DOI: 10.5061/dryad.h2082
title: Data from: Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex

description: 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.
description: Raw sequence
 readsRaw 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.ReadsByIndividual.zipSequence AlignmentsAlignments for 4 mitochondrial fragments and 23 nuclear loci.Alignments.zipRAxML_mtDNARAxML infiles and results for analysis of 4 mtDNA fragments.BEAST_mtDNABEAST xml file and results from analysis of 4 mtDNA fragments.*BEAST_nDNAStarbeast xml file and results from two separate runs analyzing 23 nDNA loci.*BEAST_regionStarbeast xml file and results from analysis of 6 geograhpic regions across the P. streckeri/P. illinoensis species complex using 23 nDNA loci.BEAST_DivTimeDatafiles and results from divergence time estimation in BEAST using family-level hylid sequences and fossil calibrations.IMa2Infiles and results from isolation with migration analyses conducted in IMa2 for divergence time estimation.Msats_294indMicrosatellite dataset with 14 loci genotyped for 294 individuals, and results from PCoA analysis of 228 individuals conducted in Genalex.ArlequinDatafiles and results from Arlequin for Mantel tests and AMOVAs.Migrate-nInfile, 24 parameter files, and 24 output files from population models tested in Migrate-n.