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

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Sample collection information, single nucleotide polymorphism, and microsatellite data for white-tailed ptarmigan across the species range generated in the Molecular Ecology Lab during 2016 This data release comprises a dataset that contains sample collection information and microsatellite genotypes, and another dataset that contains single nucleotide polymorphism (SNP) genotypes with sample collection information for populations of white-tailed ptarmigan across the species' range. There is also an additional file (accession numbers.xlsx) linking samples to accession numbers in Genbank. This data was collected in order to address the following: The delineation of intraspecific units that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Neutral genetic variation has served as the primary data source for delineating units for... Categories: Data; Tags: Alaska, Alberta, British Columbia, Colorado, Microsatellites, All tags... Montana, Mt. Evans, New Mexico, Rocky Mountain National Park, USGS Science Data Catalog (SDC), Utah, Vancouver, Washington, Yukon Territory, biological population management, biota, genetic diversity, Fewer tags Population genetic data for two species of tiger beetles, Habroscelimorpha dorsalis dorsalis and H. d. media This dataset includes microsatellite genotypes for 44 collections of Habroscelimorpha dorsalis dorsalis and 14 collections of H. d. media distributed from Massachusetts to Florida, United States. Categories: Data; Tags: Florida, Massachusetts, biota, genetic diversity, tiger beetle Cleome lutea and Machaeranthera canescens seed transfer zones and distribution on the Colorado Plateau, US 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 lutea (syn. Peritoma lutea) and Machaeranthera canescens (syn. Dieteria canescens). 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 follows... Tags: Arizona, California, Cleome lutea (syn. Peritoma lutea), Colorado, Ecology, All tags... Genetics, Geography, Information Sciences, Intermountain West, Machaeranthera canescens (syn. Dieteria canescens), Nebraska, Nevada, New Mexico, North America, South Dakota, USGS Science Data Catalog (SDC), USGS:5fb567c1d34eb413d5e13a9c, United States, United States, 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 Genotype Data for Eastern Massasauga Rattlesnakes (Sistrurus catenatus) from Bois Blanc Island, Michigan at 15 Microsatellite DNA Loci We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. These data are from 102 individual Eastern Massasauga Rattlesnakes sampled at Bois Blanc Island, Michigan and genotyped at 15 microsatellite loci. Samples were collected as part of a study to examine functional connectivity for the Eastern Massasauga. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration... Categories: Data; Tags: Bois Blanc island, Ecology, Lake Huron, Land Use Change, Michigan, All tags... USGS Science Data Catalog (SDC), Wildlife Biology, biological population management, biota, endangered species, environment, evolution, genetic diversity, genetics, genotype, loci, microsatellite, Fewer tags Whole genome sequencing of three North American large-bodied birds The data release details the samples, methods, and raw data used to generate high-quality genome assemblies for greater sage-grouse (Centrocercus urophasianus), white-tailed ptarmigan (Lagopus leucura), and trumpeter swan (Cygnus buccinator). The raw data have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), the authoritative repository for public biological sequence data, and are not included in this data release. Instead, the accessions that link to those data via the NCBI portal (www.ncbi.nlm.nih.gov) are provided herein. The release consists of a single file, sample.metadata.txt, which maps NCBI accessions to the samples sequenced and the different... Tags: Ecology, Genetics, North America, USGS Science Data Catalog (SDC), Wildlife Biology, All tags... biota, genetic diversity, genetics, ornithology, Fewer tags Red Lionfish DNA data collected from Florida, USA and around the invasive distribution from 2007 to 2016 Red lionfish (Pterois volitans) have become a successful invasive predator across the Northwestern Atlantic, Caribbean, and Gulf of Mexico (GoM). Previous investigations have identified the southeast coast of Florida as the original site of introduction, but