DOI: 10.5061/dryad.79cnp5j39
title: Data from: Population structure and species delimitation in the Wehrle’s salamander complex

description: 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.
description: Blood samples and tail tips were collected from 24 individuals
 from 20 populations of the <em>P. wehrlei</em>
 complex. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue
 Kits (Qiagen Corp., Valencia, CA). All samples were processed at the
 Florida State University Center for Anchored Phylogenomics using a hybrid
 enrichment protocol (Lemmon et al. 2012). Briefly, each sample was
 sonicated to an average fragment size of 150–300 bp using a Covaris E220
 focused ultrasonicator. Library preparation and indexing were done on a
 Beckman-Coulter Biomex FXp liquid-handling robot according to Meyer
 & Kircher (2010). Pooled libraries were enriched with an Agilent
 Custom SureSelect kit that contained amphibian-specific probes (Heinicke
 et al. 2018). After enrichment, samples were pooled for sequencing on one
 PE150 lane of an Illumina HiSeq 2000. Raw sequencing reads were filtered
 for quality, de-multiplexed, and assembled following Lemmon et al. (2012).
 Sequences were aligned using MAFFT (Katoh and Standley 2013), and the loci
 were phased using read overlap information in a Bayesian approach (Pyron
 et al. 2016; Booker et al. 2022).
description: # Data from: Population structure and species delimitation in the Wehrle’s
 salamander complex
 [https://doi.org/10.5061/dryad.79cnp5j39](https://doi.org/10.5061/dryad.79cnp5j39) ## Description of the data and file structure Included: (1) The sequence data, with each locus in a separate Fasta file (319 loci) (2) Two replicate datasets with Single Nucleotide Polymorphisms (SNPs) obtained from the sequence data. Singletons (i.e., SNPs that are only polymorphic within a single individual) were excluded from the SNP dataset, and three loci that only possessed singletons were excluded (316 loci total remained). To select SNPs, we ranked them at each locus based on the amount of missing data, then randomly selected one SNP from the set with the least missing data. Selecting one SNP per locus is advantageous because it reduces or eliminates linkage disequilibrium among loci. Up to three individuals at each site were allowed to have missing data, which retained most of our loci (313 total). We made several replicate datasets. These two highlight the largest range of variation we observed.