Michael J. Adams, Adam R. Backlin, Adrianne Brand, Colleen Emery, Robert N. Fisher, Jillian Elizabeth Fleming, Brad Glorioso, Daniel A. Grear, Evan H. Campbell Grant, Patrick M. Kleeman, David Miller, Erin L. Muths, Christopher Pearl, Jennifer Rowe, Caitlin Teresa Rumrill, J. Hardin Waddle, Megan Winzeler, Kelly L. Smalling
By
Ecosystems Mission Area, Water Resources Mission Area, Contaminant Biology, Toxic Substances Hydrology, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, National Wildlife Health Center, New Jersey Water Science Center, Northern Rocky Mountain Science Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center
Keeping the heat on: Weighted surveillance for Chytrid fungus (Batrachochytirum dendrobatidis) in Dixie Valley toads (Anaxyrus [= Bufo] williamsi)
Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecu
Authors
Matthew J. Forrest, Brian J. Halstead, Daniel A. Grear, Patrick M. Kleeman, Brian D. Todd, Oliver J. Miano, Kris D. Urquhart
Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century
Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with climate change.
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Gary M. Fellers
Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat.Aims: We sought to model the occupancy dynamics of the Dixie Valley toad (Anaxyrus
Authors
Jonathan P. Rose, Patrick M. Kleeman, Brian J. Halstead
Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting our knowle
Authors
Brian J. Halstead, Patrick M. Kleeman, Graziella Vittoria DiRenzo, Jonathan P. Rose
Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity
Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians
Authors
Beth A. Reinke, Hugo Cayuela, Fredric J. Janzen, Jean-François Lemaitre, Jean-Michel Gaillard, A. Michelle Lawing, John B. Iverson, Ditte G Christiansen, Iñigo Martínez-Solano, Gregorio Sánchez-Montes, Jorge Gutiérrez-Rodríguez, Francis L Rose, Nicola J. Nelson, Susan Keall, Alain J Crivelli, Theodoros Nazirides, Annegret Grimm-Seyfarth, Klaus Henle, Emiliano Mori, Gaëtan Guiller, Rebecca Homan, Anthony Olivier, Erin L. Muths, Blake R. Hossack, Xavier Bonnet, David Pilliod, Marieke Lettink, Tony Whitaker, Benedikt R. Schmidt, Michael G. Gardner, Marc Cheylan, Françoise Poitevin, Ana Golubović, Ljiljana Tomović, Dragan Arsovski, Richard A Griffiths, Jan W. Arntzen, Jean-Pierre Baron, Jean-François Le Galliard, Thomas Tully, Luca Luiselli, Massimo Capula, Lorenzo Rugiero, Rebecca McCaffery, Lisa A Eby, Briggs-Gonzalez; Venetia, Frank Mazzotti, David M. Pearson, Brad A. Lambert, David M. Green, Nathalie Jreidini, Claudio Angelini, Graham Pyke, Jean-Marc Thirion, Pierre Joly, Jean-Paul Léna, Tony Tucker, Col Limpus, Pauline Priol, Aurélien Besnard, Pauline Bernard, Kristin Stanford, Richard S. King, Justin M Garwood, Jaime Bosch, Franco Souza, Jaime Bertoluci, Shirley Famelli, Kurt Grossenbacher, Omar Lenzi, Kathleen Matthews, Sylvain Boitaud, Deanna H. Olson, Tim Jessop, Graeme Gillspie, Jean Clobert, Murielle Richard, Andrés Valenzuela-Sánchez, Gary M. Fellers, Patrick M. Kleeman, Brian J. Halstead, Evan H. Campbell Grant, Phillip G Byrne, Thierry Frétey, Gernard Le Garff, Pauline Levionnois, John C. Maerz, Julian Pichenot, Kurtulus Olgun, Nazan Üzüm, Aziz Avcı, Claude Miaud, Johan Elmberg, Gregory P Brown, Richard Shine, Nathan F Bendik, Lisa O'Donnell, Courtney L. Davis, Michael J Lannoo, Rochelle M Stiles, Robert M Cox, Aaron M Reedy, Daniel A. Warner, Eric Bonnaire, Kristine Grayson, Roberto Ramos-Targarona, Eyup Baskale, David J. Muñoz, John Measey, F. Andre de Villiers, Will Selman, Victor Ronget, Anne M. Bronikowski, David A W Miller
Multi-scale patterns in occurrence of an ephemeral pool-breeding amphibian
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas la
Authors
Brian J. Halstead, Jonathan P. Rose, Denise Clark, Patrick M. Kleeman, Robert N. Fisher
Conservation implications of spatiotemporal variation in the terrestrial ecology of Western spadefoots
Conservation of species reliant on ephemeral resources can be especially challenging in the face of a changing climate. Western spadefoots (Spea hammondii) are small burrowing anurans that breed in ephemeral pools, but adults spend the majority of their lives underground in adjacent terrestrial habitat. Western spadefoots are of conservation concern throughout their range because of habitat loss,
Authors
Brian J. Halstead, Katherine L. Baumberger, Adam R. Backlin, Patrick M. Kleeman, Monique Nicole Wong, Elizabeth Gallegos, Jonathan P. Rose, Robert N. Fisher
Metal accumulation varies with life history, size, and development of larval amphibians