no region-wide genetic study has directly addressed the question of introduction location(s). This dataset includes previously unpublished red lionfish samples (n = 237) from six locations: The Bahamas, Florida Keys, Northwest Florida, North Carolina, Panama, and Southeast Florida. Sequences archived in NCBI from other locations in the Northern Region, Caribbean, and Gulf of Mexico basins were used in the analyses (N = 1558). Previously published sequences were... Categories: Data; Tags: Aquatic Biology, Caribbean, Caribbean Sea, Genetics, Gulf of Mexico, All tags... North Atlantic, Southeast Florida, USGS Science Data Catalog (SDC), Western Atlantic Ocean, biota, genetic diversity, invasion pathway, invasive species, mitochondrial marker, nuclear microsatellite marker, Fewer tags Genetic data and genetic network attributes for rangewide Greater Sage-grouse network constructed in 2018 (ver. 2.0, December 2022) Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided towards nodes integral to connectivity. The greater sage-grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on spatially discrete leks that must remain connected by genetic exchange for population persistence. We genotyped 5,950 individuals, from 1,200 greater sage-grouse leks distributed across the entire species’ geographic range. We found a small world network composed of 458 nodes connected by 14,481 edges that are described here. The files associated... Categories: Data, Data Release - Revised; Tags: USGS Science Data Catalog (SDC), Western North America, biological population management, biota, centrality, All tags... genetic diversity, graph theory, multi-scale conservation prioritization, network theory, Fewer tags Population genetic data for wild Brook Trout (Salvelinus fontinalis) from the Midwestern United States and selected domestic strains This dataset includes microsatellite genotypes for 8,454 brook trout from 188 wild Midwestern populations and 26 hatchery strains of both Midwest and eastern (Atlantic seaboard) origin. Each individual was genotyped at either 5 or 7 loci. Categories: Data; Tags: Aquatic Biology, Genetics, Genetics, Midwest, USGS Science Data Catalog (SDC), All tags... biota, brook trout, genetic diversity, microsatellites, Fewer tags Penstemon grahamii genetic data from a dryland region of the western United States 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... Tags: Botany, Colorado, Ecology, Genetics, Geography, All tags... Information Sciences, Penstemon grahamii, USGS Science Data Catalog (SDC), Utah, adaptation, biogeography, biota, demographics, demography, ecosystem management, ecosystem restoration, environmental gradients, evolution, genetic diversity, native plant materials development, native species, phylogeny, phylogeography, population structure, restoration, seed transfer guidelines, Fewer tags Microsatellite genotypes for Lake Sturgeon (Acipenser fulvescens) Eggs and Larvae from Constructed Reefs in the St. Clair-Detroit River System (2015-2016) This dataset contains the physical collection information (e.g., sample location, date, gear type) and microsatellite DNA genotype of egg and larval Lake Sturgeon collected in the St. Clair and Detroit rivers in 2015 and 2016. Individuals were genotyped for 18 microsatellite loci (13 disomic and 5 polysomic). Alleles (base pair sizes) were recorded as presence absence scores (1:present, 2:absent, 0:missing data) for all previously observed alleles. Thus individual genotypes were recorded as pseudo diploid dominant phenotypes resulting in individual vectors of length n=205 for each genotyped egg or larval individual. Categories: Data; Tags: Acipenser, Acipenser fulvescens, Acipenseridae, Anthropogenic, Anthropogenic Rock, All tags... Anthropogenic Rock Reef Substrate, Anthropogenic Rock Rubble, Anthropogenic Substrate, Aquatic Biology, Aquatic Setting, Artificial reef, Assessments, Biological Occurrence, Data Content Subjects, Data Content Types, Detroit, Detroit River, Dredge Deposit, Dredge Disturbance, Dredged/Excavated Channel, Fishes, Fishing from Shore, Fishing with Benthic Mobile Gear, Genetics, Grassy Island, Great Lakes, Habitat, Harvesting Living Resources, Huron, Lacustrine, Lake Saint Clair, Lake St. Clair, Living Resources, Macomb, Michigan, Middle Channel Saint Clair River, Motorized Boating, North Channel Saint Clair River, Pelagic Fishing, Port Huron, Recreational Nonextractive /Cultural