Toward automatic reconstruction of a highly resolved tree of life

Science

Volumn 311, Issue 5765, 2006, Pages 1283-1287

  Ciccarelli, Francesca D ^a,b,c   Doerks, Tobias ^a   Von Mering, Christian ^a   Creevey, Christopher J ^a   Snel, Berend ^d   Bork, Peer ^a,e  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

^c FIRC INSTITUTE OF MOLECULAR ONCOLOGY   (Italy)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^e MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; GENE TRANSFER; GENES; THERMOPHORESIS;

AUTOMATABLE PROCEDURE; BRANCH LENGTHS; COMMON ANCESTOR; INTERDOMAIN DISCREPANCIES; ORTHOLOGS; PHYLOGENETIC RESOLUTION; TAXONOMIC CLASSIFICATION;

BIODIVERSITY;

EVOLUTION; PHYLOGENY; TAXONOMY;

ARTICLE; AUTOMATION; GENE SEQUENCE; GENE TRANSFER; GENOME; GRAM POSITIVE BACTERIUM; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLUM; PRIORITY JOURNAL; PROTEOBACTERIA;

AMINO ACYL-TRNA SYNTHETASES; ANIMALS; ARCHAEA; BACTERIA; COMPUTATIONAL BIOLOGY; EUKARYOTIC CELLS; EVOLUTION; GENE TRANSFER, HORIZONTAL; GENOME; INVERTEBRATES; PHYLOGENY; PLANTS; PROTEIN BIOSYNTHESIS; RIBOSOMAL PROTEINS; VERTEBRATES;

DELTAPROTEOBACTERIA; POSIBACTERIA;

EID: 33644700003     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1123061     Document Type: Article

References (31)

1. F. Delsuc et al., Nat. Rev. Genet. 6, 361 (2005).
2. W. F. Doolittle, Science 284, 2124 (1999).
3. J. P. Gogarten et al., Mol. Biol. Evol. 19, 2226 (2002).
4. J. R. Brown et al., Nat. Genet. 28, 281 (2001).
5. D. M. Hillis et al., Syst. Biol. 52, 124 (2003).
6. H. Philippe, C. J. Douady, Curr. Opin. Microbiol. 6, 498 (2003).
7. V. Daubin, N. A. Moran, H. Ochman, Science 301, 829 (2003).
8. Materials and methods are available on Science Online.
9. R. Jain et al., Proc. Natl. Acad. Sci. U.S.A. 96, 3801 (1999).
10. E. V. Koonin et al., Trends Genet. 12, 334 (1996).
11. C. G. Kurland, S. G. E. Andersson, Microbiol. Mol. Biol. Rev. 64, 786 (2000).
12. Y. I. Wolf et al., Genome Res. 9, 689 (1999).
13. C. Brochier et al., Trends Genet. 16, 529 (2000).
14. A detailed version of the tree in Fig. 2, including bootstrap support values and branch lengths, is available at www.bork.embl.de/tree_of_life/.
15. A. L. Koch, Trends Microbiol. 11, 166 (2003).
16. F. Raible et al., Science 310, 1325 (2005).
17. P. Hugenholtz et al., J. Bacteriol. 180, 4765 (1998).
18. D. Honda et al., J. Mol. Evol. 48, 723 (1999).
19. K. W. Nägeli, Allg. Schweiz. Ges. Gesammten Naturwiss. 10, 45 (1849).
20. C. Brochier et al., Genome Biol. 6, R42 (2005).
21. A. Adoutte et al., Proc. Natl. Acad. Sci. U.S.A. 97, 4453 (2000).
22. K. M. Halanych, Annu. Rev. Ecol. Evol. Syst. 35, 229 (2004).
23. H. Philippe et al., Mol. Biol. Evol. 22, 1246 (2005).
24. G. K. Philip et al., Mol. Biol. Evol. 22, 1175 (2005).
25. J. Felsenstein, Syst. Zool. 27, 401 (1978).
26. D. P. Kreil, C. A. Ouzounis, Nucleic Acids Res. 29, 1608 (2001).
27. K. T. Konstantinidis, J. M. Tiedje, J. Bacteriol. 187, 6258 (2005).
28. N. A. Moran, Proc. Natl. Acad. Sci. U.S.A. 93, 2873 (1996).
29. S. G. E. Andersson, C. G. Kurland, Trends Microbiol. 6, 263 (1998).
30. D. E. Wildman et al., Proc. Natl. Acad. Sci. U.S.A. 100, 7181 (2003).
31. We thank S. Hooper for help in designing trees and are grateful to members of the Bork group as well as T. Gibson, M. Gouy, M. Huynen, A. Budd, and M. Wolf for stimulating discussions. This work was supported in part by Bundesministerium fuer Bildung und Forschung (Nationales Genomforschungsnetz grant 01GR04S4 to P.B.) and by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek.