Phylogenetics and the cohesion of bacterial genomes

Science

Volumn 301, Issue 5634, 2003, Pages 829-832

  Daubin, Vincent ^a   Moran, Nancy A ^a   Ochman, Howard ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; ECOLOGY; GENE TRANSFER;

COHESION;

GENES;

BACTERIUM; GENE TRANSFER; GENOME; PHYLOGENETICS;

ADAPTATION; ARTICLE; BACTERIAL GENOME; GENE DISRUPTION; GENE SEQUENCE; GENE TRANSFER; MOLECULAR INTERACTION; NONHUMAN; ORTHOLOGY; PHYLOGENY; PRIORITY JOURNAL;

BACTERIA; CHLAMYDOPHILA PNEUMONIAE; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; EVOLUTION; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENES, RRNA; GENOME, BACTERIAL; LIKELIHOOD FUNCTIONS; PHYLOGENY; RECOMBINATION, GENETIC; RNA, BACTERIAL; RNA, RIBOSOMAL; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0042027842     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1086568     Document Type: Article

References (30)

1. H. Ochman, J. G. Lawrence, E. A. Groisman, Nature 405, 299 (2000).
2. J. R. Brown, W. F. Doolittle, Microbiol. Mol. Biol. Rev. 61, 456 (1997).
3. R. Jain, M. C. Rivera, J. A. Lake, Proc. Natl. Acad. Sci. U.S.A. 96, 3801 (1999).
4. C. L. Nesbo, Y. Boucher, W. F. Doolittle, J. Mol. Evol. 53, 340 (2001).
5. O. Zhaxybayeva, J. P. Gogarten, BMC Genomics 3, 4 (2002).
6. J. Raymond, O. Zhaxybayeva, J. P. Gogarten, S. Y. Gerdes, R. E. Blankenship, Science 298, 1616 (2002).
7. W. F. Doolittle, Science 284, 2124 (1999).
8. M. C. Rivera, R. Jain, J. E. Moore, J. A. Lake, Proc. Natl. Acad. Sci. U.S.A. 95, 6239 (1998).
9. W. F. Doolittle, Trends Cell Biol. 9, M5 (1999).
10. J. P. Gogarten, W. F. Doolittle, J. G. Lawrence, Mol. Biol. Evol. 19, 2226 (2002).
11. D. Graur, W. A. Hide, W.-H. Li, Nature 351, 649 (1991).
12. D. Huchon et al., Mol. Biol. Evol. 19, 1053 (2002).
13. S. B. Hedges, L. L. Poling, Science 283, 998 (1999).
14. S. Hughes, D. Mouchiroud, J. Mol. Evol. 53, 70 (2001).
15. A. R. Mushegian, E. V. Koonin, Proc. Natl. Acad. Sci. U.S.A. 93, 10268 (1996).
16. L B. Koski, G. B. Golding, J. Mol. Evol. 52, 540 (2001).
17. H. Shimodaira, M. Hasegawa, Mol. Biol. Evol. 16, 1114 (1999).
18. K. Strimmer, A. von Haeseler, Mol. Biol. Evol. 13, 964 (1996).
19. For each set of orthologs, both nucleotide and amino acid alignments were evaluated. Both methods yielded very similar results, and only the results based on nucleotide sequences are presented. Specifically, the protein alignments did not yield significantly smaller numbers of nonresolving or LGT topologies. The more permissive (17) Kishino-Hasegawa test, either two-sided (28) or one-sided (29), produced very similar results.
20. K. L. Millman, S. Tavare, D. Dean, J. Bacteriol. 183, 5997 (2001).
21. D. S. Guttman, D. E. Dykhuizen, Science 266, 1380 (1994).
22. D. E. Dykhuizen, L. Green, J. Bacteriol. 173, 7257 (1991).
23. H. Philippe, E. Douzery, J. Mamm. Evol. 2, 133 (1994).
24. J. Adachi, M. Hasegawa, Mol. Phylogenet. Evol. 6, 72 (1996).
25. S. F. Altschul et al., Nucleic Acids Res. 25, 3389 (1997).
26. A protein was considered absent from a genome when it had no match >10% of the bit score of the protein against itself. A protein was considered present in a genome when it had a match >50% of the bit score of the protein against itself, based on the BLOSUM62 matrix. Losses estimate the probability that a gene present in the common ancestor of the three taxa (ABC) was lost in one. Because gene gains greatly outnumber gene losses in all quartets (except B. aphidicola), the probability of overestimating gene acquisition, due to independent loss by two taxa, is very low.
27. J. G. Lawrence, H. Ochman, Proc. Natl. Acad. Sci. U.S.A. 95, 9413 (1998).
28. H. Kishino, M. Hasegawa, J. Mol. Evol. 29, 170 (1989).
29. N. Goldman, J. P. Anderson, A. G. Rodrigo, Syst. Biol. 49, 652 (2000).
30. We thank S. Santos, E. Lerat, and two anonymous reviewers for comments. This research was supported by U.S. Department of Energy grant DEFG0301ER63147 (H.O.).