Improving animal phylogenies with genomic data

Trends in Genetics

Volumn 27, Issue 5, 2011, Pages 186-195

  Telford, Maximilian J ^a   Copley, Richard R ^b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEHYDROGENASE SUBUNIT 5; MICRORNA; OXIDOREDUCTASE; UNCLASSIFIED DRUG;

ANIMAL GENETICS; COELOMATA; ECDYSOZOA; GENE SEQUENCE; GENE STRUCTURE; HUMAN; MEASUREMENT ERROR; MOLECULAR EVOLUTION; MORPHOLOGY; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; PRIORITY JOURNAL; REVIEW; TAXONOMY;

ANIMALS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME; HUMANS; MODELS, GENETIC; PHYLOGENY;

ANIMALIA;

EID: 79955109773     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2011.02.003     Document Type: Review

References (83)

1. Budd G., Jensen S. A critical reappraisal of the fossil record of the bilaterian phyla. Biol. Rev. Camb. Philos. Soc. 2000, 75:253-295.
2. Philippe H., et al. Can the Cambrian explosion be inferred through molecular phylogeny?. Development 1994, (Suppl.):15-25.
3. Rokas A., et al. Animal evolution and the molecular signature of radiations compressed in time. Science 2005, 310:1933-1938.
4. Telford M.J. Cladistic analyses of molecular characters: the good, the bad and the ugly. Contrib. Zool. 2002, 71:93-100.
5. Consortium C.e.S. Genome sequencing of the nematode C.elegans: a platform for investigating biology. Science 1998, 282:2012-2018.
6. Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science 2000, 287:2185-2195.
7. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. International Human Genome Sequencing Consortium.
8. Adoutte A., et al. The new animal phylogeny: reliability and implications. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:4453-4456.
9. Aguinaldo A.M., et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997, 387:489-493.
10. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
11. Philippe H., et al. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 2005, 5:50.
12. Blair J.E., et al. The evolutionary position of nematodes. BMC Evol. Biol. 2002, 2:7.
13. Wolf Y.I., et al. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 2004, 14:29-36.
14. Copley R.R., et al. Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. Evol. Dev. 2004, 6:164-169.
15. Philippe H., et al. Phylogenomics restores traditional views on deep animal relationships. Curr. Biol. 2009, 19:706-712.
16. Philippe H., et al. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 2005, 22:1246-1253.
17. Holton T.A., Pisani D. Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol. Evol. 2010, 2:310-324.
18. Delsuc F., et al. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 2005, 6:361-375.
19. Webster B.L., et al. Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan. Evol. Dev. 2006, 8:502-510.
20. Lartillot N., et al. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol. Biol. 2007, 7(Suppl. 1):S4.
21. Lartillot N., Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 2004, 21:1095-1109.
22. Ciccarelli F.D., et al. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287.
23. Rokas A., Holland P.W.H. Rare genomic changes as a tool for phylogenetics. Trends Evol. Ecol. 2000, 15:454-459.
24. Telford M.J., Budd G.E. The place of phylogeny and cladistics in Evo-Devo research. Int. J. Dev. Biol. 2003, 47:479-490.
25. Rogozin I.B., et al. Analysis of rare amino acid replacements supports the Coelomata clade. Mol. Biol. Evol. 2007, 24:2594-2597.
26. Rogozin I.B., et al. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol. Direct 2008, 3:7.
27. Rogozin I.B., et al. Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. Mol. Biol. Evol. 2007, 24:1080-1090.
28. Zheng J., et al. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol. Biol. Evol. 2007, 24:2583-2592.
29. Swofford D.L., et al. Phylogenetic inference. Molecular Systematics 1996, 407-514. Sinauer. 2nd edn. D.M. Hillis (Ed.).
30. Felsenstein J. PHYLIP (Phylogeny Inference Package) 2005.
31. Dollo L. Les lois de l'évolution. Bull. de la Soc. Belge de Geologie Paléontologie et d'Hydrologie 1893, 7:164-166.
32. Irimia M., et al. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol. Biol. Evol. 2007, 24:1604-1607.
33. Roy S.W., Irimia M. Rare genomic characters do not support Coelomata: intron loss/gain. Mol. Biol. Evol. 2008, 25:620-623.
34. Roy S.W., Irimia M. Rare genomic characters do not support Coelomata: RGC_CAMs. J. Mol. Evol. 2008, 66:308-315.
35. Roy S.W., Gilbert W. Resolution of a deep animal divergence by the pattern of intron conservation. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:4403-4408.
36. Heimberg A.M., et al. microRNAs reveal the interrelationships of hagfish, lampreys and gnathostomes and the nature of the ancestral vertebrate. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:19379-19383.
37. Rota-Stabelli O., et al. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc. R. Soc. Lond. B. 2011, 278:298-306.
38. Heimberg A.M., et al. microRNAs and the advent of vertebrate morphological complexity. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:2946-2950.
39. Philippe H., et al. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 2011, 470:255-258.
