Deep genomic-scale analyses of the metazoa reject coelomata: Evidence from single-and multigene families analyzed under a supertree and supermatrix paradigm

Genome Biology and Evolution

Volumn 2, Issue 1, 2010, Pages 310-324

  Holton, Thérèse A ^a   Pisani, Davide ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

Bayes factors; Coelomata; Ecdysozoa; Outgroup selection; Phylogenomics; Supermatrix; Supertrees

Indexed keywords

PROTEIN;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; EUKARYOTE; GENETIC DATABASE; GENETICS; GENOMICS; INVERTEBRATE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY;

ANIMALS; BAYES THEOREM; DATABASES, GENETIC; EUKARYOTA; EVOLUTION, MOLECULAR; GENOMICS; INVERTEBRATES; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; PROTEINS;

ANIMALIA; ANNELIDA; COELOMATA; ECDYSOZOA; LOPHOTROCHOZOA; METAZOA; MOLLUSCA; NEMATODA; PANARTHROPODA; PRIAPULIDAE; PROTOSTOMIA;

EID: 77958450862     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq016     Document Type: Article

References (72)

1. Aguinaldo A M A, et al. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:489-493.
2. Archie JW. 1989. A randomization test for phylogenetic information in systematic data. Syst Zool. 38:219-225.
3. Baum BR. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon. 41:3-10.
4. Belinky F, Cohen O, Huchon D. 2010. Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol Biol Evol. 27:441-451.
5. Blair JE, Ikeo K, Gojobori T, Hedges SB. 2002. The evolutionary position of nematodes. BMC Evol Biol. 2:7.
6. Bourlat SJ, Nielsen C, Economou AE, Telford MJ. 2008. Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Mol Phylogenet Evol. 49:23-31.
7. Brinkmann H, Philippe H. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artefacts in ancient phylogenies. Mol Biol Evol. 16:817-825.
8. Burleigh JG, Driskell AC, Sanderson MJ. 2006. Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst Biol. 55:426-440.
9. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
10. Copley RR, Aloy P, Russell RB, Telford MJ. 2004. Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. Evol Dev. 6:164-169.
11. Cotton JA, Page R D M. 2004. Tangled trees from molecular markers: reconciling conflict between phylogenies to build molecular supertrees. In: Bininda-Emonds ORP, editor. Phylogenetic supertrees: combining information to reveal the tree of life. Dordrecht (The Netherlands): Kluwer Academic. p. 107-125.
12. Creevey CJ, et al. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci. 271:2551-2558.
13. Creevy CJ, McInerney JO. 2005. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics. 21:390-392.
14. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375.
15. Dopazo H, Dopazo J. 2005. Genome-scale evidence of the nematodearthropod clade. Genome Biol. 6: R41.
16. Dopazo H, Santoyo J, Dopazo J. 2004. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics. 20: i116-i121.
17. Dunn CW, et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452:745-749.
18. Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584.
19. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 27:401-410.
20. Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package) version 3.67. Seattle (WA): Department of Genome Sciences, University of Washington.
21. Fitzpatrick DA, Logue ME, Stajich JE, Butler G. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol. 6:99.
22. Guindon S, Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
23. Halanych KM. 2004. The new view of animal phylogeny. Annu Rev Ecol Evol Sys. 35:229-256.
24. Halanych KM, et al. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science. 267:1641-1643.
25. Hejnol A, et al. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc R Soc B Biol Sci. 276:4261-4270.
26. Hyman LH. 1940. The invertebrates. Vol. 1: Protozoa through Ctenophora. New York: McGraw-Hill.
27. Irimia M, Maeso I, Penny D, Garcia-Fernàndez J, Roy SW. 2007. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol. 24:1604-1607.
28. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22:225-231.
29. Jenner RA, Schram FR. 1999. The grand game of metazoan phylogeny: rules and strategies. Biol Rev Camb Philos Soc. 74:121-142.
30. Kass RE, Raftery AE. 1995. Bayes factors. J Am Stat Assoc. 90:773-795.
31. Keane TM, Creevy CJ, Pentony MM, Naughton TJ, McInerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6:29.
32. Kluge AG. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst Zool. 38:7-25.
33. 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.
34. Lartillot N, Philippe H. 2008. Improvement of molecular phylogenetic inference and the phylogeny of the Bilateria. Philos Trans R Soc Lond B. 363:1463-1472.
