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 sea-cliff bedstraw (Galium buxifolium) data set contains two types of information, formatted as CSV worksheets: 1) Spatial coordinates (WGS 84) of known population occurrences on Santa Cruz and San Miguel Islands, California, as of 2006 (sensitive locality information); 2) Demographic data measured at four populations growing on Santa Cruz Island. Three of the populations were measured in 2005 and 2006, the fourth was measured in 2005, 2006, 2008, 2010, 2011, and 2014.

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.

A shapefile representing greater sage-grouse (hereafter sage-grouse) space use and lek abundance in the Bi-State Distinct Population Segment (DPS) of California and Nevada. These data were derived by combining a kernel density estimation of sage-grouse lek abundance combined with another raster representing distance to lek. The 85 percent isopleth was then used to define "high space-use."

A shapefile representing greater sage-grouse (hereafter sage-grouse) space use and lek abundance in the Bi-State Distinct Population Segment (DPS) of California and Nevada. These data were derived by combining a kernel density estimation of sage-grouse lek abundance combined with another raster representing distance to lek. The 85 percent isopleth was then used to define "high space-use."

Greater sage-grouse (Centrocercus urophasianus; hereinafter sage-grouse) is a sagebrush obligate species and widely considered an indicator species for sagebrush ecosystems and other sagebrush-dependent species (Hanser and Knick, 2011; Prochazka and others, 2023). Sagebrush ecosystems are threatened by a wide range of disturbances and anthropogenic factors, including climate change, severe drought, altered wildfire regimes, expansion of invasive species, and anthropogenic development. Collectively, these threats have led to reduced ecological integrity and sage-grouse habitat quality within the sagebrush biome (Doherty and others, 2022). Steady and long-term declines in sage-grouse populations have led to large-scale efforts to improve population performance and prevent additional loss of habitat for sage-grouse and other sagebrush-dependent species (Coates and others, 2021). Due to their complex space use and habitat selection patterns during different life stages, requirements for large intact tracts of sagebrush, declining population trends, and status as a proposed protected species, sage-grouse have become integral to land management and conservation policy throughout the western United States (Western Association of Fish and Wildlife Agencies, 2015; Doherty and others, 2022). References cited: Coates, P.S., Prochazka, B.G., Aldridge, C.L., O’Donnell, M.S., Edmunds, D.R., Monroe, A.P., Hanser, S.E., Wiechman, L.A., and Chenaille, M.P., 2023, Range-wide population trend analysis for greater sage-grouse (Centrocercus urophasianus)-Updated 1960-2022: U.S. Geological Survey Data Report 1175, 17 p., accessed December 7, 2023, at [Available at https://doi.org/10.3133/dr1175.] Doherty, K., Theobald, D.M., Bradford, J.B., Wiechman, L.A., Bedrosian, G., Boyd, C.S., Cahill, M., Coates, P.S., Creutzburg, M.K., Crist, M.R., Finn, S.P., Kumar, A.V., Littlefield, C.E., Maestas, J.D., Prentice, K.L., Prochazka, B.G., Remington, T.E., Sparklin, W.D., Tull, J.C., Wurtzebach, Z., and Zeller, K.A., 2022, A sagebrush conservation design to proactively restore America’s sagebrush biome: U.S. Geological Survey Open-File Report 2022-1081, 38 p., accessed December 6, 2023, at https://doi.org/10.3133/ofr20221081. Hanser, S.E., and Knick, S.T., 2011, Greater sage-grouse as an umbrella species for shrubland passerine birds-A multiscale assessment, chap. 19 in Knick, S.T., eds., Greater sage grouse-Ecology and conservation of a landscape species and its habitats: University of California Press, p. 474-487. [Available at https://doi.org/10.1525/california/9780520267114.003.0020.] Prochazka, B.G., Coates, P.S., O’Donnell, M.S., Edmunds, D.R., Monroe, A.P., Ricca, M.A., Wann, G.T., Hanser, S.E., Wiechman, L.A., Doherty, K.E., Chenaille, M.P., and Aldridge, C.L., 2023, A targeted annual warning system developed for the conservation of a sagebrush indicator species: Ecological Indicators, v. 148. [Available at https://doi.org/10.1016/j.ecolind.2023.110097.] Western Association of Fish and Wildlife Agencies, 2015, Greater sage-grouse population trends: an analysis of lek count databases 1965-2015: Cheyenne, Wyo., Western Association of Fish and Wildlife Agencies, 55 p., accessed 07 12, 2023, at https://ir.library.oregonstate.edu/concern/technical_reports/ng451p621

