DOI: 10.5061/dryad.12546
title: Data from: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

description: Frogs (Anura) are one of the most diverse groups of vertebrates and
 comprise nearly 90% of living amphibian species. Their worldwide
 distribution and diverse biology make them well-suited for assessing
 fundamental questions in evolution, ecology, and conservation. However,
 despite their scientific importance, the evolutionary history and tempo of
 frog diversification remain poorly understood. By using a molecular
 dataset of unprecedented size, including 88-kb characters from 95 nuclear
 genes of 156 frog species, in conjunction with 20 fossil-based
 calibrations, our analyses result in the most strongly supported phylogeny
 of all major frog lineages and provide a timescale of frog evolution that
 suggests much younger divergence times than suggested by earlier studies.
 Unexpectedly, our divergence-time analyses show that three species-rich
 clades (Hyloidea, Microhylidae, and Natatanura), which together comprise
 ∼88% of extant anuran species, simultaneously underwent rapid
 diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB).
 Moreover, anuran families and subfamilies containing arboreal species
 originated near or after the KPB. These results suggest that the K–Pg mass
 extinction may have triggered explosive radiations of frogs by creating
 new ecological opportunities. This phylogeny also reveals relationships
 such as Microhylidae being sister to all other ranoid frogs and African
 continental lineages of Natatanura forming a clade that is sister to a
 clade of Eurasian, Indian, Melanesian, and Malagasy lineages.
 Biogeographical analyses suggest that the ancestral area of modern frogs
 was Africa, and their current distribution is largely associated with the
 breakup of Pangaea and subsequent Gondwanan fragmentation.
description: Phylogenetic matrix (164
 species dataset)Phylogenetic matrix
 containing aligned DNA sequences for 95 nuclear coding loci (88,302 bp)
 for 164 species of frogs, including details on character partitions and
 best-fit models of evolution for the partitions.164sp_95_genes_88302_2N_20170615.nexusPhylogenetic matrix (309 species dataset)Phylogenetic matrix containing aligned DNA sequences for 95 nuclear coding loci (88,386 bp) for 309 species of frogs, including details on character partitions and best-fit models of evolution for the partitions.309sp_95_genes_88386_2N_20170615.nexusMaximum likelihood phylogeny of 309 speciesMaximum likelihood phylogeny generated using partitioned analysis in RAxML for 309 species, including 145 species for which data were obtained via GenBank.RAxML_309sp.treMaximum likelihood phylogeny of 164 speciesMaximum likelihood phylogeny generated using partitioned analysis in RAxML for 164 species.RAxML_164sp.treChronogram of 309 speciesChronogram generated in MCMCTREE using the maximum likelihood phylogeny generated via RAxML for 309 species, including 145 species for which data were obtained via GenBank.Chronogram_309sp.treChronogram of 164 speciesChronogram generated in MCMCTREE using the maximum likelihood phylogeny generated via RAxML for 164 species.Chronogram_164sp.treCollection of maximum likelihood gene trees with bootstrap replicatesMaximum likelihood phylogeny generated via RAxML and associated nonparametric bootstrap replicates for each gene in our 95-locus dataset.gene_trees.zip