Filters: Tags: Genetic diversity (X)
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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),
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...
The newly described Gunnison sage-grouse (Centrocercus minimus) is a species of concern for management because of marked declines in distribution and abundance due to the loss and fragmentation of sagebrush habitat. This has caused remaining populations to be unusually small and isolated. We utilized mitochondrial DNA sequence data and data from 8 nuclear microsatellites to assess the extent of population subdivision among Gunnison sage-grouse populations in southwestern Colorado and southeastern Utah, USA. We found a high degree of population structure and low amounts of gene flow among all pairs of populations except the geographically adjacent Gunnison and Curecanti populations. Population structure for Gunnison...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Centrocercus minimus,
Colorado,
Gunnison sage-grouse,
Journal of Wildlife Management,
The Wildlife Society,
Data used to generate figure 2 A for the cited paper. Sequence divergence was calculated as DA, Neiâs net number of nucleotide differences between each pair of collection locations, where the average number of differences between individuals among locations is corrected for the average number of differences within each location [61]. For datasets where multiple loci were sequenced, pairwise distances were averaged across loci after normalization.
Utility scale renewable energy development projects are currently proposed across the deserts of the Southwestern United States. Agencies that manage biological resources must understand the potential impacts of these projects and infrastructure (e.g., transmission corridors, substations, access roads, etc.) in order to select appropriate development sites and to mitigate for anticipated effects. Of major concern is determining how future development will impact wildlife movement and genetic exchange among core protected areas and whether increased fragmentation will impact species' abilities to adapt to changing environmental conditions. The adaptive and evolutionary potential of a species is ultimately dependent...
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,...
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.
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:...
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...
This data set describes nuclear microsatellite genotypes derived from eleven autosomal loci (Lar24, Lar12, Lar26, Lar19, Rbg13, K16, Rbg18, Hg18, Hg16, Hg25, Rbg29). A total of 651 Larus gulls were examined for this study with samples collected throughout North America, Europe, Russia, and South America.
Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids...
Utility scale renewable energy development projects are currently proposed across the deserts of the Southwestern United States. Agencies that manage biological resources must understand the potential impacts of these projects and infrastructure (e.g., transmission corridors, substations, access roads, etc.) in order to select appropriate development sites and to mitigate for anticipated effects. Of major concern is determining how future development will impact wildlife movement and genetic exchange among core protected areas and whether increased fragmentation will impact species' abilities to adapt to changing environmental conditions. The adaptive and evolutionary potential of a species is ultimately dependent...
Utility scale renewable energy development projects are currently proposed across the deserts of the Southwestern United States. Agencies that manage biological resources must understand the potential impacts of these projects and infrastructure (e.g., transmission corridors, substations, access roads, etc.) in order to select appropriate development sites and to mitigate for anticipated effects. Of major concern is determining how future development will impact wildlife movement and genetic exchange among core protected areas and whether increased fragmentation will impact species' abilities to adapt to changing environmental conditions. The adaptive and evolutionary potential of a species is ultimately dependent...
Utility scale renewable energy development projects are currently proposed across the deserts of the Southwestern United States. Agencies that manage biological resources must understand the potential impacts of these projects and infrastructure (e.g., transmission corridors, substations, access roads, etc.) in order to select appropriate development sites and to mitigate for anticipated effects. Of major concern is determining how future development will impact wildlife movement and genetic exchange among core protected areas and whether increased fragmentation will impact species' abilities to adapt to changing environmental conditions. The adaptive and evolutionary potential of a species is ultimately dependent...
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...
This dataset includes microsatellite genotypes for 16 collections of tiger beetles (Ellipsoptera puritana) distributed in Connecticut and Maryland, United States.
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.
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...
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...
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