Assessing the root of bilaterian animals with scalable phylogenomic methods

Proceedings of the Royal Society B: Biological Sciences

Volumn 276, Issue 1677, 2009, Pages 4261-4270

  Hejnol, Andreas ^a   Obst, Matthias ^b   Stamatakis, Alexandros ^c   Ott, Michael ^c   Rouse, Greg W ^d   Edgecombe, Gregory D ^e   Martinez, Pedro ^f   Baguñà, Jaume ^f   Bailly, Xavier ^g   Jondelius, Ulf ^h   Wiens, Matthias ⁱ   Müller, Werner E G ⁱ   Seaver, Elaine ^a   Wheeler, Ward C ^j   Martindale, Mark Q ^a   Giribet, Gonzalo ^k   Dunn, Casey W ^l  

^a UNIVERSITY OF HAWAII   (United States)

^b GÖTEBORG UNIVERSITY   (Sweden)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^f UNIVERSITY OF BARCELONA   (Spain)

^g STATION BIOLOGIQUE   (France)

^h SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

ⁱ JOHANNES GUTENBERG UNIVERSITY   (Germany)

^j DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^k HARVARD UNIVERSITY   (United States)

^l BROWN UNIVERSITY   (United States)

more..

Author keywords

Acoelomorpha; Ctenophora; Cycliophora Xenoturbella; Nemertodermatida; Phylogenomics

Indexed keywords

ANCESTRY; ECOLOGICAL MODELING; EVOLUTIONARY BIOLOGY; GENE; LIFE HISTORY; METAZOAN; MORPHOLOGY; PHYLOGENETICS;

ACOELA; ARTICLE; CYCLIOPHORA; DEUTEROSTOMIA; ECTOPROCTA; ENTOPROCTA; EVOLUTION; GENE SEQUENCE; METAZOON; NEMERTODERMATIDA; NONHUMAN; PHYLOGENY; PLATYHELMINTH; PRIORITY JOURNAL; XENOTURBELLA;

ACOELA; ACOELOMORPHA; ANIMALIA; BILATERIA; BRYOZOA; CTENOPHORA (COELENTERATES); CYCLIOPHORA; DEUTEROSTOMIA; ENTOPROCTA; METAZOA; NEMERTODERMATIDA; PLATYHELMINTHES; XENOTURBELLA;

EID: 72749099971     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2009.0896     Document Type: Article

References (45)

