The Pipid Root

• DOI: 10.1093/sysbio/sys039
• Publication Date: 2012-03-23T01:30:01Z
• Authors: Adam J. Bewick; Frédéric J. J. Chain; Joseph Heled; Ben J. Evans
• Keywords: Phylogenomics; Molecular clock; Divergence (linguistics); Coalescent theory

The estimation of phylogenetic relationships is an essential component understanding evolution. Accurate difficult, however, when internodes are short and old, genealogical discordance common due to large ancestral effective population sizes or structure, homoplasy prevalent. Inference divergence times also hampered by unknown uneven rates evolution, the incomplete fossil record, uncertainty in between extant lineages, age fossils. Ideally, these challenges can be overcome developing "phylogenomic" data sets analyzing them with methods that accommodate features evolutionary process, such as discordance, recurrent substitution, recombination, gene flow after speciation among sampled unsampled taxa, variation rates. In some problems, it possible use information independent fossils, geological identify putative triggers for diversification whose associated estimated then compared a posteriori ages history pipid frog genera Pipa, Hymenochirus, Silurana, Xenopus, instance, characterized many analytical challenges. These frogs diversified dozens millions years ago, they have relatively rich their distributions span continental plates well record ancient connectivity, there considerable disagreement across studies relationships. We used high throughput sequencing public databases generate phylogenomic set which we using multilocus coalescence methods. collected sequence from Xenopus outgroup taxon Rhinophrynus dorsalis coding 113 autosomal regions, averaging ∼300 bp length (range: 102-1695 bp) portion mitochondrial genome. Analysis multiple approaches recovers strong support ((Xenopus, Silurana)(Pipa, Hymenochirus)) topology, geologically calibrated time estimates consistent affinities results provide new insights into biogeography chronology during breakup Gondwanaland illustrate how may necessary tackle tough problems molecular systematics. [Coalescence; tree; high-throughout sequencing; lineage sorting; pipid; species Xenopus.].