40. Hillis D.M. SINEs of the perfect character. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:9979-9981.
41. Papillon D., et al. Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome. Mol. Biol. Evol. 2004, 21:2122-2129.
42. Dunn C.W., et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
43. Hejnol A., et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. Lond. B. 2009, 276:4261-4270.
44. Philippe H., Telford M.J. Large-scale sequencing and the new animal phylogeny. Trends Ecol. Evol. (Amst.) 2006, 21:614-620.
45. Cook C.E., et al. Hox genes and the phylogeny of the arthropods. Curr. Biol. 2001, 11:759-763.
46. Friedrich M., Tautz D. rDNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 1995, 376:165-167.
47. Pisani D., et al. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol. 2004, 2:1.
48. Janssen R., Budd G.E. Gene expression suggests conserved aspects of Hox gene regulation in arthropods and provides additional support for monophyletic Myriapoda. Evodevo 2010, 1:4.
49. Telford M.J., Thomas R.H. Demise of the Atelocerata?. Nature 1995, 376:123-124.
50. Telford M.J., et al. The evolution of the Ecdysozoa. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008, 363:1529-1537.
51. Stollewerk A., Simpson P. Evolution of early development of the nervous system: a comparison between arthropods. Bioessays 2005, 27:874-883.
52. Chipman A.D., Stollewerk A. Specification of neural precursor identity in the geophilomorph centipede Strigamia maritima. Dev. Biol. 2006, 290:337-350.
53. Rota-Stabelli O., Telford M.J. A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol. Phylogenet. Evol. 2008, 48:103-111.
54. Budd G.E., Telford M.J. The origin and evolution of the arthropods. Nature 2009, 457:812-817.
55. Delsuc F., et al. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006, 439:965-968.
56. Ruppert E.E. Key characters uniting hemichordates and chordates: homologies or homoplasies?. Can. J. Zool. 2005, 83:8-23.
57. Bourlat S.J., et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 2006, 444:85-88.
58. Delsuc F., et al. Additional molecular support for the new chordate phylogeny. Genesis 2008, 46:592-604.
59. Putnam N.H., et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 2007, 317:86-94.
60. Telford M.J., Holland P.W.H. Evolution of 28S ribosomal DNA in chaetognaths: duplicate genes and molecular phylogeny. J. Mol. Evol. 1997, 44:135-144.
61. Ryan J.F., et al. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the Parahoxozoa. EvoDevo 2010, 1:9.
62. Pang K., et al. Gegnomic insights into Wnt signalling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi. EvoDevo 2010, 1:10.
63. Podar M., et al. A molecular phylogentic framework for the phylum Ctenophora using 18S genes. Mol. Phyl. Evol. 2001, 21:218-2230.
64. Regier J.C., et al. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010, 463:1079-1083.
65. Studer R.A., Robinson-Rechavi M. Large-scale analysis of orthologs and paralogs under covarion-like and constant but different models of amino acids evolution. Mol. Biol. Evol. 2010, 27:2618-2627.
66. Rokas A., et al. Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Insect Mol. Biol. 1999, 8:527-530.
67. Srivastava M., et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 2010, 466:720-726.
68. Denoeud F., et al. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 2010, 330:1381-1385.
69. Kawashima T., et al. Domain shuffling and the evolution of vertebrates. Genome Res. 2009, 19:1393-1403.
70. Gough J. Convergent evolution of domain architectures (is rare). Bioinformatics 2005, 15:1464-1471.
71. King N., et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 2008, 451:783-788.
72. Sebé-Pedrós A., et al. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol. Biol. Evol. 2011, 28:1241-1254.
73. Matus D., et al. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Curr. Biol. 2006, 16:R575-576.
74. Telford M.J., Holland P.W. The phylogenetic affinities of the chaetognaths: a molecular analysis. Mol. Biol. Evol. 1993, 10:660-676.
75. Marletaz F., et al. Chaetognath phylogenomics: a protostome with deuterostome-like development. Curr. Biol. 2006, 16:R577-R578.
76. de Rosa R., et al. Hox genes in brachiopods and priapulids and protostome evolution. Nature 1999, 399:772-776.
77. Nielsen C. Animal Evolution. Interrelationships of the Living Phyla 2001, Oxford University Press.
78. Halanych K.M., et al. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 1995, 267:1641-1643.
79. Halanych K.M. Convergence in the feeding apparatuses of Lophophorates and pterobranch Hemichordates revealed by 18S rDNA: an interpretation. Biol. Bull. 1996, 190:1-5.
80. Ruiz Trillo I., et al. Acoel flatworms: earliest extant bilaterian metazoans, not members of Platyhelminthes. Science 1999, 283:1919-1923.
81. Egger B., et al. To be or not to be a flatworm: the acoel controversy. PLoS ONE 2009, 4:e5502.
82. Sperling E.A., et al. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol. Biol. Evol. 2009, 26:2261-2274.
83. Peterson K.J., et al. MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion. BioEssays 2009, 31:736-747.