The limits of the metapopulation: Lineage fragmentation in a widespread terrestrial salamander (Plethodon cinereus)
Abstract
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.
README: 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, < 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).