Filters: Tags: Genetic diversity (X)
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The use of molecular techniques for the assessment of familial relationships among social species of mammals has become relatively commonplace. However, some species represent poor candidates for such studies due to naturally low levels of genetic diversity, leading to unacceptably large standard errors associated with estimates of relatedness. Here, we report on a preliminary study of genetic diversity within two populations of a social species of ground squirrel, Gunnison's prairie dog (Cynomys gunnisoni) using DNA fingerprinting. We observed low levels of diversity in the form of large mean coefficients of genetic similarity among individuals occupying the same population. Overall similarity, determined from...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: American Society of Mammalogists,
Cynomys gunnisoni,
DNA fingerprinting,
Journal of Mammalogy,
genetic diversity,
The Mogollon Narrowheaded gartersnake (Thamnophis rufipunctatus) and the Northern Mexican gartersnake (Thamnophis eques megalops) are both listed as Threatened under the Federal Endangered Species Act. Both species have a strong association with aquatic habitats, and these habitats have been highly altered from impoundments, land-use changes, and the introduction and spread of non-native aquatic species, which have contributed to declines in Arizona and New Mexico over the last 30-40 years. We characterized 125 microsatellite loci per species to generate genetic toolsets for use in long term genetic monitoring of populations. We evaluated microsatellite loci for missing data and several variability thresholds, which...
Categories: Data;
Tags: Arizona,
DNA sequencing,
Genetics,
New Mexico,
USGS Science Data Catalog (SDC),
These data show the multilocus genotypes, gender, and midline carapace length (MCL) for desert tortoises (Gopherus agassizii) sampled in the central portion of the Mojave desert tortoise range. This data supports the following publication: Dutcher, K.E., Vandergast, A.G., Esque, T.C., Mitelberg, A., Matocq, M.D., Heaton, J.S. and Nussear, K.E., Genes in space: what Mojave Desert tortoise genetics can tell us about landscape connectivity. Conservation Genetics, pp.1-15.
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,
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.
Two independent sampling methods were used to collect genetic samples from grizzly bears (Ursus arctos): (i) hair traps—corrals of barbed wire with lure in the center systematically distributed using an 8 x 8 km (1998, 2000) or 7 x 7 km (2004) grid and (ii) bear rubs—naturally occurring trees or other objects that bears rub on fitted with barbed wire (1998–2000, 2004, and 2009–2012). From 1998 to 2000, sampling occurred on 8000 km2 in the northern extent of the Northern Continental Divide Ecosystem (NCDE), whereas systematic and consistent, ecosystem-wide sampling occurred in 2004 and 2009–2012. In total, there were 6160 confirmed grizzly bear detections, leading to the identification of 1115 unique individual genotypes...
Categories: Data;
Types: Citation;
Tags: Glacier National Park,
Northern Continental Divide Ecosystem,
USGS Science Data Catalog (SDC),
genetic diversity,
genotype,
These data reflect nuclear microsatellite genotypes for specimens of yellow rails (Coturnicops noveboracensis) sampled in 2005-2008. Data from six populations are included.
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,
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...
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.
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