DOI: 10.5061/dryad.23rc0
title: Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

description: The field of phylogenetics is changing rapidly with the application of
 high-throughput sequencing to non-model organisms. Cost-effective use of
 this technology for phylogenetic studies, which often include a relatively
 small portion of the genome but several taxa, requires strategies for
 genome partitioning and sequencing multiple individuals in parallel. In
 this study we estimated a multilocus phylogeny for the North American
 chorus frog genus Pseudacris using anonymous nuclear loci that were
 recently developed using a reduced representation library approach. We
 sequenced 27 nuclear loci and three mitochondrial loci for 44 individuals
 on 1/3 of an Illumina MiSeq run, obtaining 96.5% of the targeted amplicons
 at less than 20% of the cost of traditional Sanger sequencing. We found
 heterogeneity among gene trees, although four major clades (Trilling Frog,
 Fat Frog, crucifer, and West Coast) were consistently supported, and we
 resolved the relationships among these clades for the first time with
 strong support. We also found discordance between the mitochondrial and
 nuclear datasets that we attribute to mitochondrial introgression and a
 possible selective sweep. Bayesian concordance analysis in BUCKy and
 species tree analysis in *BEAST produced largely similar topologies,
 although we identify taxa that require additional investigation in order
 to clarify taxonomic and geographic range boundaries. Overall, we
 demonstrate the utility of a reduced representation library approach for
 marker development and parallel tagged sequencing on an Illumina MiSeq for
 phylogenetic studies of non-model organisms.
description: Nexus_alignmentsNexus files of analyzed regions for 27 anonymous nuclear loci and 3 mitochondrial fragmentsMrBayes gene tree resultsInput files and consensus trees from MrBayes gene tree analyses.MB.zipBUCKy infiles and resultsBUCKy infiles and results from Bayesian concordance analysis of 26 nuclear loci.BUCKy-a01.zipRAxML_26nucDNAInfile and results from RAxML analysis of concatenated nuclear DNA (26 anonymous loci).RAxML_mtDNA-partitionedInfile and results from analysis of 3 mitochondrial gene fragments.Starbeast analysis - 44 tipsStarbeast xml file and results from species tree analysis with every individual as a tip.SB-44taxa.zipStarbeast Species TreeStarbeast xml file and results from species tree analysis.SB-speciesTree.zipScript for making infilesPython script used for making infiles for RAxML, MrBayes, and *BEAST analyses. Input is a nexus file with a MrBayes block appended; output are infiles for: RAxML with randomly-chosen allele for nuclear loci, MrBayes files for gene tree analyses with either all alleles or randomly-chosen allele for heterozygotes; *BEAST files with either all alleles or randomly-chosen allele for heterozygotes.Manipulator1.7.pyIllumina Read DataIllumina MiSeq paired reads by individual for 44 individuals (40 Pseudacris, 2 Hyla cinerea, 2 Acris gryllus). IDs correspond to those in Table 1 of the publication.Illumina-Reads.zip