DOI: 10.5061/dryad.r31sg
title: Data from: Highly variable reproductive isolation among pairs of Catostomus species

description: Hybridization between diverged taxa tests the strength of reproductive
 isolation and can therefore reveal mechanisms of reproductive isolation.
 However, it remains unclear how consistent reproductive isolation is
 across species' ranges and to what extent reproductive isolation
 might remain polymorphic as species diverge. To address these questions,
 we compared outcomes of hybridization across species pairs of Catostomus
 fishes in three rivers in the Upper Colorado River basin, where an
 introduced species, C. commersoni, hybridizes with at least two native
 species, C. discobolus and C. latipinnis. We observed substantial
 heterogeneity in outcomes of hybridization, both between species pairs and
 across geographically separate rivers within each species pair. We also
 observed hybridization of additional related species with our focal
 species, suggesting that reproductive isolation in this group involves
 interactions of multiple evolutionary and ecological factors. These
 findings suggest that a better understanding of the determinants of
 variation in reproductive isolation is needed and that studies of
 reproductive isolation in hybrids should consider how the dynamics and
 mechanisms of reproductive isolation vary over ecological space and over
 evolutionary time. Our results also have implications for the conservation
 and management of native catostomids in the Colorado River basin.
 Heterogeneity in outcomes of hybridization suggests that the threat posed
 by hybridization and genetic introgression to the persistence of native
 species probably varies with extent of reproductive isolation, both across
 rivers and across species pairs.
description: VCF
 fileThis is the raw VCF file
 containing all 32,978 variant genetic sites initially identified from
 assembled reads.variants_0.5.vcfnames_common_variants_0.5This file is the formatted input file for entropy, the hierarchical Bayesian model used in this study. The file contains data for a subset of SNPs, in a simplified genotype likelihood format. SNPs in this file have a minor allele frequency &gt;0.05, and a maximum of 1 alternate allele. This file also contains only one locus per contig.artificial reference genomeThis artificial reference genome was constructed via a de novo assembly (using DNAstar's smng) of a subset of 25 million short sequence reads, distributed across all taxa. We then assembled short reads to thissplit_sucker_ref_long.fastaAllele frequenciesThis file gives allele frequencies at 4095 genetic loci for 21 different populations of fish, spanning 5 species. This is the input file for calculation of Nei's D and construction of a neighbor joining tree, visualizing genetic distance among populations.ID_afreq_matrix.txtR script for Nei's DThis is an R script that calculates Nei's genetic distance between pairs of populations, using allele frequencies. The input file for this script is "ID_afreq_matrix.txt"distAnalysis.RLocationsApproximate latitude and longitude of samped populations. NOTE: these are estimated from maps, and do not represent exact sampling locations, as GPS coordinates were not taken in the field.locations.csvlib1_sucker_barcode_keyBarcode-ID pairs for individual fish for lane 1 of sequencing. (Please note that there are individuals included in this barcode file that belong to a different project, and are not discussed in the related paper. )lib2_sucker_barcode_keyBarcode-ID pairs for individual fish for lane 2 of sequencing. (Please note that there are individuals included in this barcode file that belong to a different project, and are not discussed in the related paper. )AssembliesThis is a tarred (compressed) file that contains assemblies to an artificial reference genome. When untarred, this file will contain &gt;800 files in .bam format, one for each individual fish. These files were produced using bwa (Burrows-Wheeler Aligner, Li and Durbin 2009).assembled.tgz