10.5061/DRYAD.1QT0K
Barrow, Lisa N.
University of New Mexico
Lemmon, Alan R.
Florida State University
Lemmon, Emily Moriarty
Florida State University
Data from: Targeted sampling and target capture: assessing phylogeographic
concordance with genome-wide data
Dryad
dataset
2018
hybrid enrichment
Hyla cinerea
discordance
Anaxyrus terrestris
Lithobates sphenocephalus
Hyla squirella
Rana sphenocephala
barrier testing
National Science Foundation
https://ror.org/021nxhr62
DGE0952090, DEB1311144
2018-03-20T01:44:33Z
2018-03-20T01:44:33Z
en
https://doi.org/10.1093/sysbio/syy021
277845319 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 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
Southeastern U.S.
Southeastern United States