Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

Abstract

BackgroundPorous 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.ResultsWe 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.ConclusionsComplex 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.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1197-y) contains supplementary material, which is available to authorized users.

Genome-wide local ancestries discriminate homoploid hybrid speciation from secondary introgression in the red wolf (Canidae:Canis rufus)

“…1B). Our observations agree with prior studies in underscoring the presence of 'tree 229 compression,' or a branch lengths reduced/ distorted due to an inability to partition introgressed 230 fron non-introgressed ancestries (Leache et al 2014;Bangs et al 2018). 231…”

Defining Relictual Biodiversity: Conservation Units in Speckled Dace (Cyprinidae:Rhinichthys osculus) of the Greater Death Valley Ecosystem

“…Finally, genomic tools have demonstrated the previously unknown hybrid status of 618 Amargosa Canyon SPD. Hybridization has been commonplace among desert fishes (Bangs, Douglas, Mussmann, & Douglas, 2018) and has served as a mechanism of speciation (Gerber, 620 Tibbets, & Dowling, 2001), but can also erode species boundaries (Chafin, Douglas, Martin, & Douglas, 2019). Additionally, anthropogenic climate change has induced hybridization among 622 divergent species (Canestrelli et al, 2017;Muhlfeld et al, 2014), and thus represents a post-Pleistocene evolutionary mechanism inherent to western North America (Woodhouse, Meko, 624 MacDonald, Stahle, & Cook, 2010).…”

Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

“…Indeed, historic introgression with Sonora Sucker was 556 detected in all Virgin River samples, as reflected in the elevated hybrid index and low interspecies heterozygosity ( Figure 5B). Although the Sonora Sucker proportion is reduced, it is 558 nevertheless significant based on previous D-statistic tests (Bangs et al, 2018b) and hybrid index values for all samples ( Figure 5B). 560…”

“…The quantification of molecular variability in both catostomids is a key element in delimiting species-boundaries, management units, and historic patterns of reticulation. Here we 136 build upon previous work (Bangs et al, 2018b) by applying species delimitation methods, phylogenomic (i.e., concatenated and multispecies coalescence), and population genomic 138 approaches (i.e., Bayesian clustering and hybrid detection) to identify potential species rangewide, but with special focus on the Little Colorado River. In this regard, the impacts of divergent 140 life histories, as well as the role of stream capture and hybridization, are particularly germane with regard to the breadth and depth of differentiation found within each.…”