Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger SalamanderAmbystoma 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: 30
Survey Data for Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in Siskiyou County, California, 2023-2024 Survey Data for Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in Siskiyou County, California, 2023-2024
These data contain information about the sites, visits, and transects surveyed for Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in Siskiyou County, California, 2023-2024. The survey sites were near locations of recent (since 2005) historical occurrence of the salamanders and were designed to separate occurrence, availability on the surface, and...
Stream Characteristics and Species Data for Foothill Yellow-legged Frogs in Southern San Benito and Western Fresno Counties, California, 2019-2021 Stream Characteristics and Species Data for Foothill Yellow-legged Frogs in Southern San Benito and Western Fresno Counties, California, 2019-2021
These data contain information on stream characteristics (intermittency and temperature), vegetation (canopy and algal cover), amphibian, reptile, and fish observations, and pathogen (amphibian chytrid fungus, Batrachochytrium dendrobatidis) prevalence, all of which are relevant for the suitability of streams in Pinnacles National Park for the reintroduction of foothill yellow-legged...
Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022 Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022
These data include capture and survey information for a meadow population of endangered Sierra Nevada yellow-legged frogs (Rana sierrae) at Yosemite National Park, California, USA, 2003-2022. The data also include remotely sensed weather covariates related to winter severity (annual April snow water equivalent) and drought severity (Palmer drought severity index) to evaluate their...
Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA 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 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.
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore 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)...
Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022 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 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 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...
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park 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...
Multi-State Occurrence Data and Predictors for Amphibians in Yosemite National Park (2007-2021) 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...
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021 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...
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger SalamanderAmbystoma 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: 44
Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations
Disease, alone or combined with other stressors such as habitat loss and contaminants, affects wildlife populations worldwide. However, interactions among stressors and how they affect demography and populations remain poorly understood. The amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) is a sometimes-lethal pathogen linked with population declines and extirpations of...
Authors
Morgan P. Kain, Blake R. Hossack, Kelly Smalling, Brian J. Halstead, Daniel Grear, David Miller, Michael Adams, Adam Backlin, William Barichivich, Collin A. Eagles-Smith, Colleen Emery, Jillian Fleming, Robert N. Fisher, Elizabeth Gallegos, Duoa J. Lor, Patrick Kleeman, Erin L. Muths, Ty Pan, Christopher Pearl, Charles W. Robinson, Caitlin Rumrill, Brian Tornabene, J. Hardin Waddle, Susan Walls, Evan Campbell Grant
Pan-amphibia distribution of the fungal parasite Batrachochytrium dendrobatidis varies with species and temperature Pan-amphibia distribution of the fungal parasite Batrachochytrium dendrobatidis varies with species and temperature
Batrachochytrium dendrobatidis (Bd) is a globally distributed fungal pathogen of amphibians that has contributed to one of the largest disease-related biodiversity losses in wildlife. Bd is regularly viewed through the lens of a global wildlife epizootic because the spread of highly virulent genetic lineages has resulted in well-documented declines and extinctions of multiple amphibian...
Authors
Daniel Grear, Michael Adams, Adam Backlin, William Barichivich, Adrianne Brand, Gary Bucciarelli, Daniel Calhoun, Tara Chestnut, Jon Davenport, Andrew E Dietrich, Graziella DiRenzo, Robert N. Fisher, Brad Glorioso, Evan Campbell Grant, Brian J. Halstead, Marc Hayes, Blake R. Hossack, Morgan Kain, Patrick Kleeman, Jeffrey M. Lorch, Brome McCreary, David A.W. Miller, Brittany A. Mosher, Erin L. Muths, Christopher Pearl, Charles H. Robinson, Mark Roth, Jennifer Rowe, Walter Sadinski, Brent H. Sigafus, Iga Stasiak, Samuel Sweet, Hardin Waddle, Susan Walls, Gregory Watkins-Colwell, Lori Williams, Megan Winzeler
Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence
Sierra Nevada ecosystems have been influenced by fire for millennia; however, increasing wildfire size and frequency may yield unforeseen consequences on wildlife populations and their distribution. Foothill yellow-legged frogs Rana boylii have declined in portions of their range and are considered a species of conservation concern. We surveyed streams for foothill yellow legged frogs in...
Authors
Brian J. Halstead, Patrick Kleeman, Jonathan Rose
Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA.
Non-native plants can affect communities through direct competition, and by providing refuge to seed predators, creating apparent competition with native plants. Ammophila arenaria (European beachgrass) has been introduced to coastal dune habitats throughout the western United States where it forms dense monocultures, stabilizes dunes, and alters abiotic and biotic conditions. The...
