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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

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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)
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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)
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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.
Learn More
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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)
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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...
Learn More
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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)
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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)
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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...
Learn More
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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)
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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: 38

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 a few loc
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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

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-LoCoH) ho
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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

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)

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.
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Western Ecological Research Center (WERC)

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.
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Forest and Rangeland Ecosystem Science Center

San Francisco Gartersnake Fecundity Data from San Mateo County, California Collected from 2019-2022

Adult female San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) were captured and examined using an ultrasound device to determine if they were gravid and count the number of embryos in those that were. Morphological data including length and mass were collected for each snake, along with the date of capture and a study site identifier. These data support the following publication: Rose
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Western Ecological Research Center (WERC)

Demographic Parameter Estimates for San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) for Fitting an Integral Projection Model

A study comparing reintroduction scenarios for the San Francisco gartersnake (Thamnophis sirtalis tetrataenia), an endangered subspecies native to San Mateo County and Santa Cruz County in northern California. Models for snake survival, growth, fecundity, and reproductive status were used to construct a demographic population model. Data are posterior distributions for demographic parameters from
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Western Ecological Research Center (WERC)

Egg Mass Counts from Foothill Yellow-Legged Frogs (Rana boylii) in California from 1992-2021

We compiled time series of egg mass counts (an index of adult female abundance) from Rana boylii populations in 36 focal streams and fit a Multiple Population Viability Analysis (MPVA) model to quantify how streamflow metrics, stream temperature, and surrounding land cover affect population growth. In addition, data on streamflow, stream temperature, and surrounding land cover for each stream were
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Western Ecological Research Center (WERC)

Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California, 2022 and 2023

Locations of sites at which U.S. Geological Survey (USGS) biologists surveyed for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023 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 legless li
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Western Ecological Research Center (WERC)

Western Pond Turtle (Emys [Actinemys] marmorata) Observations at Point Reyes National Seashore and Golden Gate National Recreation Area

These data represent incidental observations of western pond turtles (Emys [Actinemys] marmorata) collected by the U.S. Geological Survey, Western Ecological Research Center, at Point Reyes National Seashore and Golden Gate National Recreation Area between 1993 and 2014. These data do not have associated survey effort, and are intended to represent incidental observations, rather than a random, sy
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Western Ecological Research Center (WERC)

Survival Data for Translocated Adults and Captive-Reared Juvenile Giant Gartersnakes in Sacramento County, California (2018-2021)

The dataset consists of two csv files one for adult snakes and one for captive-reared juvenile snakes. The data contains start times (when snakes entered the study) and end times (when snakes died or were censored from the study) for survival analysis. The data also contains general information about the individual snakes (id, snout-vent length, treatment group, whether or not they were translocat
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Western Ecological Research Center (WERC)

Multi-State Occurrence Data and Predictors for Amphibians in Yosemite National Park (2007-2021)

These data include field-collected observations of the occurrence of adult and larval amphibians at 174 sites in 14 watersheds at Yosemite National Park from 2007 through 2021. Also included in the data are potential variables affecting site occurrence, probability of reproduction, and probability of detection of amphibians, including static site-specific variables like site size and elevation, an
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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.
 

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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: 94

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 research,
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Brian J. Halstead, Kelly Smalling, Blake R. Hossack
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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

Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted
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Andrea J. Adams, C. Kamoroff, Daniel R. Norton, R. L. Grasso, Brian J. Halstead, Patrick M. Kleeman, C. Mengelt, K. Powelson, T. Seaborn, C.S. Goldberg
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California

Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles (Actinemys marmorata) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand the distrib
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Brian J. Halstead, Patrick M. Kleeman, Caren S. Goldberg, Jonathan P. Rose
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd
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A.M. Belasen, R.A. Peek, A.J. Adams, I.D. Russell, M.E. De León, Michael J. Adams, J. Bettaso, K.G.H. Breedveld, A. Catenazzi, C.P. Dillingham, Daniel A. Grear, Brian J. Halstead, P.G. Johnson, Patrick M. Kleeman, M.S. Koo, C.W. Koppl, J.D. Lauder, G. Padgett-Flohr, J. Piovia-Scott, K.L. Pope, V. Vredenburg, M. Westphal, K. Wiseman, S.J. Kupferberg
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Ecosystems Mission Area, National Wildlife Health Center, Western Ecological Research Center (WERC)

