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
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.
Western Spadefoot Habitat Selection Based on Radio Telemetry in Orange County, California 2019
We conducted a radio telemetry study of adult western spadefoots (Spea hammondii) at 2 sites in southern California to characterize their survival, behavior, and movements from breeding through aestivation to inform conservation and management for the species.
These data support the following publication:
Halstead, B.J., Baumberger, K.L., Backlin, A.R., Kleeman, P.M., Wong, M.N., Gallegos, E.
Code and Data Files to Construct an Integral Projection Model for Giant Gartersnakes (Thamnophis gigas) in the Sacramento Valley, California, 1995-2017
This dataset includes data on the growth, fecundity, and survival of Giant Gartersnakes (Thamnophis gigas) in the Sacramento Valley of California from 1995-2017. In addition, the dataset includes R code to replicate the Integral Projection Model construction and analysis presented in the paper "Demographic drivers of population growth in a threatened snake" by Rose et al.
Time to detection data for Point Reyes pond-breeding amphibians, 2017
Occupancy models provide a reliable method of estimating species distributions while accounting for imperfect detectability. The cost of accounting for false absences is that detection and nondetection surveys typically require repeated visits to a site or multiple-observer techniques. More efficient methods of collecting data to estimate detection probabilities would allow additional sites to be
Filter Total Items: 24
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
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
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
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
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
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,
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
Combining genetic and demographic monitoring better informs conservation of an endangered urban snake
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
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
Estimating the survival of unobservable life stages for a declining frog with a complex life-history
Demographic models enhance understanding of drivers of population growth and inform conservation efforts to prevent population declines and extinction. For species with complex life histories, however, parameterizing demographic models is challenging because some life stages can be difficult to study directly. Integrated population models (IPMs) empower researchers to estimate vital rates for orga
Time-to-detection occupancy methods: Performance and utility for improving efficiency of surveys
Occupancy methods propelled the quantitative study of species distributions forward by separating the observation process, or the imperfect detectability of species, from the ecological processes of interest governing species distributions. Occupancy studies come at a cost, however: the collection of additional data to account for nondetections at sites where the species is present. The most commo
Distribution of giant gartersnakes (Thamnophis gigas) in the Sacramento–San Joaquin Delta, California, 2018–2019
SummaryWe examined the occurrence of giant gartersnakes in the Sacramento–San Joaquin Delta, California, in 2018 and 2019. We made eight captures of seven giant gartersnakes (three females, four males) in 2018, and six captures of six giant gartersnakes (four females, two males) in 2019. Detection probabilities were exceedingly low despite using methods that achieve much higher detection probabili
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 publishe
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
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, 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.Western Spadefoot Habitat Selection Based on Radio Telemetry in Orange County, California 2019
We conducted a radio telemetry study of adult western spadefoots (Spea hammondii) at 2 sites in southern California to characterize their survival, behavior, and movements from breeding through aestivation to inform conservation and management for the species. These data support the following publication: Halstead, B.J., Baumberger, K.L., Backlin, A.R., Kleeman, P.M., Wong, M.N., Gallegos, E.Code and Data Files to Construct an Integral Projection Model for Giant Gartersnakes (Thamnophis gigas) in the Sacramento Valley, California, 1995-2017
This dataset includes data on the growth, fecundity, and survival of Giant Gartersnakes (Thamnophis gigas) in the Sacramento Valley of California from 1995-2017. In addition, the dataset includes R code to replicate the Integral Projection Model construction and analysis presented in the paper "Demographic drivers of population growth in a threatened snake" by Rose et al.Time to detection data for Point Reyes pond-breeding amphibians, 2017
Occupancy models provide a reliable method of estimating species distributions while accounting for imperfect detectability. The cost of accounting for false absences is that detection and nondetection surveys typically require repeated visits to a site or multiple-observer techniques. More efficient methods of collecting data to estimate detection probabilities would allow additional sites to be - Publications
Filter Total Items: 24
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. SaHot, 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 (AnaxyrusRural 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 rangIntegrating 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–rMulti-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 laConservation 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,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 mecCombining genetic and demographic monitoring better informs conservation of an endangered urban snake
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 geneticWater 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 foEstimating the survival of unobservable life stages for a declining frog with a complex life-history
Demographic models enhance understanding of drivers of population growth and inform conservation efforts to prevent population declines and extinction. For species with complex life histories, however, parameterizing demographic models is challenging because some life stages can be difficult to study directly. Integrated population models (IPMs) empower researchers to estimate vital rates for orgaTime-to-detection occupancy methods: Performance and utility for improving efficiency of surveys
Occupancy methods propelled the quantitative study of species distributions forward by separating the observation process, or the imperfect detectability of species, from the ecological processes of interest governing species distributions. Occupancy studies come at a cost, however: the collection of additional data to account for nondetections at sites where the species is present. The most commoDistribution of giant gartersnakes (Thamnophis gigas) in the Sacramento–San Joaquin Delta, California, 2018–2019
SummaryWe examined the occurrence of giant gartersnakes in the Sacramento–San Joaquin Delta, California, in 2018 and 2019. We made eight captures of seven giant gartersnakes (three females, four males) in 2018, and six captures of six giant gartersnakes (four females, two males) in 2019. Detection probabilities were exceedingly low despite using methods that achieve much higher detection probabili - Software
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 publisheCode 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