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

Abstract

Disclosure statement:Authors have nothing to disclose.Abstract (242/250) Species are an indisputable unit for biodiversity conservation, yet their delimitation is fraught 2 with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern 4 North America. Three species were originally defined according to subtle morphological differences with weak diagnostic power, with traditional genetic analyses failing to support the 6 nominal species. Consequently, the complex was re-defined as a single polytypic unit, with the proposed 'threatened' status of two putative species withdrawn at the federal level. Here, we 8 utilized dense spatial and genomic sampling (N=387 and >22k loci) to re-evaluate the status of the complex, based on SNP-based coalescent and polymorphism-aware phylogenetic models. In 10 doing so, all three species were supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To understand this discrepancy with past studies, we 12 categorized evolutionary mechanisms driving discordance. We tested (and subsequently rejected) prior hypotheses suggesting that phylogenetic discord in the complex was hybridization-driven. 14 Instead, we found the G. robusta complex to have diverged within the 'anomaly zone' of tree space and, as such, have accumulated inconsistent patterns of diversity which have confounded 16 prior studies. After extending these analyses with phylogeographic modeling, we propose that this is reflective of a rapid radiation promoted by Plio-Pleistocene tectonism. Our results not only 18 support resurrection of the three species as distinct entities, but also offer an empirical example of how phylogenetic discordance can be categorized in other recalcitrant taxa. 20 between G. robusta from the upper and lower basins of the Colorado River ecosystem (Chafin et 130 al. 2019). One species, Gila elegans, is extirpated from the wild, thus samples were provided by the 132 Southwestern Native Aquatic Resources and Recovery Center (Dexter, NM). The genus Ptychocheilus served to root the Gila clade within the broader context of western leuciscids 134 (Schönhuth et al. 2012, 2014, 2018). 8 136 Reduced-representation sequencing Genomic DNA was extracted using either PureGene® or DNeasy® kits (Qiagen Inc.) and 138 quantified via fluorometer (Qubit™; Thermo-Fisher Scientific). Library preparations followed the published ddRAD protocol (Peterson et al. 2012). Restriction enzyme and size-selection 140 ranges were first screened using an in silico procedure (Chafin et al. 2018), with the target fragment sizes further optimized by quantifying digests for 15 representative samples on an 142 Agilent 2200 TapeStation. Final library preparations were double-digested using a high-fidelity PstI (5'-CTGCAG-3') and MspI (5'-CCGG-3') following manufacturer's protocols (New 144 England Biosciences). Digests were purified using bead purification (Ampure XP; Beckman-Coul...

Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout

“…We note, however, that inferred divergence times are likely skewed by introgression (e.g. figure 6c), but that the exact nature of this effect is unclear [101]. Parameter estimates for all analyses post burn-in were >600.…”

“…geomorphic) events may have driven co-divergence, we used the program ECOEVOLITY [99], which employs a Bayesian method to compute probabilities on the number of independent divergences across a series of pairwise comparisons. Because ECOEVOLITY is most consistent when analyzing both constant and polymorphic sites [99, 100], we sampled full-locus alignments (excluding sites with either >25% missing data globally or per-population) using the phylip2ecoevolity.pl script from Chafin et al [101]. The event model followed a Dirichlet process, with the prior probability distribution for the number of divergence events skewed towards a model of complete independence (i.e.…”

Taxonomic hypotheses and the biogeography of speciation in the Tiger Whiptail complex (Aspidoscelis tigris: Squamata, Teiidae)

“…The CD5 model identified potential cryptic lineages within a clade comprising A. t. tigris and A. t. punctilinealis, although sample sizes representing this group were limited. Of note, A. t. tigris and A. t. punctilinealis were not reciprocally monophyletic, however assigning causality of this to hybridization/ intergradation, stochastic lineage sorting, or a lack of phylogenetic signal requires additional data (Chafin et al 2020). Again, we suggest a more in-depth examination using a larger panel of molecular markers so as to confirm or reject continued recognition of A. t. tigris as distinct from A. t. punctilinealis, and likewise to adjudicate recognition of A. t. mundus from A. t. septentrionalis.…”

Taxonomic hypotheses and the biogeography of speciation in the Tiger Whiptail complex (Aspidoscelis tigris: Squamata, Teiidae)

“…This is because the North American southwest was essentially defined by tectonism and subsequent climatic oscillations, with phylogeographic/ phylogenetic reverberations manifest within the endemic biodiversity (Douglas et al, 2016;Holycross & Douglas, 2007;Mussmann et al, 2020;Sullivan et al, 2014). Ancillary genetic footprints of hybridization, diversification, and rapid demographic change have also become increasingly apparent in modern evaluations (Chafin et al, 2020;Bangs et al, 2020a;Bangs et al, 2020b;Douglas et al, 2006).…”

“…Opportunities for biotic exchange (or alternatively, vicariant events) hinged largely upon drainage evolution (e.g., Chafin et al, 2020;Douglas et al, 1999). Small-bodied terrestrial vertebrates were also involved in these biogeograpnic opportunities, despite the fact that the Colorado River had long been hypothesized as a vicariant barrier to dispersal (e.g.…”