Deriving the Genomic Tree of Life in the Presence of Horizontal Gene Transfer: Conditioned Reconstruction

Molecular Biology and Evolution

Volumn 21, Issue 4, 2004, Pages 681-690

  Lake, James A ^a,b   Rivera, Maria C ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Conditioned reconstruction; Conditioning genomes; Genome fusions; Horizontal gene transfer; Paralinear logdet distances; Tree of life

Indexed keywords

ARTICLE; ARTIFACT; GENE SEQUENCE; GENOME; HORIZONTAL GENE TRANSFER; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PROBABILITY; TAXON; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME; GENOMICS; SEQUENCE ALIGNMENT;

ANIMALIA; METAZOA; PROKARYOTA;

EID: 1842505237     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh061     Document Type: Article

References (30)

1. Baldauf, S. L., and J. D. Palmer. 1990. Evolutionary transfer of the chloroplast tufa gene to the nucleus. Nature 344:262-265.
2. Campbell, A. M. 2000. Lateral gene transfer in prokaryotes. Theoret. Popul. Biol. 57:71-77.
3. Charlebois, R. L., R. K. Singh, C. C.-Y. Chan-Weiher et al. (26 co-authors). 2000. Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome 43:116-136.
4. Dickerson, R. E. 1980. Structural conservatism in proteins over three billion years: cytochrome with a touch of collagen. Pp. 227-249 in R. Srinivasan, ed. Diffraction and related studies. Pergamon Press, Oxford and New York.
5. Doolittle, W. F. 1999a. Lateral genomics. Trends Genet. 15:M5-M8.
6. -. 1999b. Phylogenetic classification and the universal tree. Science 284:2124-2128.
7. Eisen, J. A. 2000. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr. Opin. Microbiol. 3:475-480.
8. Fitz-Gibbon, S. T., and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218-4222.
9. Gogarten, J. P., W. F. Doolittle, and J. G. Lawrence. 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19:2226-2238.
10. Gray, M. W., G. Burger, and B. F. Lang. 1999. Mitochondrial evolution. Science 283:1476-1481.
11. Gupta, R. S. 1998. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 62:1435-1491.
12. House, C. H., and S. T. Fitz-Gibbon. 2002. Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J. Mol. Evol. 54:539-547.
13. Karlin, S., J. Mrazek, and A. M. Campbell. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179:3899-3913.
14. Lake, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences-paralinear distances. Proc. Natl. Acad. Sci. USA 91:1455-1459.
15. -. 1995. Calculating the probability of multitaxon evolutionary trees-bootstrappers gambit. Proc. Natl. Acad. Sci. USA 92:9662-9666.
16. -. 1997. Phylogenetic inference: How much evolutionary history is knowable? Mol. Biol. Evol. 14:213-219.
17. -. 1998. Optimally recovering rate variation information from genomes and sequences: pattern filtering. Mol. Biol. Evol. 15:1224-1231.
18. Lake, J. A., E. Henderson, M. W. Clark, and A. T. Matheson. 1982. Mapping evolution with ribosome structure-intralineage constancy and inter-lineage variation. Proc. Natl. Acad. Sci. USA Biol. Sci. 79:5948-5952.
19. Lawrence, J. G. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
20. Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
21. Martin, W., and M. Muller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.
22. Montague, M. G., and C. A. Hutchison. 2000. Gene content phylogeny of herpesviruses. Proc. Natl. Acad. Sci. USA 97:5334-5339.
23. Ochman, H. 2001. Lateral and oblique gene transfer. Curr. Opin. Genet. Dev. 11:616-619.
24. Ochman, H., and I. B. Jones. 2000. Evolutionary dynamics of fall genome content in Escherichia coli. EMBO J. 19:6637-6643.
25. Rivera, M. C., R. Jain, J. E. Moore, and J. A. Lake. 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA 95:6239-6244.
26. Rivera, M. C., and J. A. Lake. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74-76.
27. Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-110.
28. Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quarter maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
29. Tekaia, F., A. Lazcano, and B. Dujon. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:550-557.
30. Woese, C. R. 1981. Archaebacteria. Sci. Am. 244:98-105.