Phylogenomics Revives Traditional Views on Deep Animal Relationships

Current Biology

Volumn 19, Issue 8, 2009, Pages 706-712

  Philippe, Hervé ^a   Derelle, Romain ^b   Lopez, Philippe ^b   Pick, Kerstin ^c,e   Borchiellini, Carole ^f   Boury Esnault, Nicole ^f   Vacelet, Jean ^f   Renard, Emmanuelle ^f   Houliston, Evelyn ^b   Quéinnec, Eric ^b   Da Silva, Corinne ^g   Wincker, Patrick ^g   Le Guyader, Hervé ^b   Leys, Sally ^h   Jackson, Daniel J ^c,i   Schreiber, Fabian ^d   Erpenbeck, Dirk ^e   Morgenstern, Burkhard ^c,d   Wörheide, Gert ^e   Manuel, Michaël ^b  

^a Universite de Montreal   (Canada)

^b SORBONNE UNIVERSITÉ   (France)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

^d Inst fuer Mikrobiologie und Genetik   (Germany)

^e UNIVERSITY OF MUNICH   (Germany)

^f AIX MARSEILLE UNIVERSITY   (France)

^g Genoscope   (France)

^h UNIVERSITY OF ALBERTA   (Canada)

ⁱ UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

EVO_ECOL

Indexed keywords

NUCLEAR PROTEIN;

ANIMAL; ARTICLE; CLASSIFICATION; EVOLUTION; GENETICS; GENOMICS; MORPHOGENESIS; PHYLOGENY; SPONGE (PORIFERA);

ANIMALS; BODY PATTERNING; EVOLUTION; GENOMICS; NUCLEAR PROTEINS; PHYLOGENY; PORIFERA;

ANIMALIA; BILATERIA; CNIDARIA; COELENTERATA; CTENOPHORA (COELENTERATES); EUMETAZOA; METAZOA; PLACOZOA; PORIFERA;

EID: 65249099546     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2009.02.052     Document Type: Article

References (44)

