Additional molecular support for the new chordate phylogeny

Abstract

Summary: 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. genesis 46:592-604, 2008. V V C 2008 Wiley-Liss, Inc.

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

“…This is a quite conservative method for sorting genes that aims to detect novelty in the protein sequence space (10,57,62). The number and choice of internodes in the phylogeny are a result of balancing the robustness of these internodes in phylogenetic studies (32,(63)(64)(65)(66)(67)(68), the availability of sequence data for the sequence similarity searches, and the importance of evolutionary transitions (Table S2). Our consensus phylogenies span 16 evolutionary levels (phylostrata) for Arabidopsis thaliana, 18 for Danio rerio, and 20 for Drosophila melanogaster, starting from the origin of cellular organisms (ps1).…”

Genomic data do not support comb jellies as the sister group to all other animals

“…When analyzing phylogenomic datasets, proper modeling of the amino acid substitution process is crucial because the use of overly simplistic models can lead to inaccurate phylogenetic inferences (reviewed in [13][14][15][16][17]. For example, the monophyly of Chordata was not confidently resolved from phylogenomic data until sophisticated substitution models were applied (18,19). The most commonly used models assume the substitution process is the same in all sites of a protein (site-homogeneous) (e.g., 20).…”

Chordate origins and evolution

“…Importantly, although chordate topologies may have changed, integrity of the subphylum has been reaffirmed, albeit, perhaps, at the surprising price of destabilizing deuterostomes as a natural group (Delsuc et al, 2008). This point is discussed in this special issue along with the account of challenging morphological and molecular similarities observed between Xenoturbella and Acoelomorph flatworms (Bourlat et al, 2003;Cameron et al, 2000;Delsuc et al, 2008;Philippe et al, 2007;Telford, 2008).…”

“…These novel ideas have been subjected to thorough testing and the Olfactores hypothesis has received further support (Bourlat et al, 2006;Delsuc et al, 2006Delsuc et al, , 2008Dunn et al, 2008;Swalla and Smith, 2008). In contrast, the unorthodox assembly of cephalochordates and echinoderms, which initially raised suspicions about chordate monophyly (Delsuc et al, 2006), was not confirmed (Bourlat et al, 2006;Delsuc et al, 2008).…”