Data from: Targeted sampling and target capture: assessing phylogeographic concordance with genome-wide data
Barrow, Lisa N., University of New Mexico
Lemmon, Alan R., Florida State University
Lemmon, Emily Moriarty, Florida State University
Published Mar 20, 2018 on Dryad.
Cite this dataset
Barrow, Lisa N.; Lemmon, Alan R.; Lemmon, Emily Moriarty (2018). Data from: Targeted sampling and target capture: assessing phylogeographic concordance with genome-wide data [Dataset]. Dryad. https://doi.org/10.5061/dryad.1qt0k
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 >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.
Mitochondrial Datasets and Results
Mitochondrial alignments and RAxML results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
RAxML Concatenated Alignments and Results
RAxML Concatenated Alignments and Results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
RAxML GeneTree 2alleles Alignments and Results. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
Python 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.
SNP datasets for each species and summary table of SNP information. Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala.
Phylogeographic Concordance Factor analyses
Phylogeographic 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.
Probes for Anchored Hybrid Enrichment
Alignments 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.
Gene 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.
Input files and resulting trees from SVDQuartets species tree analyses.
Supporting information including supplementary methods on probe design and supplementary tables and figures.
National Science Foundation, Award: DGE0952090, DEB1311144