35. Littlewood DT, Olsen PD, Telford MJ, Herniou EA, Riutort M. 2001. Elongation factor 1-alpha sequences alone do not assist in resolving the position of the acoela within the metazoa. Mol Biol Evol. 18:437-442.
36. Löytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science. 320:1632-1635.
37. Lynch M. 2007. The origins of genome architecture. Sunderland (MA): Sinauer Associates.
38. Margush T, McMorris FR. 1981. Consensus n-trees. Bull Math Biol. 43:239-244.
39. McInerney JO, Cotton JA, Pisani D. 2008. The prokaryotic tree of life: past, present... and future? Trends Ecol Evol. 23:276-281.
40. Moore BR, Smith SA, Donoghue MJ. 2006. Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping. Syst Biol. 55:662-676.
41. Nielsen C. 2001. Animal evolution, interrelationships of the living phyla. Oxford: Oxford University Press.
42. Peterson KJ, Cotton JA, Gehling JG, Pisani D. 2008. The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philos Trans R Soc Lond B Biol Sci. 363:1435-1443.
43. Philip GK, Creevy CJ, McInerney JO. 2005. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support got the Coelomata than Ecdysozoa. Mol Biol Evol. 22:1175-1184.
44. Philippe H, Brinkmann H, Martinez P, Riutort M, Baguñà J. 2007. Acoel flatworms are not platyhelminthes: evidence from phylogenomics. PLoS One. 2: e717.
45. Philippe H, et al. 2009. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 19:706-712.
46. Philippe H, Lartillot N, Brinkmann H. 2005. Multi gene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 22:1246-1253.
47. Pisani D. 2004. Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda. Syst Biol. 53:978-989.
48. Pisani D, Cotton JA, McInerney JO. 2007. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol. 24:1752-1760.
49. Pisani D, Wilkinson M. 2002. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst Biol. 51:151-155.
50. Ragan MA. 1992. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol. 1:53-58.
51. Rambaut A, Drummond AJ. 2007. Tracer v1.4. [Internet]. Available from: http://beast.bio.ed.ac.uk/Tracer.
52. Robinson M, Gouy M, Gautier C, Mouchiroud D. 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol Biol Evol. 15:1091-1098.
53. Rogozin IB, Thomson K, Csürös M, Carmel L, Koonin EV. 2008. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol Direct. 3:7.
54. Rogozin IB, Wolf YI, Carmel L, Koonin EV. 2007. Analysis of rare amino acid replacements supports the Coelomata clade. Mol Biol Evol. 24:2594-2597.
55. Rokas A, Carroll SB. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol. 22:1337-1344.
56. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572-1574.
57. Rosenberg MS, Kumar S. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci U S A. 98:10751-10756.
58. Rota-Stabelli O, Telford MJ. 2008. A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for the Mandibulata over Myriochelata using mitogenomics. Mol Phylogenet Evol. 48:103-111.
59. Roy SW, Irimia M. 2008. Rare genomic characters do not support Coelomata: intron loss/gain. Mol Biol Evol. 25:620-623.
60. Ruiz-Trillo I, Riutort M, Littlewood D T J, Herniou EA, Baguna J. 1999. Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes. Science. 283:1919-1923.
61. Semple C, Steel M. 2003. Phylogenetics. New York: Oxford University Press.
62. Sperling EA, Peterson KJ, Pisani D. 2009. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol Biol Evol. 26:2261-2274.
63. Sperling EA, Robinson JM, Pisani D, Peterson KJ. 2010. Where's the glass? Biomarkers, molecular clocks and microRNAs suggest a 200 million year missing precambrian fossil record of siliceous sponge spicules. Geobiology. 8:24-36.
64. * and other methods). Version 4. Sunderland (MA): Sinauer Associates Inc.
65. Telford MJ, Bourlat SJ, Economou A, Papillon D, Rota-Stabelli O. 2008. The evolution of the Ecdysozoa. Philos Trans R Soc Lond B Biol Sci. 363:1529-1537.
66. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
67. Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics. 24:1540-1541.
68. Wilkinson M, Cotton JA. 2006. Supertree methods for building the tree of life: divide-and-conquer approaches to large phylogenetic problems. In: Hodkinson T, Parnell J, Waldren S, editors. Towards the tree of life: taxonomy and systematics of large and species rich taxa. Systematic Association special volume. CRC Press. p. 61-75.
69. Wolf YI, Rogozin IB, Koonin EV. 2004. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 14:29-36.
70. Yang Z. 2006. Computational molecular evolution. Oxford series in ecology and evolution. New York: Oxford University Press.
71. Zheng J, Rogozin IB, Koonin EV, Przytycka TM. 2007. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol. 24:2583-2592.
72. Zilversmit M, O'Grady P, Desalle R. 2002. Shallow genomics, phylogenetics, and evolution in the family Drosophilidae. Pac Symp Biocomput. 7:512-523.