DOI: 10.5061/dryad.ct362tv
title: Data from: Genetic structure and the history of chub in the Alvord Basin

description: Knowledge of the distribution of genetic resources within and among taxa
 is prerequisite for development of management strategies which facilitate
 conservation of those resources. We used restriction-site associated DNA
 (RAD) sequencing to survey genetic variation in Alvord Chub and Borax Lake
 Chub from the Alvord Basin in southeastern Oregon and northern Nevada,
 USA. Our specific goals were to gain an understanding of the population
 genetic structure of Alvord Chub and the relationship between this species
 and Borax Lake Chub. Despite the fact that our collections were taken from
 ponds and streams, isolated from one another by kilometers of desert, our
 results revealed that diversity in Alvord Chub was primarily distributed
 among two regional groupings, which we hypothesize to be related to
 habitat changes following the end of the most recent glaciation event,
 approximately 10 thousand years ago. Our results further revealed that
 Alvord Chub and Borax Lake Chub shared common ancestors during that
 glaciation event, and that divergence between the two may have been
 sympatric. Finally, we observed evidence that the clade containing Alvord
 Chub and Borax Lake Chub was isolated from its closest extant relative,
 the Tui chub, during the Miocene Epoch, when volcanic flows were forming
 the mountains surrounding what became the Alvord Basin. These results will
 be useful for informing conservation strategies for Alvord Chub, and
 provide new insights regarding the role of these species in the
 evolutionary legacy of the region.
description: Supplementary File
 1Bash
 scripts used to handle raw sequence data, identify loci, and call
 genotypes.SF1_CompositeScript.txtSupplementary File 2List of samples examined by collection. Samples that were removed during analysis, and the reason for each, are indicated.SF2_SamplesExamined.xlsxSupplementary File 3List of loci identified as outliers, including allele frequencies, and BLAST results for each.SF3_OutlierLoci.xlsxSupplementary File 4RAD genotype data for the full set of 4,969 loci in genepop format. Sample names correspond to the 'Alias' column in Supplementary File 2.SF4_RADgenepop.txtSupplementary File 5RAD genotype data for 4,931 loci in genepop format. This file is similar to Supplementary File 4, except that the outlier loci have been removed here. Sample names correspond to the 'Alias' column in Supplementary File 2.SF5_RADgenepop-sel.txtSupplementary File 6Microsatellite genotype data in genepop format. Names of individuals correspond to the 'Sample Name' field in Supplementary File 2.SF6_MicrosatGenepop.txtSTACKS catalog fileDNA sequences and metadata for consensus loci created using the scripts presented in Supplementary File 1. This catalog file was generated using the cstacks script in STACKS. Detailed information regarding the file format is available in the STACKS user manual (http://catchenlab.life.illinois.edu/stacks/manual/).Data1_batch_1.catalog.tags.tsvRAD genotype data in variant call formatRAD genotype data resulting from the pipeline presented in Supplementary File 1, in variant call format. Locus names correspond to those listed in the catalog file (Data1_batch_1.catalog.tags.tsv). This file was produced using the populations script in STACKS.Data2_batch_1.vcf