Dr. Jonathan Rose conducts research on the population ecology reptiles and amphibians, with the goal of informing conservation of these taxa.
Jonathan analyzes capture-mark-recapture, occupancy, and movement data in a Bayesian framework, to estimate species' demographic vital rates, distributions, and space use. Jonathan is particularly interested in how species respond to changes in land cover and land use, and how species can persist in fragmented, human-dominated landscapes. Current projects include studying how the availability of aquatic habitat affects the demography and distribution of threatened Giant Gartersnakes (Thamnophis gigas) in the Sacramento Valley, California; population studies of endangered San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia); estimating the occupancy of Western Pond Turtles (Actinemys marmorata) in rice-growing regions of the Sacramento Valley; and modeling the distribution and population dynamics of amphibians of conservation concern in northern California.
RESEARCH INTERESTS
- Conservation Biology
- Population Ecology
- Herpetology
- Landscape Ecology
EDUCATION
- B.S. in Biology, University of Iowa, 2007
- M.A. in Geography, University of Iowa, 2010
- Ph.D. in Ecology, University of California, Davis, 2016
Google Scholar
Science and Products
Filter Total Items: 15
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:
Scho
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
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
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
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
Data 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)
These data represent the results of trapping efforts for native northwestern pond turtles (Actinemys marmorata) and non-native red-eared sliders (Trachemys scripta elegans) in wetlands and irrigation canals in agricultural regions of the Sacramento Valley in 2018 and the Sacramento-San Joaquin River Delta in 2019. In addition to detection data for these two turtle species, the dataset includes hab
USGS Occupancy Surveys for Dixie Valley Toads, Anaxyrus williamsi, in Churchill County, Nevada from April 2018 to May 2021
Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. The Dixie Valley Toad (Anaxyrus williamsi) is a recently described anuran species endemic to desert spring wetlands in the Dixie Valley, Churchill County, Nevada, USA. Given this species was only recently recognized as distinct from Anaxyrus boreas, little is
Time to First Detection of Northwestern Pond Turtles and Red-eared Sliders by Bait Type in the Sacramento Valley, California, 2018
These data provide the time to first detection in days of Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans) by trapping location and bait type in the Sacramento Valley, California, in 2018. Bait types evaluated include sardines and dry cat food. Only location, species, and bait type combinations that resulted in captures are included.
These data a
Growth and Capture-Mark-Recapture Data for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia, in San Mateo County, California from 2007 to 2020
This dataset includes records of captures of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) collected at five sites from 2007 to 2020. The data include measurements of snake snout-vent length to estimate growth patterns, snake sex, and the record of all captures of individual snakes for estimating capture probability, availability for capture, and survival.
These data support the fo
Western Spadefoot Survey Data in Northern and Central California (2019)
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas la
San Francisco Gartersnake (Thamnophis sirtalis tetrataenia) Genomic and Demographic Data from San Mateo County and Northeastern Santa Cruz County Collected Between 2016 - 2018
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic
Northwestern Pond Turtle Survey Data in Northern California Forest Streams (2021)
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
Filter Total Items: 28
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
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
Are canned sardines or dry cat food more effective as bait for capturing Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans)?
During an occupancy study of Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans) in California’s Sacramento Valley in 2018, we tested the relative effectiveness of 2 bait types: sardines packed in soybean oil and Meow Mix® Original Choice dry cat food. We sampled 116 sites with 2 traps each: one baited with sardines and one baited with dry cat food. Sa
Authors
Alexandria M Fulton, Jonathan P. Rose, Brian J. Halstead
Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat.Aims: We sought to model the occupancy dynamics of the Dixie Valley toad (Anaxyrus
Authors
Jonathan P. Rose, Patrick M. Kleeman, Brian J. Halstead
Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting our knowle
Authors
Brian J. Halstead, Patrick M. Kleeman, Graziella Vittoria Direnzo, Jonathan P. Rose
Rural turtles: Estimating the occupancy of Northwestern Pond Turtles and non-native red-eared sliders in agricultural habitats in California's Sacramento Valley and Sacramento-San Joaquin River Delta
The Northwestern Pond Turtle (Actinemys marmorata; WPT) was once widespread throughout the Sacramento Valley and the Sacramento-San Joaquin River Delta. Much of its historical range has been converted into agricultural land, reducing and altering aquatic habitat and surrounding uplands. Red-eared Sliders (Trachemys scripta elegans; RES) have been introduced throughout much of the existing WPT rang
Authors
Jonathan P. Rose, Brian J. Halstead, Alexandria M. Fulton
Integrating growth and survival models for flexible estimation of size-dependent survival in a cryptic, endangered snake
Estimates of demographic rates for animal populations and individuals have many applications for ecological and conservation research. In many animals, survival is size-dependent, but estimating the form of the size–survival relationship presents challenges. For elusive species with low recapture rates, individuals’ size will be unknown at many points in time. Integrating growth and capture–mark–r
Authors
Jonathan P. Rose, Richard Kim, Elliot James Schoenig, Patrick C. Lien, Brian J. Halstead
