Hilaria jamesii data for the Colorado Plateau of the southwestern United States
Data for journal manuscript: The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States
Dates
Publication Date
2020-01-10
Time Period
2017
Citation
Massatti, R., 2020, Hilaria jamesii data for the Colorado Plateau of the southwestern United States: U.S. Geological Survey data release, https://doi.org/10.5066/P9CNFWOX.
Summary
These data were compiled to investigate the demographic, phylogeographic, and adaptation history of Hilaria jamesii. The data release consists of three tab delimited text files that may be used to infer population structure or putative adaptive loci (hija_adaptation_dataset.stru), relationships among sampling localities (hija_phylogeny_dataset.phylip), or genetic diversity statistics (hija_diversity_stats.vcf). All files record 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 [...]
Summary
These data were compiled to investigate the demographic, phylogeographic, and adaptation history of Hilaria jamesii. The data release consists of three tab delimited text files that may be used to infer population structure or putative adaptive loci (hija_adaptation_dataset.stru), relationships among sampling localities (hija_phylogeny_dataset.phylip), or genetic diversity statistics (hija_diversity_stats.vcf). All files record 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.
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Related External Resources
Type: Related Primary Publication
The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States
The purpose of these data are to describe the population structure, intraspecific relationships, genetic diversity, and putative adaptive loci in Hilaria jamesii. With knowledge of these patterns, we investigated the phylogeographic history of the species and how that history related to its historical and contemporary patterns of adaptation to regional environmental gradients. The datasets archived herein can be used to further investigate evolutionary or ecological processes that affect Hilaria jamesii, or they may be used to reconfirm the patterns reported in Massatti and Knowles 2020 (see Larger Work Citation). Ultimately, these data will be used to inform restoration management decisions regarding seed transfer guidelines and native plant materials development.
Rights
The author(s) of these data request that data users contact them regarding intended use and to assist with understanding limitations and interpretation. Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty.