DOI: 10.5061/dryad.dv41ns22q
title: The limits of the metapopulation: Lineage fragmentation in a widespread terrestrial salamander (Plethodon cinereus)

description: In vicariant species formation, divergence results primarily from periods
 of allopatry and restricted gene flow. Widespread species harboring
 differentiated, geographically distinct sublineages offer a window into
 what may be a common mode of species formation, whereby a species
 originates, spreads across the landscape, then fragments into multiple
 units. However, incipient lineages usually lack reproductive barriers that
 prevent their fusion upon secondary contact, blurring the boundaries
 between a single, large metapopulation-level lineage and multiple
 independent species. Here we explore this model of species formation in
 the Eastern Red-backed Salamander (Plethodon cinereus), a widespread
 terrestrial vertebrate with at least six divergent mitochondrial clades
 throughout its range. Using anchored hybrid enrichment data, we applied
 phylogenomic and population genomic approaches to investigate patterns of
 divergence, gene flow, and secondary contact. Genomic data broadly match
 most mitochondrial groups but reveal mitochondrial introgression and
 extensive admixture at several contact zones. While species delimitation
 analyses in BPP supported five lineages of P. cinereus, genealogical
 divergence indices (gdi) were highly sensitive to the inclusion of admixed
 samples and the geographic representation of candidate species, with
 increasing support for multiple species when removing admixed samples or
 limiting sampling to a single locality per group. An analysis of
 morphometric data revealed differences in body size and limb proportions
 among groups, with a reduction of forelimb length among warmer and drier
 localities consistent with increased fossoriality. We conclude that P.
 cinereus is a single species, but one with highly structured component
 lineages of various degrees of independence.
description: # The limits of the metapopulation: Lineage fragmentation in a widespread
 terrestrial salamander (Plethodon cinereus) ###
 "Waldron\_etal\_SuppMat.pdf" Contains supplementary figures
 (S1-S20), brief supplementary table descriptions (S1-S7), and extended
 Materials and Methods. # Folders: Supplementary Tables Contains
 Supplementary Tables S1-S7 in Excel workbook format. Data Contains raw
 data and input files for analyses in this paper: Data/BPP Contains
 "./sequences" and "./analyses" subfolders with input
 sequence data and analysis subfolders, respectively, using all samples
 (allSamples), all samples after excluding admixed samples (dropAdmix), or
 one sampled per genetic group (oneSamp). Analyses A00, A01, and A11
 included two independent runs, r1 and r2 (with control files). Datafeems
 Input files for fEEMS. Data/Gene_trees Gene trees of 308 loci used for
 ASTRAL and SNaQ, estimated in RAxML. Data/Morphology_raw_data Raw
 morphological data, and mean annual temperature, mean annual
 precipitation, and elevation extracted for the coordinates of each sample
 All samples are included here (including juveniles, &lt; 32 mm SVL, which
 were not analyzed). METADATA tab of workbook provides column descriptions.
 Data/Nexus_files Nexus formatted sequence alignments for phased data of
 Plethodon cinereus (N=38 individuals) and Plethodon serratus (N=3). With
 phasing, each sample includes two sequences ("_seq1" and
 "_seq2"). Subolders include all 351 loci prior to filtering, and
 only the 308 loci retained for downstream analyses using DNA sequences.
 Data SNPs All SNPs extracted from DNA sequences, used for PCA. Sample
 names were abbreviated. Data STRUCTURE Structure input file of a single
 SNP per locus extracted from DNA sequences. Sample names were abbreviated.
 Data TreeMix TreeMix input files for analyses of each sample treated as a
 tip, for all samples or excluding admixed samples, as well as for an
 analysis lumping individuals by group ("n28_K5.gz). Data trees
 Concatenated-sequence phylogenies using BEAST2 and RAxML, each with or
 without admixed samples included. BEAST trees represent maximum clade
 credibility trees (MCCT).