Amphibian larvae are commonly used as indicators of aquatic ecosystem health because they are susceptible to contaminants. However, there is limited information on how species characteristics and trophic position influence contaminant loads in larval amphibians. Importantly, there remains a need to understand whether grazers (frogs and toads [anurans]) and predators (salamanders) provide comparabl
Authors
Kelly L. Smalling, Emily Bea Oja, Danielle M. Cleveland, Jon D Davenport, Collin A. Eagles-Smith, Evan H. Campbell Grant, Patrick M. Kleeman, Brian J. Halstead, Kenzi M Stemp, Brian J. Tornabene, Zachary J Bunnell, Blake R. Hossack
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii).
This repository specifically contains code to reproduce analyses in:
Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and Wildlife Ma
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California
The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys and samplin
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore
This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript:
Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park
The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variab
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021
-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model published by Duart
Science and Products
Filter Total Items: 24
Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA
These data were collected to assess the occurrence of foothill yellow-legged frogs (Rana boylii) in 2022, one year after the 2021 Dixie Fire in northeastern California, USA. The data included herein are those required to replicate the occupancy analysis presented in the manuscript, cited in the larger work. Additional site data are included in the manuscript itself.
Captures and Trapping Effort for Deer Mice (Peromyscus sonoriensis) at Point Reyes National Seashore, California, USA from 2021 to 2022
These data represent trapping effort and captures of deer mice at Point Reyes National Seashore, Marin County, California. Deer mice were captured and marked with ear tags to allow identification of individuals. The location of captures can be used in a spatially explicit capture recapture model to estimate density of mice and how mouse density varies by site and habitat type.
Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
Mercury concentrations in amphibian tissues across the United States, 2016-2021
Comma-separated values (.csv) file containing data related to amphibian sampling across the United States between 2016 and 2021. Data files contain mercury concentrations in amphibian and dragonfly tissues, mercury concentrations in sediment, as well as amphibian morphometrics, and habitat and climate characteristics where the samples were collected.
Western Pond Turtle (Emys [Actinemys] marmorata) Observations at Point Reyes National Seashore and Golden Gate National Recreation Area
These data represent incidental observations of western pond turtles (Emys [Actinemys] marmorata) collected by the U.S. Geological Survey, Western Ecological Research Center, at Point Reyes National Seashore and Golden Gate National Recreation Area between 1993 and 2014. These data do not have associated survey effort, and are intended to represent incidental observations, rather than a random, sy
Multi-State Occurrence Data and Predictors for Amphibians in Yosemite National Park (2007-2021)
These data include field-collected observations of the occurrence of adult and larval amphibians at 174 sites in 14 watersheds at Yosemite National Park from 2007 through 2021. Also included in the data are potential variables affecting site occurrence, probability of reproduction, and probability of detection of amphibians, including static site-specific variables like site size and elevation, an
USGS Occupancy Surveys for Dixie Valley Toads, Anaxyrus williamsi, in Churchill County, Nevada from April 2018 to May 2021
Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. The Dixie Valley Toad (Anaxyrus williamsi) is a recently described anuran species endemic to desert spring wetlands in the Dixie Valley, Churchill County, Nevada, USA. Given this species was only recently recognized as distinct from Anaxyrus boreas, little is
Temperature and Relative Conductivity at Sampling Locations in the Dixie Valley, Churchill County, Nevada, 2019-2021
These data provide temperatures and relative conductivity to determine the presence or absence of water at specific locations in Dixie Meadows, Dixie Valley, Churchill County, Nevada, 2019-2021.
Concentrations of pesticides in silicone bands as passive samplers and sediment in Pinnacles National Park and Bureau of Land Management lands in San Benito County, California, 2019-2021
To better understand the potential pesticide exposure, samples were collected from locations along two creeks in Pinnacles National Park and four creeks in nearby Bureau of Land Management (BLM) lands. Silicone bands were used as passive sampling devices (PSD) staked in the creek and above in the air (above the water line). Sampling was conducted in the summer from 2019 to 2021. PSDs were deployed
Western Spadefoot Survey Data in Northern and Central California (2019)
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas la
Amphibian chytrid swab data from Mendocino County, California (2016 - 2020)
This dataset includes results from external skin swabbing of Rana boylii and Dicamptodon tenebrosus to test for the fungus Batrachochytrium dendrobatidis from Fox Creek in Mendocino County, California, in 2016-2020. Morphological measurements of swabbed animals were recorded, and Rana boylii had a unique identifier (pit tag) inserted beneath their skin for identification in future capture events.
Northwestern Pond Turtle Survey Data in Northern California Forest Streams (2021)
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander is a A dark brown salamander with yellow spots.
Ambystoma californiense - California Tiger Salamander is a A dark brown salamander with yellow spots.
Pacific Chorus Frog
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Point Reyes National Seashore.
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Point Reyes National Seashore.
Pacific Chorus Frog
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Lassen Volcanic National Park.
A Pacific chorus frog (Pseudacris regilla) in a meadow located in Lassen Volcanic National Park.
Filter Total Items: 40
From eDNA to decisions using a multi-method approach to restoration planning in streams
Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted
Authors
Andrea J. Adams, C. Kamoroff, Daniel R. Norton, R. L. Grasso, Brian J. Halstead, Patrick M. Kleeman, C. Mengelt, K. Powelson, T. Seaborn, C.S. Goldberg
Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California
Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles (Actinemys marmorata) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand the distrib
Authors
Brian J. Halstead, Patrick M. Kleeman, Caren S. Goldberg, Jonathan P. Rose
Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog
Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd
Authors
A.M. Belasen, R.A. Peek, A.J. Adams, I.D. Russell, M.E. De León, Michael J. Adams, J. Bettaso, K.G.H. Breedveld, A. Catenazzi, C.P. Dillingham, Daniel A. Grear, Brian J. Halstead, P.G. Johnson, Patrick M. Kleeman, M.S. Koo, C.W. Koppl, J.D. Lauder, G. Padgett-Flohr, J. Piovia-Scott, K.L. Pope, V. Vredenburg, M. Westphal, K. Wiseman, S.J. Kupferberg
Broad-scale assessment of methylmercury in adult amphibians
Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scal
Authors
Brian J. Tornabene, Blake R. Hossack, Brian J. Halstead, Collin A. Eagles-Smith, Michael J. Adams, Adam R. Backlin, Adrianne Brand, Colleen Emery, Robert N. Fisher, Jillian Elizabeth Fleming, Brad Glorioso, Daniel A. Grear, Evan H. Campbell Grant, Patrick M. Kleeman, David Miller, Erin L. Muths, Christopher Pearl, Jennifer Rowe, Caitlin Teresa Rumrill, J. Hardin Waddle, Megan Winzeler, Kelly L. Smalling
By
Ecosystems Mission Area, Water Resources Mission Area, Contaminant Biology, Toxic Substances Hydrology, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, National Wildlife Health Center, New Jersey Water Science Center, Northern Rocky Mountain Science Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center
Keeping the heat on: Weighted surveillance for Chytrid fungus (Batrachochytirum dendrobatidis) in Dixie Valley toads (Anaxyrus [= Bufo] williamsi)
Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecu
Authors
Matthew J. Forrest, Brian J. Halstead, Daniel A. Grear, Patrick M. Kleeman, Brian D. Todd, Oliver J. Miano, Kris D. Urquhart
Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century
Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with climate change.
