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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...
Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail ( Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11...
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Clapper Rail,
Fragmentation,
Microsatellites,
Population declines,
Ridgway’s rail,
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.
The Mogollon Narrowheaded gartersnake (Thamnophis rufipunctatus) and the Northern Mexican gartersnake (Thamnophis eques megalops) are both listed as Threatened under the Federal Endangered Species Act. Both species have a strong association with aquatic habitats, and these habitats have been highly altered from impoundments, land-use changes, and the introduction and spread of non-native aquatic species, which have contributed to declines in Arizona and New Mexico over the last 30-40 years. We characterized 125 microsatellite loci per species to generate genetic toolsets for use in long term genetic monitoring of populations. We evaluated microsatellite loci for missing data and several variability thresholds, which...
Categories: Data;
Tags: Arizona,
DNA sequencing,
Genetics,
New Mexico,
USGS Science Data Catalog (SDC),
Microsatellite data formatted for the software CONVERT, which includes dataset numerical IDs, sampling site names, and locus identifiers. Rows 291-294 provides information about the allele size ranges and repeat motif for each locus. Missing data are coded as ?.
Categories: Data;
Types: Citation;
Tags: California,
Carrizo Plain,
Cuyama River Watershed,
Gambelia sila,
Panoche Plateau,
Genetic samples in the form of a small blood sample were collected from 263 Bell’s vireos (Vireo bellii) in drainages throughout southern and central California, Arizona, southern Nevada, and southwestern Utah. We used population genomic techniques to delineate the range limit between the Least Bell’s Vireo (V. b. pusillus) and its conspecific geographical neighbor, the Arizona Bell’s Vireo (V. b. arizonae). This study provides a taxonomic classification of individuals sampled where the two subspecies meet. Moreover, it allows an estimate of genetic diversity and trends in both taxa, estimates sources and levels of dispersal and gene flow among drainages, and allows us to assess progress of recovery and effectiveness...
Microsatellite STRUCTURE input file that corresponds with the samples in the ‘refSampleLoc’ worksheet. Missing data are coded as -999.
Categories: Data;
Types: Citation;
Tags: California,
Carrizo Plain,
Cuyama River Watershed,
Gambelia sila,
Panoche Plateau,
This dataset contains genomic records from 184 California Gnatcatchers (Polioptila californica) collected at 18 sites in southern California (USA), 13 sites in Baja California (Mexico), and 17 sites in Baja California Sur (Mexico). Genomic markers were generated from ddRAD loci (Peterson and others, 2012) and analyzed using the Stacks v2.53 (Catchen and others, 2013) pipeline. The genotypes for all samples are provided in a VCF file with 84,125 independent loci and 7 percent missing data. A companion file is provided with sample names and occurrence designations. These files may be opened and edited in a text editor program, such as Notepad (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population...
Location information regarding samples taken for each individual.
Categories: Data;
Types: Citation;
Tags: California,
Carrizo Plain,
Cuyama River Watershed,
Gambelia sila,
Panoche Plateau,
The recency of large-scale land conversion in California’s San Joaquin Desert raises the probability that the region’s numerous endemic species still retain genetic signatures of historical population connectivity. If so, genomic data can serve as a guidance tool for conserving lands that once supported habitat for gene movement. We studied the genetic structuring of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, to (1) test whether patterns of population admixture could be used to delimit former habitat corridors in the pre-converted landscape, (2) evaluate whether restriction site associated DNA sequencing (RADseq) from a subset of samples can resolve structure at the same...
Types: Citation;
Tags: California,
Carrizo Plain,
Cuyama River Watershed,
Gambelia sila,
Panoche Plateau,
Location information regarding samples taken for each individual.
Categories: Data;
Types: Citation;
Tags: California,
Carrizo Plain,
Cuyama River Watershed,
Gambelia sila,
Panoche Plateau,
Location information regarding samples taken for each individual. This data sheet is to be used in conjunction with the 'Convert' file.
Categories: Data;
Types: Citation;
Tags: California,
Carrizo Plain,
Cuyama River Watershed,
Gambelia sila,
Panoche Plateau,
We used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia). As Thamnophis sirtalis tetrataenia is listed as endangered by the U.S. Fish and Wildlife Service (USFWS), sensitive location information can be made available upon request by contacting Brian J. Halstead and/or Amy G. Vandergast.
Categories: Data;
Tags: San Francisco Peninsula,
San Mateo County,
Santa Clara County,
Santa Cruz County,
Thamnophis,
This dataset includes location, field measurements, and descriptions of 330 Uma inornata sampled for the research study entitled “Sampling Across 20 Years (1996–2017) Reveals Loss of Diversity and Genetic Connectivity in the Coachella Valley Fringe-Toed Lizard (Uma inornata)”. Field sampling occurred between March and September of 2017 and between April and June of 2018. Lizards were located by visually searching dune habitat in all major populations. Sites included Windy Point, Willow Hole, Train Station, Whitewater, and the South Coachella Valley Preserve. In addition, satellite populations in the Indio Hills and individuals salvaged from Section 24 and translocated to Stebbin’s Dune were also sampled. Lizards...
Categories: Data;
Tags: Riverside,
USGS Science Data Catalog (SDC),
Wildlife Biology,
animal populations,
biota,
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