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Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida

Nature volume 444, pages 85–88 (2006)Cite this article

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 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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Figure 1: Phylogenetic analyses of 170 nuclear proteins and 13 mitochondrial proteins support a monophyletic chordate clade and an independent deuterostome phylum of Xenoturbellida.

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Acknowledgements

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.

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Authors and Affiliations

  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, OX3 7BN, Oxford, UK

    Thorhildur Juliusdottir & Richard R. Copley

  3. Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th Street, Illinois, 60637, Chicago, USA

    Christopher J. Lowe & Jochanan Aronowicz

  4. Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Massachusetts, 02115, Boston, USA

    Robert Freeman & Eric S. Lander

  5. Department of Molecular and Cell Biology, University of California, Berkeley, 142 Life Sciences Addition #3200, California, 94720-3200, Berkeley, 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, St Augustine, 9505 Ocean Shore Boulevard, Florida, 32080, USA

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

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  1. Sarah J. Bourlat
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Corresponding author

Correspondence to Maximilian J. Telford.

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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 www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Materials

Details of additional Materials and Methods and Supplementary Figures 1 to 5. (PDF 282 kb)

Supplementary Data 1

Nexus format file of aligned and concatenated nuclear EST sequences. Further annotation within file. Part 1 (TXT 717 kb)

Supplementary Data 2

Nexus format file of aligned and concatenated nuclear EST sequences. Further annotation within file. Part 2 (TXT 518 kb)

Supplementary Data 3

Nexus format file of aligned and concatenated nuclear EST sequences. Further annotation within file. Part 3 (TXT 426 kb)

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. (TXT 869 kb)

Supplementary Data 5

Nexus format file of aligned and concatenated mitochondrial protein coding gene nucleotide sequences. Further annotation within file. (TXT 795 kb)

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. (TXT 132 kb)

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Bourlat, S., Juliusdottir, T., Lowe, C. et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85–88 (2006). https://doi.org/10.1038/nature05241

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