DOI: 10.5061/dryad.1qt0k
title: Data from: Targeted sampling and target capture: assessing phylogeographic concordance with genome-wide data

description: Comparative phylogeography provides the necessary framework to examine the
 factors influencing population divergence, persistence, and change over
 time. Avise (2000) outlined four aspects of concordance that result when
 data exhibit significant phylogeographic signal: concordance among sites
 within a locus, among multiple loci within a species, among multiple
 species within a region, and between genetic patterns and established
 biogeographic provinces. To fully address each aspect of concordance, we
 combined target capture of a set of orthologous loci with targeted
 geographic sampling of multiple species, thus removing any variability
 introduced by using different genetic markers and heterogeneous sampling
 distributions. We used hybrid enrichment and high-throughput sequencing of
 four anuran species sampled from 36 congruent localities in the
 Southeastern U.S. Coastal Plain, a region that represents one of the
 classic systems in phylogeography. In total, we recovered &gt;375 of
 the same nuclear loci across species and assembled mitochondrial genomes,
 resulting in one of the most comprehensive comparative phylogeographic
 datasets in any region or taxon to date. We used these data to evaluate
 concordance, compare genetic structure across species, and test previously
 described biogeographic features in the region including major river
 drainages and suture zones. We then applied a recently-developed framework
 to quantify concordance across species using phylogeographic concordance
 factors. For the four species examined, which have higher dispersal and
 potentially limited structure compared to many amphibians, we found poor
 resolution in individual nuclear gene trees even with long (~1400 bp)
 nuclear sequences. The mitochondrial and multi-locus nuclear datasets,
 however, produced similar patterns within species, indicated high
 discordance among species, and suggested little correspondence of genetic
 patterns with putative biogeographic barriers. Variation in the
 phylogeographic structure detected may be related to differences in
 natural history, in that the two habitat generalists exhibited less
 structure. Our study demonstrates the utility of combining target capture,
 which is highly repeatable and produces comparable datasets, with a
 targeted sampling strategy to quantify phylogeographic concordance across
 diverse taxa in a region with a complex history.
description: Mitochondrial Datasets
 and ResultsMitochondrial alignments
 and RAxML results. Note that Lithobates sphenocephalus (Lsp) = Rana
 sphenocephalaMitochondrial.zipRAxML Concatenated Alignments and ResultsRAxML Concatenated Alignments and Results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephalaRAxML_Concatenated.zipRAxML GeneTree 1allele AlignmentsRAxML 1-allele Alignments. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephalaRAxML_GeneTree_1allele.zipRAxML GeneTree 2alleles Alignments and ResultsRAxML GeneTree 2alleles Alignments and Results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephalaRAxML_GeneTree_2alleles.zipPython scriptsPython scripts for extracting SNPs from 1-allele RAxML (phylip) files; and script for summarizing bootstrap values from RAxML 2-allele results. Additional details are commented in each script.Python_scripts.zipSNP datasetsSNP datasets for each species and summary table of SNP information. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala.SNP_datasets.zipPhylogeographic Concordance Factor analysesPhylogeographic Concordance Factor analyses and results. Includes SNAPP results for nuclear datasets, *BEAST results for mitochondrial datasets, (4-region and 5-region models for each), and PCF results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala.PCFs.zipProbes for Anchored Hybrid EnrichmentAlignments and probe sequences used for anchored hybrid enrichment of anurans. Alignments are labeled by locus number and include sequences for Xenopus tropicalis (ind 1), Pseudacris feriarum (ind 2), Pseudacris nigrita (ind 3), Rana sphenocephala (ind 4). The 120-bp probe sequences and associated names are provided in "Amp2_XenRanNigFer.txt" and the key file associates the probe name with the locus number, species (ind 1-4), and site within the alignment.Probes.zipASTRAL2_Locus-SelectionGene trees and output files from Astral species tree analyses. Loci were ranked based on informative sites and bootstrap support, and analyses were conducted with the "best" 20, 40, 80, 160, and all loci, as well as all loci removing outliers based on tree distance.SVDQuartetsInput files and resulting trees from SVDQuartets species tree analyses.Supporting InformationSupporting information including supplementary methods on probe design and supplementary tables and figures.Barrow_TargetMS_March2018_SupportingInfo.docx