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.

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