Multi-scale patterns in occurrence of an ephemeral pool-breeding amphibian
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas la
Authors
Brian J. Halstead, Jonathan P. Rose, Denise Clark, Patrick M. Kleeman, Robert N. Fisher
Projecting the remaining habitat for the western spadefoot (Spea hammondii) in heavily urbanized southern California
Extensive urbanization in coastal southern California has reduced natural habitat in this biodiversity hotspot. To better conserve ecological communities, state and federal agencies, along with local jurisdictions and private stakeholders, developed regional conservation plans for southern California. Although many protected areas exist within this region, the patchwork nature of these protected a
Authors
Jonathan P. Rose, Brian J. Halstead, Robert H. Packard, Robert N. Fisher
Conservation implications of spatiotemporal variation in the terrestrial ecology of Western spadefoots
Conservation of species reliant on ephemeral resources can be especially challenging in the face of a changing climate. Western spadefoots (Spea hammondii) are small burrowing anurans that breed in ephemeral pools, but adults spend the majority of their lives underground in adjacent terrestrial habitat. Western spadefoots are of conservation concern throughout their range because of habitat loss,
Authors
Brian J. Halstead, Katherine L. Baumberger, Adam R. Backlin, Patrick M. Kleeman, Monique Nicole Wong, Elizabeth Gallegos, Jonathan P. Rose, Robert N. Fisher
A tale of two valleys: Endangered species policy and the fate of the giant gartersnake
By the mid-20th Century, giant gartersnakes (Thamnophis gigas) had lost more than 90% of their Central Valley marsh habitat and were extirpated from more than two-thirds of their range. This massive habitat loss led to their inclusion in the inaugural list of rare species under the California Endangered Species Act (CESA). Listing under the CESA provided giant gartersnakes legal protection and mec
Authors
Brian J. Halstead, Patricia Valcarcel, Richard Kim, Anna Jordan, Jonathan P. Rose, Shannon Skalos, Gabriel Reyes, Julia Ersan, Michael L. Casazza, Allison Essert, Alexandria M Fulton
Water temperature and availability shape the spatial ecology of a hot springs endemic toad
Desert amphibians are limited to exploiting ephemeral resources and aestivating or to inhabiting scarce refuges of permanent water, such as springs. Understanding how amphibians use these resources is essential for their conservation. Dixie Valley Toads (Anaxyrus williamsi) are precinctive to a small system of cold and hot springs in the Dixie Valley, Nevada, USA. The toads have been petitioned fo
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Kristen J Fouts
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 (
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
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park
The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variab
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021
-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model published by Duart
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
Science and Products
- Data
Filter Total Items: 15
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: SchoDemographic 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 fromEgg 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 wereSurvey 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 liMulti-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, anData 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)
These data represent the results of trapping efforts for native northwestern pond turtles (Actinemys marmorata) and non-native red-eared sliders (Trachemys scripta elegans) in wetlands and irrigation canals in agricultural regions of the Sacramento Valley in 2018 and the Sacramento-San Joaquin River Delta in 2019. In addition to detection data for these two turtle species, the dataset includes habUSGS Occupancy Surveys for Dixie Valley Toads, Anaxyrus williamsi, in Churchill County, Nevada from April 2018 to May 2021
Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. The Dixie Valley Toad (Anaxyrus williamsi) is a recently described anuran species endemic to desert spring wetlands in the Dixie Valley, Churchill County, Nevada, USA. Given this species was only recently recognized as distinct from Anaxyrus boreas, little isTime to First Detection of Northwestern Pond Turtles and Red-eared Sliders by Bait Type in the Sacramento Valley, California, 2018
These data provide the time to first detection in days of Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans) by trapping location and bait type in the Sacramento Valley, California, in 2018. Bait types evaluated include sardines and dry cat food. Only location, species, and bait type combinations that resulted in captures are included. These data aGrowth and Capture-Mark-Recapture Data for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia, in San Mateo County, California from 2007 to 2020
This dataset includes records of captures of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) collected at five sites from 2007 to 2020. The data include measurements of snake snout-vent length to estimate growth patterns, snake sex, and the record of all captures of individual snakes for estimating capture probability, availability for capture, and survival. These data support the foWestern Spadefoot Survey Data in Northern and Central California (2019)
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas laSan Francisco Gartersnake (Thamnophis sirtalis tetrataenia) Genomic and Demographic Data from San Mateo County and Northeastern Santa Cruz County Collected Between 2016 - 2018
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of geneticNorthwestern Pond Turtle Survey Data in Northern California Forest Streams (2021)
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California. - Publications
Filter Total Items: 28
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 naturAuthorsJonathan 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. HalsteadSierra 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.AuthorsBrian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Gary M. FellersAre canned sardines or dry cat food more effective as bait for capturing Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans)?
