DOI: 10.5061/dryad.0rxwdbs7q
title: Traversing the Great Lakes: Post-glacial colonization by a widespread terrestrial salamander

description: Aims: Glacial retreat at the end of the Pleistocene epoch opened vast
 expanses of emergent habitat in the northern hemisphere that were
 colonized by opportunistic taxa. However, species that undergo
 post-glacial expansion may have originated from one or several glacial
 refugia. We inferred the post-glacial expansion history of the Eastern
 Red-backed Salamander (Plethodon cinereus), a fully terrestrial species
 with a vast distribution despite severe dispersal limitations. Previous
 studies indicated populations south of the glacial boundary at the eastern
 and western limits of the distribution were closely related, suggesting
 either multiple refugia or an extraordinary post-glacial expansion event.
 Location: Eastern North America. Taxon: Plethodon cinereus (Green, 1818),
 Caudata: Plethodontidae. Methods: We collected ddRAD-seq data
 from 106 individuals throughout the distribution of P. cinereus. We
 estimated phylogeographic structure, including finer-scale structure among
 the post-glacial populations. To test the origins and routes of
 colonization, we used ecological niche modeling, population trees, and
 analyses of directional range expansion. Results: Analyses
 supported our hypothesis of a southeastern glacial refugium, with
 northward expansion along the Eastern Seaboard prior to westward invasion
 into the Great Lakes region, including southwestern expansion into
 unglaciated areas at the western end of the distribution. However, a
 distinct subgroup in the northwestern portion of the range raises the
 possibility of a second refugium near the ice-free Driftless Area. Main
 conclusions: Based on our results, we hypothesize a southeastern refugium
 from which most of today’s northern populations undertook extensive
 post-glacial colonization. Our results indicate a geographically
 non-linear colonization history for P. cinereus.
description: Phylogeographic data represent ddRAD-seq for 106 samples of
 <em>Plethodon cinereus</em>. See Materials
 and Methods of Waldron et al. (2024) for details.
description: # Traversing the Great Lakes: Post-glacial colonization by a widespread
 terrestrial salamander ## Supplementary materials for Waldron et al.
 (2024) - Journal of Biogeography ##### Supplementary Figures "Figure
 S1.png" - sNMF and tess3 evaluation of K values "Figure
 S2.png" - sNMF and tess3 results across K=1-10 for N=106 "Figure
 S3.png" - PCA axis 1+3 "Figure S4.png" - sNMF and tess3
 results across K=1-10 for N=80 "Figure S5.pdf" - TreeMix
 evaluation of m values "Figure S6.pdf" - TreeMix results across
 m=1-5 "Supplementary Figure Legends.docx" - full legends #####
 Supplementary Tables "Table.S1.xlsx" - Sample information
 "Table.S2.xlsx" - PCR conditions for ddRAD ## SNP data
 "./SNP-data/all_OG_108_90_mac3.stru" - SNP data N=106+outgroup
 "./SNP-data/all_noOG_106_90_mac3.stru" - SNP data N=106
 "./SNP-data/UN_80_90_mac3.stru" - SNP data N=80
 "./SNP-data/SNP-data-info.txt" - additional information about
 SNP files ##### 'rangeExpansion' simulation of get.all.psi()
 function
 "./rangeExpansion-simData/rangeExpansion-simulatedData.R" - R
 script to test directionality index
 "./rangeExpansion-simData/simcoords.csv" - toy example of
 outgroup plus two eastern populations and two western populations, two
 samples per population "./rangeExpansion-simData/simsnps.csv" -
 SNP data for toy example; eastern pops fixed or heterozygous for derived
 alleles; western populations fixed for derived alleles
 "./rangeExpansion-simData/results-uncorrected-psi.png" - raw
 results without changing sign of psi or modifying function
 "./rangeExpansion-simData/results-corrected-psi.png" - results
 after changing sign of psi or modifying function