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Gary M. Fellers
Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat.Aims: We sought to model the occupancy dynamics of the Dixie Valley toad (Anaxyrus
Authors
Jonathan P. Rose, Patrick M. Kleeman, Brian J. Halstead
Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting our knowle
Authors
Brian J. Halstead, Patrick M. Kleeman, Graziella Vittoria DiRenzo, Jonathan P. Rose
Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity
Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians
Authors
Beth A. Reinke, Hugo Cayuela, Fredric J. Janzen, Jean-François Lemaitre, Jean-Michel Gaillard, A. Michelle Lawing, John B. Iverson, Ditte G Christiansen, Iñigo Martínez-Solano, Gregorio Sánchez-Montes, Jorge Gutiérrez-Rodríguez, Francis L Rose, Nicola J. Nelson, Susan Keall, Alain J Crivelli, Theodoros Nazirides, Annegret Grimm-Seyfarth, Klaus Henle, Emiliano Mori, Gaëtan Guiller, Rebecca Homan, Anthony Olivier, Erin L. Muths, Blake R. Hossack, Xavier Bonnet, David Pilliod, Marieke Lettink, Tony Whitaker, Benedikt R. Schmidt, Michael G. Gardner, Marc Cheylan, Françoise Poitevin, Ana Golubović, Ljiljana Tomović, Dragan Arsovski, Richard A Griffiths, Jan W. Arntzen, Jean-Pierre Baron, Jean-François Le Galliard, Thomas Tully, Luca Luiselli, Massimo Capula, Lorenzo Rugiero, Rebecca McCaffery, Lisa A Eby, Briggs-Gonzalez; Venetia, Frank Mazzotti, David M. Pearson, Brad A. Lambert, David M. Green, Nathalie Jreidini, Claudio Angelini, Graham Pyke, Jean-Marc Thirion, Pierre Joly, Jean-Paul Léna, Tony Tucker, Col Limpus, Pauline Priol, Aurélien Besnard, Pauline Bernard, Kristin Stanford, Richard S. King, Justin M Garwood, Jaime Bosch, Franco Souza, Jaime Bertoluci, Shirley Famelli, Kurt Grossenbacher, Omar Lenzi, Kathleen Matthews, Sylvain Boitaud, Deanna H. Olson, Tim Jessop, Graeme Gillspie, Jean Clobert, Murielle Richard, Andrés Valenzuela-Sánchez, Gary M. Fellers, Patrick M. Kleeman, Brian J. Halstead, Evan H. Campbell Grant, Phillip G Byrne, Thierry Frétey, Gernard Le Garff, Pauline Levionnois, John C. Maerz, Julian Pichenot, Kurtulus Olgun, Nazan Üzüm, Aziz Avcı, Claude Miaud, Johan Elmberg, Gregory P Brown, Richard Shine, Nathan F Bendik, Lisa O'Donnell, Courtney L. Davis, Michael J Lannoo, Rochelle M Stiles, Robert M Cox, Aaron M Reedy, Daniel A. Warner, Eric Bonnaire, Kristine Grayson, Roberto Ramos-Targarona, Eyup Baskale, David J. Muñoz, John Measey, F. Andre de Villiers, Will Selman, Victor Ronget, Anne M. Bronikowski, David A W Miller
Multi-scale patterns in occurrence of an ephemeral pool-breeding amphibian
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas la
Authors
Brian J. Halstead, Jonathan P. Rose, Denise Clark, Patrick M. Kleeman, Robert N. Fisher
Conservation implications of spatiotemporal variation in the terrestrial ecology of Western spadefoots
Conservation of species reliant on ephemeral resources can be especially challenging in the face of a changing climate. Western spadefoots (Spea hammondii) are small burrowing anurans that breed in ephemeral pools, but adults spend the majority of their lives underground in adjacent terrestrial habitat. Western spadefoots are of conservation concern throughout their range because of habitat loss,
Authors
Brian J. Halstead, Katherine L. Baumberger, Adam R. Backlin, Patrick M. Kleeman, Monique Nicole Wong, Elizabeth Gallegos, Jonathan P. Rose, Robert N. Fisher
Metal accumulation varies with life history, size, and development of larval amphibians
Amphibian larvae are commonly used as indicators of aquatic ecosystem health because they are susceptible to contaminants. However, there is limited information on how species characteristics and trophic position influence contaminant loads in larval amphibians. Importantly, there remains a need to understand whether grazers (frogs and toads [anurans]) and predators (salamanders) provide comparabl
Authors
Kelly L. Smalling, Emily Bea Oja, Danielle M. Cleveland, Jon D Davenport, Collin A. Eagles-Smith, Evan H. Campbell Grant, Patrick M. Kleeman, Brian J. Halstead, Kenzi M Stemp, Brian J. Tornabene, Zachary J Bunnell, Blake R. Hossack
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii).
This repository specifically contains code to reproduce analyses in:
Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and Wildlife Ma
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California
The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys and samplin
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore
This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript:
Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park
The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variab
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021
-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model published by Duart