Data from: Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex
Barrow, Lisa N., Florida State University
Bigelow, Alyssa T., Florida State University
Phillips, Christopher A., University of Illinois System
Lemmon, Emily Moriarty, Florida State University
Published Aug 10, 2015 on Dryad.
Cite this dataset
Barrow, Lisa N.; Bigelow, Alyssa T.; Phillips, Christopher A.; Lemmon, Emily Moriarty (2015). Data from: Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex [Dataset]. Dryad. https://doi.org/10.5061/dryad.h2082
Fragmented species complexes provide an interesting system for investigating biogeographic history and the present distribution of genetic variation. Recent advances in sequencing technology and statistical phylogeography enable the collection and rigorous analysis of large multilocus data sets, but designing studies that produce meaningful phylogeographic inferences remains challenging. We implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex. The Illinois chorus frog (Pseudacris illinoensis), originally described as a subspecies of the broadly distributed Strecker's chorus frog (Pseudacris streckeri), occurs in small, disjunct regions associated with scarce sand prairie habitats that have been impacted by human development. We used high-throughput sequencing to develop and collect a multitiered genetic data set comprised of three different marker types (23 anonymous nuclear sequence loci, four mitochondrial genes and 14 microsatellite loci) designed to address questions across different evolutionary timescales. Phylogenetic analyses uncovered a deep divergence between populations in the Edwards Plateau of central Texas and all other P. streckeri/P. illinoensis populations, but suggest the disjunct distribution of P. illinoensis occurred more recently. Our best-supported migration model is consistent with the hypothesis that central Texas represented a refugium from which populations expanded via multiple routes. This model also indicates that disjunct northern and southern regions of P. illinoensis should be considered genetically distinct management units. Our study provides an evolutionary context for future studies and conservation efforts in P. illinoensis and demonstrates the utility of model-based approaches for phylogeographic inference.
Raw sequence reads
Raw Illumina sequence reads for 34 individuals, demultiplexed by individual barcode tags. Within each individual, PCR products from 23 nuclear loci and 4 mitochondrial loci were pooled and sequenced. Individual numbers, barcodes, and Field Numbers/localities corresponding to Table S1 are included in the ReadMe file.
Alignments for 4 mitochondrial fragments and 23 nuclear loci.
RAxML infiles and results for analysis of 4 mtDNA fragments.
BEAST xml file and results from analysis of 4 mtDNA fragments.
Starbeast xml file and results from two separate runs analyzing 23 nDNA loci.
Starbeast xml file and results from analysis of 6 geograhpic regions across the P. streckeri/P. illinoensis species complex using 23 nDNA loci.
Datafiles and results from divergence time estimation in BEAST using family-level hylid sequences and fossil calibrations.
Infiles and results from isolation with migration analyses conducted in IMa2 for divergence time estimation.
Microsatellite dataset with 14 loci genotyped for 294 individuals, and results from PCoA analysis of 228 individuals conducted in Genalex.
Datafiles and results from Arlequin for Mantel tests and AMOVAs.
Infile, 24 parameter files, and 24 output files from population models tested in Migrate-n.