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: 18
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 to Fit an Integrated Population Model for the Foothill Yellow-legged Frog, Rana boylii, in Northern California
These data include egg mass counts and adult capture-mark-recapture histories for Foothill Yellow-legged frogs (Rana boylii) at two streams in northern California. Data were collected from the South Fork Eel River and its tributary, Fox Creek, from 1993-2019. Data from Hurdygurdy Creek were collected from 2002-2008.
This code and data support the following publication:
Rose, JP, Kupferberg, SJ
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. published in Journal of W
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: 29
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
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
Authors
Jonathan P. Rose, Sarah Kupferberg, Clara A Wheeler, Patrick M. Kleeman, Brian J. Halstead
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
Authors
Brian J. Halstead, Jonathan P. Rose, Patrick M. Kleeman
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
Authors
Kristen J. Fouts, Richard Kim, Anna C. Jordan, Alexandria M. Fulton, Jonathan P. Rose, Julia S. M. Ersan, Brian J. Halstead
Integrating multiple data sources and multi-scale land-cover data to model the distribution of a declining amphibian
Determining the spatial scale at which landscape features influence population persistence is an important task for conservation planning. One challenge is that sampling biases confound factors that influence species occurrence and survey effort. Recent developments in Point Process Models (PPMs) enable researchers to disentangle the sampling process from ecological drivers of species' distributio
Authors
Jonathan P. Rose, Brian J. Halstead, Robert N. Fisher
Demographic factors affecting population growth in giant gartersnakes
Demographic models provide insight into which vital rates and life stages contribute most to population growth. Integral projection models (IPMs) offer flexibility in matching model structure to a species’ demography. For many rare species, data are lacking for key vital rates, and uncertainty might dissuade researchers from attempting to build a demographic model. We present work that highlights
Authors
Jonathan P. Rose, Julia Ersan, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Monitoring protocol development and assessment for narrowly endemic toads in Nevada, 2018
Several species and subspecies of toads are endemic to small spring systems in the Great Basin, and their restricted ranges and habitat extent make them vulnerable to environmental perturbations. Very little is known about several of these toad populations, so a group of stakeholders including the U.S. Geological Survey, U.S. Fish and Wildlife Service, Bureau of Land Management, Nevada Department
Authors
Brian J. Halstead, Patrick M. Kleeman, Adam Duarte, Jonathan P. Rose, Kris Urquhart, Chad Mellison, Kevin Guadalupe, Melanie Cota, Rachel Van Horne, Alexa Killion, Kelsey Ruehling
Conservation reliance of a threatened snake on rice agriculture
Conservation-reliant species require perpetual management by humans to persist. But do species that persist largely in human-dominated landscapes actually require conditions maintained by humans? Because most extant populations of giant gartersnakes (Thamnophis gigas) inhabit the highly modified rice agricultural regions of the Sacramento Valley, we sought to evaluate whether giant gartersnakes ar
Authors
Brian J. Halstead, Jonathan P. Rose, Gabriel Reyes, Glenn D. Wylie, Michael L. Casazza
Time-to-detection occupancy modeling: An efficient method for analyzing the occurrence of amphibians and reptiles
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
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose
Integrating growth and capture–mark–recapture models reveals size‐dependent survival in an elusive species
Survival is a key vital rate for projecting the viability of wild populations. Estimating survival is difficult for many rare or elusive species because recapture rates of marked individuals are low, and the ultimate fate of individuals is unknown. Low recapture rates for many species have made it difficult to accurately estimate survival, and to evaluate the importance of individual and environme
Authors
Jonathan P. Rose, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Findings from a preliminary investigation of the effects of aquatic habitat (water) availability on giant gartersnake (Thamnophis gigas) demography in the Sacramento Valley, California, 2014–17
The giant gartersnake (Thamnophis gigas) is a semi-aquatic species of snake precinctive to the Central Valley of California. Because the Central Valley has experienced a substantial loss of wetland habitat, giant gartersnake populations are largely found in aquatic habitats associated with rice agriculture. In dry years, less water may be available for rice agriculture, resulting in less aquatic h
Authors
Jonathan P. Rose, Julia S. M. Ersan, Gabriel A. Reyes, K. Benjamin Gustafson, Alexandria M. Fulton, Kristen J. Fouts, Raymund F. Wack, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Reproductive frequency and size-dependence of fecundity in the Giant Gartersnake (Thamnophis gigas)
How reproductive output changes with age or size is a key life-history trait that can affect which demographic rates most influence population growth. Although many studies have investigated the reproductive ecology of gartersnakes, we know little about reproduction in the threatened Giant Gartersnake, Thamnophis gigas. We used X-radiography to determine reproductive status and estimated fecundity
Authors
Jonathan P. Rose, Julia Ersan, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Science and Products
Filter Total Items: 18
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 to Fit an Integrated Population Model for the Foothill Yellow-legged Frog, Rana boylii, in Northern California
These data include egg mass counts and adult capture-mark-recapture histories for Foothill Yellow-legged frogs (Rana boylii) at two streams in northern California. Data were collected from the South Fork Eel River and its tributary, Fox Creek, from 1993-2019. Data from Hurdygurdy Creek were collected from 2002-2008.
