Genetic Data for Plantago ovata in the Mojave Desert
Dates
Publication Date
2020-12-16
Time Period
2020
Citation
Shryock, D.F., Washburn, L.K., DeFalco, L.A., and Esque, T.C., 2020, Genetic and habitat data for Plantago ovata in the Mojave Desert: U.S. Geological Survey data release, https://doi.org/10.5066/P92XN5OW.
Summary
These datasets were developed to represent the genetic diversity, and population structure of Plantago ovata in the Mojave Desert. The genetic datasets record genetic variation at an individual level, with the file structures varying based on the programs within which the files are intended to be edited. The .genepop file can be viewed in GENEPOP software (Rousset 2008) or imported into R statistical software (https://www.R-project.org/) using the adegenet package (Jombart and Ahmed 2011). The .vcf file can be loaded into the Stacks population program (Catchen et al. 2013) to calculate genetic diversity statistics. References: Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool [...]
Summary
These datasets were developed to represent the genetic diversity, and population structure of Plantago ovata in the Mojave Desert. The genetic datasets record genetic variation at an individual level, with the file structures varying based on the programs within which the files are intended to be edited. The .genepop file can be viewed in GENEPOP software (Rousset 2008) or imported into R statistical software (https://www.R-project.org/) using the adegenet package (Jombart and Ahmed 2011). The .vcf file can be loaded into the Stacks population program (Catchen et al. 2013) to calculate genetic diversity statistics.
References:
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics. Molecular Ecology, 22(11), 3124–3140.
Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi:10.1093/bioinformatics/btr521
Rousset, F., 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Molecular Ecology. Resources 8: 103-106.
The purpose of these data are to represent genetic diversity, population structure, and the geographic distribution of Plantago ovata in the Mojave Desert. Based on these datasets, we investigated patterns of putative local adaptation in the species and developed seed transfer zones reflecting areas within which seeds may be transferred with limited risk of maladaptation. These datasets can be used to further investigate the genetic structure of Plantago ovata in appropriate genetics software.
