DOI: 10.5061/dryad.d3q3220
title: Data from: Hybridization drives genetic erosion in sympatric desert fishes of western North America

description: Many species have evolved or currently coexist in sympatry due to
 differential adaptation in a heterogeneous environment. However,
 anthropogenic habitat modifications can either disrupt reproductive
 barriers or obscure environmental conditions which underlie fitness
 gradients. In this study, we evaluated the potential for an
 anthropogenically-mediated shift in reproductive boundaries that separate
 two historically sympatric fish species (Gila cypha and G. robusta)
 endemic to the Colorado River Basin using ddRAD sequencing of 368
 individuals. We first examined the integrity of reproductive isolation
 while in sympatry and allopatry, then characterized hybrid ancestries
 using genealogical assignment tests. We tested for localized erosion of
 reproductive isolation by comparing site-wise genomic clines against
 global patterns and identified a breakdown in the drainage-wide pattern of
 selection against interspecific heterozygotes. This, in turn, allowed for
 the formation of a hybrid swarm in one tributary, and asymmetric
 introgression where species co-occur. We also detected a weak but
 significant relationship between genetic purity and degree of consumptive
 water removal, suggesting a role for anthropogenic habitat modifications
 in undermining species boundaries or expanding historically limited
 introgression. In addition, results from basin-wide genomic clines
 suggested that hybrids and parental forms are adaptively non-equivalent.
 If so, then a failure to manage for hybridization will exacerbate the
 long-term extinction risk in parental populations. These results reinforce
 the role of anthropogenic habitat modification in promoting interspecific
 introgression in sympatric species by relaxing divergent selection. This,
 in turn, underscores a broader role for hybridization in decreasing global
 biodiversity within rapidly deteriorating environments.
description: Supplementary
 materialsSupplementary figures
 S1-S7GilaUB_SuppMat_submit_29May19.docxgila_ub.vcf.tar.gzVCF file for running admixture. Analyses were completed using an open source pipeline by Steve Mussman, available at https://github.com/stevemussmann/admixturePipeline, which completes per-locus filtering (e.g. by coverage, minor allele freuency) internally using command-line options.gila_ub_snps.tarData files containing an all-SNP alignment (in pyRAD .snps format), unlinked SNPs (=1 sampled per locus) in phylip format, and a filtered unlinked SNP alignment in phylip format. A filtered dataset of unlinked SNPs were used to run STRUCTURE and DAPC. See Methods for more details.gila_ub.loci.tar.gzFull-locus alignments for all retained loci assembled by pyRAD, in pyRAD's .loci formatgila_ub.str.tar.gzSTRUCTURE formatted unlinked SNPsgila_ub_introgress.tar.gzGzipped tar archive containing input files and R code for running genomic cline analysesgila_newhyb.tar.gzOutputs and datafiles for running newhybrids and associated power analyses in the hybriddetective R packagegila_ub_sra_metadataSample metadata for linking between NCBI SRA accession names (raw data) and sample names in datasets used for analyses