Filters: Tags: Genetic diversity (X) > Categories: Data (X)
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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...
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.
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...
This data set contains genetic information collected from eelgrass (Zostera marina) populations along the Pacific coast of North America from Alaska to Baha California. A total of 447 samples were collected comprising 401 unique individuals (genets) and 46 clones (ramets) from which 10 microsatellite DNA loci were obtained.
Categories: Data;
Types: Citation;
Tags: Angiosperms (Flowering Plants),
AquaticEcosystems,
Bahia Magdelena,
Bahia San Quintin,
Biological Classification,
Reported here are the metabarcoding read numbers and biomass data assessed from a fish community in a southern Florida pond in Pinecrest Gardens after invasive species eradication and native restocking in 2017 and 2018 in linear regression models. This dataframe contains the number of fish of each species identified, their measured lengths estimated population surface area, and the number of metabarcoding reads (with SD and COV) for each species observed from the sampling date.
Categories: Data;
Tags: Ecology,
Genetics,
Genetics,
Southern Florida,
USGS Science Data Catalog (SDC),
These are genetic data collected from replicated samples of 21 Enteroctopus (E. dofleini or a cryptic lineage) in Prince William Sound Alaska to evaluate tissue type, DNA extraction method, and time until analyses are completed on data reliability. Data collected from all samples include two microsatellites identified as possible lineage indicators, and nine microsatellite loci previously identified as polymorphic in both lineages. DNA sequence data from 528 bp of the octopine dehydrogenase (OCDE) gene were also collected.
Categories: Data;
Tags: Amino Acid Oxidoreductases,
Animals/Invertebrates,
Bald Head Chris Island,
Biodiversity,
Biodiversity,
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...
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...
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),
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,
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.
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 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),
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:...
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.
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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