1. Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
2. Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
3. Department of Organismal Biology and Anatomy, 1027 E. 57th Street, University of Chicago, Chicago, Illinois 60637, USA
4. Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
5. University of California, Berkeley, Department of Molecular and Cell Biology, 142 Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
6. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
7. Royal Swedish Academy of Sciences, Kristineberg Marine Research Station, Fiskebäckskil, S 450 34, Sweden
8. The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St Augustine, Florida 32080, USA

Correspondence to: Maximilian J. Telford¹ The Xenotubella mitochondrial genome sequence has GenBank Accession number DQ832701. Xenoturbella ESTs have accession numbers EC906293-EC907475 and novel Saccoglossus ESTs used in this project have accession number EE111315-EE122968. Novel Solaster ESTs used in this project have accession numbers EE122969-EE123339. Alignments used are available for download as Supplementary Information or on request from M.J.T. Correspondence and requests for materials should be addressed to M.J.T. (Email: m.telford@ucl.ac.uk).

Abstract

Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella¹. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of chordate classes and a sea urchin have indicated that urochordates might be the closest invertebrate sister group of vertebrates, rather than cephalochordates, as traditionally believed^{2, 3, 4, 5}. More remarkable is the suggestion that cephalochordates are closer to echinoderms than to vertebrates and urochordates, meaning that chordates are paraphyletic². To study the relationships among all deuterostome groups, we have assembled an alignment of more than 35,000 homologous amino acids, including new data from a hemichordate, starfish and Xenoturbella. We have also sequenced the mitochondrial genome of Xenoturbella. We support the clades Olfactores (urochordates and vertebrates) and Ambulacraria (hemichordates and echinoderms⁶). Analyses using our new data, however, do not support a cephalochordate and echinoderm grouping and we conclude that chordates are monophyletic. Finally, nuclear and mitochondrial data place Xenoturbella as the sister group of the two ambulacrarian phyla¹. As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four.

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