Phylogenomic assessment of microhylid frogs reveals widespread taxonomic confusion in the Asterophryinae and establishes the timing of diversification in Australia

Microhylid frogs are a hyper-diverse family thought to have radiated explosively around the Cretaceous-Paleogene boundary. Roughly half of microhylid species richness is concentrated into a single subfamily, the Asterophryinae, which is centered in New Guinea and surrounds, and has been a rich source for species discovery over the past 50 years. However, resolving Asterophryinae phylogenetics has remained a challenge, with frequent taxonomic reshuffling. To address this instability, we generated a sequence-capture molecular dataset to investigate the phylogenetics of the group. This included 71 species of Asterophryinae, across 13 of 17 recognized genera representing extensive sampling of the New Guinea radiation and full sampling of Australian microhylid species. Our dated species tree supports an explosive diversification of microhylids in New Guinea near the start of the Miocene, approximately 20 million years ago. Asterophryinae expansion into northern Australia occurred much later ([~]10 ma) and is marked by well supported clades of Austrochaperina and Cophixalus that show temporally consistent splits from their New Guinea sister taxa. Our phylogeny allows us to identify several instances of polyphyly, which are at odds with our current understanding of intergeneric relationships within the Asterophryinae. We suggest that this confusion is a result of rapid radiation and morphological variability across some poorly defined genera. This work establishes a reliable phylogenetic framework that can form a foundation for a more stable taxonomy of the Asterophryinae. HighlightsO_LIA phylogenomic assessment of the globally distributed frog family Microhylidae C_LIO_LIThe subfamily Asterophryinae radiated explosively in New Guinea C_LIO_LIAustralian species represent two distinct clades C_LIO_LIAssignments of species to genera by morphological means are often unreliable C_LI