Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs.

The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MYA. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.

Molecular phylogenetics and dating of the problematic New Guinea microhylid frogs (Amphibia: Anura) reveals elevated speciation rates and need for taxonomic reclassification.

Asterophryinae is a large monophyletic subfamily of Anurans containing over 300 species distributed across one of the world's most geologically active areas - New Guinea and its satellite islands, Australia and the Philippines. The tremendous ecological and morphological diversity of this clade, with apparent specializations for burrowing, terrestrial, semi-aquatic, and arboreal lifestyle, suggests an evolutionary process of adaptive radiation. Despite this spectacular diversity, this and many other questions of evolutionary processes have received little formal study because until now the phylogeny of this spececies-rich clade has remained uncertain. Here we reconstruct a phylogeny for Asterophryinae with greatly increased taxon and genetic sampling relative to prior studies. We use Maximum Likelihood and Bayesian Inference methods to produce the most robust and comprehensive phylogeny to date containing 155 species using 3 nuclear and 2 mitochondrial loci. We also perform a time calibration analysis to estimate the age of the clade. We find support for the monophyly of Asterophryinae as well as need for taxonomic reclassification of several genera. Furthermore, we find increased rates of speciation across the clade supporting the hypothesis of rapid radiation. Lastly, we found that adding taxa to the analysis produced more robust phylogenetic results over adding loci.