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

Abstract

The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double‐digest restriction site‐associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robustaComplex) in the Colorado River

“…S2 and S3 , Supplementary Material online; following Evanno et al 2005 ), as computed using Phylo Networks ( Solís-Lemus and Ané 2016 ; Solís-Lemus et al 2017 ). An alternative test using D -statistics (computed in Comp- D; Mussmann, Douglas, Bangs, et al 2020 ) also supported introgression between G. elegans and G. seminuda ( = 0.302 across 86,400 tests; table1 ), as did analogous tests using distance-based networks ( supplementary fig. S3 , Supplementary Material online) and the H -statistic output by Hy De ( Blischak et al 2018 ).…”

“…D -statistics ( Green et al 2010 ; Eaton and Ree 2013 ) were calculated using Comp- D v 2018-06-28 ( Mussmann, Douglas, Bangs, et al 2020 ). To further test hypotheses of reticulation, we used quartet concordance factors (CFs) as input for phylogenetic network inference using the S Na Q algorithm ( Phylo Networks v 0.8.0; Solís-Lemus and Ané 2016 ; Solís-Lemus et al 2017 ).…”

“…Here, historical or persistent gene flow both compresses apparent divergence in species-trees ( Leache, Harris, et al 2014 ) and similarly drives a predominance of AGTs which can supersede “correct” branching patterns in some regions of parameter space ( Long and Kubatko 2018 ). The result is a confounding effect on the adequate delineation of phylogenetic groupings (e.g., a necessary step of biodiversity conservation), as well as a limitation in the downstream analysis of affected species trees ( Bastide et al 2018 ; Luo et al 2018 ; Morales and Carstens 2018 ; Bangs et al 2020 ).…”

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta complex) in the Colorado River

“…Here, historical or persistent gene flow both compresses apparent divergence in species-trees (Leache et al 2014b) and similarly drives a predominance of AGTs which can supercede 'correct' branching patterns in some regions of parameter space (Long and Kubatko 2018). The result is a confounding effect on the adequate delineation of phylogenetic groupings (e.g., a necessary step of biodiversity conservation), as well as a limitation in the downstream analysis of affected species trees (Bastide et al 2018;Luo et al 2018;Morales and Carstens 2018;Bangs et al 2020).…”

Brown trout phylogenetics: A persistent mirage towards (too) many species

“…This includes fish species complexes in sticklebacks (Guo et al, 2019), roaches (Baumsteiger et al, 2017), cichlids (e.g. Willis, 2017), suckers (Bangs et al, 2020), topminnows (Duvernell et al, 2019) and coregonids (Coregonus ardeti species flock; Ackiss et al, 2020). Based on several thousand polymorphisms, Copus et al (2018) proposed reducing the Gila robusta complex to a single species.…”