A dataset of amphibian species in U.S. National Parks

National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park u
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Benjamin Lafrance, Andrew M. Ray, Robert N. Fisher, Evan H. Campbell Grant, Charles Shafer, David Beamer, Stephen Frank Spear, Todd W Pierson, Jon M. Davenport, Matthew L. Niemiller, R. Alexander Pyron, Brad Glorioso, William Barichivich, Brian J. Halstead, Kory Roberts, Blake R. Hossack
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Ecosystems Mission Area, Northern Rocky Mountain Science Center, Eastern Ecological Science Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center

Broad-scale assessment of methylmercury in adult amphibians

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scal

Authors
Brian J. Tornabene, Blake R. Hossack, Brian J. Halstead, Collin A. Eagles-Smith, Michael J. Adams, Adam R. Backlin, Adrianne Brand, Colleen Emery, Robert N. Fisher, Jillian Elizabeth Fleming, Brad Glorioso, Daniel A. Grear, Evan H. Campbell Grant, Patrick M. Kleeman, David Miller, Erin L. Muths, Christopher Pearl, Jennifer Rowe, Caitlin Teresa Rumrill, J. Hardin Waddle, Megan Winzeler, Kelly L. Smalling
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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

Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models

For endangered species persisting in a few populations, reintroductions to unoccupied habitat are a popular conservation action to increase viability in the long term. Identifying the reintroduction strategy that is most likely to result in viable founder and donor populations is essential to optimally use resources available for conservation. The San Francisco gartersnake (Thamnophis sirtalis tet
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Jonathan P. Rose, Richard Kim, Elliot James Schoenig, Patrick C. Lien, Brian J. Halstead
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Priority research needs to inform amphibian conservation in the Anthropocene

The problem of global amphibian declines has prompted extensive research over the last three decades. Initially, the focus was on identifying and characterizing the extent of the problem, but more recently efforts have shifted to evidence-based research designed to identify best solutions and to improve conservation outcomes. Despite extensive accumulation of knowledge on amphibian declines, there
Authors
Evan H. Campbell Grant, Staci M. Amburgey, Brian Gratwicke, Victor Acosta Chaves, Anat M. Belasen, David Bickford, Carsten Brühl, Natalie E. Calatayud, Nick Clemann, Simon Clulow, Jelka Crnobrnja-Isailovic, Jeff Dawson, David A. De Angelis, C. Kenneth Dodd, Annette Evans, Gentile Francesco Ficetola, Mattia Falaschi, Sergio González-Mollinedo, David M. Green, Roseanna Gamlen-Greene, Richard A. Griffiths, Brian J. Halstead, Craig Hassapakis, Geoffrey Heard, Catharina Karlsson, Tom Kirschey, Blake Klocke, Tiffany A. Kosch, Sophia Kusterko Novaes, Luke Linhoff, John C. Maerz, Brittany A. Mosher, Katherine M O'Donnell, Leticia M. Ochoa-Ochoa, Deanna H. Olson, Kristiina Ovaska, J. Dale Roberts, Aimee J. Silla, Tariq Stark, Jeanne Tarrant, R. Upton, Judit Vörös, Erin L. Muths
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Ecosystems Mission Area, Species Management Research Program, Eastern Ecological Science Center, Fort Collins Science Center, Western Ecological Research Center (WERC)

Identifying drivers of population dynamics for a stream breeding amphibian using time series of egg mass counts

The decline in amphibian populations is one of the starkest examples of the biodiversity crisis. For stream breeding amphibians, alterations to natural flow regimes by dams, water diversions, and climate change have been implicated in declines and extirpations. Identifying drivers of amphibian declines requires long time series of abundance data because amphibian populations can exhibit high natur
Authors
Jonathan P. Rose, Sarah J. Kupferberg, Ryan A. Peek, Don Ashton, James B. Bettaso, Steven Bobzien, Ryan M. Bourque, Koen G.H. Breedveld, Alessandro Catenazzi, Joseph E. Drennan, Earl Gonsolin, Marcia Grefsrud, Andrea E. Herman, Matthew R. House, Matt R. Kluber, Amy J. Lind, Karla R. Marlow, Alan Striegle, Michael van Hattem, Clara A. Wheeler, Jeffery T. Wilcox, Kevin D. Wiseman, Brian J. Halstead
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Keeping the heat on: Weighted surveillance for Chytrid fungus (Batrachochytirum dendrobatidis) in Dixie Valley toads (Anaxyrus [= Bufo] williamsi)

