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Brian Halstead

Dr. Brian Halstead is a Research Wildlife Biologist with the Western Ecological Research Center.

He focuses on conservation of reptiles and amphibians, particularly applications of population ecology to species conservation. In particular, he combines field methods like capture-mark-recapture and radio telemetry with flexible Bayesian hierarchical models to learn about demographic parameters and the individual, biotic, and environmental variables that affect them. Central themes of his research include the influence of land use, climate, and biotic interactions on species distributions and demographic rates; the behavioral response of individuals to habitat change; and providing relevant information for wildlife conservation to resource managers and private landowners. Currently, Dr. Halstead's research focuses on the effects of water availability on the distribution, behavior, and demography of giant gartersnakes (Thamnophis gigas); the response of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) to grazing and management of aquatic invasive species; and the influence of abiotic and biotic variables on the distribution and demography of amphibian populations in northern California. Additional research projects include the distribution, growth, and demography of island night lizards (Xantusia riversiana) on San Nicolas Island and monitoring Townsend’s big-eared bat (Corynorhinus townsendii) maternal colonies at Point Reyes National Seashore.

RESEARCH INTERESTS

  • Population Ecology
  • Conservation Biology
  • Herpetology
  • Bayesian Statistics

Education and Certifications

  • B.S. in Biology, Carroll College (Waukesha, WI), 1999

  • Ph.D. in Biology, University of South Florida, 2008

Science and Products

Aerial view of five gulls, with grey backs and wings and white heads and tails, flying over the ocean

Birds, Bats, and Beyond: Networked Wildlife Tracking in the Southern California Bight

Seabird and bat researchers from the USGS Western Ecological Research Center are teaming up to study how flying animals move through the marine environment. This Bureau of Ocean Energy Management supported project will add 25 remote telemetry stations to the existing global Motus Wildlife Tracking System, representing the largest single investment in coastal and offshore Motus infrastructure on...
By
Species Management Research Program, Western Ecological Research Center (WERC)
Birds, Bats, and Beyond: Networked Wildlife Tracking in the Southern California Bight

Birds, Bats, and Beyond: Networked Wildlife Tracking in the Southern California Bight

Seabird and bat researchers from the USGS Western Ecological Research Center are teaming up to study how flying animals move through the marine environment. This Bureau of Ocean Energy Management supported project will add 25 remote telemetry stations to the existing global Motus Wildlife Tracking System, representing the largest single investment in coastal and offshore Motus infrastructure on...
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Bats benefit from maintaining a close-knit roosting group.

Tracking Bats and Coronaviruses

Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to tracking bats and coronaviruses. Select tabs above for related items.
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Fort Collins Science Center, National Wildlife Health Center, Western Ecological Research Center (WERC)
Tracking Bats and Coronaviruses

Tracking Bats and Coronaviruses

Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to tracking bats and coronaviruses. Select tabs above for related items.
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SFGS

Ecology and Conservation of Reptiles

This project improves our understanding of the ecology of reptiles in California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of reptiles to understand factors that affect where they are found and how populations change. He further explores the relationships of reptiles with their abiotic and...
By
Ecosystems Mission Area, Species Management Research Program, Western Ecological Research Center (WERC)
Ecology and Conservation of Reptiles

Ecology and Conservation of Reptiles

This project improves our understanding of the ecology of reptiles in California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of reptiles to understand factors that affect where they are found and how populations change. He further explores the relationships of reptiles with their abiotic and...
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Image: California Red-legged Frog

Ecology and Conservation of Amphibians in Northern California

This project improves our understanding of the ecology of amphibians in northern California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of amphibians to understand factors that affect where amphibians are found and how populations change. He further explores the relationships of amphibians with...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Western Ecological Research Center (WERC)
Ecology and Conservation of Amphibians in Northern California

Ecology and Conservation of Amphibians in Northern California

This project improves our understanding of the ecology of amphibians in northern California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of amphibians to understand factors that affect where amphibians are found and how populations change. He further explores the relationships of amphibians with...
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hoary bat