1. Baguñà, J. & Riutort, M. 2004 The dawn of bilaterian animals: the case of acoelomorph flatworms. Bioessays 26, 1046-1057. (doi:10.1002/bies.20113) (Pubitemid 39424808)
2. Bourlat, S. J. & Hejnol, A. 2009 Acoels. Curr. Biol. 19, R279-R280.
3. Bourlat, S. J., Nielsen, C., Lockyer, A. E., Littlewood, D. T. J. & Telford, M. J. 2003 Xenoturbella is a deuterostome that eats molluscs. Nature 424, 925-928. (doi:10.1038/nature01851) (Pubitemid 37051680)
4. Bourlat, S. J. et al. 2006 Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85-88. (doi:10.1038/nature05241)
5. Castresana, J. 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552.
6. Cavalier-Smith, T. 1998 A revised six-kingdom system of life. Biol. Rev. 73, 203-266. (doi:10.1017/S0006323198005167)
7. Chen, F., Mackey, A. J., Vermunt, J. K. & Roos, D. S. 2007 Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2, e383. (doi:10.1371/journal.pone.0000383)
8. Dunn, C. W. et al. 2008 Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745-749. (doi:10.1038/nature06614)
9. Edgar, R. C. 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113. (doi:10.1186/1471-2105-5-113)
10. Egger, B. et al. 2009 To be or not to be a flatworm: the acoel controversy. PLoS ONE 4, e5502. (doi:10.1371/journal.pone.0005502)
11. Ehlers, U. 1985 Das phylogenetische System der Plathelminthes. Stuttgart, Germany: Gustav Fischer.
12. Franzén, A. & Afzelius, B. 1987 The ciliated epidermis of Xenoturbella bocki (Platyhelminthes, Xenoturbellida) with some phylogenetic considerations. Zool. Scripta 16, 9-17. (doi:10.1111/j.1463-6409.1987.tb00046.x)
13. Funch, P. & Kristensen, R. M. 1995 Cycliophora is a new phylum with affinities to Entoprocta and Ectoprocta. Nature 378, 711-714. (doi:10.1038/378711a0) (Pubitemid 26001941)
14. Giribet, G., Dunn, C. W., Edgecombe, G. D., Hejnol, A., Martindale, M. Q. & Rouse, G. W. 2009 Assembling the spiralian tree of life. In Animal evolution: genes, genomes, fossils and trees (eds M. J. Telford & D. T. J. Littlewood), pp. 52-64. Oxford, UK: Oxford University Press.
15. Haszprunar, G. 1996 Plathelminthes and Plathelminthomorpha - paraphyletic taxa. J. Zool. Syst. Evol. Res. 34, 41-48.
16. Hausdorf, B., Helmkampf, M., Meyer, A., Witek, A., Herlyn, H., Bruchhaus, I., Hankeln, T., Struck, T. H. & Lieb, B. 2007 Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta. Mol. Biol. Evol. 24, 2723-2729. (doi:10.1093/molbev/msm214)
17. Hejnol, A. & Martindale, M. Q. 2008a Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature 456, 382-386. (doi:10.1038/nature07309)
18. Hejnol, A. & Martindale, M. Q. 2008b Acoel development supports a simple planula-like urbilaterian. Phil. Trans. R. Soc. B 363, 1493-1501. (doi:10.1098/rstb.2007.2239)
19. Jondelius, U., Ruiz-Trillo, I., Baguñà, J. & Riutort, M. 2002 The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zool. Scripta 31, 201-215. (doi:10.1046/j.1463-6409.2002.00090. x) (Pubitemid 34285649)
20. Lundin, K. 1998 The epidermal ciliary rootlets of Xenoturbella bocki (Xenoturbellida) revisited: new support for a possible kinship with the Acoelomorpha (Platyhelminthes). Zool. Scripta 27, 263-270. (doi:10.1111/j.1463- 6409.1998.tb00440.x) (Pubitemid 28374062)
21. Lundin, K. 2001 Degenerating epidermal cells in Xenoturbella bocki (phylum uncertain). Nemertodermatida and Acoela (Platyhelminthes). Belgian J. Zool. 131, 153-157.
22. Lundin, K. & Hendelberg, J. 1996 Degenerating epidermal bodies ('pulsatile bodies') in Meara stichopi (Plathelminthes, Nemertodermatida). Zoomorphology 116, 1-5. (doi:10.1007/BF02526924)
23. Malakhov, V. V. 1990 Description of the development of Ascopodaria discreta (Coloniales, Barentsiidae) and discussion of the Kamptozoa status in the animal kingdom. Zool. Zh. 69, 20-30.
