Additional molecular support for the new chordate phylogeny

Genesis

Volumn 46, Issue 11, 2008, Pages 592-604

  Delsuc, Frédéric ^a,b   Tsagkogeorga, Georgia ^a,b   Lartillot, Nicolas ^c   Philippe, Hervé ^c  

^a UNIV MONTPELLIER   (France)

^b INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Cephalochordates; Chordates; Deuterostomes; Evolution; Jack knife; Olfactores; Phylogenomics; Ribosomal RNA; Tunicates

Indexed keywords

RIBOSOME RNA;

AMINO ACID SUBSTITUTION; ARTICLE; BAYES THEOREM; CHORDATA; DEVELOPMENTAL BIOLOGY; EVOLUTION; GENETIC ANALYSIS; GENETIC CONSERVATION; HYPOTHESIS; MAXIMUM LIKELIHOOD METHOD; METAZOON; MOLECULAR PHYLOGENY; MONOPHYLY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; TAXONOMY; VERTEBRATE;

ANIMALS; BIOLOGICAL EVOLUTION; CHORDATA, NONVERTEBRATE; GENOMICS; PHYLOGENY; RNA, RIBOSOMAL; VERTEBRATES;

CHORDATA; DEUTEROSTOMIA; UROCHORDATA; VERTEBRATA;

EID: 67149095243     PISSN: 1526954X     EISSN: 1526968X     Source Type: Journal    
DOI: 10.1002/dvg.20450     Document Type: Article

References (83)