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecu
Authors
Matthew J. Forrest, Brian J. Halstead, Daniel A. Grear, Patrick M. Kleeman, Brian D. Todd, Oliver J. Miano, Kris D. Urquhart
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Ecosystems Mission Area, National Wildlife Health Center, Western Ecological Research Center (WERC)

Survival and establishment of captive-reared and translocated giant gartersnakes after release

Many imperiled species face increasing extinction risk that requires interventional management like translocation or captive rearing. The use of translocations to successfully restore or create populations requires that animals survive at recipient sites, information that is often lacking for imperiled species and that can be risky to acquire if not obtained before a species has dwindled in number
Authors
Allison M. Nguyen, Brian D Todd, Brian J. Halstead
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century

Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with climate change.
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Gary M. Fellers
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

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 temperatur
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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

The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys and samplin
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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

This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point
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Western Ecological Research Center (WERC)

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 gartersnake (
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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 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. This code
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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 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

The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variab
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Western Ecological Research Center (WERC)

Code to analyze survival data for Giant gatersnakes, Thamnophis gigas in Sacramento County, California from 2018 to 2021

The purpose of this study was to estimate the survival of giant gartersnakes (Thamnophis gigas) prior to and following translocation, as well as to evaluate the use of captive rearing as a conservation tool for giant gartersnakes. We used Kaplan-Meier and Cox Proportional Hazards models to estimate survival rates and estimate the effects of group identity (marsh donor, rice donor, and translocatio
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Western Ecological Research Center (WERC)

Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021

-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model published by Duart
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Western Ecological Research Center (WERC)

Code to analyze Capture-Mark-Recapture data of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia)

Code files "growth_analysis.R" -An R script to fit the von Bertalanffy growth model to growth data from San Francisco gartersnakes. The von Bertalanffy growth model is fit using JAGS software (Plummer 2003), and is based on the model presented in Armstrong and Brooks (2013). "survival_analysis.R" -An R script to fit the robust-design Cormack-Jolly-Seber model to capture-mark-recapture data from
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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

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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)
link

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...
Learn More
link
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)
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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.
Learn More
link
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)
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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...
Learn More
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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)
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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)
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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)
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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: 38

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 a few loc
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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

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-LoCoH) ho
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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

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)

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.
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Western Ecological Research Center (WERC)

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.
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Forest and Rangeland Ecosystem Science Center

San Francisco Gartersnake Fecundity Data from San Mateo County, California Collected from 2019-2022

Adult female San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) were captured and examined using an ultrasound device to determine if they were gravid and count the number of embryos in those that were. Morphological data including length and mass were collected for each snake, along with the date of capture and a study site identifier. These data support the following publication: Rose
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Western Ecological Research Center (WERC)

Demographic Parameter Estimates for San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) for Fitting an Integral Projection Model

A study comparing reintroduction scenarios for the San Francisco gartersnake (Thamnophis sirtalis tetrataenia), an endangered subspecies native to San Mateo County and Santa Cruz County in northern California. Models for snake survival, growth, fecundity, and reproductive status were used to construct a demographic population model. Data are posterior distributions for demographic parameters from
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Western Ecological Research Center (WERC)

Egg Mass Counts from Foothill Yellow-Legged Frogs (Rana boylii) in California from 1992-2021

We compiled time series of egg mass counts (an index of adult female abundance) from Rana boylii populations in 36 focal streams and fit a Multiple Population Viability Analysis (MPVA) model to quantify how streamflow metrics, stream temperature, and surrounding land cover affect population growth. In addition, data on streamflow, stream temperature, and surrounding land cover for each stream were
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Western Ecological Research Center (WERC)

Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California, 2022 and 2023

Locations of sites at which U.S. Geological Survey (USGS) biologists surveyed for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023 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 legless li
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Western Ecological Research Center (WERC)

Western Pond Turtle (Emys [Actinemys] marmorata) Observations at Point Reyes National Seashore and Golden Gate National Recreation Area

These data represent incidental observations of western pond turtles (Emys [Actinemys] marmorata) collected by the U.S. Geological Survey, Western Ecological Research Center, at Point Reyes National Seashore and Golden Gate National Recreation Area between 1993 and 2014. These data do not have associated survey effort, and are intended to represent incidental observations, rather than a random, sy
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Western Ecological Research Center (WERC)

Survival Data for Translocated Adults and Captive-Reared Juvenile Giant Gartersnakes in Sacramento County, California (2018-2021)