Bat Research in California

The primary goal of this bat research program is to develop projects that increase our understanding of basic ecology and natural history of western bat species, while simultaneously providing needed data to inform conservation measures and management decisions in the West. Dr. Brian Halstead, together with Gabriel Reyes, studies the habitat and resource selection, movement ecology, demography...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Western Ecological Research Center (WERC)
Bat Research in California

Bat Research in California

The primary goal of this bat research program is to develop projects that increase our understanding of basic ecology and natural history of western bat species, while simultaneously providing needed data to inform conservation measures and management decisions in the West. Dr. Brian Halstead, together with Gabriel Reyes, studies the habitat and resource selection, movement ecology, demography...
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Photo of waterbirds feeding at a flooded agricultural field.

Dixon Field Station

WERC scientists at the Dixon Field Station conduct studies from the San Francisco Bay-Delta in California to the Great Basin spanning California and Nevada.
By
Western Ecological Research Center (WERC)
Dixon Field Station

Dixon Field Station

WERC scientists at the Dixon Field Station conduct studies from the San Francisco Bay-Delta in California to the Great Basin spanning California and Nevada.
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Filter Total Items: 52

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...
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California

Locations of sites at which U.S. Geological Survey (USGS) biologists surveyed for Temblor legless lizards (Anniella alexanderae) from 2022 to 2025 and the results of those surveys. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond a few localities. Surveys were designed to gather information on the distribution of Temblor...
By
Western Ecological Research Center (WERC)

Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model

These data represent the results of surveys for western spadefoots in southern California, including both presence and non-detection data. In addition, data include environmental covariates that were hypothesized to influence the occurrence of western spadefoots, such as land cover and distance to aquatic features. These data support the following publication: Rose, J.P., Halstead, B.J...
By
Western Ecological Research Center (WERC)

Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023 (ver. 2.0, July 2025) Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023 (ver. 2.0, July 2025)

These data support a study modeling the growth, capture, and survival of giant gartersnakes (Thamnophis gigas). We captured giant gartersnakes inhabiting rice irrigation canals in the Sacramento Valley, California, USA from 2018 to 2023. We analyzed capture-mark-recapture data from 19 populations of giant gartersnakes sampled with an integrated growth-survival model. We tested how growth...
By
Western Ecological Research Center (WERC)

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.
By
Western Ecological Research Center (WERC)

Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023 Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023

This dataset contains the survey effort by U.S. Geological Survey (USGS) biologists sampling for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023, the results of those surveys, and environmental covariates relevant to detection and occupancy of this species. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond...
By
Western Ecological Research Center (WERC)

Home Range and Movement Metric Data of Resident and Translocated Giant Gartersnakes (Thamnophis gigas) in Sacramento, CA, USA, in 2018 to 2021 Home Range and Movement Metric Data of Resident and Translocated Giant Gartersnakes (Thamnophis gigas) in Sacramento, CA, USA, in 2018 to 2021

The dataset consists of two csv files one for home range and net displacement analysis for adult snakes with at least 20 locations collected during the study period and one for the analysis of movement metrics for all adult snakes in the study. The home range data contains the calculated 100 percent and 95 percent minimum convex polygons (MCP) and 95 percent adaptive local convex hull (a...
By
Western Ecological Research Center (WERC)

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.
By
Western Ecological Research Center (WERC)

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)...
By
Western Ecological Research Center (WERC)

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.
By
Western Ecological Research Center (WERC)
USGS Science in Point Reyes National Seashore (California)
USGS Science in Point Reyes National Seashore (California)

USGS Science in Point Reyes National Seashore (California)

USGS Science in Point Reyes National Seashore (California)

Interviews with staff at Point Reyes National Seashore tell how this National Park Service unit uses USGS science to educate visitors, and manage the park.
 

