Polioptila californica Genotype Data from California, USA and Baja California, Mexico
Dates
Publication Date
2022-05-02
Time Period
2021
Citation
Wood, D.A., and Vandergast, A.G., 2022, Polioptila californica genotype data from California, USA and Baja California, Mexico: U.S. Geological Survey data release, https://doi.org/10.5066/P9MB2YE2.
Summary
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 [...]
Summary
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.
These data support the following publication:
Vandergast, A.G., Kus, B.E., Wood, D.A., Milano, E.R., and Preston, K.L., 2022. Subspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation. Evolutionary Applications. https://doi.org/10.1111/eva.13429
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.
Special Note:
The extent shown in the map preview is from eBird:
Fink, D., T. Auer, A. Johnston, M. Strimas-Mackey, O. Robinson, S. Ligocki, W. Hochachka, L. Jaromczyk, C. Wood, I. Davies, M. Iliff, L. Seitz. 2021. eBird Status and Trends, Data Version: 2020; Released: 2021. Cornell Lab of Ornithology, Ithaca, New York. https://doi.org/10.2173/ebirdst.2020
Click on title to download individual files attached to this item.
cagn_metadata.xml Original FGDC Metadata
View
37.03 KB
application/fgdc+xml
cagn_sample_info.txt
10.65 KB
text/plain
cagn_CAGN_genotypes.vcf
479.33 MB
text/x-vcard
Related External Resources
Type: Related Primary Publication
Subspecies differentiation and range‐wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation
Questions pertaining to the intended use of, or assistance with understanding limitations or interpretation of these data are to be directed to the individuals/organization listed in the Point of Contact section. Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Purpose
These data were collected to assess the distribution of genetic diversity within and among occurrences of the endangered California Gnatcatcher (Polioptila californica) and explore its evolutionary relationship to recognized subspecific with adjacent distribution in Baja California, using genome-wide genetic markers. The dataset archived herein can be used to further investigate evolutionary or ecological processes that affect these sampled occurrences of Polioptila californica, or they may be used to reconfirm the patterns reported in Vandergast et al. 2022 (see Larger Work Citation).
