Genetic and Habitat 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, population structure, and geographic distribution of Plantago ovata in the Mojave Desert. This data release consists of two tab-delimited text files representing the genetic diversity and structure of Plantago ovata (.genepop and .vcf), and two raster spatial datasets (GeoTIFF) reflecting predicted habitat for the species within 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. Each file contains 13,111 SNPs genotyped in 748 individuals. The genepop file can be viewed in GENEPOP software (Rousset 2008) or imported into R statistical [...]
Summary
These datasets were developed to represent the genetic diversity, population structure, and geographic distribution of Plantago ovata in the Mojave Desert. This data release consists of two tab-delimited text files representing the genetic diversity and structure of Plantago ovata (.genepop and .vcf), and two raster spatial datasets (GeoTIFF) reflecting predicted habitat for the species within 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. Each file contains 13,111 SNPs genotyped in 748 individuals. 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. The raster datasets represent the predicted suitability of habitat for Plantago ovata within the Mojave Desert mapping extent and the standard error among alternative habitat models. They can be viewed in any appropriate mapping software. Analyses used to create the habitat layer can be replicated with the accompanying R script.
These data support the following publication:
Shryock, D.F., Washburn, L.K., DeFalco, L.A. and Esque, T.C., 2020. Harnessing landscape genomics to identify future‐climate resilient genotypes in a desert annual. Molecular Ecology.
References:
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics., 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 datasets 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 or to map the species geographic distribution in an appropriate GIS.