1. Abedin M, King N. 2008. The premetazoan ancestry of cadherins. Science 319:946-948.
2. Adoutte A, Balavoine G, Lartillot N, Lespinet O, Prud'homme B, de Rosa R. 2000. The new animal phylogeny: Reliability and implications. Proc Natl Acad Sci USA 97:4453-4456.
3. Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387:489-493.
4. Bassham S, Cañestro C, Postlethwait JH. 2008. Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages. BMC Biol 6:35.
5. Bassham S, Postlethwait JH. 2005. The evolutionary history of placodes: A molecular genetic investigation of the larvacean urochordate Oikopleura dioica. Development 132:4259-4272.
6. Baurain D, Brinkmann H, Philippe H. 2007. Lack of resolution in the animal phylogeny: Closely spaced cladogeneses or undetected systematic errors? Mol Biol Evol 24:6-9.
7. Blair JE, Hedges SB. 2005. Molecular phylogeny and divergence times of deuterostome animals. Mol Biol Evol 22:2275-2284.
8. Blanquart S, Lartillot N. 2008. A site- and time-heterogeneous model of amino acid replacement. Mol Biol Evol 25:842-858.
9. Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ. 2006. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444:85-88.
10. Cameron CB, Garey JR, Swalla BJ. 2000. Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla. Proc Natl Acad Sci USA 97:4469-4474.
11. Cañestro C, Postlethwait JH. 2007. Development of a chordate anterior-posterior axis without classical retinoic acid signaling. Dev Biol 305:522-538.
12. Cañestro C, Postlethwait JH, Gonzalez-Duarte R, Albalat R. 2006. Is retinoic acid genetic machinery a chordate innovation? Evol Dev 8:394-406.
13. Cañestro C, Yokoi H, Postlethwait JH. 2007. Evolutionary developmental biology and genomics. Nat Rev Genet 8:932-942.
14. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552.
15. Cavender JA, Felsenstein J. 1987. Invariants of phylogenies in a simple case with discrete states. J Classif 4:57-71.
16. Conway-Morris S. 2003. The Cambrian "explosion" of metazoans and molecular biology:Would Darwin be satisfied? Int J Dev Biol 47:505-515.
17. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439:965-968.
18. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6:361-375.
19. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sorensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
20. Edvardsen RB, Lerat E, Maeland AD, Flat M, Tewari R, Jensen MF, Lehrach H, Reinhardt R, Seo HC, Chourrout D. 2004. Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica. J Mol Evol 59:448-457.
21. Felsenstein J. 2001. PHYLIP (Phylogenetic Inference Package) version 3.6. (distributed by the author). Seattle: Department of Genetics, University of Washington.
22. Felsenstein J. 2004. Inferring phylogenies. Sunderland, MA, USA: Sinauer Associates, Inc. 645 p.
23. Fu X, Adamski M, Thompson EM. 2008. Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Mol Biol Evol 25:1067-1080.
24. Gee H. 2001. Deuterostome phylogeny: the context for the origin and evolution of the vertebrates. In: Ahlberg PE, editor. Major events in early vertebrate evolution: Palaeontology, phylogeny, genetics, and development. London: Taylor and Francis. pp 1-14.
25. Halanych KM. 1995. The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data. Mol Phylogenet Evol 4:72-76.
26. Halanych KM. 2004. The new view of animal phylogeny. Annu Rev Ecol Evol Syst 35:229-256.
27. Halanych KM, Bacheller JD, Aguinaldo AM, Liva SM, Hillis DM, Lake JA. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 267:1641-1643.
28. Hartmann S, Vision TJ. 2008. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol 8:95.
29. Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ. 2008. MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci USA 105:2946-2950.
30. Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF. 2006. The expansion of the metazoan microRNA repertoire. BMC Genomics 7:25.
31. Holland LZ. 2007. Developmental biology: A chordate with a difference. Nature 447:153-155.
32. Holland LZ, Gibson-Brown JJ. 2003. The Ciona intestinalis genome: When the constraints are off. Bioessays 25:529-532.
33. Ikuta T, Yoshida N, Satoh N, Saiga H. 2004. Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development. Proc Natl Acad Sci USA 101:15118-15123.
34. Jefferies RPS. 1991. Two types of bilateral symmetry in the Metazoa: Chordate and bilaterian. In: Bock GR, Marsh J, editors. Biological asymmetry and handedness. Chichester: Wiley. pp 94-127.
35. Jeffery WR. 2006. Ascidian neural crest-like cells: Phylogenetic distribution, relationship to larval complexity, and pigment cell fate. J Exp Zoolog B Mol Dev Evol 306:470-480.
36. Jeffery WR. 2007. Chordate ancestry of the neural crest: New insights from ascidians. Semin Cell Dev Biol 18:481-491.
37. Jeffery WR, Strickler AG, Yamamoto Y. 2004. Migratory neural crest-like cells form body pigmentation in a urochordate embryo. Nature 431:696-699.
38. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: The beginning of incongruence? Trends Genet 22:225-231.
39. Jimenez-Guri E, Philippe H, Okamura B, Holland PWH. 2007. Buddenbrockia is a Cnidarian worm. Science 317:116-118.
40. Jobb G, von Haeseler A, Strimmer K. 2004. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4:18.
41. Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7 Suppl 1:S4.
42. Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21:1095-1109.