24. Marcus, E. 1939 Bryozoarios marinhos brasileiros III. Boletim da Faculdade de filosofia, ciências e letras, Universidade di Sao Paolo, Zoologia 3, 113-299.
25. Nielsen, C. 2001 Animal evolution. New York, NY: Oxford University Press.
26. Paps, J., Baguñà, J. & Riutort, M. 2009 Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proc. R. Soc. B 276, 1245-1254.
27. Passamaneck, Y. & Halanych, K. M. 2006 Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly. Mol. Phylogenet. Evol. 40, 20-28. (doi:10.1016/j.ympev.2006.02.001)
28. Pedersen, K. & Pedersen, L. 1988 Ultrastructural observations on the epidermis of Xenoturbella bocki Westblad, 1949, with a discusion of epidermal cytoplasmic filament systems of Invertebrates. Acta Zool. 69, 231-246.
29. Perseke, M., Hankeln, T., Weich, B., Fritzsch, G., Stadler, P. F., Israelsson, O., Bernhard, D. & Schlegel, M. 2007 The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. Theory Biosci. 126, 35-42. (doi:10.1007/s12064-007-0007-7) (Pubitemid 46835782)
30. Philippe, H., Brinkmann, H., Martinez, P., Riutort, M. & Baguñà, J. 2007 Acoel flatworms are not Platyhelminthes: evidence from phylogenomics. PLoS ONE 2, e717. (doi:10.1371/journal.pone.0000717)
31. Philippe, H. et al. 2009 Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19, 706-712. (doi:10.1016/j.cub.2009.02.052)
32. Raikova, O. I., Reuter, M., Jondelius, U. & Gustafsson, M. K. S. 2000 An immunocytochemical and ultrastructural study of the nervous and muscular systems of Xenoturbella westbladi (Bilateria inc. sed.). Zoomorphology 120, 107-118. (doi:10.1007/s004350000028)
33. Raikova, O. I., Reuter, M. & Justine, L. 2001 Contributions to the phylogeny and systematics of the Acoelomorpha. In Interrelationships of the Platyhelminthes (eds D. T. J. Littlewood & R. A. Bray), pp. 13-23. London, UK: Taylor & Francis.
34. Reisinger, E. 1972 Die Evolution des Orthogons der Spiralier und das Archicölomatenproblem. Z. Zool. Syst. Evolutionsforsch. 10, 1-43. (doi:10.1111/j.1439-0469.1972.tb00783.x)
35. Remane, A. 1950 Die Entstehung der Metamerie der Wirbellosen. Zool. Anz. Suppl. 14, 18-23.
36. Ruiz-Trillo, I., Riutort, M., Littlewood, D. T. J., Herniou, E. A. &Baguñà, J. 1999 Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes. Science 283, 1919-1923. (doi:10.1126/science.283.5409.1919)
37. Ruiz-Trillo, I., Paps, J., Loukota, M., Ribera, C., Jondelius, U., Baguñà, J. & Riutort, M. 2002 A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc. Natl Acad. Sci. USA 99, 11 246-11 251. (doi:10.1073/pnas.172390199)
38. Schierwater, B., Eitel, M., Jakob, W., Osigus, H. J., Hadrys, H., Dellaporta, S. L., Kolokotronis, S. O. & Desalle, R. 2009 Concatenated analysis sheds light on early metazoan evolution and fuels a modern 'urmetazoon' hypothesis. PLoS Biol. 7, e20. (doi:10.1371/journal.pbio.1000020)
39. Smith, S. A. & Dunn, C. W. 2008 Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24, 715-716. (doi:10.1093/bioinformatics/btm619)
40. Srivastava, M. et al. 2008 The Trichoplax genome and the nature of placozoans. Nature 454, 955-960. (doi:10.1038/nature07191)
41. Stamatakis, A. & Ott, M. 2008 Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures. Phil. Trans. R. Soc. B 363, 3977-3984. (doi:10.1098/rstb.2008. 0163)
42. Thorley, J. L. & Wilkinson, M. 1999 Testing the phylogenetic stability of early tetrapods. J. Theor. Biol. 200, 343-344. (doi:10.1006/jtbi. 1999.0999)
43. van Dongen, S. 2000 Graph clustering by flow simulation. PhD thesis, University of Utrecht, Holland.
44. Wallberg, A., Curini-Galletti, M., Ahmadzadeh, A. & Jondelius, U. 2007 Dismissal of Acoelomorpha: Acoela and Nemertodermatida are separate early bilaterian clades. Zoolog. Scripta 36, 509-523. (doi:10.1111/j.1463-6409.2007. 00295.x) (Pubitemid 47373559)
45. Westblad, E. 1949 Xenoturbella bocki n. g., n. sp., a peculiar, primitive Turbellarian type. Arkiv för Zool. 1, 3-29.