Use, Sailing, Saint Clair, Saint Clair River, Shipping, Shore Use, St. Clair, St. Clair-Detroit, Substrate, Transportation, USGS Science Data Catalog (SDC), United States, Wayne, Western Lake Erie, animals, anthropogenic agents of coastal change, aquatic ecosystems, biological features, biological laboratory methods, biological observations, biological resources, biology, biota, biota, canal, capturing (animals), channels, chordates, conservation, construction, cultural resources, data processing, datasets, discipline, dredge spoils disposal, dredging operations, ecological change, ecosystem monitoring, ecosystem restoration, ecosystems, endemic species, environment, environmental assessment, eukaryotes, feature type, field inventory and monitoring, field methods, field observation, field sampling, fish, fish eggs, fish larvae, fisheries, fishery resources, food resources, freshwater ecosystems, genetic diversity, genetics, genotype, habitats, hot topics, hydrographic features, ichthyology, ichthyoplankton, inland fishery resources, inlandWaters, laboratory methods, landform, life sciences, management methods, methods, native species, natural resources, nekton and plankton, organism groupings (non-taxonomic), organisms, physiographic features, population and community ecology, population dynamics, product types, ray-finned fish ["bony fish"], recreational fishery resources, reef, reefs, regions, research method, resource management, resources, river, river basin development, river systems, rivers, sciences, shipping channels, species conservation, streams, sturgeon, topics, transportation resources, trapping, vertebrates, water resources, wetland destruction, zoology, Fewer tags 'Viva' native plant material data in support of restoration and conservation These data were compiled to investigate the evolutionary history of Hilaria jamesii, Hilaria mutica, and Hilaria rigida. The data release consists of two tab delimited text files that may be used to infer population structure (viva_structure.stru) or relationships among sampling localities (viva.phylip). Files record genetic variation on an individual (.stru) or sampling locality (.phylip) level. These files may be opened and edited in a text editor program, such as Notepad ++ (PC) or BBEdit (Mac). The .phylip file can be uploaded to phyML or SVDQuartets to generate a tree-based visualization of relationships ( http://www.atgc-montpellier.fr/phyml/ or https://paup.phylosolutions.com, repectively). The .stru file... Tags: Arizona, Botany, California, Colorado, Colorado Plateau, All tags... Ecology, Genetics, Geography, Great Basin, Hilaria jamesii, Hilaria mutica, Hilaria rigida, Information Sciences, Intermountain West, Kansas, Mojave Desert, Nevada, New Mexico, North America, Poaceae, Texas, USGS Science Data Catalog (SDC), Utah, Wyoming, adaptation, biogeography, biota, demographics, demography, ecosystem management, ecosystem management, ecosystem restoration, evolution, genetic diversity, genetics, hybridization, indigenous plants, native plant materials development, native species, phylogeny, phylogeography, population genetics, population structure, remediation, restoration, seed transfer guidelines, seeds, western United States, Fewer tags Population genetic data for three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana This dataset includes microsatellite genotypes for 16 collections of tiger beetles (Ellipsoptera puritana) distributed in Connecticut and Maryland, United States and 44 collections of Habroscelimorpha dorsalis dorsalis and 14 collections of H. d. media distributed from Massachusetts to Florida, United States. Categories: Data; Tags: Connecticut, Ecology, Genetics, Maryland, USGS Science Data Catalog (SDC), All tags... biota, genetic diversity, tiger beetle, Fewer tags Nuclear microsatellite genotypes of six populations of yellow rail (Coturnicops noveboracensis) sampled 2005-2008 These data reflect nuclear microsatellite genotypes for specimens of yellow rails (Coturnicops noveboracensis) sampled in 2005-2008. Data from six populations are included. Tags: Canada, Ecology, Genetics, Manitoba, Michigan, All tags... Minnesota, North America, Oregon, Quebec, USGS Science Data Catalog (SDC), Wildlife Biology, Wisconsin, biodiversity, biota, birds, environment, genetic diversity, genetics, genotype, ornithology, wildlife biology, Fewer tags 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 1 2 »