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Oenothera deltoides Genotype Data from Contra Costa County, California in 2019

February 23, 2022

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, 2011) to calculate genetic diversity statistics, or loaded into R, using vcfR (Knaus and Grunwald, 2017), for further analysis.

These data support the following publication:
Thorne, K.M., and Vandergast, A.G., 2021, Distribution, abundance, and genomic diversity of the endangered Antioch Dunes evening-primrose (Oenothera deltoides subsp. howellii) surveyed in 2019: U.S. Geological Survey Open-File Report 2021-1017, 40 p., https://doi.org/10.3133/ofr20211017.

References:
Catchen, J., Bassham, S., Wilson, T., Currey, M., O'Brien, C., Yeates, Q., and Cresko, W. A., 2013, The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular ecology, 22(11), 2864-2883.
Knaus, B.J., and Grunwald, N.J., 2017, Vcfr: a package to manipulate and visualize variant call format data in R. Molecular ecology resources, 17(1), 44-53.
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., and Hoekstra, H. E., 2012, Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLOS ONE 7(5): e37135.

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