Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

Abstract

Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich—35 reciprocally monophyletic clades versus 22 recognized species—than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sampled. We conceived and implemented a sampling regime combining level IV ecoregions and independent river drainages to yield a geographic grid for comprehensive recovery of all genealogically exclusive clades. We sampled over 550 populations throughout the distribution of Desmognathus in the eastern United States of America and generated mitochondrial DNA sequence data (mtDNA; 1,991 bp) for 536 specimens. A Bayesian phylogenetic reconstruction of the resulting haplotypes revealed forty-five reciprocally monophyletic clades, eleven of which have never been included in a comprehensive phylogenetic reconstruction, and an additional three not represented in any molecular systematic survey. Although general limitations associated with mtDNA data preclude new species delineation, we profile each of the 45 clades and assign names to 10 new clades (following a protocol for previous clade nomenclature). We also redefine several species complexes and erect new informal species complexes. Our dataset, which contains topotypic samples for nearly every currently recognized species and most synonymies, will offer a robust framework for future efforts to delimit species within Desmognathus.

Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

“…Second, specimens of valentinei from the southern Pascagoula and Escatawpa drainages of Mississippi and Alabama form a reciprocally monophyletic group exhibiting almost no gene flow with valentinei . Distinctiveness of this lineage was noted in previous analyses with more limited sampling (Beamer & Lamb, 2020; Means et al, 2017; Pyron et al, 2020). We, therefore, recognize it as valentinei B, a newly delimited mito‐nuclear candidate species.…”

“…Others, such as a deep‐time reticulation involving the lineage ancestral to aeneus + imitator, were unexpected and not reflected in present‐day mitochondrial patterns (Pyron et al, 2020). Other clear instances of mitochondrial capture, such as fuscus E with haplotypes from auriculatus C (Beamer & Lamb, 2020), were not recovered by the preliminary network analyses. Therefore, a population‐level genomic assessment of species boundaries and admixture combined with known instances of mitochondrial capture is needed to quantify an accurate species delimitation model and an estimate of quantifiable hybridization events.…”

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation*

“…2009). We note that some recent studies suggest that D. auriculatus , D. conanti, D. fuscus , and D. ocoee may contain additional cryptic species that we have not included here (Beamer and Lamb 2008, 2020; Tilley et al. 2013; Pyron et al.…”

Understanding “Alexandrian” extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders

“…This may suggest that the panhandle segment was indeed also D. auriculatus A, and that stream-dwelling D. auriculatus A suffered disproportionately from the unknown forces of decline compared to swamp-dwelling populations. Both swamp-and stream-dwelling populations previously assigned to Desmognathus "auriculatus" in the extreme western part of their range in Texas and Louisiana also apparently declined around the same time, though all recent genetic samples from this area have been referred to D. conanti E (Hibbitts et al 2015;Beamer and Lamb 2020).…”

“…Most historical peninsular records (Fig. 1; Table 1; see Neill 1951) occurred in a distinct river drainage (St. Johns) and Level IV Ecoregion (75c Central Florida Ridges and Uplands/75d Eastern Florida Flatwoods) from the more northerly extant populations (Means et al 2017;Beamer and Lamb 2020). Other populations to the west from the Ala a and Wacassassa Rivers near Tampa (Fig.…”