Salt marsh bird's-beak and Point Reyes bird's-beak single nucleotide polymorphism genotype data from California, USA and Baja California, MX
This dataset contains 58 samples from 10 occurrences of Chloropyron maritimum subsp. maritimum (salt marsh bird's-beak), and 2 occurrences of Chloropyron maritimum subsp. palustre (Point Reyes bird's-beak). Genomic markers were generated from ddRAD loci and analyzed using the Stacks v2.68 pipeline. The genotypes for all samples are provided in a VCF file with 18,031 loci . A companion sample data file is provided with sample names, and occurrence designations, and other data. 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 to calculate genetic diversity statistics, or loaded into R, using vcfR, for further analysis.
Short sequence reads generated for this project are publicly available under NCBI BioProject accession PRJNA1227921 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1227921) and PRJNA1227546 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1227546). Variant call format (VCF) and comma‑separated values (CSV) files derived from these reads are provided within this ScienceBase data release (https://doi.org/10.5066/P15ZVKBA).
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Complete Metadata
| accessLevel | public |
|---|---|
| bureauCode |
[ "010:12" ] |
| contactPoint |
{ "fn": "U.S. Geological Survey, Western Ecological Research Center", "@type": "vcard:Contact", "hasEmail": "mailto:gs-b-werc_data_management@usgs.gov" } |
| description | This dataset contains 58 samples from 10 occurrences of Chloropyron maritimum subsp. maritimum (salt marsh bird's-beak), and 2 occurrences of Chloropyron maritimum subsp. palustre (Point Reyes bird's-beak). Genomic markers were generated from ddRAD loci and analyzed using the Stacks v2.68 pipeline. The genotypes for all samples are provided in a VCF file with 18,031 loci . A companion sample data file is provided with sample names, and occurrence designations, and other data. 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 to calculate genetic diversity statistics, or loaded into R, using vcfR, for further analysis. Short sequence reads generated for this project are publicly available under NCBI BioProject accession PRJNA1227921 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1227921) and PRJNA1227546 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1227546). Variant call format (VCF) and comma‑separated values (CSV) files derived from these reads are provided within this ScienceBase data release (https://doi.org/10.5066/P15ZVKBA). |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Digital Data", "format": "XML", "accessURL": "https://doi.org/10.5066/P15ZVKBA", "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.6aac2bac1ba49b6a17baa51f.xml" } ] |
| identifier | http://datainventory.doi.gov/id/dataset/USGS_6aac2bac1ba49b6a17baa51f |
| keyword |
[ "Carpinteria", "Grizzly Bay", "Jacoby", "Mad River", "Morro Bay", "Newport Bay", "Point Mugu", "San Quintin", "Tijuana Estuary", "USGS:6aac2bac1ba49b6a17baa51f", "abundance", "adaptation", "annual plant", "biota", "habitat suitability", "population structure", "remediation", "restoration", "sea level rise", "sea-level change", "single nucleotide polymorphisms" ] |
| modified | 2026-09-28T00:00:00Z |
| publisher |
{ "name": "U.S. Geological Survey", "@type": "org:Organization" } |
| spatial | -124.1491, 30.453874, -116.0327, 40.86596 |
| theme |
[ "geospatial" ] |
| title | Salt marsh bird's-beak and Point Reyes bird's-beak single nucleotide polymorphism genotype data from California, USA and Baja California, MX |