By
Core Science Systems, Ecosystems, Natural Hazards, Coastal and Marine Hazards and Resources Program, Earthquake Hazards, National Land Imaging Program, Landslide Hazards, Climate Adaptation Science Centers, Wildlife Program, Pacific Coastal and Marine Science Center, Western Ecological Research Center (WERC), Communications and Publishing

USGS Science in Point Reyes National Seashore (California)

USGS Science in Point Reyes National Seashore (California)

Interviews with staff at Point Reyes National Seashore tell how this National Park Service unit uses USGS science to educate visitors, and manage the park.
 

By
Core Science Systems, Ecosystems, Natural Hazards, Coastal and Marine Hazards and Resources Program, Earthquake Hazards, National Land Imaging Program, Landslide Hazards, Climate Adaptation Science Centers, Wildlife Program, Pacific Coastal and Marine Science Center, Western Ecological Research Center (WERC), Communications and Publishing
Filter Total Items: 103

Using periodic matrix models to simulate the effectiveness of alternative reintroduction strategies for lizards on a seasonal tropical island Using periodic matrix models to simulate the effectiveness of alternative reintroduction strategies for lizards on a seasonal tropical island

Conservation translocations and reintroductions are widely used to improve conservation outcomes for declining species. Reintroductions are unlikely to be successful if the threats that led to the extirpation of the focal species, such as non-native predators, have not been ameliorated. The non-native brown treesnake (Boiga irregularis) was introduced to Guam in the mid-20th century and...
Authors
Jonathan Rose, Brian Halstead, Melia Nafus
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Eastern Ecological Science Center

Do watershed conditions or local climate play a larger role in determining regional stream salamander distributions? Do watershed conditions or local climate play a larger role in determining regional stream salamander distributions?

Anthropogenic influences like land use and climate variability interact with natural heterogeneity to influence the persistence of stream salamanders. Using occupancy modeling in the southern Appalachian Mountains, we investigated the influence of land use, climate, and physical context (e.g., drainage area, elevation) on stream salamander occupancy, noting species, and life stage...
Authors
Kristen Cecala, Brian J. Halstead, James S. McGrory, John Maerz
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

Effects of invasive American bullfrogs and their removal on Northwestern pond turtles Effects of invasive American bullfrogs and their removal on Northwestern pond turtles

The American bullfrog (Rana catesbeiana) is an invasive species globally significant for its role as a generalist predator in freshwater systems. Native turtles are among the species eaten by bullfrogs, and turtle populations are slow to recover from this impact. We examined the effects of bullfrogs and their removal on Northwestern pond turtles (Actinemys marmorata) at four sites in...
Authors
Sidney Woodruff, Robert Grasso, Brian Halstead, Brian Todd
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, National Wildlife Health Center

Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California

Reintroductions are used worldwide to increase the viability of species and restore native ecological communities. The success of reintroductions is usually judged by the establishment of self-sustaining populations, restoration of naturally occurring ecological communities, and the species resuming its ecological function. Recovery for the endangered San Francisco gartersnake (SFGS...
Authors
Jonathan Rose, Elliot Schoenig, Richard Kim, Allison Nguyen, Brian J. Halstead
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

Effects of harmful algal blooms on amphibians and reptiles are under-reported and under-represented Effects of harmful algal blooms on amphibians and reptiles are under-reported and under-represented

Harmful algal blooms (HABs) are a persistent and increasing problem globally, yet we still have limited knowledge about how they affect wildlife. Although semi-aquatic and aquatic amphibians and reptiles have experienced large declines and occupy environments where HABs are increasingly problematic, their vulnerability to HABs remains unclear. To inform monitoring, management, and future...
Authors
Brian J. Halstead, Kelly Smalling, Blake R. Hossack
By
Water Resources Mission Area, Ecosystems Mission Area, New Jersey Water Science Center, Northern Rocky Mountain Science Center, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC), Pacific Northwest Environmental DNA Laboratory

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, National Wildlife Health Center, Western Ecological Research Center (WERC)
Filter Total Items: 15

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...
By
Western Ecological Research Center (WERC)

Code to estimate effects of rice growing on growth and survival of giant gartersnakes, Thamnophis gigas Code to estimate effects of rice growing on growth and survival of giant gartersnakes, Thamnophis gigas

