DOI: 10.5061/dryad.3qd54
title: Data from: The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

description: BACKGROUND: Understanding the causes underlying heterogeneity of molecular
 evolutionary rates among lineages is a long-standing and central question
 in evolutionary biology. Although several earlier studies showed that
 modern frogs (Neobatrachia) experienced an acceleration of mitochondrial
 gene substitution rates compared to non-neobatrachian relatives, no
 further characterization of this phenomenon was attempted. To gain new
 insights on this topic, we sequenced the complete mitochondrial genomes
 and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five
 neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga
 (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae),
 Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti
 (Sooglossidae). These represent major clades not included in previous
 mitogenomic analyses, and most of them are remarkably species-poor
 compared to other neobatrachians. RESULTS: We reconstructed a fully
 resolved and robust phylogeny of extant frogs based on the new
 mitochondrial and nuclear sequence data, and dated major cladogenetic
 events. The reconstructed tree recovered Heleophryne as sister group to
 all other neobatrachians, Australasian Lechriodus and South American
 Calyptocephalella formed a clade that was the sister group to
 Nobleobatrachia, and the Seychellois Sooglossus was recovered as the
 sister group of Ranoides. We used relative-rate tests and direct
 comparison of branch lengths from mitochondrial and nuclear-based trees to
 demonstrate that both mitochondrial and nuclear evolutionary rates are
 significantly higher in all neobatrachians compared to their
 non-neobatrachian relatives, and that such rate acceleration started at
 the origin of Neobatrachia. CONCLUSIONS: Through the analysis of the
 selection coefficient (ω) in different branches of the tree, we found
 compelling evidence of relaxation of purifying selection in
 neobatrachians, which could (at least in part) explain the observed higher
 mitochondrial and nuclear substitution rates in this clade. Our analyses
 allowed us to discard that changes in substitution rates could be
 correlated with increased mitochondrial genome rearrangement or
 diversification rates observed in different lineages of neobatrachians.
description: Neobatrachia_combined_aminoacidCombined mitochondrial and nuclear data set with protein-coding genes translated into amino acidsNeobatrachia_mt_aminoacidMitochondril data set with protein-coding genes translated into amino acidsNeobatrachia_nuc_aminoacidNuclear data set with protein-coding genes translated into amino acidsNeobatrachia_combined_nucleotideCombined mitochondrial and nuclear data set at the nucleotide level. First and third codon positions of mitochondrial protein-coding genes and third codon positions of nuclear protein-coding genes have been removed.Neobatrachia_mt_nucleotideMitochondrial nucleotide data set, including all codon positions of protein-coding genes.Neobatrachia_nuc_nucleotideNuclear nucleotide data set, including all codon positions of protein-coding genes.Neobatrachia_Beast_fileInput file used for BEAST analyses.