Astragalus species complex genetic data from southeast Utah (Grand County and San Juan County), USA
These data were compiled to investigate the evolutionary history of Astragalus iselyi, A. sabulosus var. sabulosus, and A. sabulosus var. vehiculus. The data release consists of six text files. One file is a bash script (astragalus_MLE_msms.sh) for generating simulated genetic data. Four files contain individual-level (astragalus.fasta, astragalus.nothin.recode.vcf, astragalus.recode.vcf) or population-level (astragalus_dadi.txt) information on genetic variation. One file contains sampling site-specific data for various soil and climatic variables (astragalus_env.txt). The .vcf files contain the full sequence information that is contained in the other files, but the file structures vary based on the programs used for analysis. 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 et al. 2013) or VCFtools (Danecek et al. 2011) to calculate genetic diversity statistics (astragalus.nothin.recode.vcf contains multiple genetic variants per locus, whereas astragalus.recode.vcf contains only one genetic variant per locus).The astragalus_dadi.txt file can be used as an input file with the program dadi (Gutenkunst et al. 2009) to infer population history. Finally, astragalus.fasta can be loaded as an input file into RAxML (Stamatakis 2008) to perform phylogenetic analyses.
Citation Information
| Publication Year | 2021 |
|---|---|
| Title | Astragalus species complex genetic data from southeast Utah (Grand County and San Juan County), USA |
| DOI | 10.5066/P93SRC7M |
| Authors | Matthew R Jones, Daniel E Winkler, Robert T Massatti |
| Product Type | Data Release |
| Record Source | USGS Digital Object Identifier Catalog |
| USGS Organization | Southwest Biological Science Center - Flagstaff, AZ, Headquarters |
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AimEvolutionary radiations are central to the origin and maintenance of biodiversity, yet we rarely understand how they are jointly shaped by demography and ecological opportunity. Astragalus is the largest plant genus in the world and is disproportionately comprised of rare species restricted to narrow geographic and ecological regions. Here, we explored the demographic and ecological mechanismsAuthorsMatthew Richard Jones, Daniel E. Winkler, Robert Massatti - Connect