Data from: Genetic structure and the history of chub in the Alvord Basin

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