The New Chordate Phylogeny Strengthened by Better Models and More Phylogenomic Data

Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates as the most basal lineage. These results were robust to both gene sampling and missing data. New analyses of ribosomal rRNA also recovered Olfactores when compositional bias was alleviated. These phylogenetic results have important implications for interpreting chordate evolution in light of recent advances from evolutionary developmental biology and genomics.

Reference: Delsuc F., Tsagkogeorga G., Lartillot N. & Philippe H. (2008). Additional molecular support for the new chordate phylogeny. Genesis 46: 592-604.