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    • Polioptila californica genotype data from California, USA and Baja California, Mexico

    Metadata Updated: October 30, 2025

    This dataset contains genomic records from 184 California Gnatcatchers (Polioptila californica) collected at 18 sites in southern California (USA), 13 sites in Baja California (Mexico), and 17 sites in Baja California Sur (Mexico). 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 84,125 independent loci and 7 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 Grunwald, 2017), for further analysis. References: Catchen J., Hohenlohe P.A., Bassham S., Amores A., Cresko W.A. Stacks-an analysis tool set for population genomics. Molecular Ecology. 2013; 22:3124-3140. Knaus, B.J, Grunwald N.J. vcfr: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources. 2016; 17:44-53. Peterson B.K., Weber J.N., Kay E.H., Fisher H.S., Hoekstra H.E. Double Digest RADseq-an inexpensive method for de novo SNP discovery and genotyping in model and non-model species: PLoS ONE. 2012; 7:e37135.

    Access & Use Information

    Public: This dataset is intended for public access and use. License: No license information was provided. If this work was prepared by an officer or employee of the United States government as part of that person's official duties it is considered a U.S. Government Work.

    Downloads & Resources

    Dates

    Metadata Created Date September 14, 2025
    Metadata Updated Date October 30, 2025

    Metadata Source

    Harvested from DOI USGS DCAT-US

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date September 14, 2025
    Metadata Updated Date October 30, 2025
    Publisher U.S. Geological Survey
    Maintainer
    Identifier http://datainventory.doi.gov/id/dataset/usgs-6255f2b8d34e21f8276f4ae3
    Data Last Modified 2022-06-17T00:00:00Z
    Category geospatial
    Public Access Level public
    Bureau Code 010:12
    Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
    Metadata Catalog ID https://ddi.doi.gov/usgs-data.json
    Schema Version https://project-open-data.cio.gov/v1.1/schema
    Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
    Harvest Object Id 48d232d6-96f7-41b4-acc8-5a24b6b25e32
    Harvest Source Id 2b80d118-ab3a-48ba-bd93-996bbacefac2
    Harvest Source Title DOI USGS DCAT-US
    Metadata Type geospatial
    Old Spatial -120, 22, -109, 34.5
    Source Datajson Identifier True
    Source Hash bb6fbf421850db3f5412d05ecbe3984af62624db500498433448c80fce444d97
    Source Schema Version 1.1
    Spatial {"type": "Polygon", "coordinates": -120, 22, -120, 34.5, -109, 34.5, -109, 22, -120, 22}

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