DOI: 10.5061/dryad.3rc02
title: Data from: The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

description: Inferring the evolutionary history of lineages often becomes difficult
 when gene histories are in conflict with each other. Introgression, for
 example, can cause DNA sequences from one species to be more similar to
 sequences of a different species and lead to incongruence amongst gene
 trees. However, incorporating congruent and incongruent locus-specific
 phylogenetic estimates with the geographical distribution of lineages may
 provide valuable insight into evolutionary processes important to
 speciation. In this study, we investigated mitochondrial introgression
 within the Hyla eximia group to better understand its role in illuminating
 the evolutionary history and phylogeography of these treefrogs. We
 reconstructed and compared the matrilineal history of the Hyla eximia
 group with estimates of evolutionary history inferred from nuclear genes.
 We tested for introgression within the mitochondrial and nuclear genes
 using a posterior predictive checking approach. Reconstructions of the
 species tree based on the mitochondrial DNA (mtDNA) and nuclear DNA data
 were strongly discordant. Introgression between lineages was widespread in
 the mtDNA data set (145 occurrences amongst 11 of the 16 lineages), but
 uncommon in the nuclear genes (12 occurrences amongst four of the 16
 lineages). Nonetheless, the geographical structuring of mtDNA within
 species provides valuable information on biogeographical areas, ancient
 areas of hybridization, and unique histories of lineages within the
 H. eximia group. These results suggest that the combination of nuclear,
 mitochondrial, and spatial information can provide a more complete picture
 of ‘how evolutionary history played out’, particularly in cases where
 mitochondrial introgression is known to occur.
description: Hyla eximia group full
 mtDNA data setNexus file with aligned
 mtDNA sequences generated from 130 samples. See ReadMe file to match
 sample names with species and voucher specimens.Hyla_mtDNA_all.nexHyla eximia group phased cryB data set used in *BEAST analysesNexus file with final alignment of phased cryB sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.cryba_NEXUS.nexusHyla eximia group phased POMC data set used in *BEAST analysesNexus file with final alignment of phased POMC sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.pomc_NEXUS.nexusHyla eximia group phased tyr1 data set used in *BEAST analysesNexus file with final alignment of phased tyr1 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.tyr1_NEXUS.nexusHyla eximia group ND4 data set used in *BEAST analysesNexus file with subset of ND4 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.Hyla_ND4.nexHyla eximia group tRNA data set used in *BEAST analysesNexus file with subset of tRNA sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.Hyla_tRNA.nexHyla eximia group ATPase8 data set used in *BEAST analysesNexus file with subset of ATPase8 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.Hyla_ATP8.nexHyla eximia group ATPase6 data set used in *BEAST analysesNexus file with subset of ATPase6 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.Hyla_ATP6.nex