Filters: Tags: conservation genetics (X) > partyWithName: U.S. Geological Survey - ScienceBase (X)

Filters Date Range Past year (7) Past month (0) Past week (0) Past day (0) Custom range... To   Search Extensions Shapefile (1) Types Downloadable (1) Map Service (1) OGC WFS Layer (1) OGC WMS Layer (1) Shapefile (1) Contacts Ecosystems Rich D Inman U.S. Geological Survey Nathan A Johnson Fort Collins Science Center More... Categories Data (6) Data Release - Revised (1) Tag Types Theme (18) Place (14) USGS Scientific Topic Keyword (12) Harvest Set (14) Tag Schemes None (15) USGS Thesaurus (15) ISO 19115 Topic Category (16) Geographic Names Information System (GNIS) (2) Common geographic areas (3) USGS Biocomplexity Thesaurus (4) ISO 19115 Topic Categories (2) More... View Results as: JSON ATOM CSV

Spatial Predictions of Mojave Desert Tortoise, Sonoran Desert Tortoise and Pooled Species Habitat Suitability for present-day (1950 – 2000 yr) This dataset provides spatial predictions of habitat suitability for Gopherus agassizii (Agassiz’s desert tortoise), Gopherus morafkai (Morafka’s desert tortoise) and a pooled-species model under current conditions (1950 – 2000 yr). The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to evaluate subtle ecological niche differences between G. agassizii and G. morafkai, and identify local species-environment relationships. Spatial predictions of habitat suitability were created using MaxEnt version 3.4.0 (Phillips et al., 2006), a widely-used software for SDM in presence-background frameworks. Detailed methods are provided in Inman et al. 2019. Inman et al. 2019. Local niche... Tags: Gopherus agassizii, Gopherus morafkai, North America, North America, Western USA, All tags... animals, biota, conservation genetics, desert tortoise, deserts, ecological niche, genetics, geospatial analysis, habitats, multiscale geographically weighted regression, species distribution modelling, Fewer tags Habitat Genotype Association This dataset provides spatial predictions of clustering and the genotype association index for the Mojave genotype in local species-environment relationships of Desert Tortoises (Gopherus agassizi and Gopherus morafkaii) for individuals in the subregion encompassing the genetic sampling locations used by Edwards et al. (2015). This region offered an opportunity to explore habitat selection across the ecotone between the Mojave and Sonoran deserts and the secondary contact zone between G. agassizii and G. morafkai, and is referred to as the focal study area. The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to identify multivariate clusters and map them back to geographic space.... Tags: North America, North America, Western USA, animals, biota, All tags... conservation genetics, desert tortoise, deserts, ecological niche, genetics, geospatial analysis, habitats, multiscale geographically weighted regression, species distribution modelling, Fewer tags Molecular resources for investigating relationships among freshwater mussels (Bivalvia: Unionoida) with a focus on the genus Alasmidonta Longstanding taxonomic uncertainties have limited conservation efforts for species currently assigned to the freshwater mussel genus Alasmidonta. Here, we present mitochondrial and nuclear DNA sequence data needed to assess the genus- and species-level taxonomy of Alasmidonta. These molecular data allowed us to test whether cryptic diversity exists within Alasmidonta and whether A. triangulata and A. arcula are distinct species. Details associated with specimens and DNA sequence data are provided here to provide a foundation for future research on Alasmidonta and give conservation agencies greater confidence in the findings of our work. Categories: Data; Tags: DNA sequencing, Genetics, USGS Science Data Catalog (SDC), biota, conservation genetics, All tags... cryptic species, endangered species, generic reclassification, incomplete lineage sorting, integrative taxonomy, phylogenetic systematics, species delimitation, species diversity, systematics and taxonomy, Fewer tags Local Niche Model This dataset provides spatial predictions of the pooled-SDM residuals from a multiscale geographically weighted regression model (MGWR) and the resulting local R2 values for individuals in the subregion encompassing the genetic sampling locations used by Edwards et al. (2015). This region offered an opportunity to explore habitat selection across the ecotone between the Mojave and Sonoran deserts and the secondary contact zone between G. agassizii and G. morafkai, and is referred to as the focal study area. The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to identify multivariate clusters and map them back to geographic space. Inman et al. 2019. Local niche differences predict... Tags: North America, North America, Western USA, animals, biota, All tags... conservation genetics, desert tortoise, deserts, ecological niche, genetics, geospatial analysis, habitats, multiscale geographically weighted regression, species distribution modelling, Fewer tags Molecular data used to test species boundaries, characterize phylogeographic patterns of genetic diversity, and guide the Endangered Species Act listing decision for a North American freshwater mussel species complex Here we provide the molecular datasets and metadata associated with specimens used in the investigation of species boundaries and phylogeographic structure of two freshwater mussels, one common (Pleurobema sintoxia) and one being considered for protection under the Endangered Species Act (Pleurobema rubrum). Categories: Data; Tags: Eastern United States, Genetics, USGS Science Data Catalog (SDC), biota, conservation genetics, All tags... endangered species, freshwater mussels, phylogeography, species delimitation, Fewer tags Genetic analyses of Astragalus sect. Humillimi data in the southwest USA These data were compiled to support effective conservation for species within Astragalus sect. Humillimi. Two species, A. cremnophylax