This repository specifically contains code to reproduce analyses in: Rose, J.P., Nguyen, A.M., Jordan, A.C., Macias, D.A., Schoenig, E.J., Napolitano G.R., Kim, R., Ersan, J.S.M., Fulton, A.M., and Halstead, B.J. 2025. Rice cultivation supports growth and survival of a threatened semi-aquatic reptile. In review.
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam

This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae

This repository contains code to fit Multi-scale Occupancy Models to survey data for Temblor legless lizards (Anniella alexanderae) This repository specifically contains code to reproduce analyses in: Rose, J.P., Camp, S.M., Sheikh, Z.N., Johnson, C.B., Lei, S.H., Napolitano, G.R., Schoenig, E.J., Macias, D.A., Jordan, A.C., and Halstead, B.J. 2024. Multi-scale occupancy surveys reveal...
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

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)...
By
Western Ecological Research Center (WERC)

Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia

This repository contains code to fit Integral Projection Models and simulate population reintroductions for San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) This repository specifically contains code to reproduce analyses in: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C., and Halstead, B.J. in-review. Comparing reintroduction strategies for the endangered San Francisco...
By
Western Ecological Research Center (WERC)

Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California

Code to fit a Multiple Population Viability Analysis (MPVA) to time series of Foothill yellow-legged frog (Rana boylii) egg mass counts. Rose, J.P., and Halstead, B.J., 2023, Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California: U.S. Geological Survey software release, https://doi.org/10.5066/P9QWX2GR...
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Western Ecological Research Center (WERC)

Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019) Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019)

Code to reproduce analyses of turtle occupancy in the Sacramento Valley and Sacramento-San Joaquin River Delta
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Western Ecological Research Center (WERC)

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...
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Western Ecological Research Center (WERC)
WERC Scientists Find that Threatened Snakes Depend on Agriculture (TWS Wildlife News)

WERC Scientists Find that Threatened Snakes Depend on Agriculture (TWS Wildlife News)

SACRAMENTO – A new study shows how giant gartersnakes use Central Valley rice fields

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A Unified Research Strategy for Disease Management

A Unified Research Strategy for Disease Management

As wildlife diseases increase globally, an understanding of host-pathogen relationships can elucidate avenues for management and improve conservation...

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Incoming! Learn about Bats with the USGS WERC

Incoming! Learn about Bats with the USGS WERC

Around Halloween, USGS celebrates bats and other "spooky" creatures by sharing some of its research on these fascinating creatures! Check out social...

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Science and Products

Aerial view of five gulls, with grey backs and wings and white heads and tails, flying over the ocean

Birds, Bats, and Beyond: Networked Wildlife Tracking in the Southern California Bight

Seabird and bat researchers from the USGS Western Ecological Research Center are teaming up to study how flying animals move through the marine environment. This Bureau of Ocean Energy Management supported project will add 25 remote telemetry stations to the existing global Motus Wildlife Tracking System, representing the largest single investment in coastal and offshore Motus infrastructure on...
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Species Management Research Program, Western Ecological Research Center (WERC)
Birds, Bats, and Beyond: Networked Wildlife Tracking in the Southern California Bight

Birds, Bats, and Beyond: Networked Wildlife Tracking in the Southern California Bight

Seabird and bat researchers from the USGS Western Ecological Research Center are teaming up to study how flying animals move through the marine environment. This Bureau of Ocean Energy Management supported project will add 25 remote telemetry stations to the existing global Motus Wildlife Tracking System, representing the largest single investment in coastal and offshore Motus infrastructure on...
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Bats benefit from maintaining a close-knit roosting group.