The dataset consists of two csv files one for adult snakes and one for captive-reared juvenile snakes. The data contains start times (when snakes entered the study) and end times (when snakes died or were censored from the study) for survival analysis. The data also contains general information about the individual snakes (id, snout-vent length, treatment group, whether or not they were translocat
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Western Ecological Research Center (WERC)

Multi-State Occurrence Data and Predictors for Amphibians in Yosemite National Park (2007-2021)

These data include field-collected observations of the occurrence of adult and larval amphibians at 174 sites in 14 watersheds at Yosemite National Park from 2007 through 2021. Also included in the data are potential variables affecting site occurrence, probability of reproduction, and probability of detection of amphibians, including static site-specific variables like site size and elevation, an
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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.
 

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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: 94

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 research,
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Brian J. Halstead, Kelly Smalling, Blake R. Hossack
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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

Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted
Authors
Andrea J. Adams, C. Kamoroff, Daniel R. Norton, R. L. Grasso, Brian J. Halstead, Patrick M. Kleeman, C. Mengelt, K. Powelson, T. Seaborn, C.S. Goldberg
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California

Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles (Actinemys marmorata) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand the distrib
Authors
Brian J. Halstead, Patrick M. Kleeman, Caren S. Goldberg, Jonathan P. Rose
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd
Authors
A.M. Belasen, R.A. Peek, A.J. Adams, I.D. Russell, M.E. De León, Michael J. Adams, J. Bettaso, K.G.H. Breedveld, A. Catenazzi, C.P. Dillingham, Daniel A. Grear, Brian J. Halstead, P.G. Johnson, Patrick M. Kleeman, M.S. Koo, C.W. Koppl, J.D. Lauder, G. Padgett-Flohr, J. Piovia-Scott, K.L. Pope, V. Vredenburg, M. Westphal, K. Wiseman, S.J. Kupferberg
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Ecosystems Mission Area, National Wildlife Health Center, Western Ecological Research Center (WERC)

A dataset of amphibian species in U.S. National Parks

National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park u
Authors
Benjamin Lafrance, Andrew M. Ray, Robert N. Fisher, Evan H. Campbell Grant, Charles Shafer, David Beamer, Stephen Frank Spear, Todd W Pierson, Jon M. Davenport, Matthew L. Niemiller, R. Alexander Pyron, Brad Glorioso, William Barichivich, Brian J. Halstead, Kory Roberts, Blake R. Hossack
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Ecosystems Mission Area, Northern Rocky Mountain Science Center, Eastern Ecological Science Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center

Broad-scale assessment of methylmercury in adult amphibians

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scal

Authors
Brian J. Tornabene, Blake R. Hossack, Brian J. Halstead, Collin A. Eagles-Smith, Michael J. Adams, Adam R. Backlin, Adrianne Brand, Colleen Emery, Robert N. Fisher, Jillian Elizabeth Fleming, Brad Glorioso, Daniel A. Grear, Evan H. Campbell Grant, Patrick M. Kleeman, David Miller, Erin L. Muths, Christopher Pearl, Jennifer Rowe, Caitlin Teresa Rumrill, J. Hardin Waddle, Megan Winzeler, Kelly L. Smalling
By
Ecosystems Mission Area, Water Resources Mission Area, Contaminant Biology, Toxic Substances Hydrology, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, National Wildlife Health Center, New Jersey Water Science Center, Northern Rocky Mountain Science Center, Western Ecological Research Center (WERC), Wetland and Aquatic Research Center

Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models

For endangered species persisting in a few populations, reintroductions to unoccupied habitat are a popular conservation action to increase viability in the long term. Identifying the reintroduction strategy that is most likely to result in viable founder and donor populations is essential to optimally use resources available for conservation. The San Francisco gartersnake (Thamnophis sirtalis tet
Authors
Jonathan P. Rose, Richard Kim, Elliot James Schoenig, Patrick C. Lien, Brian J. Halstead
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Priority research needs to inform amphibian conservation in the Anthropocene

The problem of global amphibian declines has prompted extensive research over the last three decades. Initially, the focus was on identifying and characterizing the extent of the problem, but more recently efforts have shifted to evidence-based research designed to identify best solutions and to improve conservation outcomes. Despite extensive accumulation of knowledge on amphibian declines, there
Authors
Evan H. Campbell Grant, Staci M. Amburgey, Brian Gratwicke, Victor Acosta Chaves, Anat M. Belasen, David Bickford, Carsten Brühl, Natalie E. Calatayud, Nick Clemann, Simon Clulow, Jelka Crnobrnja-Isailovic, Jeff Dawson, David A. De Angelis, C. Kenneth Dodd, Annette Evans, Gentile Francesco Ficetola, Mattia Falaschi, Sergio González-Mollinedo, David M. Green, Roseanna Gamlen-Greene, Richard A. Griffiths, Brian J. Halstead, Craig Hassapakis, Geoffrey Heard, Catharina Karlsson, Tom Kirschey, Blake Klocke, Tiffany A. Kosch, Sophia Kusterko Novaes, Luke Linhoff, John C. Maerz, Brittany A. Mosher, Katherine M O'Donnell, Leticia M. Ochoa-Ochoa, Deanna H. Olson, Kristiina Ovaska, J. Dale Roberts, Aimee J. Silla, Tariq Stark, Jeanne Tarrant, R. Upton, Judit Vörös, Erin L. Muths
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Ecosystems Mission Area, Species Management Research Program, Eastern Ecological Science Center, Fort Collins Science Center, Western Ecological Research Center (WERC)

Identifying drivers of population dynamics for a stream breeding amphibian using time series of egg mass counts

The decline in amphibian populations is one of the starkest examples of the biodiversity crisis. For stream breeding amphibians, alterations to natural flow regimes by dams, water diversions, and climate change have been implicated in declines and extirpations. Identifying drivers of amphibian declines requires long time series of abundance data because amphibian populations can exhibit high natur
Authors
Jonathan P. Rose, Sarah J. Kupferberg, Ryan A. Peek, Don Ashton, James B. Bettaso, Steven Bobzien, Ryan M. Bourque, Koen G.H. Breedveld, Alessandro Catenazzi, Joseph E. Drennan, Earl Gonsolin, Marcia Grefsrud, Andrea E. Herman, Matthew R. House, Matt R. Kluber, Amy J. Lind, Karla R. Marlow, Alan Striegle, Michael van Hattem, Clara A. Wheeler, Jeffery T. Wilcox, Kevin D. Wiseman, Brian J. Halstead
By
Ecosystems Mission Area, Western Ecological Research Center (WERC)

Keeping the heat on: Weighted surveillance for Chytrid fungus (Batrachochytirum dendrobatidis) in Dixie Valley toads (Anaxyrus [= Bufo] williamsi)

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecu
Authors
Matthew J. Forrest, Brian J. Halstead, Daniel A. Grear, Patrick M. Kleeman, Brian D. Todd, Oliver J. Miano, Kris D. Urquhart
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Ecosystems Mission Area, National Wildlife Health Center, Western Ecological Research Center (WERC)

Survival and establishment of captive-reared and translocated giant gartersnakes after release

Many imperiled species face increasing extinction risk that requires interventional management like translocation or captive rearing. The use of translocations to successfully restore or create populations requires that animals survive at recipient sites, information that is often lacking for imperiled species and that can be risky to acquire if not obtained before a species has dwindled in number
Authors
Allison M. Nguyen, Brian D Todd, Brian J. Halstead
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century

Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with climate change.
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Gary M. Fellers
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Ecosystems Mission Area, Western Ecological Research Center (WERC)

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 temperatur
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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

The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys and samplin
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

This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point
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Western Ecological Research Center (WERC)

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 gartersnake (
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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 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. This code
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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 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

The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variab
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Western Ecological Research Center (WERC)

Code to analyze survival data for Giant gatersnakes, Thamnophis gigas in Sacramento County, California from 2018 to 2021

The purpose of this study was to estimate the survival of giant gartersnakes (Thamnophis gigas) prior to and following translocation, as well as to evaluate the use of captive rearing as a conservation tool for giant gartersnakes. We used Kaplan-Meier and Cox Proportional Hazards models to estimate survival rates and estimate the effects of group identity (marsh donor, rice donor, and translocatio
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Western Ecological Research Center (WERC)

Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021

-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model published by Duart
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Western Ecological Research Center (WERC)

Code to analyze Capture-Mark-Recapture data of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia)

Code files "growth_analysis.R" -An R script to fit the von Bertalanffy growth model to growth data from San Francisco gartersnakes. The von Bertalanffy growth model is fit using JAGS software (Plummer 2003), and is based on the model presented in Armstrong and Brooks (2013). "survival_analysis.R" -An R script to fit the robust-design Cormack-Jolly-Seber model to capture-mark-recapture data from
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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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