var. cremnophylax and A. humillimus are federally listed as endangered taxa. The data provided herein were used to resolve the relationaships among taxa, the population structure within taxa, and genetic diversity within taxa. The data are provided in a STRUCTURE-formatted file that includes taxa, individuals, sampling localities, and the genotype scores per individual for 690 Amplified Fragment Length Polymorphisms (AFLPs). Tags: Arizona, Astragalus sect. Humillimi;, Botany, Colorado Plateau, Ecology, All tags... Fabaceae, Genetics, Grand Canyon National Park, Information Sciences, New Mexico, USGS Science Data Catalog (SDC), biota, conservation genetics, phylogenetics, southwestern United States, Fewer tags Greater sage-grouse genetic warning system, western United States (ver 1.1, January 2023) Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species’ conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., fine-scale) with low genetic diversity relative... Categories: Data Release - Revised; Tags: California, Centrocercus urophasianus, Colorado, Greater sage-grouse, Idaho, All tags... Montana, Nevada, North Dakota, Oregon, South Dakota, USGS Science Data Catalog (SDC), United States, Utah, Washington, Wyoming, adaptive management, biota, boundaries, conservation genetics, genetic diversity, genetic monitoring, hierarchical sampling units, population monitoring, western United States, Fewer tags Gunnison sage-grouse predicted gene flow (conductance) surfaces, Colorado, United States Habitat fragmentation and degradation impacts an organism's ability to navigate the landscape, ultimately resulting in decreased gene flow and increased extinction risk. Understanding how landscape composition impacts gene flow (i.e., connectivity) and interacts with scale is essential to conservation decision-making. We used a landscape genetics approach implementing a recently developed statistical model based on the generalized Wishart probability distribution to identify the primary landscape features affecting gene flow and estimate the degree to which each component influences connectivity for Gunnison sage-grouse (Centrocercus minimus). We were interested in two spatial scales: among distinct populations... Tags: Centrocercus minimus, Colorado, Ecology, Gunnison sage-grouse, USGS Science Data Catalog (SDC), All tags... United States, Utah, Wildlife Biology, adaptive management, biota, conservation genetics, gene flow, genetic connectivity, landscape genetics, western United States, Fewer tags Reduced representation sequencing and genotyping of Arizona Toads (Anaxyrus microscaphus) from the southwestern United States The dataset consists of genotypes (diploid base calls at variant sites) at 3,601 anonymous sites of the Arizona Toad (Anaxyrus microscaphus) nuclear genome. The genotyped samples are representative of the range of the species and its major population units, and the genotyped loci have a high degree of completeness. This data release consists of several files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All NCBI-derived accessions... Tags: Arizona, Ecology, Genetics, Nevada, New Mexico, All tags... USGS Science Data Catalog (SDC), Utah, Wildlife Biology, biota, conservation genetics, genetics, vertebrate zoology, Fewer tags Amplicon sequencing of pollen foraged by Bombus affinis for compositional analysis This study generated genetic 'barcode' data using high-throughput sequencing to characterize pollen collected by the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were associated with a single Bombus affinis colony within a structure in Red Wing, Minnesota, USA, as previously described by Boone et al. (2022). This data release consists of two tab-delimited files: 1) sample.metadata.txt includes sample identifiers and accessions assigned by the National Center for Biotechnology Information (NCBI), the authoritative repository for publicly funded genetic data in the United States. These accessions can be used individually to obtain raw sequencing data or sample information at www.ncbi.nih.nlm.gov.... Tags: Botany, Ecology, Genetics, Minnesota, USGS Science Data Catalog (SDC), All tags... biota, conservation genetics, genetics, invertebrate zoology, Fewer tags Environmental Explanatory Variables This dataset provides the environmental explanatory variables used to explore spatial patterns in species-environment relationships in Gopherus agassizii and Gopherus morafkai across the subregion encompassing the genetic sampling locations used by Edwards et al. (2015). This region offered an opportunity to explore habitat selection across the ecotone between the Mojave and Sonoran deserts and the secondary contact zone between G. agassizii and G. morafkai, and is referred to as the focal study area. The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to identify multivariate clusters and map them back to geographic space. Inman et al. 2019. Local niche differences predict... Tags: North America, North America, Western USA, animals, biota, All tags... conservation genetics, desert tortoise, deserts, ecological niche, genetics, geospatial analysis, habitats, multiscale geographically weighted regression, species distribution modelling, Fewer tags Molecular, morphological, and distributional data supporting the recognition of an undescribed freshwater mussel endemic to the Edwards Plateau in the Colorado River basin The widespread distribution of Strophitus undulatus, as well as high intraspecific morphological variation, has led previous authors to doubt the taxon is representative of a single species. Here we provide detailed information for all the freshwater mussels and associated DNA sequence data utilized to test species boundaries in S. undulatus. These molecular data, in combination with morphological data and results from species distribution models, support the recognition of an undescribed freshwater mussel species endemic to streams along the Edwards Plateau in the Colorado River basin in