This dataset contains 253 samples from 11 occurrences of Chloropyron molle subsp. molle, and 3 occurrences of Chloropyron molle hispidum. Genomic markers were generated from ddRAD loci and analyzed using the Stacks v2.60 pipeline. The genotypes for all samples are provided in a VCF file with 40,707 independent loci . A companion sample data file is provided with sample names, and occurrence designations, and other data. 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 program to calculate genetic diversity statistics, or loaded into R, using vcfR, for further analysis.

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 program (Catchen and others, 2013) to calculate genetic diversity statistics, or loaded into R, using vcfR (Knaus and Grunwald, 2017), for further analysis. References: Catchen J., Hohenlohe P.A., Bassham S., Amores A., Cresko W.A. Stacks-an analysis tool set for population genomics. Molecular Ecology. 2013; 22:3124-3140. Knaus, B.J, Grunwald N.J. vcfr: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources. 2016; 17:44-53. Peterson B.K., Weber J.N., Kay E.H., Fisher H.S., Hoekstra H.E. Double Digest RADseq-an inexpensive method for de novo SNP discovery and genotyping in model and non-model species: PLoS ONE. 2012; 7:e37135.

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 program (Catchen and others, 2013) to calculate genetic diversity statistics, or loaded into R, using vcfR (Knaus and Grunwald, 2017), for further analysis. References: Catchen J., Hohenlohe P.A., Bassham S., Amores A., Cresko W.A. Stacks-an analysis tool set for population genomics. Molecular Ecology. 2013; 22:3124-3140. Knaus, B.J, Grunwald N.J. vcfr: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources. 2016; 17:44-53. Peterson B.K., Weber J.N., Kay E.H., Fisher H.S., Hoekstra H.E. Double Digest RADseq-an inexpensive method for de novo SNP discovery and genotyping in model and non-model species: PLoS ONE. 2012; 7:e37135.

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.

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.

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.

These data show multilocus genotypes, banding age, and territory for coastal cactus wrens (Campylorhynchus brunneicapillus) sampled in coastal Southern California between 2009 and 2019.

These data show multilocus genotypes, banding age, and territory for coastal cactus wrens (Campylorhynchus brunneicapillus) sampled in coastal Southern California between 2009 and 2019.

These data show multilocus genotypes for Chylismia brevipes sampled from natural populations throughout the Mojave Desert of California, Nevada, and Arizona from 2016 to 2019. The data release contains two vcf files with SNPs from single-end Restriction-site associated DNA sequencing (RADSeq), which differ in the restriction enzyme used during sequencing. One file contains PstI genotypes, and the other SbfI genotypes.