This code and data support the following publication:
Rose, JP, Kupferberg, SJ
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. published in Journal of W
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: 29
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
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
Authors
Jonathan P. Rose, Sarah Kupferberg, Clara A Wheeler, Patrick M. Kleeman, Brian J. Halstead
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
Authors
Brian J. Halstead, Jonathan P. Rose, Patrick M. Kleeman
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
Authors
Kristen J. Fouts, Richard Kim, Anna C. Jordan, Alexandria M. Fulton, Jonathan P. Rose, Julia S. M. Ersan, Brian J. Halstead
Integrating multiple data sources and multi-scale land-cover data to model the distribution of a declining amphibian
Determining the spatial scale at which landscape features influence population persistence is an important task for conservation planning. One challenge is that sampling biases confound factors that influence species occurrence and survey effort. Recent developments in Point Process Models (PPMs) enable researchers to disentangle the sampling process from ecological drivers of species' distributio
Authors
Jonathan P. Rose, Brian J. Halstead, Robert N. Fisher
Demographic factors affecting population growth in giant gartersnakes
Demographic models provide insight into which vital rates and life stages contribute most to population growth. Integral projection models (IPMs) offer flexibility in matching model structure to a species’ demography. For many rare species, data are lacking for key vital rates, and uncertainty might dissuade researchers from attempting to build a demographic model. We present work that highlights
Authors
Jonathan P. Rose, Julia Ersan, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Monitoring protocol development and assessment for narrowly endemic toads in Nevada, 2018
Several species and subspecies of toads are endemic to small spring systems in the Great Basin, and their restricted ranges and habitat extent make them vulnerable to environmental perturbations. Very little is known about several of these toad populations, so a group of stakeholders including the U.S. Geological Survey, U.S. Fish and Wildlife Service, Bureau of Land Management, Nevada Department
Authors
Brian J. Halstead, Patrick M. Kleeman, Adam Duarte, Jonathan P. Rose, Kris Urquhart, Chad Mellison, Kevin Guadalupe, Melanie Cota, Rachel Van Horne, Alexa Killion, Kelsey Ruehling
Conservation reliance of a threatened snake on rice agriculture
Conservation-reliant species require perpetual management by humans to persist. But do species that persist largely in human-dominated landscapes actually require conditions maintained by humans? Because most extant populations of giant gartersnakes (Thamnophis gigas) inhabit the highly modified rice agricultural regions of the Sacramento Valley, we sought to evaluate whether giant gartersnakes ar
Authors
Brian J. Halstead, Jonathan P. Rose, Gabriel Reyes, Glenn D. Wylie, Michael L. Casazza
Time-to-detection occupancy modeling: An efficient method for analyzing the occurrence of amphibians and reptiles
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
Authors
Brian J. Halstead, Patrick M. Kleeman, Jonathan P. Rose
Integrating growth and capture–mark–recapture models reveals size‐dependent survival in an elusive species
Survival is a key vital rate for projecting the viability of wild populations. Estimating survival is difficult for many rare or elusive species because recapture rates of marked individuals are low, and the ultimate fate of individuals is unknown. Low recapture rates for many species have made it difficult to accurately estimate survival, and to evaluate the importance of individual and environme
Authors
Jonathan P. Rose, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Findings from a preliminary investigation of the effects of aquatic habitat (water) availability on giant gartersnake (Thamnophis gigas) demography in the Sacramento Valley, California, 2014–17
The giant gartersnake (Thamnophis gigas) is a semi-aquatic species of snake precinctive to the Central Valley of California. Because the Central Valley has experienced a substantial loss of wetland habitat, giant gartersnake populations are largely found in aquatic habitats associated with rice agriculture. In dry years, less water may be available for rice agriculture, resulting in less aquatic h
Authors
Jonathan P. Rose, Julia S. M. Ersan, Gabriel A. Reyes, K. Benjamin Gustafson, Alexandria M. Fulton, Kristen J. Fouts, Raymund F. Wack, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead
Reproductive frequency and size-dependence of fecundity in the Giant Gartersnake (Thamnophis gigas)
How reproductive output changes with age or size is a key life-history trait that can affect which demographic rates most influence population growth. Although many studies have investigated the reproductive ecology of gartersnakes, we know little about reproduction in the threatened Giant Gartersnake, Thamnophis gigas. We used X-radiography to determine reproductive status and estimated fecundity
Authors
Jonathan P. Rose, Julia Ersan, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead