Filters: Tags: Genetic diversity (X) > partyWithName: U.S. Geological Survey - ScienceBase (X)

Filters Date Range Past year (9) Past month (0) Past week (0) Past day (0) Custom range... To   Search Extensions Shapefile (1) Types Map Service (4) OGC WFS Layer (4) OGC WMS Layer (4) OGC WMS Service (3) Downloadable (1) Shapefile (1) Contacts Ecosystems U.S. Geological Survey Robert T Massatti Amy Vandergast Western Ecological Research Center More... Categories Data (25) Data Release - Revised (2) Tag Types Theme (47) Place (47) USGS Scientific Topic Keyword (35) Harvest Set (42) Tag Schemes USGS Thesaurus (43) None (33) Common geographic areas (19) Geographic Names Information System (GNIS) (11) ISO 19115 Topic Category (35) Marine Realms Information Bank (MRIB) keywords (3) USGS Biocomplexity Thesaurus (9) More... View Results as: JSON ATOM CSV

Microsatellite genotypes for desert tortoise (Gopherus agassizii) from scat (2016-2018) These data show the multilocus genotypes, as well as extraction and sample genotype quality assessments for desert tortoise (Gopherus agassizii) scat samples. These data support the following publication: Mitelberg, A., Vandergast, A.G., Nussear, K.E., Dutcher, K. and Esque, T.C., 2019. Development of a Genotyping Protocol for Mojave Desert Tortoise Scat. Chelonian Conservation and Biology. https://doi.org/10.2744/CCB-1394.1. Categories: Data; Tags: California, Genetics, Mojave Desert, Nevada, USGS Science Data Catalog (SDC), All tags... biological population management, biota, genetic diversity, genotype, reptiles, Fewer tags Genetically informed seed transfer zones for Pleuraphis jamesii, Sphaeralcea parvifolia, and Sporobolus cryptandrus across the Colorado Plateau and adjacent regions These data were compiled to provide seed transfer and native plant materials development guidance to managers and practitioners across the Colorado Plateau and in adjacent regions. This data release contains empirical seed transfer zones derived from molecular genetic data for Pleuraphis jamesii (syn. Hilaria jamesii), Sphaeralcea parvifolia, and Sporobolus cryptandrus. Pleuraphis jamesii and Sphaeralcea parvifolia show distinct population structure (i.e., genetic differentiation) across their ranges ; as such, seed transfer zones reflect both patterns of genetic differentiation and information on each species' unique adaptations to climatic gradients. Sporobolus cryptandrus did not display discrete population structure... Tags: Arizona, Botany, California, Colorado, Colorado Plateau, All tags... Ecology, Genetics, Geography, Information Sciences, Kansas, Nevada, New Mexico, Oklahoma, Pleuraphis jamesii (syn. Hilaria jamesii), Sphaeralcea parvifolia, Sporobolus cryptandrus, Texas, USGS Science Data Catalog (SDC), Utah, Wyoming, adaptation, biogeography, biota, climatic gradients, differentiation, environmental restoration, flora restoration, genetic differentiation, genetic diversity, genetic resources, genetic variation, molecular genetic data, native plant, population differentiation, restoration, seed accessions, seed strategies, seed transfer, seed transfer zones, Fewer tags Oenothera deltoides Genotype Data from Contra Costa County, California in 2019 This dataset contains 212 samples from 8 Oenothera deltoides subsp. howellii occurrences, 3 occurrences of the unknown taxon- clade X, and 3 occurrences of related Oenothera deltoides subsp. cognata. 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 2,693 independent loci and 15 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,... Tags: Antioch Dunes National Wildlife Refuge, Antioch Dunes evening-primrose, California, Genetics, North America, All tags... San Francisco Bay-Delta, Sand dune ecosystem, USGS Science Data Catalog (SDC), Western United States, biota, ddRADseq, evolution, genetic diversity, hybrid, population structure, rare plant, Fewer tags Genotypes of Atlantic Sturgeon collected from Canada to Georgia used in the development of a genetic baseline This dataset includes microsatellite genotypes for 2510 Atlantic sturgeon from 18 different populations distributed from Canada to Georgia. Each individual was genotyped at 12 loci. Additional information about sex, capture date, and size are also provided. Categories: Data; Tags: Aquatic Biology, Atlantic Sturgeon, Atlantic coast, Ecology, Genetics, All tags... USGS Science Data Catalog (SDC), environment, genetic diversity, microsatellite, population genetics, Fewer tags Genetic Data for Plantago ovata in the Mojave Desert These datasets were developed to represent the genetic diversity, and population structure of Plantago ovata in the Mojave Desert. The genetic datasets record genetic variation at an individual level, with the file structures varying based on the programs within which the files are intended to be edited. The .genepop file can be viewed in GENEPOP software (Rousset 2008) or imported into R statistical software (https://www.R-project.org/) using the adegenet package (Jombart and Ahmed 2011). The .vcf file can be loaded into the Stacks population program (Catchen et al. 2013) to calculate genetic diversity statistics. References: Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks:... Categories: Data; Tags: Arizona, California, Mojave, Nevada, Utah, All tags... adaptation, biota, evolution, genetic diversity, native plant materials development, native species, restoration, seed transfer zones, Fewer tags Greater sage-grouse network-prioritized functional connectivity cumulative current map (raster) Conserving genetic connectivity is fundamental to species persistence, yet rarely is made actionable into spatial planning for imperiled species. Climate change and habitat degradation have added urgency to embrace connectivity into networks of protected areas. Our two-step process integrates a network model with a functional connectivity model, to identify population centers important to maintaining genetic connectivity then to delineate those pathways most likely to facilitate connectivity thereamong for the greater sage-grouse (Centrocercus urophasianus); a species of conservation concern ranging across eleven western U.S. states and into two Canadian provinces. This replicable process yielded spatial action... Tags: Ecology, USGS Science Data Catalog (SDC), Western North America, Wildlife Biology, biological population management, All tags... genetic diversity, geospatial analysis, protected areas, spatial analysis, wildlife biology, wildlife population management, Fewer tags Targeted amplicon resequencing of chelonid alphaherpesvirus 5 from tumor samples collected from Chelonia mydas (green turtle) inhabiting Hawaiian and Florida coastal waters The files in this data release are the processed DNA consensus sequence alignment files for the chelonid herpesvirus 5 (ChHV-5) genome plus 66 open reading frames representing protien-coding genes. DNA was extracted from tumor biopsies from green sea turtles (Chelonias mydas) with fibropapillomatosis sampled from Florida and Hawaii coastal waters. We used high-throughput short-read sequencing (Illumina MiSeq and Ion Torrent Personal Genome Machine) of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. The raw sequence data is available at the NCBI Sequence Read Archive under bioproject number PRJNA360405, including... Tags: Class Reptilia, DNA sequencing, Earth, Oceans, Atlantic, North Atlantic, Earth, Oceans, Pacific, Family Cheloniidae, All tags... Family Herpesviridae, Florida, Indian River County, Martin County, Sarasota, Genetic Diversity, Genetics, Genus Chelonia, Genus Scutavirus, Green Sea Turtle, Hawaii, Hilo, Hawaii, Maui County 2, Hawaii, Oahu, Honolulu County, Infrakingdom Deuterostomia, Infraphylum Gnathostomata, Kingdom Animalia, Order Herpesvirales, Order Testudines, Phylum Chordata, Species Chelonia mydas, Species Chelonid alphaherpesvirus 5, Subfamily Alpheherpesvirinae, Subfamily Cheloniinae, Subkingdom Bilateria, Suborder Cryptodira, Subphylum Vertebrata, Superclass Tetrapoda, Superfamily Chelonioidea, USGS Science Data Catalog (SDC), Virology, Wildlife Disease, biota, disease research, endangered species, genetics, marine biology, polymerase chain reaction, reptiles, sea turtles, virology, viruses, Fewer tags Population genetic data for tiger beetles Ellipsoptera puritana This dataset includes microsatellite genotypes for 16 collections of tiger beetles (Ellipsoptera puritana) distributed in Connecticut and Maryland, United States. Categories: Data; Tags: Connecticut, Maryland, biota, genetic diversity, tiger beetle Microsatellite Genotypes for Coastal Cactus Wrens (Campylorhynchus brunneicapillus) from Southern California, 2009-2019 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 support the following publication: Vandergast, A.G., Kus, B.E., Smith, J.G. and Mitelberg, A., 2022. Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California. Conservation Science and Practice, 4(9), p.e12780. https://doi.org/10.1111/csp2.12780. Categories: Data; Tags: Genetics, Southern California Coastal, USGS Science Data Catalog (SDC), Wildlife Biology, biological population management, All tags... biota, birds, endemic species, genetic diversity, genotype, human impacts, native species, shrubland ecosystems, Fewer tags Polioptila californica Genotype Data from California, USA and Baja California, Mexico 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... Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: Baja California, Mexico, North America, Southern California, USGS Science Data Catalog (SDC), All tags... Western United States, Wildlife Biology, biota, ddRADseq, endangered species, evolution, genetic diversity, Fewer tags Carex specuicola genomic data for the southern Colorado Plateau Desert These data were compiled to investigate the demographic and phylogeographic of Carex specuicola. Objectives of our study were to understand the demographic and dispersal history of Carex specuicola across hanging gardens, the hybridization history between Carex specuicola and Carex utahensis, and the population structure of Carex specuicola across its distribution. The data release consists of three tab delimited text files that may be used to infer population structure and diversity (CASP.stru), relationships among sampling localities Carex.phylip), or genetic diversity statistics and demographic history (Carex.snps.vcf). These data represent genetic variation on an individual (.stru and .vcf) or sampling locality... Tags: Arizona, Botany, Carex specuicola, Colorado, Colorado Plateau, All tags... Colorado Plateau Desert, Ecology, Genetics, Geography, Information Sciences, New Mexico, Soil Sciences, USGS Science Data Catalog (SDC), Utah, alleles, biodiversity, biogeography, biota, data release, demographic history, demographics, evolution, field sampling, genetic data, genetic diversity, genetic loci, genetic variation, genetics, hanging gardens, native species, phylogeny, phylogeography, population diversity, population dynamics, population structure, sampling locality, southwestern United States, Fewer tags Empirical Seed Transfer Zones for Plantago ovata in the Mojave Desert Seed sourcing strategies that incorporate spatially explicit genetic information promote effective revegetation by reducing genetic risk factors, such as maladaptation, outbreeding, and inbreeding depression. Molecular markers represent an increasingly robust and cost- efficient data source for uncovering patterns of adaptive divergence in high-priority species to support restoration decision making. This project uses marker-based genetic analyses to develop empirical seed transfer zones for species that have been genotyped at a wide range of sites in the Mojave Desert. Empirical seed transfer zones delineate areas within which seeds may be transferred with limited risk of maladaptation or outbreeding depression.... Categories: Data; Tags: Arizona, Botany, California, Mojave, NDVI amplitude, All tags... Nevada, USGS Science Data Catalog (SDC), Utah, atmospheric and climatic processes, climatologyMeteorologyAtmosphere, environment, genetic diversity, local adaptation, normalized difference vegetation index, restoration, Fewer tags Microsatellite data for American bullfrogs in the Yellowstone River Montana, 2013-2017 We used 7 microsatellites to characterize the invasion genetics of 528 American bullfrogs sampled from the Yellowstone River floodplain (Montana). American bullfrog samples were collected from a 140 km section of the Yellowstone River near Billings, MT in 2013 - 2017. Categories: Data; Tags: Billings, Montana, USGS Science Data Catalog (SDC), Yellowstone, aquatic biology, All tags... biota, genetic diversity, invasive species, river systems, Fewer tags Mitochondrial and microsatellite genetic data from Cape Sable seaside sparrow feather samples collected 2011-2018 The federally endangered Cape Sable seaside sparrow (Ammospiza maritima mirabilis) is endemic to the Greater Everglades ecosystem in southern Florida. The subspecies inhabits the fragmented freshwater marl prairies and contains six subpopulations (A-F), named for management purposes, since genetic information is lacking. To evaluate genetic connectivity and inform management decisions, feather samples were collected between 2011 and 2018 from 108 sparrows across five subpopulations (A-E). Sequence data for four mitochondrial DNA markers (N = 36–69) and 12 nuclear microsatellite loci (N = 55) are provided. The mitochondrial markers used were Cytochrome b (Cytb), control region D-loop, NADH dehydrogenase 2 (ND2),... Categories: Data; Tags: DNA sequencing, Everglades, Genetics, Shark River slough, Southern Florida, All tags... USGS Science Data Catalog (SDC), biological population management, birds, genetic diversity, genotype, Fewer tags Astragalus species complex genetic data from southeast Utah (Grand County and San Juan County), USA These data were compiled to investigate the evolutionary history of Astragalus iselyi, A. sabulosus var. sabulosus, and A. sabulosus var. vehiculus. The data release consists of six text files. One file is a bash script (astragalus_MLE_msms.sh) for generating simulated genetic data. Four files contain individual-level (astragalus.fasta, astragalus.nothin.recode.vcf, astragalus.recode.vcf) or population-level (astragalus_dadi.txt) information on genetic variation. One file contains sampling site-specific data for various soil and climatic variables (astragalus_env.txt). The .vcf files contain the full sequence information that is contained in the other files, but the file structures vary based on the programs used... Tags: Biological phenomena, Botany, Colorado Plateau, DNA sequencing, Ecology, All tags... Evolution (biology), Evolutionary genetics, Genetics, Geography, Grand County, Information Sciences, Intermountain West, San Juan County, USGS Science Data Catalog (SDC), Utah, adaptation, biota, demography, evolution, genetic diversity, genetic diversity, genomics, geography, native species, native species, phylogenetics, phylogeography, population structure, rare species, western United States, Fewer tags Empirical and Provisional Seed Transfer Zones for the Mojave Desert and Surrounding Regions (ver. 2.0, January 2021) Empirical evidence that local adaptation and home-site advantages are frequent across plant taxa has increased recognition that local adaptation plays a fundamental role in shaping plant responses to seed transfer (i.e., when plant materials are introduced to a site during restoration). Use of maladapted plant materials can lead to poor project outcomes if propagules exhibit poor germination or seedling survival, low population fitness, inbreeding or outbreeding depression. Accounting for local adaptation in restoration designs is a promising approach for increasing revegetation effectiveness, particularly in drylands where extreme environmental variation potentially drives high levels of selection. Consequently,... Tags: Arizona, California, Colorado, Colorado Plateau, Great Basin, All tags... Mojave Desert, Nevada, New Mexico, Sonoran Desert, USGS Science Data Catalog (SDC), Utah, atmospheric and climatic processes, biota, genetic diversity, genetic variation, geospatial analysis, local adaptation, native plant, restoration, seed transfer zone, Fewer tags Bighorn sheep Ovine HD array genotypes from National Parks, 2004-2011 Between 2004 and 2011 bighorn sheep were darted in Glacier National Park and in Dinosaur National Monument. Blood was drawn. These are the genotypes resulting from an Ovine HD array from the bighorns. The first 3 columns refers to bighorn sheep identifiers: 'Herd_Unit', 'IndID', and 'AgencyID'. IndID is the identifier assigned at Montana State University. Subsequent columns each represent a locus, with the values in the locus representing the allele. Categories: Data; Tags: Crown of the Continent, Dinosaur National Monument, Glacier National Park, Rocky Mountains, USGS Science Data Catalog (SDC), All tags... bighorn sheep, biological population management, biota, ecology, genetic diversity, genetics, population and community ecology, ungulates, wildlife biology, wildlife disease, Fewer tags Genetically informed seed transfer zones for Astragalus lonchocarpus, Cleome serrulata, and Heliomeris multiflora across the Colorado Plateau and adjacent regions These data were compiled to provide seed transfer and native plant materials development guidance to managers and practitioners across the Colorado Plateau and in adjacent regions. This data release contains empirical seed transfer zones derived from molecular genetic data for Cleome serrulata (syn. Peritoma serrulata), Heliomeris multiflora, and Astragalus lonchocarpus. These species show distinct population structure (i.e., genetic differentiation) across their ranges; as such, seed transfer zones reflect both patterns of genetic differentiation and information on each species' unique adaptations to climatic gradients. These shapefile data may support successful restoration outcomes if, for example, seed transfer... Categories: Data; Types: Downloadable, Map Service, OGC WFS Layer, OGC WMS Layer, Shapefile; Tags: Arizona, Astragalus lonchocarpus, Botany, Cleome serrulata (syn. Peritoma serrulata), Colorado, All tags... Colorado Plateau, Ecology, Genetics, Geography, Heliomeris multiflora, Information Sciences, Intermountain West, Nevada, New Mexico, North America, USGS Science Data Catalog (SDC), United States, Utah, Wyoming, adaptation, air temperature, biogeography, biota, climatic gradients, data release, differentiation, effects of climate change, environment, environmental restoration, field inventory and monitoring, flora restoration, genetic differentiation, genetic diversity, genetic resources, genetic variation, mean annual precipitation, molecular biology, molecular genetic data, native plant, native species, natural resource management, plants (organisms), population and community ecology, population differentiation, population dynamics, precipitation (atmospheric), precipitation seasonality, restoration, seed accessions, seed strategies, seed transfer, seed transfer zones, species diversity, species' adaptations, temperature seasonality, Fewer tags Plant genetic structure data from riparian areas within the Grand Canyon region in northern Arizona These data represent nuclear microsatellite data collected from four riparian plant species that occur in and around Grand Canyon National Park: Populus fremontii (POFR), Salix gooddingii (SAGO), Salix exigua (SAEX), and Prosopis glandulosa (PRGL). These data were collected for population genetic analysis to help inform native plant material development in Grand Canyon National Park. Leaf samples were collected at sites spanning 470 km of the Colorado River between Glen Canyon Dam and Lake Mead and in tributaries. Known revegetation areas were not sampled. We aimed to collect leaf tissue from at least 15 individuals at each sample site. If there were fewer than 15 individuals per species at a site, leaf tissue was... Tags: Arizona, Botany, Colorado River, Ecology, Genetic diversity, All tags... Genetics, Geography, Glen Canyon, Glen Canyon Dam, Grand Canyon, Grand Canyon National Park, Information Sciences, Lake Mead, Nuclear microsatellite, Population characteristics, USGS Science Data Catalog (SDC), biogeography, biota, conservation genetics, cottonwood, genetics, mesquite, northern Arizona, plants (organisms), population and community ecology, population genetics, riparian plants, southwestern U.S., southwestern United States, wetland ecosystems, willow, Fewer tags Empirical Seed Transfer Zones for Sphaeralcea ambigua in the Mojave Desert Seed sourcing strategies that incorporate spatially explicit genetic information promote effective revegetation by reducing genetic risk factors, such as maladaptation, outbreeding, and inbreeding depression. Molecular markers represent an increasingly robust and cost- efficient data source for uncovering patterns of adaptive divergence in high-priority species to support restoration decision making. This project uses marker-based genetic analyses to develop empirical seed transfer zones for species that have been genotyped at a wide range of sites in the Mojave Desert. Empirical seed transfer zones delineate areas within which seeds may be transferred with limited risk of maladaptation or outbreeding depression.... Tags: Arizona, California, Mojave, Nevada, Sphaeralcea ambigua, All tags... Utah, atmospheric and climatic processes, biota, genetic diversity, genetic variation, local adaptation, native plant, restoration, seed transfer zone, Fewer tags « 1 2 3 »