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 averagi..., Blood samples and tail tips were collected from 24 individuals from 20 populations of the P. wehrlei 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..., , # 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). ...