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To understand the genetic structure of six rare plant species (Acanthomintha ilicifolia, Baccharis vanessae, Chloropyron maritimum ssp. maritimus, Deinandra conjugens, Dicranostegia orcuttiana, Monardella viminea), we obtained samples from known occurrences in San Diego County, prepared and sequenced ddRAD genomic libraries, and developed and analyzed a panel of genetic markers to assess population diversity and divergence. We provide this SNP genotype dataset in Structure format, produced in Stacks v2.0b8, for future monitoring efforts and population genetic analysis. These data support the following publication: Milano, E.R., and Vandergast, A.G., 2018, Population genomic surveys for six rare plant species in...
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Botany,
Genetics,
San Diego,
USGS Science Data Catalog (SDC),
biological population management, All tags...
ddRADseq,
endangered species,
genetic diversity,
plants (organisms), Fewer tags
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These data represent stem growth from whitebark pine at 27 sites in the Sierra Nevada of California. Values for stem growth were derived from increment cores, processed following standard methods. Samples were also compared against a genomic data collected at the same trees. These data support the following publication: van Mantgem, P.J., Milano, E.R., Dudney, J., Nesmith, J.C.B, Vandergast, A.G., and Zald, H.S.J., 2023. Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California. Ecology and Evolution. https://doi.org/10.1002/ece3.10072.
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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
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