Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex

Abstract

Accurate species delimitation is critical for biodiversity studies. However, species complexes characterized by introgression, high levels of population structure and subtle phenotypic differentiation can be challenging to delimit. Here, we report on a molecular systematic investigation of the woodland salamanders Plethodon wehrlei and Plethodon punctatus, which traditionally have been placed in the Plethodon wehrlei species group. To quantify patterns of genetic variation, we collected genetic samples from throughout the range of both species, including 22 individuals from nine populations of P. punctatus, and 60 individuals from 26 populations of P. wehrlei. From these samples, we sequenced three mtDNA loci (5596 base pairs) and five nuclear loci (3377 base pairs). We inferred time-calibrated gene trees and species trees using BEAST 2.4.6, and we delimited putative species using a Bayesian implementation of the general mixed Yule-coalescent model (bGMYC) and STRUCTURE.Finally, we validated putative species using the multispecies coalescent as implemented in Bayesian Phylogenetics and Phylogeography (BPP). We found substantial phylogeographic diversity in P. wehrlei, including multiple geographically cohesive clades and an inferred mitochondrial common ancestor at 11.5 myr (95% HPD: 9.6-13.6 myr) that separated populations formerly assigned to P. dixi from all other populations. We also found that P. punctatus is deeply nested within P. wehrlei, rendering the latter paraphyletic. After discussing the challenges faced by modern species delimitation methods, we recommend retaining P. punctatus because it is ecologically and phenotypically distinct. We further recommend that P. dixi be recognized as a valid species. |KUCHTA eT Al.

Phylogeography ofDictyota fasciolaandDictyota mediterranea(Dictyotales, Phaeophyceae): unexpected patterns on the Atlantic-Mediterranean marine transition and taxonomic implications

“…The only possibility to accept the two currently recognized species would imply considering D. mediterranea as a paraphyletic taxon. Anacladogenetic speciation processes—often rendering ancestral paraphyletic taxa—have already been proposed to explain similar phylogenetic patterns (e.g., Hörandl, 2006; Crawford, 2010; Kuchta, Brown & Highton, 2018; Smith, Ooi & Clark, 2018). In this scenario, some taxonomy-genetic conflict should be taken into account: a few individuals of both species are nested with individuals of the other species (Fig.…”

Peer Review #1 of "Phylogeography of Dictyota fasciola and Dictyota mediterranea (Dictyotales, Phaeophyceae): unexpected patterns on the Atlantic-Mediterranean marine transition and taxonomic implications (v0.1)"

“…Anacladogenetic speciation processes -often rendering ancestral paraphyletic taxa-have already been proposed to explain similar phylogenetic patterns (e.g. Hörandl, 2006;Crawford, 2010;Kuchta et al, 2018;Smith et al, 2018). In this scenario, some taxonomy-genetic conflict should be taken into account: a few individuals of both species are nested with individuals of the other species (Fig.…”

An integrative multi-approach workflow resolves species limits in the southernmost members of theLiolaemus kingiigroup (Squamata: Liolaemini)

“…When a species originates, especially if it originates relatively quickly (as evidenced with the short branches that separate them), or on the periphery of another species' range, the ancestral taxon will usually be rendered paraphyletic (Kuchta et al, 2018). However, over time, gene trees are expected to experience a transition to monophyly in a rate proportional to effective population sizes and rates of migration among populations (Baum and Shaw, 1995;Kuchta et al, 2018). Our study suggests that this and other Liolaemus species are at various points along this transition…”

“…This also raises the question that most current SDL methods based on this model do not account for introgressive hybridization (see below), isolation by distance (IBD) and ancient population structure (Barley et al, 2018). In the context of these "worst-cases scenarios" (Kuchta et al, 2018), such methods include simplifying assumptions that can lead them to fail with such complex patterns (Carstens et al, 2013;Kuchta et al, 2018). Nevertheless, the multispecies coalescent is the most objective approach available to explore species limits using genome-wide data (Fujita et al, 2012;Leaché et al, 2014Leaché et al, , 2019Villamil et al, 2019), and, given previous taxonomic treatments and geographical concordance, we are confident of the results obtained with these methodologies.…”