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 San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. We also used temporally sampled datasets to examine the magnitude of genetic change over time.

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 San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. We also used temporally sampled datasets to examine the magnitude of genetic change over time.

These data include site information for call count stations used to monitor secretive marshbirds, specifically Yuma Ridgway's rail (Rallus obsoletus yumanensis), at and near the Salton Sea and Sonny Bono Salton Sea National Wildlife Refuge (SBSSNWR) in 2016 and complete count information for four species of secretive marshbird [Yuma Ridgway's rail, Virginia rail (Rallus limicola), Sora (Porzana carolina), American bittern (Botaurus lentiginosus)], detected among surveys at those sites between March 8 and April 17, 2016. Also included is location information from Yuma Ridgway’s rails marked with radio-downloaded GPS transmitters and tracked between April 4 and November 17, 2016.

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 spatial scale as mtDNA and microsatellite data collected on the full sample, and (3) inform recovery efforts lacking direction from genetics. Cluster and tree-based analyses reveal a recent shared history between many populations that are now isolated, and that contemporary structure is linked to geophysical features that influence precipitation patterns and locations of former suitable habitat. Past hybridization with the sister species Gambelia wislizenii in southern San Joaquin Desert has generated a stable, but now-isolated population with different species identities for the mtDNA and nuclear genomes. The three marker types converged on similar themes, despite substantially fewer samples in the RADseq datasets; however, RADseq inferences were sensitive to dataset assembly filters that account for sequencing error, particularly cluster assignments. We suggest ways in which these data can be used to improve recovery efforts for G. sila and offer guidelines for RADseq dataset assembly in studies of intraspecific population structure.

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.

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.

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.

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.

This dataset contains records of Gulf of Mexico (GOM) blue crab (Callinectes sapidus), white shrimp (Litopenaeus setiferus), brown shrimp (Farfantepenaeus aztecus), and fishes which can be used to quantify their population abundances and distributions. The data set contains existing data as a baseline and supplemental data from continued sampling. It contains records of early life stage blue crab, white shrimp, brown shrimp, and fishes (measurements and counts) from beach seine and trawl samples across the north GOM in the central Gulf States that were collected using standardized sampling methods. Data also include habitat assessments such as descriptions, georeferencing information, and abiotic factors (DO, salinity, temperature).

Six metrics were used to determine Population Vulnerability: global population size, annual occurrence in the California Current System (CCS), percent of the population present in the CCS, threat status, breeding score, and annual adult survival. Global Population size (POP)—to determine population size estimates for each species we gathered information tabulated by American Bird Conservancy, Birdlife International, and other primary sources. Proportion of Population in CCS (CCSpop)—for each species, we generated the population size within the CCS by averaging region-wide population estimates, or by combining state estimates for California, Oregon, and Washington for each species (if estimates were not available for a region or state, “NA” was recorded in place of a value) and then dividing the CCSpop value by the estimated global population size (POP) to yield the percentage of the population occurring in the CCS. Annual Occurrence in the CCS (AO)—for each species, we estimated the number of months per year within the CCS and binned this estimate into three categories: 1–4 months, 5–8 months, or 9–12 months. Threat Status (TS)—for each species, we used the International Union for Conservation of Nature (IUCN) species threat status (IUCN 2014) and the U.S. Fish and Wildlife national threat status lists (USFWS 2014) to determine TS values for each species. If available, we also evaluated threat status values from state and international agencies. Breeding Score (BR)—we determined the degree to which a species breeds and feeds its young in the CCS according to 3 categories: breeds in the CCS, may breed in the CCS, or does not breed in the CCS. Adult Survival (AS)—for each species, we referenced information to estimate adult annual survival, because adult survival among marine birds in general is the most important demographic factor that can affect population growth rate and therefore inform vulnerability. These data support the following publication: Adams, J., Kelsey, E.C., Felis J.J., and Pereksta, D.M., 2016, Collision and displacement vulnerability among marine birds of the California Current System associated with offshore wind energy infrastructure: U.S. Geological Survey Open-File Report 2016-1154, 116 p., https://doi.org/10.3133/ofr20161154. These data were revisied in June 2017 and the revision published in August 2017. Please be advised to use CCS_vulnerability_FINAL_VERSION_v9_PV.csv