Carex specuicola genomic data for the southern Colorado Plateau Desert

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 (http://www.atgc-montpellier.fr/phyml/). 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.本数据集汇编旨在研究岩生薹草（Carex specuicola）的种群动态与系统地理学特征。本研究的目标为阐明岩生薹草在各类悬垂花园生境中的种群动态与扩散历史、岩生薹草与犹他薹草（Carex utahensis）的杂交演化历史，以及岩生薹草在其分布范围内的种群遗传结构。本次发布的数据包含三个制表符分隔的文本文件，可分别用于推断种群结构与遗传多样性（CASP.stru）、采样点间的演化关系（Carex.phylip），以及计算遗传多样性统计量与种群动态历史（Carex.snps.vcf）。这些数据分别从个体水平（.stru与.vcf文件）与采样点水平（.phylip文件）反映了遗传变异情况。Carex.snps.vcf文件包含了另外两个文件的全部信息，但不同文件的结构需适配各自对应的分析软件。上述文件可通过文本编辑器打开并编辑，例如PC端的Notepad++与Mac端的BBEdit。可将Carex.snps.vcf文件导入Stacks种群分析程序（Catchen等人，2013）以计算遗传多样性统计量。可将Carex.phylip文件上传至phyML平台以生成演化关系的树形可视化结果（http://www.atgc-montpellier.fr/phyml/）。CASP.stru文件可用于STRUCTURE程序（Falush等人，2007）以估算种群遗传结构。本数据集的样本采集工作于2020年完成，采样材料取自美国亚利桑那州与犹他州四角落区域的悬垂花园生境。本次数据采集由美国地质调查局与迪弗标本馆的研究人员完成，他们实地走访了各悬垂花园生境，并从单株植物上采集了叶片组织。