Oenothera deltoides genotype data from Contra Costa County, California in 2019
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, 2013) to calculate genetic diversity statistics, or loaded into R, using vcfR (Knaus and Grünwald, 2017), for further analysis. These data support the following publication:
Complete Metadata
| accessLevel | public |
|---|---|
| bureauCode |
[
"010:12"
]
|
| contactPoint |
{
"fn": "Data Manager",
"@type": "vcard:Contact",
"hasEmail": "mailto:fresc_outreach@usgs.gov"
}
|
| description | 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, 2013) to calculate genetic diversity statistics, or loaded into R, using vcfR (Knaus and Grünwald, 2017), for further analysis. These data support the following publication: |
| distribution |
[
{
"@type": "dcat:Distribution",
"title": "Digital Data",
"format": "XML",
"accessURL": "https://doi.org/10.5066/P93VYTF5",
"mediaType": "application/http",
"description": "Landing page for access to the data"
},
{
"@type": "dcat:Distribution",
"title": "Original Metadata",
"format": "XML",
"mediaType": "text/xml",
"description": "The metadata original format",
"downloadURL": "https://data.usgs.gov/datacatalog/metadata/USGS.605a3ba0d34e18948831d8ae.xml"
}
]
|
| identifier | http://datainventory.doi.gov/id/dataset/USGS_605a3ba0d34e18948831d8ae |
| keyword |
[
"Antioch Dunes National Wildlife Refuge",
"Antioch Dunes evening-primrose",
"California",
"North America",
"San Francisco Bay-Delta",
"Sand dune ecosystem",
"USGS:605a3ba0d34e18948831d8ae",
"Western United States",
"biota",
"ddRADseq",
"evolution",
"genetic diversity",
"hybrid",
"population structure",
"rare plant"
]
|
| modified | 2021-12-23T00:00:00Z |
| publisher |
{
"name": "U.S. Geological Survey",
"@type": "org:Organization"
}
|
| spatial | -122.3700, 37.7100, -121.5300, 38.0900 |
| theme |
[
"Geospatial"
]
|
| title | Oenothera deltoides genotype data from Contra Costa County, California in 2019 |
