Broad phylogenomic sampling improves resolution of the animal tree of life

Nature

Volumn 452, Issue 7188, 2008, Pages 745-749

  Dunn, Casey W ^a,l   Hejnol, Andreas ^a   Matus, David Q ^a   Pang, Kevin ^a   Browne, William E ^a   Smith, Stephen A ^b   Seaver, Elaine ^a   Rouse, Greg W ^c   Obst, Matthias ^d   Edgecombe, Gregory D ^e   Sørensen, Martin V ^f   Haddock, Steven H D ^g   Schmidt Rhaesa, Andreas ^h   Okusu, Akiko ⁱ   Kristensen, Reinhardt Møbjerg ^f   Wheeler, Ward C ^j   Martindale, Mark Q ^a   Giribet, Gonzalo ^k  

^a UNIVERSITY OF HAWAII   (United States)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d GÖTEBORG UNIVERSITY   (Sweden)

^e DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^f UNIVERSITY OF COPENHAGEN   (Denmark)

^g MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^h UNIVERSITY OF HAMBURG   (Germany)

ⁱ SIMMONS COLLEGE   (United States)

^j DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^k HARVARD UNIVERSITY   (United States)

^l BROWN UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANNELID; BIVALVE; EVOLUTION; GENE EXPRESSION; GENOMICS; MORPHOLOGY; NEMATODE; PHYLOGENY; SAMPLING; TREE;

ANIMAL GENETICS; ANNELID WORM; ARTHROPOD; ARTICLE; CLADISTICS; EXPRESSED SEQUENCE TAG; MOLECULAR EVOLUTION; MOLLUSC; MOLTING; MONOPHYLY; MORPHOLOGY; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PHYLUM; PRIORITY JOURNAL; SAMPLING;

ANIMALIA; ANNELIDA; ARTHROPODA; BRACHIOPODA; CTENOPHORA (COELENTERATES); ECDYSOZOA; ECHIURA; LOPHOTROCHOZOA; METAZOA; MOLLUSCA; NEMERTEA; ONYCHOPHORA; PHORONIFORMEA; PROTOSTOMIA; SIPUNCULIDA; TARDIGRADA;

EID: 42149157760     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature06614     Document Type: Article

References (41)

1. Giribet, G. Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion? Mol. Phylogenet. Evol. 24, 345-357 (2002).
2. Halanych, K. M. The new view of animal phylogeny. Ann. Rev. Ecol. Evol. Sys. 35, 229-256 (2004).
3. Aguinaldo, A. M. A. et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489-493 (1997).
4. Halanych, K. M. et al. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 267, 1641-1643 (1995).
5. Schmidt-Rhaesa, A. Tardigrades - Are they really miniaturized dwarfs? Zool. Anz. 240, 549-555 (2001).
6. Philippe, H. & Telford, M. J. Large-scale sequencing and the new animal phylogeny. Trends Ecol. Evol. 21, 614-620 (2006).
7. Bourlat, S. J. et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85-88 (2006).
8. Delsuc, F. et al. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965-968 (2006).
9. Philippe, H., Lartillot, N. & Brinkmann, H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22, 1246-1253 (2005).
10. Philippe, H. et al. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21, 1740-1752 (2004).
11. Lartillot, N. & Philippe, H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095-1109 (2004).
12. Philip, G. K., Creevey, C. J. & McInerney, J. O. 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 for the Coelomata than Ecdysozoa. Mol. Biol. Evol. 22, 1175-1184 (2005).
13. Rokas, A., Kruger, D. & Carroll, S. B. Animal evolution and the molecular signature of radiations compressed in time. Science 310, 1933-1938 (2005).
14. Baurain, D., Brinkmann, H. & Philippe, H. Lack of resolution in the animal phylogeny: closely spaced cladogenesis or undetected systematic errors? Mol. Biol. Evol. 24, 6-9 (2006).
15. Philippe, H. et al. Acoel flatworms are not Platyhelminthes: evidence from phylogenomics. PLoS One 2, e717 (2007).
16. Blair, J. E. et al. The evolutionary position of nematodes. BMC Evol. Biol. 2, 1-7 (2002).
17. Thorley, J. L. & Wilkinson, M. Testing the phylogenetic stability of early tetrapods. J. Theor. Biol. 200, 343-344 (1999).
18. Giribet, G., Distel, D. L., Polz, M., Sterrer, W. & Wheeler, W. C. Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology. Syst. Biol. 49, 539-562 (2000).
19. Telford, M. J., Wise, M. J. & Gowri-Shankar, V. Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the Bilateria. Mol. Biol. Evol. 22, 1129-1136 (2005).
20. Struck, T. H. et al. Annelid phylogeny and the status of Sipuncula and Echiura. BMC Evol. Biol. 7, 57 (2007).
21. Giribet, G. et al. Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons. Proc. Natl Acad. Sci. USA 103, 7723-7728 (2006).
22. Conway Morris, S. & Peel, J. S. Articulated Halkieriids from the Lower Cambrian of North Greenland and their role in early protostome evolution. Phil. Trans. R. Soc. Lond. B 347, 305-358 (1995).
23. Nielsen, C. Animal Evolution, Interrelationships of the Living Phyla 2nd edn (Oxford Univ. Press, Oxford, 2001).
24. Giribet, G., Edgecombe, G. D. & Wheeler, W. C. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157-161 (2001).
25. Mallatt, J. M., Garey, J. R. & Shultz, J. W. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31, 178-191 (2004).
26. Hwang, U. W. et al. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413, 154-157 (2001).
27. Freeman, G. & Martindale, M. Q. The origin of mesoderm in phoronids. Dev. Biol. 252, 301-311 (2002).
28. van Dongen, S. A cluster algorithm for graphs. National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam. Technical Report INS-R0010 (Stichting Mathematisch Centrum, Amsterdam, 2000).
29. Enright, A. J., Van Dongen, S. & Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584 (2002).
30. Smith, S. A.& Dunn, C. W. Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics doi:10.1093/bioinformatics/btm619 (2008).
31. Parkinson, J. et al. PartiGene - constructing partial genomes. Bioinformatics 20, 1398-1404 (2004).
32. Thompson, J. D., Higgins, D. G. & Gibson, T. J. 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 (1994).
33. Marchler-Bauer, A. et al. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33 (Database issue), D192-D196 (2005).
34. Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
35. van Dongen, S. Graph Clustering by Flow Simulation. PhD thesis, Univ. Utrecht (2000).
36. Swofford, D. L. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) Version 4 (Sinauer Associates, Sunderland, Massachusetts, 2003).
37. Edgar, R. C. & Journals, O. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
38. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552 (2000).
39. Roure, B., Rodriguez-Ezpeleta, N. & Philippe, H. SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics. BMC Evol. Biol. 7, S2 (2007).
40. Huelsenbeck, J. P. & Ronquist, F. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17, 754-755 (2001).
41. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).