Résumé
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. Despite the inclusion of 25 taxa
representing all major lineages, the monophyly of deuterostomes remained
poorly supported. The implications of these phylogenetic results for
interpreting chordate evolution are discussed in light of recent advances
from evolutionary developmental biology and genomics.