A large-scale phylogeny of Microhylidae inferred from a combined dataset of 121 genes and 427 taxa

The phylogenetic relationships of Microhylidae, the third largest family of extant frogs, have been difficult to resolve. In the past decade, large amounts of sequence data have been deposited for almost every microhylid genus, but no study has attempted to combine these data to reconstruct a comprehensive phylogeny for this family. In this study, we sequenced 20 near-complete or partial microhylid mitochondrial genomes and integrated them with all available sequences of Microhylidae from GenBank to construct a supermatrix containing 121 genes (14 mitochondrial and 107 nuclear protein-coding genes). The combined dataset is 112,328 characters long (average sequence data length per species = 7829 bp), includes 427 microhylid taxa, and covers all but three genera of the entire family. This dataset provides strong support for the traditional classification of 11 nominal subfamilies and improves the phylogenetic resolution of the relationships among subfamilies. The African subfamily Phrynomerinae is the sister group of all the other microhylids, and the African subfamily Hoplophryninae is the sister taxon to a clade comprising the remaining 9 subfamilies. At the genus level, our analyses confirm the monophyly of most but not all microhylid genera. In summary, we present a new large-scale phylogeny of microhylid frogs that should be valuable for addressing their classification and for comparative evolutionary studies.