Tracking Bats and Coronaviruses

Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to tracking bats and coronaviruses. Select tabs above for related items.
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Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Fort Collins Science Center, National Wildlife Health Center, Western Ecological Research Center (WERC)
Tracking Bats and Coronaviruses

Tracking Bats and Coronaviruses

Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to tracking bats and coronaviruses. Select tabs above for related items.
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SFGS

Ecology and Conservation of Reptiles

This project improves our understanding of the ecology of reptiles in California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of reptiles to understand factors that affect where they are found and how populations change. He further explores the relationships of reptiles with their abiotic and...
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Ecosystems Mission Area, Species Management Research Program, Western Ecological Research Center (WERC)
Ecology and Conservation of Reptiles

Ecology and Conservation of Reptiles

This project improves our understanding of the ecology of reptiles in California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of reptiles to understand factors that affect where they are found and how populations change. He further explores the relationships of reptiles with their abiotic and...
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Image: California Red-legged Frog

Ecology and Conservation of Amphibians in Northern California

This project improves our understanding of the ecology of amphibians in northern California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of amphibians to understand factors that affect where amphibians are found and how populations change. He further explores the relationships of amphibians with...
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Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Western Ecological Research Center (WERC)
Ecology and Conservation of Amphibians in Northern California

Ecology and Conservation of Amphibians in Northern California

This project improves our understanding of the ecology of amphibians in northern California and evaluates methods of managing landscapes and these imperiled species. In particular, Dr. Brian Halstead examines the distribution and demography of amphibians to understand factors that affect where amphibians are found and how populations change. He further explores the relationships of amphibians with...
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hoary bat

Bat Research in California

The primary goal of this bat research program is to develop projects that increase our understanding of basic ecology and natural history of western bat species, while simultaneously providing needed data to inform conservation measures and management decisions in the West. Dr. Brian Halstead, together with Gabriel Reyes, studies the habitat and resource selection, movement ecology, demography...
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Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Western Ecological Research Center (WERC)
Bat Research in California

Bat Research in California

The primary goal of this bat research program is to develop projects that increase our understanding of basic ecology and natural history of western bat species, while simultaneously providing needed data to inform conservation measures and management decisions in the West. Dr. Brian Halstead, together with Gabriel Reyes, studies the habitat and resource selection, movement ecology, demography...
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Photo of waterbirds feeding at a flooded agricultural field.

Dixon Field Station

WERC scientists at the Dixon Field Station conduct studies from the San Francisco Bay-Delta in California to the Great Basin spanning California and Nevada.
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Western Ecological Research Center (WERC)
Dixon Field Station

Dixon Field Station

WERC scientists at the Dixon Field Station conduct studies from the San Francisco Bay-Delta in California to the Great Basin spanning California and Nevada.
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Filter Total Items: 52

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...
By
Western Ecological Research Center (WERC)

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...
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Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California

Locations of sites at which U.S. Geological Survey (USGS) biologists surveyed for Temblor legless lizards (Anniella alexanderae) from 2022 to 2025 and the results of those surveys. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond a few localities. Surveys were designed to gather information on the distribution of Temblor...
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Western Ecological Research Center (WERC)

Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model

These data represent the results of surveys for western spadefoots in southern California, including both presence and non-detection data. In addition, data include environmental covariates that were hypothesized to influence the occurrence of western spadefoots, such as land cover and distance to aquatic features. These data support the following publication: Rose, J.P., Halstead, B.J...
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Western Ecological Research Center (WERC)

Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023 (ver. 2.0, July 2025) Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023 (ver. 2.0, July 2025)

These data support a study modeling the growth, capture, and survival of giant gartersnakes (Thamnophis gigas). We captured giant gartersnakes inhabiting rice irrigation canals in the Sacramento Valley, California, USA from 2018 to 2023. We analyzed capture-mark-recapture data from 19 populations of giant gartersnakes sampled with an integrated growth-survival model. We tested how growth...
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Western Ecological Research Center (WERC)

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.
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Western Ecological Research Center (WERC)

Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023 Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023

This dataset contains the survey effort by U.S. Geological Survey (USGS) biologists sampling for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023, the results of those surveys, and environmental covariates relevant to detection and occupancy of this species. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond...
By
Western Ecological Research Center (WERC)

