DOI: 10.5061/dryad.8f1j5nd
title: Data from: Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

description: Background: Porous species boundaries can be a source of conflicting
 hypotheses, particularly when coupled with variable data and/or
 methodological approaches. Their impacts can often be magnified when
 non-model organisms with complex histories of reticulation are
 investigated. One such example is the genus Catostomus (Osteichthys,
 Catostomidae), a freshwater fish clade with conflicting morphological and
 mitochondrial phylogenies. The former is hypothesized as reflecting the
 presence of admixed genotypes within morphologically distinct lineages,
 whereas the latter is interpreted as the presence of distinct morphologies
 that emerged multiple times through convergent evolution. We tested these
 hypotheses using multiple methods, to including multispecies coalescent
 and concatenated approaches. Patterson's D-statistic was applied to
 resolve potential discord, examine introgression, and test the putative
 hybrid origin of two species. We also applied naïve binning to explore
 potential effects of concatenation. Results: We employed 14,007 loci
 generated from ddRAD sequencing of 184 individuals to derive the first
 highly supported nuclear phylogeny for Catostomus. Our phylogenomic
 analyses largely agreed with a morphological interpretation,with the
 exception of the placement of Xyrauchen texanus, which differs from both
 morphological and mitochondrial phylogenies. Additionally, our evaluation
 of the putative hybrid species C. columbianus revealed a lack
 introgression and instead matched the mitochondrial phylogeny.
 Furthermore, D-statistic tests clarified all discrepancies based solely on
 mitochondrial data, with agreement among topologies derived from
 concatenation and multispecies coalescent approaches. Extensive historic
 introgression was detected across six species-pairs. Potential endemism in
 the Virgin and Little Colorado Rivers was also apparent, and the former
 genus Pantosteus was derived as monophyletic, save for C. columbianus.
 Conclusions: Complex reticulated histories detected herein support the
 hypothesis that introgression was responsible for conflicts that occurred
 within the mitochondrial phylogeny, and explains discrepancies found
 between it and previous morphological phylogenies. Additionally, the
 hybrid origin of C. columbianus was refuted, but with the caveat that more
 fine-grain sampling is still needed. Our diverse phylogenomic approaches
 provided largely concordant results, with naïve binning useful in
 exploring the single conflict. Considerable diversity was found within
 Catostomus across southwestern North America, with two drainages [Virgin
 River (UT) and Little Colorado River (AZ)] reflecting unique composition.
description: alignmentsZip file of all alignments used in .phy and .nex formats.ardensRaw fastq files split by individual.bondiRaw fastq files split by individual.catostomusRaw fastq files split by individual.clarkiiRaw fastq files split by individual.columbianusRaw fastq files split by individual.commersoniiRaw fastq files split by individual.insignisRaw fastq files split by individual.jordaniRaw fastq files split by individual.lahontanRaw fastq files split by individual.micropsRaw fastq files split by individual.MoxostomaRaw fastq files split by individual.plebeiusRaw fastq files split by individual.rimiculusRaw fastq files split by individual.santaanaeRaw fastq files split by individual.tahoensisRaw fastq files split by individual.texanusRaw fastq files split by individual.virescensRaw fastq files split by individual.discobolusRaw fastq files split by individual.latipinnisRaw fastq files split by individual.platyrhynchusRaw fastq files split by individual.