Jonathan Rose
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: 24
Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022 Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022
These data include capture and survey information for a meadow population of endangered Sierra Nevada yellow-legged frogs (Rana sierrae) at Yosemite National Park, California, USA, 2003-2022. The data also include remotely sensed weather covariates related to winter severity (annual April snow water equivalent) and drought severity (Palmer drought severity index) to evaluate their...
Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California
Locations of sites at which U.S. Geological Survey (USGS) biologists surveyed for Temblor legless lizards (Anniella alexanderae) from 2022 to 2025 and the results of those surveys. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond a few localities. Surveys were designed to gather information on the distribution of Temblor...
Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model
These data represent the results of surveys for western spadefoots in southern California, including both presence and non-detection data. In addition, data include environmental covariates that were hypothesized to influence the occurrence of western spadefoots, such as land cover and distance to aquatic features. These data support the following publication: Rose, J.P., Halstead, B.J...
Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023 Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023
These data support a study modeling the growth, capture, and survival of giant gartersnakes (Thamnophis gigas). We captured giant gartersnakes inhabiting rice irrigation canals in the Sacramento Valley, California, USA from 2018 to 2023. We analyzed capture-mark-recapture data from 19 populations of giant gartersnakes sampled with an integrated growth-survival model. We tested how growth...
Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA
These data were collected to assess the occurrence of foothill yellow-legged frogs (Rana boylii) in 2022, one year after the 2021 Dixie Fire in northeastern California, USA. The data included herein are those required to replicate the occupancy analysis presented in the manuscript, cited in the larger work. Additional site data are included in the manuscript itself.
Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023 Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023
This dataset contains the survey effort by U.S. Geological Survey (USGS) biologists sampling for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023, the results of those surveys, and environmental covariates relevant to detection and occupancy of this species. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond...
Captures and Trapping Effort for Deer Mice (Peromyscus sonoriensis) at Point Reyes National Seashore, California, USA from 2021 to 2022 Captures and Trapping Effort for Deer Mice (Peromyscus sonoriensis) at Point Reyes National Seashore, California, USA from 2021 to 2022
These data represent trapping effort and captures of deer mice at Point Reyes National Seashore, Marin County, California. Deer mice were captured and marked with ear tags to allow identification of individuals. The location of captures can be used in a spatially explicit capture recapture model to estimate density of mice and how mouse density varies by site and habitat type.
Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022 Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
San Francisco Gartersnake Fecundity Data from San Mateo County, California Collected from 2019-2022 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...
Demographic Parameter Estimates for San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) for Fitting an Integral Projection Model 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...
Egg Mass Counts from Foothill Yellow-Legged Frogs (Rana boylii) in California from 1992-2021 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...
Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California, 2022 and 2023 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...
Filter Total Items: 34
Increased heterozygosity and body condition result from admixed translocation of the threatened Mogollon Narrow-headed Gartersnake (Thamnophis rufipunctatus) Increased heterozygosity and body condition result from admixed translocation of the threatened Mogollon Narrow-headed Gartersnake (Thamnophis rufipunctatus)
Enhancing gene flow through translocations can be a useful tool in recovering small and isolated populations. However, it is not devoid of genetic risks, such as outbreeding depression in future generations, that can have negative consequences in terms of the establishment and mean fitness of the population. Studies that monitor the long-term effects of genetic rescue on populations in...
Authors
Dustin A. Wood, Bruce L. Christman, Randy D. Jennings, Jonathan P. Rose, Erika M. Nowak, Justin Schofer, A.G. Vandergast
Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California
Reintroductions are used worldwide to increase the viability of species and restore native ecological communities. The success of reintroductions is usually judged by the establishment of self-sustaining populations, restoration of naturally occurring ecological communities, and the species resuming its ecological function. Recovery for the endangered San Francisco gartersnake (SFGS...
Authors
Jonathan P. Rose, Elliot J. Schoenig, Richard Kim, Allison M. Nguyen, Brian J. Halstead
Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence
Sierra Nevada ecosystems have been influenced by fire for millennia; however, increasing wildfire size and frequency may yield unforeseen consequences on wildlife populations and their distribution. Foothill yellow-legged frogs Rana boylii have declined in portions of their range and are considered a species of conservation concern. We surveyed streams for foothill yellow legged frogs in...
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose
Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA.
Non-native plants can affect communities through direct competition, and by providing refuge to seed predators, creating apparent competition with native plants. Ammophila arenaria (European beachgrass) has been introduced to coastal dune habitats throughout the western United States where it forms dense monocultures, stabilizes dunes, and alters abiotic and biotic conditions. The...
Authors
Jonathan P. Rose, Lorraine S Parsons, Patrick M. Kleeman, Brian J. Halstead
Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California
Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles (Actinemys marmorata) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand...
Authors
Brian J. Halstead, Patrick M. Kleeman, Caren S. Goldberg, Jonathan P. Rose
Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models 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...
Authors
Jonathan P. Rose, Richard Kim, Elliot J. Schoenig, Patrick C. Lien, Brian J. Halstead
Identifying drivers of population dynamics for a stream breeding amphibian using time series of egg mass counts 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...
