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    Polioptila californica genotype data from California, USA and Baja...

    • gimi9.com
    • data.usgs.gov
    • +1more
    Updated Aug 21, 2022
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    (2022). Polioptila californica genotype data from California, USA and Baja California, Mexico [Dataset]. https://gimi9.com/dataset/data-gov_polioptila-californica-genotype-data-from-california-usa-and-baja-california-mexico
    Explore at:
    Dataset updated
    Aug 21, 2022
    Area covered
    Baja California, Mexico, California, United States
    Description

    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.

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Share
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TwitterTwitter
Email
Click to copy link
Link copied
Close
Cite
(2022). Polioptila californica genotype data from California, USA and Baja California, Mexico [Dataset]. https://gimi9.com/dataset/data-gov_polioptila-californica-genotype-data-from-california-usa-and-baja-california-mexico

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

Explore at:
Dataset updated
Aug 21, 2022
Area covered
Baja California, Mexico, California, United States
Description

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.

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