1. Philippe H., and Telford M. Large-scale sequencing and the new animal phylogeny. Trends Ecol. Evol. 21 (2006) 614-620
2. Philippe H., Lartillot N., and Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22 (2005) 1246-1253
3. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., et al. Broad phylogenetic sampling improves the resolution of the animal tree of life. Nature 452 (2008) 745-749
4. Borchiellini C., Manuel M., Alivon E., Boury-Esnault N., Vacelet J., and Le Parco Y. Sponge paraphyly and the origin of Metazoa. J. Evol. Biol. 14 (2001) 171-179
5. Peterson K.J., and Eernisse D.J. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Dev. 3 (2001) 170-205
6. Medina M., Collins A.G., Silberman J.D., and Sogin M.L. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc. Natl. Acad. Sci. USA 98 (2001) 9707-9712
7. Manuel M., Borchiellini C., Alivon E., Le Parco Y., Vacelet J., and Boury-Esnault N. Phylogeny and evolution of calcareous sponges: Monophyly of Calcinea and Calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry. Syst. Biol. 52 (2003) 311-333
8. Sperling E.A., Pisani D., and Peterson K.J. Poriferan paraphyly and its implications for Precambrian palaeobiology. In: Vickers-Rich P., and Komarower P. (Eds). The Rise and Fall of Ediacaran Biota (2007), Geological Society Special Publications, London 355-368
9. Nielsen C. Six major steps in animal evolution: Are we derived sponge larvae?. Evol. Dev. 10 (2008) 241-257
10. Rokas A., Krüger D., and Carroll S.B. Animal evolution and the molecular signature of radiations compressed in time. Science 310 (2005) 1933-1938
11. Schierwater B., Eitel M., Jakob W., Osigus H.-J., Hadrys H., Dellaporta S.L., Kolokotronis S.-O., and DeSalle R. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "Urmetazoon" hypothesis. PLoS Biol. 7 (2009) e1000020
12. Hedtke S.M., Townsend T.M., and Hillis D.M. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55 (2006) 522-529
13. Baurain D., Brinkmann H., and Philippe H. Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?. Mol. Biol. Evol. 24 (2007) 6-9
14. Lartillot N., and Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21 (2004) 1095-1109
15. Lartillot N., Brinkmann H., and Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol. Biol. 7 (2007) S4
16. King N., Westbrook M.J., Young S.L., Kuo A., Abedin M., Chapman J., Faircough S., Hellsten U., Isogai Y., Letunic I., et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451 (2008) 783-788
17. Ax P. Multicellular animals: A new approach to the phylogenetic order in nature (1996), Springer-Verlag, Berlin
18. Hyman L.H. The Invertebrates Volume 1-6 (1940), McGraw-Hill, New York
19. Brusca R.C., and Brusca G.J. Invertebrates. Second Edition (2003), Sinauer, Sunderland, MA
20. Adamska M., Degnan S.M., Green K.M., Adamski M., Craigie A., Larroux C., and Degnan B.M. Wnt and TGF-β expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning. PLoS One 10 (2007) e1031
21. Manuel M. Early evolution of symmetry and polarity in metazoan body plans. C. R. Biol. 332 (2009) 184-209
22. Gray J.E. Notes on the arrangement of sponges, with the description of some new genera. Proc. Zool. Soc. Lond. 1867 (1867) 492-558
23. Uriz M.-J., Turon X., Becerro M.A., and Agell G. Siliceous spicules and skeleton frameworks in sponges: Origin, diversity, ultrastructural patterns, and biological functions. Microsc. Res. Tech. 62 (2003) 279-299
24. Thiel V., Blumenberg M., Hefter J., Pape T., Pomponi S., Reed J., Reitner J., Wörheide G., and Michaelis W. A chemical view of the most ancient metazoa-biomarker chemotaxonomy of hexactinellid sponges. Naturwissenschaften 89 (2002) 60-66
25. Borchiellini C., Chombard C., Manuel M., Alivon E., Vacelet J., and Boury-Esnault N. Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Mol. Phylogenet. Evol. 32 (2004) 823-837
26. Dohrmann M., Janussen D., Reitner J., Collins A.G., and Wörheide G. Phylogeny and evolution of glass sponges (Porifera, Hexactinellida). Syst. Biol. 57 (2008) 388-405
27. In: Hooper J.N.A., and van Soest R.W.M. (Eds). Systema Porifera. A Guide to the Classification of Sponges (2002), Kluwer Academic/Plenum Publishers, New York
28. Wang X., and Lavrov D.V. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae. PLoS ONE 3 (2008) e2723
29. Boute N., Exposito J.Y., Boury-Esnault N., Vacelet J., Noro N., Miyazaki K., Yoshigato K., and Garrone R. Type IV collagen in sponges, the missing link in basement membrane ubiquity. Biol. Cell 88 (1996) 37-44
30. Boury-Esnault N., Ereskovsky A., Bézac C., and Tokina D. Larval development in Homoscleromorpha (Porifera, Demospongiae). Invertebr. Biol. 122 (2003) 187-202
31. Miller D.J., and Ball E.E. Animal evolution: Trichoplax, trees, and taxonomic turmoil. Curr. Biol. 18 (2008) R1003-R1005
32. Leuckart R. Über die Morphologie und die Verwandtschaftsverhältnisse der wirbellosen Tiere (1848), Vieweg und Sohn, Braunschweig
33. Harbison G.R. On the classification and evolution of the Ctenophora. In: Morris S.C., George J.D., Gibson R., and Platt H.M. (Eds). The Origins and Relationships of Lower Invertebrates. Systematics Association Special Volume 28 (1985), Clarendon Press, Oxford 78-100
34. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Biol. 27 (1978) 401-410
35. Srivastava M., Begovic E., Chapman J., Putnam N.H., Hellsten U., Kawashima T., Kuo A., Mitros T., Salamov A., Carpenter M.L., et al. The Trichoplax genome and the nature of placozoans. Nature 454 (2008) 955-960
36. Finnerty J.R., Pang K., Burton P., Paulson D., and Martindale M.Q. Origins of bilateral symmetry: Hox and Dpp expression in a sea anemone. Science 304 (2004) 1335-1337
37. Martindale M.Q. The evolution of metazoan axial properties. Nat. Rev. Genet. 6 (2005) 917-927
38. Matus D.Q., Pang K., Marlow H., Dunn C.W., Thomsen G.H., and Martindale M.Q. Molecular evidence for deep evolutionary roots of bilaterality in animal development. Proc. Natl. Acad. Sci. USA 103 (2006) 11195-11200
39. Seipel K., and Schmid V. Mesodermal anatomies in cnidarian polyps and medusae. Int. J. Dev. Biol. 50 (2006) 589-599
40. Lartillot N., and Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363 (2008) 1463-1472
41. Bapteste E., Brinkmann H., Lee J.A., Moore D.V., Sensen C.W., Gordon P., Durufle L., Gaasterland T., Lopez P., Muller M., et al. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99 (2002) 1414-1419
42. Rodriguez-Ezpeleta N., Brinkmann H., Burger G., Roger A.J., Gray M.W., Philippe H., and Lang B.F. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol. 17 (2007) 1420-1425
43. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
44. Roure B., Rodriguez-Ezpeleta N., and Philippe H. SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol. Biol. 7 Suppl 1 (2007) S2