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 Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century
Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with...
Authors
Brian J. Halstead, Patrick 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)? 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...
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 Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat.Aims: We sought to model the occupancy dynamics of the Dixie Valley toad...
Authors
Jonathan 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 Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting...
Authors
Brian J. Halstead, Patrick 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 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...
Authors
Jonathan P. Rose, Brian J. Halstead, Alexandria M. Fulton
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam
This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022 Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and...
Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae
This repository contains code to fit Multi-scale Occupancy Models to survey data for Temblor legless lizards (Anniella alexanderae) This repository specifically contains code to reproduce analyses in: Rose, J.P., Camp, S.M., Sheikh, Z.N., Johnson, C.B., Lei, S.H., Napolitano, G.R., Schoenig, E.J., Macias, D.A., Jordan, A.C., and Halstead, B.J. 2024. Multi-scale occupancy surveys reveal...
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California
The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys...
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore
This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice)...
Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia
This repository contains code to fit Integral Projection Models and simulate population reintroductions for San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) This repository specifically contains code to reproduce analyses in: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C., and Halstead, B.J. in-review. Comparing reintroduction strategies for the endangered San Francisco...
Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California
Code to fit a Multiple Population Viability Analysis (MPVA) to time series of Foothill yellow-legged frog (Rana boylii) egg mass counts. Rose, J.P., and Halstead, B.J., 2023, Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California: U.S. Geological Survey software release, https://doi.org/10.5066/P9QWX2GR...
Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019) Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019)
Code to reproduce analyses of turtle occupancy in the Sacramento Valley and Sacramento-San Joaquin River Delta
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park
The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g...
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021 Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021
-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model...
Code to analyze Capture-Mark-Recapture data of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) 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...
Science and Products
Filter Total Items: 24
Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022 Capture-Mark-Recapture and Covariate Data for Demography of Sierra Nevada Yellow-legged Frogs (Rana sierrae) at Summit Meadow, Yosemite National Park, California, 2003-2022
These data include capture and survey information for a meadow population of endangered Sierra Nevada yellow-legged frogs (Rana sierrae) at Yosemite National Park, California, USA, 2003-2022. The data also include remotely sensed weather covariates related to winter severity (annual April snow water equivalent) and drought severity (Palmer drought severity index) to evaluate their...
Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California
Locations of sites at which U.S. Geological Survey (USGS) biologists surveyed for Temblor legless lizards (Anniella alexanderae) from 2022 to 2025 and the results of those surveys. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond a few localities. Surveys were designed to gather information on the distribution of Temblor...
Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model Occurrence Data for the Western Spadefoot (Spea hammondii) in Southern California From 1995 to 2020 and Projected Species Distribution Model
These data represent the results of surveys for western spadefoots in southern California, including both presence and non-detection data. In addition, data include environmental covariates that were hypothesized to influence the occurrence of western spadefoots, such as land cover and distance to aquatic features. These data support the following publication: Rose, J.P., Halstead, B.J...
Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023 Growth and Capture Mark Recapture Data from Giant Gartersnakes (Thamnophis gigas) in Rice Irrigation Canals 2018 to 2023
These data support a study modeling the growth, capture, and survival of giant gartersnakes (Thamnophis gigas). We captured giant gartersnakes inhabiting rice irrigation canals in the Sacramento Valley, California, USA from 2018 to 2023. We analyzed capture-mark-recapture data from 19 populations of giant gartersnakes sampled with an integrated growth-survival model. We tested how growth...
Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA Foothill Yellow-Legged Frog (Rana boylii) 2022 Site and Survey Data In and Near the Footprint of the 2021 Dixie Fire, Northeastern California, USA
These data were collected to assess the occurrence of foothill yellow-legged frogs (Rana boylii) in 2022, one year after the 2021 Dixie Fire in northeastern California, USA. The data included herein are those required to replicate the occupancy analysis presented in the manuscript, cited in the larger work. Additional site data are included in the manuscript itself.
Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023 Occupancy Surveys for the Temblor Legless Lizard (Anniella alexanderae) in the San Joaquin Valley, California 2022 to 2023
This dataset contains the survey effort by U.S. Geological Survey (USGS) biologists sampling for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023, the results of those surveys, and environmental covariates relevant to detection and occupancy of this species. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond...
Captures and Trapping Effort for Deer Mice (Peromyscus sonoriensis) at Point Reyes National Seashore, California, USA from 2021 to 2022 Captures and Trapping Effort for Deer Mice (Peromyscus sonoriensis) at Point Reyes National Seashore, California, USA from 2021 to 2022
These data represent trapping effort and captures of deer mice at Point Reyes National Seashore, Marin County, California. Deer mice were captured and marked with ear tags to allow identification of individuals. The location of captures can be used in a spatially explicit capture recapture model to estimate density of mice and how mouse density varies by site and habitat type.
Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022 Northwestern Pond Turtle Survey Data in Northern California Forest Streams, 2021-2022
These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
San Francisco Gartersnake Fecundity Data from San Mateo County, California Collected from 2019-2022 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...
Demographic Parameter Estimates for San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) for Fitting an Integral Projection Model 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...
Egg Mass Counts from Foothill Yellow-Legged Frogs (Rana boylii) in California from 1992-2021 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...
Survey Results for Temblor Legless Lizards (Anniella alexanderae) in the San Joaquin Valley of California, 2022 and 2023 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...
Filter Total Items: 34
Increased heterozygosity and body condition result from admixed translocation of the threatened Mogollon Narrow-headed Gartersnake (Thamnophis rufipunctatus) Increased heterozygosity and body condition result from admixed translocation of the threatened Mogollon Narrow-headed Gartersnake (Thamnophis rufipunctatus)
Enhancing gene flow through translocations can be a useful tool in recovering small and isolated populations. However, it is not devoid of genetic risks, such as outbreeding depression in future generations, that can have negative consequences in terms of the establishment and mean fitness of the population. Studies that monitor the long-term effects of genetic rescue on populations in...
Authors
Dustin A. Wood, Bruce L. Christman, Randy D. Jennings, Jonathan P. Rose, Erika M. Nowak, Justin Schofer, A.G. Vandergast
Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California Assessing the Feasibility of Reintroducing San Francisco Gartersnakes (Thamnophis sirtalis tetrataenia) to La Honda Creek Open Space Preserve, San Mateo County, California
Reintroductions are used worldwide to increase the viability of species and restore native ecological communities. The success of reintroductions is usually judged by the establishment of self-sustaining populations, restoration of naturally occurring ecological communities, and the species resuming its ecological function. Recovery for the endangered San Francisco gartersnake (SFGS...
Authors
Jonathan P. Rose, Elliot J. Schoenig, Richard Kim, Allison M. Nguyen, Brian J. Halstead
Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence
Sierra Nevada ecosystems have been influenced by fire for millennia; however, increasing wildfire size and frequency may yield unforeseen consequences on wildlife populations and their distribution. Foothill yellow-legged frogs Rana boylii have declined in portions of their range and are considered a species of conservation concern. We surveyed streams for foothill yellow legged frogs in...
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose
Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA.
Non-native plants can affect communities through direct competition, and by providing refuge to seed predators, creating apparent competition with native plants. Ammophila arenaria (European beachgrass) has been introduced to coastal dune habitats throughout the western United States where it forms dense monocultures, stabilizes dunes, and alters abiotic and biotic conditions. The...
Authors
Jonathan P. Rose, Lorraine S Parsons, Patrick M. Kleeman, Brian J. Halstead
Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California
Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles (Actinemys marmorata) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand...
Authors
Brian J. Halstead, Patrick M. Kleeman, Caren S. Goldberg, Jonathan P. Rose
Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models 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...
Authors
Jonathan P. Rose, Richard Kim, Elliot J. Schoenig, Patrick C. Lien, Brian J. Halstead
Identifying drivers of population dynamics for a stream breeding amphibian using time series of egg mass counts 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...
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 Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century
Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with...
Authors
Brian J. Halstead, Patrick 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)? 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...
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 Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat.Aims: We sought to model the occupancy dynamics of the Dixie Valley toad...
Authors
Jonathan 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 Optimizing survey design for shasta salamanders (Hydromantes spp.) to estimate occurrence in little-studied portions of their range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting...
Authors
Brian J. Halstead, Patrick 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 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...
Authors
Jonathan P. Rose, Brian J. Halstead, Alexandria M. Fulton
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam
This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022 Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and...
Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae
This repository contains code to fit Multi-scale Occupancy Models to survey data for Temblor legless lizards (Anniella alexanderae) This repository specifically contains code to reproduce analyses in: Rose, J.P., Camp, S.M., Sheikh, Z.N., Johnson, C.B., Lei, S.H., Napolitano, G.R., Schoenig, E.J., Macias, D.A., Jordan, A.C., and Halstead, B.J. 2024. Multi-scale occupancy surveys reveal...
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California
The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys...
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore
This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice)...
Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia
This repository contains code to fit Integral Projection Models and simulate population reintroductions for San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) This repository specifically contains code to reproduce analyses in: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C., and Halstead, B.J. in-review. Comparing reintroduction strategies for the endangered San Francisco...
Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California
Code to fit a Multiple Population Viability Analysis (MPVA) to time series of Foothill yellow-legged frog (Rana boylii) egg mass counts. Rose, J.P., and Halstead, B.J., 2023, Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California: U.S. Geological Survey software release, https://doi.org/10.5066/P9QWX2GR...
Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019) Code to fit an occupancy model to trapping data for the northwestern pond turtle and red-eared slider in the Sacramento Valley (2018) and Sacramento-San Joaquin River Delta (2019)
Code to reproduce analyses of turtle occupancy in the Sacramento Valley and Sacramento-San Joaquin River Delta
Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park
The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g...
Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021 Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021
-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model...
Code to analyze Capture-Mark-Recapture data of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) 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...