43. Lartillot N, Philippe H. 2008. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci 363:1463-1472.
44. Lwoff A. 1944. L'évolution physiologique: Étude des pertes de fonctions chez les microorganismes. Paris: Hermann. 308 p.
45. Mallatt J, Winchell CJ. 2007. Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogenet Evol 43:1005-1022.
46. Marlétaz F, Holland LZ, Laudet V, Schubert M. 2006a. Retinoic acid signaling and the evolution of chordates. Int J Biol Sci 2:38-47.
47. Marlétaz F, Martin E, Perez Y, Papillon D, Caubit X, Lowe CJ, Freeman B, Fasano L, Dossat C, Wincker P, Weissenbach J, Le Parco Y. 2006b. Chaetognath phylogenomics: A protostome with deuterostome-like development. Curr Biol 16:R577-R578.
48. Matus DQ, Copley RR, Dunn CW, Hejnol A, Eccleston H, Halanych KM, Martindale MQ, Telford MJ. 2006. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Curr Biol 16:R575-R576.
49. Mazet F, Shimeld SM. 2005. Molecular evidence from ascidians for the evolutionary origin of vertebrate cranial sensory placodes. J Exp Zoolog B Mol Dev Evol 304:340-346.
50. Nielsen C. 2001. Animal evolution, interrelationships of the living phyla. Oxford, UK: Oxford University Press.
51. Oda H, Akiyama-Oda Y, Zhang S. 2004. Two classic cadherin-related molecules with no cadherin extracellular repeats in the cephalochordate amphioxus: Distinct adhesive specificities and possible involvement in the development of multicell-layered structures. J Cell Sci 117:2757-2767.
52. Oda H, Wada H, Tagawa K, Akiyama-Oda Y, Satoh N, Humphreys T, Zhang S, Tsukita S. 2002. A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny. Evol Dev 4:426-434.
53. Philippe H. 1993. MUST, a computer package of management utilities for sequences and trees. Nucleic Acids Res 21:5264-5272.
54. Philippe H, Delsuc F, Brinkmann H, Lartillot N. 2005a. Phylogenomics. Annu Rev Ecol Evol Syst 36:541-562.
55. Philippe H, Lartillot N, Brinkmann H. 2005b. Multigene analyses of bilaterian animals corroborate the monophyly of ecdysozoa, lophotrochozoa, and protostomia. Mol Biol Evol 22:1246-1253.
56. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D. 2004. Phylogenomics of eukaryotes: Impact of missing data on large alignments. Mol Biol Evol 21:1740-1752.
57. Philippe H, Telford MJ. 2006. Large-scale sequencing and the new animal phylogeny. Trends Ecol Evol 21:614-620.
58. Phillips MJ, Delsuc F, Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455-1458.
59. Posada D, Crandall KA. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
60. Posada D, Crandall KA. 2001. Selecting the best-fit model of nucleotide substitution. Syst Biol 50:580-601.
61. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutierrez EL, Dubchak I, Garcia-Fernandez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin IT, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064-1071.
62. R Development Core Team. 2007. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
63. Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol 56:389-399.
64. Roure B, Rodriguez-Ezpeleta N, Philippe H. 2007. SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol 7 Suppl 1:S2.
65. Rowe T. 2004. Chordate phylogeny and development. In: Cracraft J, Donoghue MJ, editors. Assembling the tree of life. Oxford: Oxford University Press. pp 384-409.
66. Ruppert EE. 2005. Key characters uniting hemichordates and chordates: Homologies or homoplasies? Can J Zool 83:8-23.
67. Schaeffer B. 1987. Deuterostome monophyly and phylogeny. Evol Biol 21:179-235.
68. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
69. Schubert M, Escriva H, Xavier-Neto J, Laudet V. 2006. Amphioxus and tunicates as evolutionary model systems. Trends Ecol Evol 21:269-277.
70. Sempere LF, Cole CN, McPeek MA, Peterson KJ. 2006. The phylogenetic distribution of metazoan microRNAs: Insights into evolutionary complexity and constraint. J Exp Zoolog B Mol Dev Evol 306:575-588.
71. Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D. 2004. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 431:67-71.
72. Steel M. 2005. Should phylogenetic models be trying to "fit an elephant"? Trends Genet 21:307-309.
73. Swalla BJ, Cameron CB, Corley LS, Garey JR. 2000. Urochordates are monophyletic within the deuterostomes. Syst Biol 49:52-64.
74. Swofford DL. 2002. PAUP*: Phylogenetic analysis using parsimony and other methods version 4.0b10. Sunderland, MA: Sinauer.
75. Telford MJ, Budd GE. 2003. The place of phylogeny and cladistics in Evo-Devo research. Int J Dev Biol 47:479-490.
76. Vienne A, Pontarotti P. 2006. Metaphylogeny of 82 gene families sheds a new light on chordate evolution. Int J Biol Sci 2:32-37.
77. Wada H, Okuyama M, Satoh N, Zhang S. 2006. Molecular evolution of fibrillar collagen in chordates, with implications for the evolution of vertebrate skeletons and chordate phylogeny. Evol Dev 8:370-377.
78. Wada H, Satoh N. 1994. Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA. Proc Natl Acad Sci USA 91:1801-1804.
79. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691-699.
80. Wiens JJ. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol 52:528-538.
81. Wiens JJ. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst Biol 54:731-742.
82. Wiens JJ. 2006. Missing data and the design of phylogenetic analyses. J Biomed Inform 39:34-42.
83. Winchell CJ, Sullivan J, Cameron CB, Swalla BJ, Mallatt J. 2002. Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Mol Biol Evol 19:762-776.