A likelihood framework to analyse phyletic patterns

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 363, Issue 1512, 2008, Pages 3903-3911

  Cohen, Ofir ^a   Rubinstein, Nimrod D ^a   Stern, Adi ^a   Gophna, Uri ^a   Pupko, Tal ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Gene content; Gene gain and loss; Genome evolution; Horizontal gene transfer; Phyletic pattern; Probabilistic evolutionary models

Indexed keywords

EVOLUTION; GENOME; MARKOV CHAIN; PHYLOGENY; STOCHASTICITY;

EID: 57149086448     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2008.0177     Document Type: Article

References (33)

1. Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. 2006 Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287.
2. Doolittle, R. F., Feng, D. F., Anderson, K. L. & Alberro, M. R. 1990 A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote. J. Mol. Evol. 31, 383-388.
3. Felsenstein, J. 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
4. Felsenstein, J. 1992 Phylogenies from restriction sites: a maximum-likelihood approach. Evol. Int. J. Org. Evol. 46, 159-173.
5. Gogarten, J. P. & Townsend, J. P. 2005 Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3, 679-687.
6. Hao, W. & Golding, G. B. 2006 The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res. 16, 636-643.
7. Jain, R., Rivera, M. C. & Lake, J. A. 1999 Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801-3806.
8. Jain, R., Rivera, M. C., Moore, J. E. & Lake, J. A. 2003 Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol. 20, 1598-1602.
9. Koonin, E. V., Makarova, K. S. & Aravind, L. 2001 Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55, 709-742.
10. Lake, J. A. & Rivera, M. C. 2004 Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol. 21, 681-690.
11. Lawrence, J. G. & Roth, J. R. 1996 Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843-1860.
12. Lerat, E., Daubin, V., Ochman, H. & Moran, N. A. 2005 Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3, e130.
13. Marri, P. R., Hao, W. & Golding, G. B. 2007 The role of laterally transferred genes in adaptive evolution. BMC Evol. Biol. 7(Suppl. 1), S8.
14. Mayrose, I., Graur, D., Ben-Tal, N. & Pupko, T. 2004 Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol. 21, 1781-1791.
15. Mira, A., Klasson, L. & Andersson, S. G. 2002 Microbial genome evolution: sources of variability. Curr. Opin. Microbiol. 5, 506-512.
16. Mirkin, B. G., Fenner, T. I., Galperin, M. Y. & Koonin, E. V. 2003 Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3, 2.
17. Nelson, K. E. et al. 1999 Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329.
18. Ochman, H., Lawrence, J. G. & Groisman, E. A. 2000 Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304.
19. Pennisi, E. 2004 Microbiology. Researchers trade insights about gene swapping. Science 305, 334-335.
20. Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. 2002 RATE4SITE: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18(Suppl. 1), S71-S77.
21. Ross, S. M. 1996 Stochastic processes. New York, NY: Wiley.
22. Snel, B., Huynen, M. A. & Dutilh, B. E. 2005 Genome trees and the nature of genome evolution. Annu. Rev. Microbiol. 59, 191-209.
23. Spencer, M., Bryant, D. & Susko, E. 2007 Conditioned genome reconstruction: how to avoid choosing the conditioning genome. Syst. Biol. 56, 25-43.
24. Syvanen, M. 1994 Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28, 237-261.
25. Tatusov, R. L. et al. 2003 The COG database: an updated version includes eukaryotes. BMC Bioinform. 4, 41.
26. Thompson, J. R., Pacocha, S., Pharino, C., Klepac-Ceraj, V., Hunt, D. E., Benoit, J., Sarma-Rupavtarm, R., Distel, D. L. & Polz, M. F. 2005 Genotypic diversity within a natural coastal bacterioplankton population. Science 307, 1311-1313.
27. Wapinski, I., Pfeffer, A., Friedman, N. & Regev, A. 2007 Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54-61.
28. Yang, Z. 1993 Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10, 1396-1401.
29. Yang, Z. 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39, 306-314.
30. Yang, Z. 1995 A space-time process model for the evolution of DNA sequences. Genetics 139, 993-1005.
31. Yang, Z. & Nielsen, R. 2000 Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17, 32-43.
32. Yang, Z. & Wang, T. 1995 Mixed model analysis of DNA sequence evolution. Biometrics 51, 552-561.
33. Zhang, J., Nielsen, R. & Yang, Z. 2005 Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22, 2472-2479.