nature.com

Xenacoelomorpha is the sister group to Nephrozoa - Nature

  • ️Hejnol, Andreas
  • ️Wed Feb 03 2016

References

  1. Dunn, C. W., Giribet, G., Edgecombe, G. D. & Hejnol, A. Animal phylogeny and its evolutionary implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395 (2014)

    Article  Google Scholar 

  2. Hejnol, A. et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B 276, 4261–4270 (2009)

    Article  PubMed  PubMed Central  Google Scholar 

  3. Srivastava, M., Mazza-Curll, K. L., van Wolfswinkel, J. C. & Reddien, P. W. Whole-body acoel regeneration is controlled by Wnt and Bmp-Admp signaling. Curr. Biol. 24, 1107–1113 (2014)

    Article  CAS  PubMed  Google Scholar 

  4. Philippe, H. et al. Acoelomorph flatworms are deuterostomes related to Xenoturbella . Nature 470, 255–258 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  5. Nielsen, C. Animal Evolution: Interrelationships of the Living Phyla (Oxford Univ. Press, 2012)

  6. Ehlers, U. Das phylogenetische System der Plathelminthes (G. Fischer, 1985)

  7. Smith, J. P. S., III, Tyler, S. & Rieger, R. M. Is the Turbellaria polyphyletic? Hydrobiologia 132, 13–21 (1986)

    Article  Google Scholar 

  8. Haszprunar, G. Plathelminthes and Plathelminthomorpha — paraphyletic taxa. J. Zool. Syst. Evol. Res. 34, 41–48 (1996)

    Article  Google Scholar 

  9. Ruiz-Trillo, I., Riutort, M., Littlewood, D. T. J., Herniou, E. A. & Baguña, J. Acoel flatworms: earliest extant bilaterian metazoans, not members of Platyhelminthes. Science 283, 1919–1923 (1999)

    Article  ADS  CAS  PubMed  Google Scholar 

  10. Steinböck, O. Ergebnisse einer von E. Reisinger & O. Steinböck mit Hilfe des Rask-Örsted fonds durchgefuhrten Reise in Grönland 1926. 2. Nemertoderma bathycola nov. gen. nov. spec., eine eigenartige Turbellarie aus der Tiefe der Diskobay: nebst einem Beitrag zur Kenntnis des Nemertinenepithels. Vidensk. Medd. Dan. Naturhist. Foren. 90, 47–84 (1930)

    Google Scholar 

  11. Paps, J., Baguñà, J. & Riutort, M. Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha. Mol. Biol. Evol. 26, 2397–2406 (2009)

    Article  CAS  PubMed  Google Scholar 

  12. Jondelius, U., Ruiz-Trillo, I., Baguñà, J. & Riutort, M. The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zool. Scr. 31, 201–215 (2002)

    Article  Google Scholar 

  13. Westblad, E. Xenoturbella bocki n.g, n.sp, a peculiar, primitive turbellarian type. Ark. Zool. 1, 3–29 (1949)

    Google Scholar 

  14. Franzén, Å. & Afzelius, B. A. The ciliated epidermis of Xenoturbella bocki (Platyhelminthes, Xenoturbellida) with some phylogenetic considerations. Zool. Scr. 16, 9–17 (1987)

    Article  Google Scholar 

  15. Ehlers, U. & Sopott-Ehlers, B. Ultrastructure of the subepidermal musculature of Xenoturbella bocki, the adelphotaxon of the Bilateria. Zoomorphology 117, 71–79 (1997)

    Article  Google Scholar 

  16. Norén, M. & Jondelius, U. Xenoturbella’s molluscan relatives…. Nature 390, 31–32 (1997)

    Article  ADS  Google Scholar 

  17. Bourlat, S. J. et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85–88 (2006)

    Article  ADS  CAS  PubMed  Google Scholar 

  18. Bourlat, S. J., Rota-Stabelli, O., Lanfear, R. & Telford, M. J. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes. BMC Evol. Biol. 9, 107 (2009)

