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 believed2,3,4,5. 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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R.R.C., T.J., M.J.T. and S.J.B. are supported by the EU Marie Curie RTN Zoonet. S.J.B. is also funded by the BBSRC. H.N. was supported by the Human Frontier Science Program Long-Term Fellowship. L.L.M. was supported by NIH and NSF grants as well as the McKnight Brain Research Foundation and the University of Florida opportunity funds. Author Contributions S.J.B. sequenced the mitochondrial genome. C.J.L., R.F., J.A., M.K. and E.S.L. generated the Saccoglossus and Solaster EST data. M.T., H.N., A.B.K., A.H. and L.L.M. generated the Xenoturbella EST data. R.R.C. and T.J. assembled the EST data. M.J.T. analysed the data and led the write-up.

Author information


  1. Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK

    • Sarah J. Bourlat
    •  & Maximilian J. Telford
  2. Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK

    • Thorhildur Juliusdottir
    •  & Richard R. Copley
  3. Department of Organismal Biology and Anatomy, 1027 E. 57th Street, University of Chicago, Chicago, Illinois 60637, USA

    • Christopher J. Lowe
    •  & Jochanan Aronowicz
  4. Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA

    • Robert Freeman
    •  & Eric S. Lander
  5. University of California, Berkeley, Department of Molecular and Cell Biology, 142 Life Sciences Addition #3200, Berkeley, California 94720-3200, USA

    • Mark Kirschner
  6. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Eric S. Lander
  7. Royal Swedish Academy of Sciences, Kristineberg Marine Research Station, Fiskebäckskil, S 450 34, Sweden

    • Michael Thorndyke
    •  & Hiroaki Nakano
  8. The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St Augustine, Florida 32080, USA

    • Andrea B. Kohn
    • , Andreas Heyland
    •  & Leonid L. Moroz


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Competing interests

The Xenoturbella 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 numbers 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. Reprints and permissions information is available at The authors declare no competing financial interests.

Corresponding author

Correspondence to Maximilian J. Telford.

Supplementary information

PDF files

  1. 1.

    Supplementary Materials

    Details of additional Materials and Methods and Supplementary Figures 1 to 5.

Text files

  1. 1.

    Supplementary Data 1

    Nexus format file of aligned and concatenated nuclear EST sequences. Further annotation within file. Part 1

  2. 2.

    Supplementary Data 2

    Nexus format file of aligned and concatenated nuclear EST sequences. Further annotation within file. Part 2

  3. 3.

    Supplementary Data 3

    Nexus format file of aligned and concatenated nuclear EST sequences. Further annotation within file. Part 3

  4. 4.

    Supplementary Data 4

    Nexus format file of aligned EST sequences. This is a concatenation of EST_PART1-3.dat after exclusion of the unreliably aligned positions as indicated in these sub files. Further annotation within file.

  5. 5.

    Supplementary Data 5

    Nexus format file of aligned and concatenated mitochondrial protein coding gene nucleotide sequences. Further annotation within file.

  6. 6.

    Supplementary Data 6

    Nexus format file of aligned and concatenated mitochondrial protein coding gene amino acid sequences after exclusion of the unreliably aligned positions as indicated in Supplementary Data 5 and subsequent translation of the remaining nucleotide sequences according to taxon specific genetic codes. Further annotation within file.

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