The limits of the metapopulation: Lineage fragmentation in a widespread terrestrial salamander (Plethodon cinereus)

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 mit..., , , # 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 ann...