Home Range and Movement Metric Data of Resident and Translocated Giant Gartersnakes (Thamnophis gigas) in Sacramento, CA, USA, in 2018 to 2021 Home Range and Movement Metric Data of Resident and Translocated Giant Gartersnakes (Thamnophis gigas) in Sacramento, CA, USA, in 2018 to 2021

The dataset consists of two csv files one for home range and net displacement analysis for adult snakes with at least 20 locations collected during the study period and one for the analysis of movement metrics for all adult snakes in the study. The home range data contains the calculated 100 percent and 95 percent minimum convex polygons (MCP) and 95 percent adaptive local convex hull (a...
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Western Ecological Research Center (WERC)

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.
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Western Ecological Research Center (WERC)

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)...
By
Western Ecological Research Center (WERC)

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.
By
Western Ecological Research Center (WERC)
USGS Science in Point Reyes National Seashore (California)
USGS Science in Point Reyes National Seashore (California)

USGS Science in Point Reyes National Seashore (California)

USGS Science in Point Reyes National Seashore (California)

Interviews with staff at Point Reyes National Seashore tell how this National Park Service unit uses USGS science to educate visitors, and manage the park.
 

By
Core Science Systems, Ecosystems, Natural Hazards, Coastal and Marine Hazards and Resources Program, Earthquake Hazards, National Land Imaging Program, Landslide Hazards, Climate Adaptation Science Centers, Wildlife Program, Pacific Coastal and Marine Science Center, Western Ecological Research Center (WERC), Communications and Publishing

USGS Science in Point Reyes National Seashore (California)

USGS Science in Point Reyes National Seashore (California)

Interviews with staff at Point Reyes National Seashore tell how this National Park Service unit uses USGS science to educate visitors, and manage the park.
 

By
Core Science Systems, Ecosystems, Natural Hazards, Coastal and Marine Hazards and Resources Program, Earthquake Hazards, National Land Imaging Program, Landslide Hazards, Climate Adaptation Science Centers, Wildlife Program, Pacific Coastal and Marine Science Center, Western Ecological Research Center (WERC), Communications and Publishing
Filter Total Items: 103

Using periodic matrix models to simulate the effectiveness of alternative reintroduction strategies for lizards on a seasonal tropical island Using periodic matrix models to simulate the effectiveness of alternative reintroduction strategies for lizards on a seasonal tropical island

Conservation translocations and reintroductions are widely used to improve conservation outcomes for declining species. Reintroductions are unlikely to be successful if the threats that led to the extirpation of the focal species, such as non-native predators, have not been ameliorated. The non-native brown treesnake (Boiga irregularis) was introduced to Guam in the mid-20th century and...
Authors
Jonathan Rose, Brian Halstead, Melia Nafus
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Eastern Ecological Science Center

Do watershed conditions or local climate play a larger role in determining regional stream salamander distributions? Do watershed conditions or local climate play a larger role in determining regional stream salamander distributions?

Anthropogenic influences like land use and climate variability interact with natural heterogeneity to influence the persistence of stream salamanders. Using occupancy modeling in the southern Appalachian Mountains, we investigated the influence of land use, climate, and physical context (e.g., drainage area, elevation) on stream salamander occupancy, noting species, and life stage...
Authors
Kristen Cecala, Brian J. Halstead, James S. McGrory, John Maerz
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

Effects of invasive American bullfrogs and their removal on Northwestern pond turtles Effects of invasive American bullfrogs and their removal on Northwestern pond turtles

The American bullfrog (Rana catesbeiana) is an invasive species globally significant for its role as a generalist predator in freshwater systems. Native turtles are among the species eaten by bullfrogs, and turtle populations are slow to recover from this impact. We examined the effects of bullfrogs and their removal on Northwestern pond turtles (Actinemys marmorata) at four sites in...
Authors
Sidney Woodruff, Robert Grasso, Brian Halstead, Brian Todd
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, National Wildlife Health Center

Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California

Reintroductions are used worldwide to increase the viability of species and restore native ecological communities. The success of reintroductions is usually judged by the establishment of self-sustaining populations, restoration of naturally occurring ecological communities, and the species resuming its ecological function. Recovery for the endangered San Francisco gartersnake (SFGS...
Authors
Jonathan Rose, Elliot Schoenig, Richard Kim, Allison Nguyen, Brian J. Halstead
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

Effects of harmful algal blooms on amphibians and reptiles are under-reported and under-represented Effects of harmful algal blooms on amphibians and reptiles are under-reported and under-represented

Harmful algal blooms (HABs) are a persistent and increasing problem globally, yet we still have limited knowledge about how they affect wildlife. Although semi-aquatic and aquatic amphibians and reptiles have experienced large declines and occupy environments where HABs are increasingly problematic, their vulnerability to HABs remains unclear. To inform monitoring, management, and future...
Authors
Brian J. Halstead, Kelly Smalling, Blake R. Hossack
By
Water Resources Mission Area, Ecosystems Mission Area, New Jersey Water Science Center, Northern Rocky Mountain Science Center, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC), Pacific Northwest Environmental DNA Laboratory

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
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

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
By
Ecosystems Mission Area, National Wildlife Health Center, Western Ecological Research Center (WERC)
Filter Total Items: 15

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...
By
Western Ecological Research Center (WERC)

Code to estimate effects of rice growing on growth and survival of giant gartersnakes, Thamnophis gigas Code to estimate effects of rice growing on growth and survival of giant gartersnakes, Thamnophis gigas

This repository specifically contains code to reproduce analyses in: Rose, J.P., Nguyen, A.M., Jordan, A.C., Macias, D.A., Schoenig, E.J., Napolitano G.R., Kim, R., Ersan, J.S.M., Fulton, A.M., and Halstead, B.J. 2025. Rice cultivation supports growth and survival of a threatened semi-aquatic reptile. In review.
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam

This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae

This repository contains code to fit Multi-scale Occupancy Models to survey data for Temblor legless lizards (Anniella alexanderae) This repository specifically contains code to reproduce analyses in: Rose, J.P., Camp, S.M., Sheikh, Z.N., Johnson, C.B., Lei, S.H., Napolitano, G.R., Schoenig, E.J., Macias, D.A., Jordan, A.C., and Halstead, B.J. 2024. Multi-scale occupancy surveys reveal...
By
Western Ecological Research Center (WERC)

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...
By
Western Ecological Research Center (WERC)

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)...
By
Western Ecological Research Center (WERC)

Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia

This repository contains code to fit Integral Projection Models and simulate population reintroductions for San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) This repository specifically contains code to reproduce analyses in: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C., and Halstead, B.J. in-review. Comparing reintroduction strategies for the endangered San Francisco...
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Western Ecological Research Center (WERC)

Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California

Code to fit a Multiple Population Viability Analysis (MPVA) to time series of Foothill yellow-legged frog (Rana boylii) egg mass counts. Rose, J.P., and Halstead, B.J., 2023, Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California: U.S. Geological Survey software release, https://doi.org/10.5066/P9QWX2GR...
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Western Ecological Research Center (WERC)

Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019) Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019)

Code to reproduce analyses of turtle occupancy in the Sacramento Valley and Sacramento-San Joaquin River Delta
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Western Ecological Research Center (WERC)

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...
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Western Ecological Research Center (WERC)
WERC Scientists Find that Threatened Snakes Depend on Agriculture (TWS Wildlife News)

WERC Scientists Find that Threatened Snakes Depend on Agriculture (TWS Wildlife News)

SACRAMENTO – A new study shows how giant gartersnakes use Central Valley rice fields

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A Unified Research Strategy for Disease Management

A Unified Research Strategy for Disease Management

As wildlife diseases increase globally, an understanding of host-pathogen relationships can elucidate avenues for management and improve conservation...

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Incoming! Learn about Bats with the USGS WERC

Incoming! Learn about Bats with the USGS WERC

Around Halloween, USGS celebrates bats and other "spooky" creatures by sharing some of its research on these fascinating creatures! Check out social...

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