Data from: Population structure and species delimitation in the Wehrle’s salamander complex

Species are the fundamental unit of biodiversity studies. However, many
species complexes are difficult to delimit, especially those characterized
by complicated patterns of population structure. Salamanders in the family
Plethodontidae often form species by slowly fragmenting across a landscape
over space and time. They thus provide many examples of species complexes
in which gradual Darwinian evolution has resulted in multiple units of
varying degrees of differentiation, including incompletely separated
lineages. Here we report on a molecular systematic investigation of
woodland salamanders in the Plethodon wehrlei group, which has recently
been split from two species into five. To quantify patterns of genetic
variation, we collected genetic samples from 24 individuals from 20
populations, including all species and representing a carefully selected
subset of previous work. From these samples, we obtained genomic data
using anchored hybrid enrichment, which resulted in 319 loci averaging
1300 base pairs in length. Biallelic single nucleotide polymorphisms
(SNPs) were randomly selected from 316 of these loci for some analyses. We
examined patterns of genetic structure using PCA, DAPC, FEEMS, and
STRUCTURE, and found that all of the recognized species formed genetic
clusters; however, P. wehrlei and P. punctatus were relatively weakly
differentiated, and STRUCTURE identified three separate clusters within P.
jacksoni. Species trees inferred using wASTRAL, BPP, and TreeMix all
recovered the same topology, with P. dixi sister to the other taxa, which
included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a
southern clade (P. jacksoni, with three separate groups). TreeMix only
inferred one gene flow event. We evaluated the candidate species using BPP
and the genealogical divergence index (gdi). While BPP delimited all
candidate species with strong support (all posterior probabilities = 1.0),
the gdi only strongly supported P. dixi and P. pauleyi, both of which have
only been recently described. We discuss the difficult problem of species
delimitation in groups that form species via range fragmentation. We also
provide a vision for future research with the aim of better testing and
diagnosing the species diversity within the P. wehrlei group.