Texas, USA. Categories: Data; Tags: Aquatic Biology, DNA sequencing, Genetics, USGS Science Data Catalog (SDC), biota, All tags... conservation genetics, cryptic species, endangered species, freshwater mussels, integrative taxonomy, phylogenetic systematics, species delimitation, species diversity, systematics and taxonomy, Fewer tags Concentrations of environmental DNA (eDNA) during sockeye salmon spawning in 2016, Hansen Creek, Alaska, USA This dataset contains environmental DNA (eDNA) concentrations and spawning adult abundances for sockeye salmon (Oncorhynchus nerka) in Hansen Creek, a small tributary in the Wood River watershed, southeast Alaska, USA. We took temporally- and spatially-replicated eDNA samples during the spawning period (mid-July through August), along with fish counts (live, naturally dead, and killed), dissolved oxygen (DO), discharge, and temperature data at each time of sampling. Samples were collected at each site before adults entered the stream, and then continued to be collected daily or every other day for the next three weeks. Categories: Data; Types: Downloadable, Map Service, OGC WFS Layer, OGC WMS Layer, Shapefile; Tags: Alaska, Aleknagik Lake, CO3, DNeasy, Hansen Creek, All tags... TaqMan MGB, USGS Science Data Catalog (SDC), United States, Wood River watershed, biota, cellulose nitrate, conservation genetics, filtration, freshwater ecosystems, genetics, inlandWaters, qPCR, water sampling, 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 Local ecological niche models, genotype associations and environmental data for desert tortoises. These data include environmental covariates used to develop species distribution models for Gopherus agassizii and Gopherus morafkai, along with PCA-reduced environmental covariates used to explore local species-environment relationships within a subregion of the ectone between the two species. We also provide the genotype association used to test the mapped clusters of multiscale geographically weighted regression coefficients against models of (i) a geographically-based taxonomic designation these two sister species, and (ii) an environmental ecoregion designation. These data support the following publication: Inman et al. 2019. Local niche differences predict genotype associations in sister taxa of desert tortoise.... Tags: Ecology, Genetics, North America, North America, USGS Science Data Catalog (SDC), All tags... Western USA, Wildlife Biology, animals, biota, conservation genetics, desert tortoise, deserts, ecological niche, genetics, geospatial analysis, habitats, multiscale geographically weighted regression, species distribution modelling, Fewer tags Molecular data and results needed to better understand codiversification of freshwater mussels (Unionidae: Quadrulini) and their parasitic larval hosts The North American freshwater mussel tribe Quadrulini has a suite of life history adaptations, however, the evolution of life histories in this group has yet to be explored using comparative phylogenetic methods. Here we provide the AHE DNA sequence alignment representing 27 species from the subfamily Ambleminae that was used to estimate a phylogenomic reconstruction of Quadrulini. Additionally, we provide a compilation of host use information and larval length and height measurements utilized to trace the evolution of life history characteristics, such as larval morphology and host attraction strategy. Phylogenetic trees are presented representing phylogenetic inference performed under Maximum Likelihood, Maximum... Categories: Data; Tags: Aquatic Biology, DNA sequencing, Genetics, USGS Science Data Catalog (SDC), biota, All tags... conservation genetics, cryptic species, endangered species, generic reclassification, incomplete lineage sorting, integrative taxonomy, phylogenetic systematics, species delimitation, species diversity, systematics and taxonomy, Fewer tags Molecular and morphological data on two species complexes in the freshwater mussel genus Cyclonaias We examined species boundaries within an imperiled group of freshwater mussels in the genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across all lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex, while underestimating diversity in the C. nodulata species complex. Here we provide all molecular, morphological, and collection information collected and analyzed in our investigation. Categories: Data; Tags: Aquatic Biology, Ecology, Genetics, USGS Science Data Catalog (SDC), biota, All tags... conservation genetics, cryptic species, generic reclassification, imperiled species, incomplete lineage sorting, integrative taxonomy, phylogenetic systematics, species delimitation, species diversity, systematics and taxonomy, Fewer tags Greater sage-grouse genetic data and R code for evaluating conservation translocations in the northwestern United States, 1992–2021 Conservation translocations are a common wildlife management tool that can be difficult to implement and evaluate for effectiveness. Genetic information can provide unique insight regarding local impact of translocations (e.g., presence and retention of introduced genetic variation) and identifying suitable source and recipient populations (e.g., adaptive similarity). We developed two genetic data sets and wrote statistical code to evaluate conservation translocation effectiveness into the isolated northwestern region of the greater sage-grouse (Centrocercus urophasianus) distribution and to retrospectively evaluate adaptive divergence among source and recipient populations. Our first data set was microsatellite-based... Tags: Centrocercus urophasianus, Ecology, Genetics, Idaho, Nevada, All tags... Oregon, USGS Science Data Catalog (SDC), United States, Washington, Wildlife Biology, biological population management, biota, conservation genetics, conservation translocation, genetic diversity, genetic monitoring, greater sage-grouse, western United States, wildlife management, wildlife population management, Fewer tags