Authors
Jonathan Rose, Lorraine S Parsons, Patrick Kleeman, Brian J. Halstead
From eDNA to decisions using a multi-method approach to restoration planning in streams 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...
Authors
Andrea Adams, C. Kamoroff, Daniel Norton, Brian J. Halstead, R. Grasso, Patrick 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 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...
Authors
Brian J. Halstead, Patrick Kleeman, Caren Goldberg, Jonathan Rose
Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog 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...
Authors
A.M. Belasen, R.A. Peek, A.J. Adams, I.D. Russell, M.E. De Leon, Michael Adams, J. Bettaso, K.G.H. Breedveld, A. Catenazzi, C.P. Dillingham, Daniel Grear, Brian J. Halstead, P.G. Johnson, Patrick 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 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...
Authors
Brian Tornabene, Blake R. Hossack, Brian J. Halstead, Collin A. Eagles-Smith, Michael Adams, Adam Backlin, Adrianne Brand, Colleen Emery, Robert N. Fisher, Jillian Fleming, Brad Glorioso, Daniel Grear, Evan Campbell Grant, Patrick Kleeman, David Miller, Erin L. Muths, Christopher Pearl, Jennifer Rowe, Caitlin Rumrill, J. 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) 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...
Authors
Matthew J. Forrest, Brian J. Halstead, Daniel Grear, Patrick Kleeman, Brian D. Todd, Oliver Miano, Kris Urquhart
Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century 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...
Authors
Brian J. Halstead, Patrick Kleeman, Jonathan Rose, Gary Fellers
Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad 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...
Authors
Jonathan Rose, Patrick Kleeman, Brian J. Halstead
Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range 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...
Authors
Brian J. Halstead, Patrick Kleeman, Graziella DiRenzo, Jonathan Rose
Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024 Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024
The code in this repository generates and analyzes directed acyclic graphs (DAGs) representing hypotheses about variables affecting the occurrence and surface availability of Plethodon salamanders in northern California; formats data from field surveys and GIS for analysis; and analyzes multi-scale occupancy models, including model selection, to evaluate the model and variables with the...
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
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 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...
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California 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...
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore 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)...
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park 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...
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021 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...
Science and Products
Filter Total Items: 30
Survey Data for Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in Siskiyou County, California, 2023-2024 Survey Data for Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in Siskiyou County, California, 2023-2024
These data contain information about the sites, visits, and transects surveyed for Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in Siskiyou County, California, 2023-2024. The survey sites were near locations of recent (since 2005) historical occurrence of the salamanders and were designed to separate occurrence, availability on the surface, and...
Stream Characteristics and Species Data for Foothill Yellow-legged Frogs in Southern San Benito and Western Fresno Counties, California, 2019-2021 Stream Characteristics and Species Data for Foothill Yellow-legged Frogs in Southern San Benito and Western Fresno Counties, California, 2019-2021
These data contain information on stream characteristics (intermittency and temperature), vegetation (canopy and algal cover), amphibian, reptile, and fish observations, and pathogen (amphibian chytrid fungus, Batrachochytrium dendrobatidis) prevalence, all of which are relevant for the suitability of streams in Pinnacles National Park for the reintroduction of foothill yellow-legged...
Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022 Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022
These data include capture and survey information for a meadow population of endangered Sierra Nevada yellow-legged frogs (Rana sierrae) at Yosemite National Park, California, USA, 2003-2022. The data also include remotely sensed weather covariates related to winter severity (annual April snow water equivalent) and drought severity (Palmer drought severity index) to evaluate their...
Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA 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 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.
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore 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)...
Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022 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 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 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...
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park 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...
Multi-State Occurrence Data and Predictors for Amphibians in Yosemite National Park (2007-2021) 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...
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021 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...
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger SalamanderAmbystoma californiense - California Tiger Salamander is a A dark brown salamander with yellow spots.
Ambystoma californiense - California Tiger Salamander
Ambystoma californiense - California Tiger SalamanderAmbystoma 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: 44
Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations
Disease, alone or combined with other stressors such as habitat loss and contaminants, affects wildlife populations worldwide. However, interactions among stressors and how they affect demography and populations remain poorly understood. The amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) is a sometimes-lethal pathogen linked with population declines and extirpations of...
