DOI: 10.5061/dryad.66mc094q
title: Data from: The pipid root

description: The estimation of phylogenetic relationships is an essential component of
 understanding evolution. Accurate phylogenetic estimation is difficult,
 however, when internodes are short and old, when genealogical discordance
 is common due to large ancestral effective population sizes or ancestral
 population structure, and when homoplasy is prevalent. Inference of
 divergence times is also hampered by unknown and uneven rates of
 evolution, the incomplete fossil record, uncertainty in relationships
 between fossil and extant lineages, and uncertainty in the age of fossils.
 Ideally these challenges can be overcome by developing large
 “phylogenomic” datasets, and by analyzing them with methods that
 accommodate features of the evolutionary process such as genealogical
 discordance, recurrent substitution, recombination, ancestral population
 structure, gene flow after speciation among sampled and unsampled taxa,
 and variation in evolutionary rates. In some phylogenetic problems it is
 possible to use information that is independent of fossils, such as the
 geological record, to identify putative triggers for diversification whose
 associated estimated divergence times can then be compared a posteriori to
 estimated relationships and ages of fossils. The history of
 diversification of pipid frog genera Pipa, Hymenochirus, Silurana, and
 Xenopus, for instance, is characterized by many of these evolutionary and
 analytical challenges. These frogs diversified dozens of millions of years
 ago, they have a relatively rich fossil record, their distributions span
 continental plates with a well characterized geological record of ancient
 connectivity, and there is considerable disagreement across studies in
 estimated evolutionary relationships. We used high throughput sequencing
 and public databases to generate a large phylogenomic dataset with which
 we estimated evolutionary relationships using multilocus coalescence
 methods. We collected sequence data from Pipa, Hymenochirus, Silurana, and
 Xenopus and the outgroup taxon Rhinophrynus dorsalis from coding sequence
 of 113 autosomal regions, averaging ~300 base pairs in length (range: 102
 – 1695 base pairs), and also a portion of the mitochondrial genome.
 Analysis of these data using multiple approaches recovers strong support
 for the ((Xenopus, Silurana)(Pipa, Hymenochirus)) topology, and
 geologically calibrated divergence time estimates that are consistent with
 estimated ages and phylogenetic affinities of many fossils. These results
 provide new insights into the biogeography and chronology of pipid
 diversification during the breakup of Gondwanaland, and illustrate how
 phylogenomic data may be necessary to tackle tough problems in molecular
 systematics.
description: Supplementary
 Information including accession numbersSuppl_Info.pdf*BEAST input file Pipa calibration JC codon modelpiponly_jc.xml*BEAST input file Pipa calibration HKY codon modelpiponly_hky.xml*BEAST input file Pipa calibration GTR codon modelpiponly_gtr.xml*BEAST input file Root calibration JC codon modelrootonly_jc.xml*BEAST input file Root calibration HKY codon modelrootonly_hky.xml*BEAST input file Root calibration GTR codon modelrootonly_gtr.xml*BEAST input file Pipa and Root calibration JC codon modelpipandroot_jc.xml*BEAST input file Pipa and Root calibration HKY codon modelpipandroot_hky.xml*BEAST input file Pipa and Root calibration GTR codon modelpipandroot_gtr.xmlBEST input file JC modelBEST_pipid_JC_114.inBEST input file HKY modelBEST_pipid_HKY_114.inBEST input file GTR modelBEST_pipid_GTR_114.in