    Google Scholar 

  19. Mwinyi, A. et al. The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis. BMC Evol. Biol. 10, 309 (2010)

    Google Scholar 

  20. Ruiz-Trillo, I., Riutort, M., Fourcade, H. M., Baguñà, J. & Boore, J. L. Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. Mol. Phylogenet. Evol. 33, 321–332 (2004)

    Article  CAS  PubMed  Google Scholar 

  21. Rouse, G., Wilson, N. G., Carvajal, J. I. & Vrijenhoek, R. C. New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature http://dx.doi.org/10.1038/nature16545 (this issue)

  22. Thomson, R. C., Plachetzki, D. C., Mahler, D. L. & Moore, B. R. A critical appraisal of the use of microRNA data in phylogenetics. Proc. Natl Acad. Sci. USA 111, E3659–E3668 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  23. Jondelius, U., Wallberg, A., Hooge, M. & Raikova, O. I. How the worm got its pharynx: phylogeny, classification and Bayesian assessment of character evolution in Acoela. Syst. Biol. 60, 845–871 (2011)

    Article  PubMed  Google Scholar 

  24. Le, S. Q., Dang, C. C. & Gascuel, O. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol. Biol. Evol. 29, 2921–2936 (2012)

    Article  CAS  PubMed  Google Scholar 

  25. Dunn, C. W. et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Mirarab, S. et al. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541–i548 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Bleidorn, C. et al. On the phylogenetic position of Myzostomida: can 77 genes get it wrong? BMC Evol. Biol. 9, 150 (2009)

    Google Scholar 

  28. Whelan, N. V., Kocot, K. M., Moroz, L. L. & Halanych, K. M. Error, signal, and the placement of Ctenophora sister to all other animals. Proc. Natl Acad. Sci. USA 112, 5773–5778 (2015)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Hejnol, A. & Martindale, M. Q. Acoel development supports a simple planula-like urbilaterian. Phil. Trans. R. Soc. B 363, 1493–1501 (2008)

    Article  PubMed  PubMed Central  Google Scholar 

  30. Laumer, C. E. et al. Spiralian phylogeny informs the evolution of microscopic lineages. Curr. Biol. 25, 2000–2006 (2015)

    Article  CAS  PubMed  Google Scholar 

  31. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnol. 29, 644–652 (2011)

    Article  CAS  Google Scholar 

  32. Ebersberger, I., Strauss, S. & von Haeseler, A. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol. Biol. 9, 157 (2009)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Lechner, M. et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 12, 124 (2011)

    Article  PubMed  PubMed Central  Google Scholar 

  34. Kocot, K. M. et al. Phylogenomics reveals deep molluscan relationships. Nature 477, 452–456 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  35. Cannon, J. T. et al. Phylogenomic resolution of the hemichordate and echinoderm clade. Curr. Biol. 24, 2827–2832 (2014)

    Article  CAS  PubMed  Google Scholar 

  36. Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Misof, B. & Misof, K. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst. Biol. 58, 21–34 (2009)

    Article  CAS  PubMed  Google Scholar 

  38. Price, M. N., Dehal, P. S. & Arkin, A. P . FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490 (2010)

  39. Kocot, K. M., Citarella, M. R., Moroz, L. L. & Halanych, K. M. PhyloTreePruner: a phylogenetic tree-based approach for selection of orthologous sequences for phylogenomics. Evol. Bioinform. Online 9, 429–435 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000)

    Article  CAS  PubMed  Google Scholar 

  41. Struck, T. H. TreSpEx-Detection of misleading signal in phylogenetic reconstructions based on tree information. Evol. Bioinform. Online 10, 51–67 (2014)

    Article  PubMed  PubMed Central  Google Scholar 

  42. Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164–1165 (2011)

    Article  CAS  PubMed  Google Scholar 

  45. Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013)

    Article  CAS  PubMed  Google Scholar 

  46. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012)

    Article  PubMed  PubMed Central  Google Scholar 

Download references