Authors
Morgan P. Kain, Blake R. Hossack, Kelly Smalling, Brian J. Halstead, Daniel Grear, David Miller, Michael Adams, Adam Backlin, William Barichivich, Collin A. Eagles-Smith, Colleen Emery, Jillian Fleming, Robert N. Fisher, Elizabeth Gallegos, Duoa J. Lor, Patrick Kleeman, Erin L. Muths, Ty Pan, Christopher Pearl, Charles W. Robinson, Caitlin Rumrill, Brian Tornabene, J. Hardin Waddle, Susan Walls, Evan Campbell Grant
Pan-amphibia distribution of the fungal parasite Batrachochytrium dendrobatidis varies with species and temperature Pan-amphibia distribution of the fungal parasite Batrachochytrium dendrobatidis varies with species and temperature
Batrachochytrium dendrobatidis (Bd) is a globally distributed fungal pathogen of amphibians that has contributed to one of the largest disease-related biodiversity losses in wildlife. Bd is regularly viewed through the lens of a global wildlife epizootic because the spread of highly virulent genetic lineages has resulted in well-documented declines and extinctions of multiple amphibian...
Authors
Daniel Grear, Michael Adams, Adam Backlin, William Barichivich, Adrianne Brand, Gary Bucciarelli, Daniel Calhoun, Tara Chestnut, Jon Davenport, Andrew E Dietrich, Graziella DiRenzo, Robert N. Fisher, Brad Glorioso, Evan Campbell Grant, Brian J. Halstead, Marc Hayes, Blake R. Hossack, Morgan Kain, Patrick Kleeman, Jeffrey M. Lorch, Brome McCreary, David A.W. Miller, Brittany A. Mosher, Erin L. Muths, Christopher Pearl, Charles H. Robinson, Mark Roth, Jennifer Rowe, Walter Sadinski, Brent H. Sigafus, Iga Stasiak, Samuel Sweet, Hardin Waddle, Susan Walls, Gregory Watkins-Colwell, Lori Williams, Megan Winzeler
Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence
Sierra Nevada ecosystems have been influenced by fire for millennia; however, increasing wildfire size and frequency may yield unforeseen consequences on wildlife populations and their distribution. Foothill yellow-legged frogs Rana boylii have declined in portions of their range and are considered a species of conservation concern. We surveyed streams for foothill yellow legged frogs in...
Authors
Brian J. Halstead, Patrick Kleeman, Jonathan Rose
Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA.
Non-native plants can affect communities through direct competition, and by providing refuge to seed predators, creating apparent competition with native plants. Ammophila arenaria (European beachgrass) has been introduced to coastal dune habitats throughout the western United States where it forms dense monocultures, stabilizes dunes, and alters abiotic and biotic conditions. The...
Authors
Jonathan Rose, Lorraine S Parsons, Patrick Kleeman, Brian J. Halstead
From eDNA to decisions using a multi-method approach to restoration planning in streams 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...
Authors
Andrea Adams, C. Kamoroff, Daniel Norton, Brian J. Halstead, R. Grasso, Patrick 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 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...
Authors
Brian J. Halstead, Patrick Kleeman, Caren Goldberg, Jonathan Rose
Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog 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...
Authors
A.M. Belasen, R.A. Peek, A.J. Adams, I.D. Russell, M.E. De Leon, Michael Adams, J. Bettaso, K.G.H. Breedveld, A. Catenazzi, C.P. Dillingham, Daniel Grear, Brian J. Halstead, P.G. Johnson, Patrick 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 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...
Authors
Brian Tornabene, Blake R. Hossack, Brian J. Halstead, Collin A. Eagles-Smith, Michael Adams, Adam Backlin, Adrianne Brand, Colleen Emery, Robert N. Fisher, Jillian Fleming, Brad Glorioso, Daniel Grear, Evan Campbell Grant, Patrick Kleeman, David Miller, Erin L. Muths, Christopher Pearl, Jennifer Rowe, Caitlin Rumrill, J. 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) 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...
Authors
Matthew J. Forrest, Brian J. Halstead, Daniel Grear, Patrick Kleeman, Brian D. Todd, Oliver Miano, Kris Urquhart
Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century 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...
Authors
Brian J. Halstead, Patrick Kleeman, Jonathan Rose, Gary Fellers
Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad 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...
Authors
Jonathan Rose, Patrick Kleeman, Brian J. Halstead
Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range 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...
Authors
Brian J. Halstead, Patrick Kleeman, Graziella DiRenzo, Jonathan Rose
Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024 Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024
The code in this repository generates and analyzes directed acyclic graphs (DAGs) representing hypotheses about variables affecting the occurrence and surface availability of Plethodon salamanders in northern California; formats data from field surveys and GIS for analysis; and analyzes multi-scale occupancy models, including model selection, to evaluate the model and variables with the...
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
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 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...
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California 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...
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore 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)...
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park 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...
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021 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...