Filters: partyWithName: Jonathan P Rose (X)
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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.A., Rose, J.P., and Fisher, R.N., 2021. Conservation implications of spatiotemporal variation in the terrestrial ecology of an ephemeral pool-breeding amphibian. The Journal of Wildlife Management.
Categories: Data;
Tags: California,
Orange County,
Southern California,
Spea hammondii,
USGS Science Data Catalog (SDC),
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.
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.
Categories: Data;
Types: Downloadable,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service,
Shapefile;
Tags: California,
Ecology,
Marin County,
Point Reyes National Seashore,
USGS Science Data Catalog (SDC),
Code for fitting Integrated Population Models was adapted from Kéry and Schaub (2012). The Goodness-of-Fit test for the egg-mass count state space model was based on Besbeas and Morgan (2014). Analyses were performed in R version 3.6.1 (R Core Team 2019). References: Besbeas, P. and Morgan, B.J., 2014. Goodness‐of‐fit of integrated population models using calibrated simulation. Methods in Ecology and Evolution, 5(12), pp.1373-1382. https://doi.org/10.1111/2041-210X.12279 Kéry, M. and Schaub, M., 2012. Bayesian population analysis using WinBUGS: a hierarchical perspective. Academic Press. R Core Team, 2019. R: a language and environment for statistical computing. https://www.r-project.org/
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 drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the population structure, genetic diversity and abundance of seven focal sites of the endangered...
A study comparing reintroduction scenarios for the San Francisco gartersnake (Thamnophis sirtalis tetrataenia), an endangered subspecies native to San Mateo County and Santa Cruz County in northern California. Models for snake survival, growth, fecundity, and reproductive status were used to construct a demographic population model. Data are posterior distributions for demographic parameters from Markov Chain Monte Carlo sampling in hierarchical Bayesian models. These data support the following publication: Rose, J.P., Kim, R., Schoening, E.J., Lien, P.C., and Halstead, B.J., 2023. Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic...
Categories: Data;
Tags: California,
San Mateo County,
USGS Science Data Catalog (SDC),
Wildlife Biology,
biota,
Capture-mark-recapture data from San Francisco Gartersnakes at five sites in San Mateo County, California in 2018. These data include capture histories, snout-vent lengths, and sex for individual snakes. R files included with the data fit closed capture-mark-recapture models to estimate the abundance of adult snakes at each site in 2018.
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 known about its ecology and habitat requirements. These data represent the results of surveys for Dixie Valley Toads conducted from April 2018 to May 2021 in Churchill County, Nevada, USA and associated covariates from surveys and study sites. The potential wetland habitat for the Dixie Valley Toad was divided into 20...
Adult female San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) were captured and examined using an ultrasound device to determine if they were gravid and count the number of embryos in those that were. Morphological data including length and mass were collected for each snake, along with the date of capture and a study site identifier. These data support the following publication: Rose, J.P., Kim, R., Schoening, E.J., Lien, P.C., and Halstead, B.J., 2023. Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models. PLoS ONE 18(10): e0292379. https://doi.org/10.1371/journal.pone.0292379
Categories: Data;
Tags: Ecology,
San Mateo County,
USGS Science Data Catalog (SDC),
Wildlife Biology,
biota,
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, Wheeler, CA, Kleeman, PM, and Halstead BJ. 2021. Estimating the survival of unobservable life stages for a declining frog with a complex life history. Ecosphere. 12(2):e03381.
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 large-scale patterns in land cover might better explain the distribution of other life stages. Using a conditional multi-scale model, we evaluated which aspects of the landscape and local environment are most strongly related to occupancy patterns of western spadefoots (Spea hammondii). These data describe the survey, pool,...
Categories: Data;
Tags: California,
USGS Science Data Catalog (SDC),
amphibians,
biota,
terrestrial ecosystems,
This dataset contains the survey effort by U.S. Geological Survey (USGS) biologists sampling for Temblor legless lizards (Anniella alexanderae) in 2022 and 2023, the results of those surveys, and environmental covariates relevant to detection and occupancy of this species. At the time of the species description, little was known about the distribution of the Temblor legless lizard beyond a few localities. Surveys were designed to gather information on the distribution of Temblor legless lizards to help inform a Species Status Assessment by the U.S. Fish and Wildlife Service. Binary values for each year indicate whether Temblor legless lizards were detected under cover boards at a site in that year (1) or were not...
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 surveyed for the same amount of effort, which would support more precise estimation of covariate effects to improve inference about underlying ecological processes. Time-to-detection surveys allow the estimation of detection probability based on a single site visit by one observer, and therefore might be an efficient technique...
Categories: Data;
Tags: California,
Ecology,
Marin County,
Point Reyes National Seashore,
USGS Science Data Catalog (SDC),
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 are supported by the following publication: Fulton, A.M., Rose, J.P., and Halstead, B.J., 2022. Are sardines or dry cat food more effective as bait for capturing Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans)? Western North American Naturalist, 82(3), p.14. https://scholarsarchive.byu.edu/wnan/vol82/iss3/14.
Categories: Data;
Tags: Sacramento Valley, California,
USGS Science Data Catalog (SDC),
Wildlife Biology,
animal behavior,
bait,
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 following publication: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C. and Halstead, B.J., 2022. Integrating growth and survival models for flexible estimation of size-dependent survival in a cryptic, endangered snake. Ecology and Evolution, 12(4), https://doi.org/10.1002/ece3.8799.
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 habitat data from each trapped site and data on the capture rate of fish, frogs, and tadpoles at each site. These data support the following publication: Fulton, A.M., Rose, J.P. and Halstead, B.J., 2022. Rural turtles: estimating the occupancy of northwestern pond turtles and non-native red-eared sliders in agricultural...
This data release 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 Wildlife Management in 2019.
This dataset includes data on the growth, fecundity, and survival of Giant Gartersnakes (Thamnophis gigas) in the Sacramento Valley of California from 1995-2017. These data support the following publication: Rose, J.P., Ersan, J.S., Wylie, G.D., Casazza, M.L. and Halstead, B.J., 2019. Demographic factors affecting population growth in giant gartersnakes. The Journal of Wildlife Management, 83(7), pp.1540-1551.
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, and dynamic variables including surveyors, when surveys occurred, and site- and year-specific weather variables. These data were used to fit the models in the accompanying publication and can be used with the associated code to replicate the results found in the publication. These data support the following publication:...
Categories: Data;
Tags: Biological Occurrence,
Ecology,
USGS Science Data Catalog (SDC),
Wildlife Biology,
Yosemite National Park,
An updated version has been published: Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Northwestern pond turtle survey data in northern California forest streams, 2021-2022: U.S. Geological Survey data release, https://doi.org/10.5066/P96GAPCC. These data are from joint visual encounter and environmental DNA (eDNA) surveys conducted for northwestern pond turtles (Actinemys marmorata) in streams on privately-owned timberlands in northern California.
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