During an occupancy study of Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans) in California’s Sacramento Valley in 2018, we tested the relative effectiveness of 2 bait types: sardines packed in soybean oil and Meow Mix® Original Choice dry cat food. We sampled 116 sites with 2 traps each: one baited with sardines and one baited with dry cat food. SaAuthorsAlexandria M Fulton, Jonathan P. Rose, Brian J. HalsteadHot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat.Aims: We sought to model the occupancy dynamics of the Dixie Valley toad (AnaxyrusAuthorsJonathan P. Rose, Patrick M. Kleeman, Brian J. HalsteadOptimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting our knowleAuthorsBrian J. Halstead, Patrick M. Kleeman, Graziella Vittoria Direnzo, Jonathan P. RoseRural turtles: Estimating the occupancy of Northwestern Pond Turtles and non-native red-eared sliders in agricultural habitats in California's Sacramento Valley and Sacramento-San Joaquin River Delta
The Northwestern Pond Turtle (Actinemys marmorata; WPT) was once widespread throughout the Sacramento Valley and the Sacramento-San Joaquin River Delta. Much of its historical range has been converted into agricultural land, reducing and altering aquatic habitat and surrounding uplands. Red-eared Sliders (Trachemys scripta elegans; RES) have been introduced throughout much of the existing WPT rangAuthorsJonathan P. Rose, Brian J. Halstead, Alexandria M. FultonIntegrating growth and survival models for flexible estimation of size-dependent survival in a cryptic, endangered snake
Estimates of demographic rates for animal populations and individuals have many applications for ecological and conservation research. In many animals, survival is size-dependent, but estimating the form of the size–survival relationship presents challenges. For elusive species with low recapture rates, individuals’ size will be unknown at many points in time. Integrating growth and capture–mark–rAuthorsJonathan P. Rose, Richard Kim, Elliot James Schoenig, Patrick C. Lien, Brian J. HalsteadMulti-scale patterns in occurrence of an ephemeral pool-breeding amphibian
Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas laAuthorsBrian J. Halstead, Jonathan P. Rose, Denise Clark, Patrick M. Kleeman, Robert N. FisherProjecting the remaining habitat for the western spadefoot (Spea hammondii) in heavily urbanized southern California
Extensive urbanization in coastal southern California has reduced natural habitat in this biodiversity hotspot. To better conserve ecological communities, state and federal agencies, along with local jurisdictions and private stakeholders, developed regional conservation plans for southern California. Although many protected areas exist within this region, the patchwork nature of these protected aAuthorsJonathan P. Rose, Brian J. Halstead, Robert H. Packard, Robert N. FisherConservation implications of spatiotemporal variation in the terrestrial ecology of Western spadefoots
Conservation of species reliant on ephemeral resources can be especially challenging in the face of a changing climate. Western spadefoots (Spea hammondii) are small burrowing anurans that breed in ephemeral pools, but adults spend the majority of their lives underground in adjacent terrestrial habitat. Western spadefoots are of conservation concern throughout their range because of habitat loss,AuthorsBrian J. Halstead, Katherine L. Baumberger, Adam R. Backlin, Patrick M. Kleeman, Monique Nicole Wong, Elizabeth Gallegos, Jonathan P. Rose, Robert N. FisherA tale of two valleys: Endangered species policy and the fate of the giant gartersnake
By the mid-20th Century, giant gartersnakes (Thamnophis gigas) had lost more than 90% of their Central Valley marsh habitat and were extirpated from more than two-thirds of their range. This massive habitat loss led to their inclusion in the inaugural list of rare species under the California Endangered Species Act (CESA). Listing under the CESA provided giant gartersnakes legal protection and mecAuthorsBrian J. Halstead, Patricia Valcarcel, Richard Kim, Anna Jordan, Jonathan P. Rose, Shannon Skalos, Gabriel Reyes, Julia Ersan, Michael L. Casazza, Allison Essert, Alexandria M FultonWater temperature and availability shape the spatial ecology of a hot springs endemic toad
Desert amphibians are limited to exploiting ephemeral resources and aestivating or to inhabiting scarce refuges of permanent water, such as springs. Understanding how amphibians use these resources is essential for their conservation. Dixie Valley Toads (Anaxyrus williamsi) are precinctive to a small system of cold and hot springs in the Dixie Valley, Nevada, USA. The toads have been petitioned foAuthorsBrian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose, Kristen J Fouts - Software
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 (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 codeCode 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) variabCode 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 DuartCode 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