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Carex specuicola genomic data for the southern Colorado Plateau Desert

September 20, 2022

These data were compiled to investigate the demographic and phylogeographic of Carex specuicola. Objectives of our study were to understand the demographic and dispersal history of Carex specuicola across hanging gardens, the hybridization history between Carex specuicola and Carex utahensis, and the population structure of Carex specuicola across its distribution. The data release consists of three tab delimited text files that may be used to infer population structure and diversity (CASP.stru), relationships among sampling localities Carex.phylip), or genetic diversity statistics and demographic history (Carex.snps.vcf). These data represent genetic variation on an individual (.stru and .vcf) or sampling locality (.phylip) level. The .vcf file contains all of the information 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) to calculate genetic diversity statistics. The .phylip file can be uploaded to phyML to generate a tree-based visualization of relationships ( The .stru file can be used in the STRUCTURE program (Falush et al. 2007) to estimate population structure. These data were collected in 2020 using leaf samples collected from hanging gardens in the Four Corners region of Arizona and Utah. These data were collected by U.S. Geological Survey and Deaver Herbarium researchers who visited hanging garden sites and sampled leaf tissues from individual plants.

Publication Year 2022
Title Carex specuicola genomic data for the southern Colorado Plateau Desert
DOI 10.5066/P9LLZ1XD
Authors Robert T Massatti
Product Type Data Release
Record Source USGS Digital Object Identifier Catalog
USGS Organization Southwest Biological Science Center - Flagstaff, AZ, Headquarters