Greater sage-grouse (Centrocercus urophasianus; hereinafter sage-grouse) is a sagebrush obligate species and widely considered an indicator species for sagebrush ecosystems and other sagebrush-dependent species (Hanser and Knick, 2011; Prochazka and others, 2023). Sagebrush ecosystems are threatened by a wide range of disturbances and anthropogenic factors, including climate change, severe drought, altered wildfire regimes, expansion of invasive species, and anthropogenic development. Collectively, these threats have led to reduced ecological integrity and sage-grouse habitat quality within the sagebrush biome (Doherty and others, 2022). Steady and long-term declines in sage-grouse populations have led to large-scale efforts to improve population performance and prevent additional loss of habitat for sage-grouse and other sagebrush-dependent species (Coates and others, 2021). Due to their complex space use and habitat selection patterns during different life stages, requirements for large intact tracts of sagebrush, declining population trends, and status as a proposed protected species, sage-grouse have become integral to land management and conservation policy throughout the western United States (Western Association of Fish and Wildlife Agencies, 2015; Doherty and others, 2022). References cited: Coates, P.S., Prochazka, B.G., Aldridge, C.L., O’Donnell, M.S., Edmunds, D.R., Monroe, A.P., Hanser, S.E., Wiechman, L.A., and Chenaille, M.P., 2023, Range-wide population trend analysis for greater sage-grouse (Centrocercus urophasianus)-Updated 1960-2022: U.S. Geological Survey Data Report 1175, 17 p., accessed December 7, 2023, at [Available at https://doi.org/10.3133/dr1175.] Doherty, K., Theobald, D.M., Bradford, J.B., Wiechman, L.A., Bedrosian, G., Boyd, C.S., Cahill, M., Coates, P.S., Creutzburg, M.K., Crist, M.R., Finn, S.P., Kumar, A.V., Littlefield, C.E., Maestas, J.D., Prentice, K.L., Prochazka, B.G., Remington, T.E., Sparklin, W.D., Tull, J.C., Wurtzebach, Z., and Zeller, K.A., 2022, A sagebrush conservation design to proactively restore America’s sagebrush biome: U.S. Geological Survey Open-File Report 2022-1081, 38 p., accessed December 6, 2023, at https://doi.org/10.3133/ofr20221081. Hanser, S.E., and Knick, S.T., 2011, Greater sage-grouse as an umbrella species for shrubland passerine birds-A multiscale assessment, chap. 19 in Knick, S.T., eds., Greater sage grouse-Ecology and conservation of a landscape species and its habitats: University of California Press, p. 474-487. [Available at https://doi.org/10.1525/california/9780520267114.003.0020.] Prochazka, B.G., Coates, P.S., O’Donnell, M.S., Edmunds, D.R., Monroe, A.P., Ricca, M.A., Wann, G.T., Hanser, S.E., Wiechman, L.A., Doherty, K.E., Chenaille, M.P., and Aldridge, C.L., 2023, A targeted annual warning system developed for the conservation of a sagebrush indicator species: Ecological Indicators, v. 148. [Available at https://doi.org/10.1016/j.ecolind.2023.110097.] Western Association of Fish and Wildlife Agencies, 2015, Greater sage-grouse population trends: an analysis of lek count databases 1965-2015: Cheyenne, Wyo., Western Association of Fish and Wildlife Agencies, 55 p., accessed 07 12, 2023, at https://ir.library.oregonstate.edu/concern/technical_reports/ng451p621

These data were compiled to investigate the evolutionary history of Graham's beardtongue (Penstemon grahamii). Objective(s) of our study were to determine the evolutionary history of P. grahamii, including ancestral population sizes, the history of population divergences, and historical connectivity. In addition, we characterized population structure, genetic diversity summary statistics, and landscape factors influencing differentiation. These data represent anonymous loci sequenced from throughout the P. grahamii genome (specifically, .vcf and .structure files). Data in these files were manipulated to represent site frequency spectra between population pairs (.data files). These data were collected in 2019 from across the P. grahamii distribution, which is located in northeastern Utah and western Colorado. Specifically, plants are located at lower elevations on the northern slope of the Book Cliffs, which forms the southern side of the Uinta Basin. These data were collected by employees of the U.S. Geological Survey. Known occurrences of P. grahamii were visited and leaf samples from individual plants were collected from across the species’ distribution. These data can be used to further investigate the genetic differentiation, genetic diversity, and evolutionary history of P. grahamii.

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.