A genetic algorithm approach to detecting lineage-specific variation in selection pressure

Molecular Biology and Evolution

Volumn 22, Issue 3, 2005, Pages 478-485

  Kosakovsky Pond, Sergei L ^a   Frost, Simon D W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Branch site model; Codon substitution model; Genetic algorithms; Lineage specific selection; Model selection

Indexed keywords

LYSOZYME;

AMINO ACID SUBSTITUTION; ARTICLE; GENETIC ALGORITHM; GENETIC SELECTION; HOMINID; HUMAN; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MONKEY; MONTE CARLO METHOD; NONHUMAN; PHYLOGENETIC TREE; POPULATION SIZE; STOP CODON;

ALGORITHMS; AMINO ACID SUBSTITUTION; ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; PRIMATES; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 14544275616     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi031     Document Type: Article

References (23)

1. Abramowitz, M., and I. Stegun, eds. 1972. Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables, 9th printing. Dover, New York.
2. Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Automatic Control 119:716-723.
3. Akaike, H. 1983. Information measures and model selection. Int. Stat. Inst. 44:139-149.
4. Brauer, M. J., M. T. Holder, L. A. Dries, D. J. Zwickl, P. O. Lewis, and D. M. Hillis. 2002. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Mol. Biol. Evol. 19:1717-1726.
5. Burnham, K. P., and D. R. Anderson. 2003. Model Selection and Multimodel Inference, 2nd ed. Springer, New York.
6. Eshelman, L. 1991. Foga-1. Morgan Kaufmann, Los Atlos, Calif.
7. Goldman, N., and Z. H. Yang. 1994. Codon-based model of nucleotide substitution for protein-coding DNA-sequences. Mol. Biol. Evol. 11:725-736.
8. Katoh, K., K. Kuma, and T. Miyata. 2001. Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J. Mol. Evol. 53:477-484.
9. Kim, Y. H., S. K. Lee, and B. R. Moon. 2003. Optimizing the order of taxon addition in phylogenetic tree construction using genetic algorithm. Genetic and Evolutionary Computation - Gecco 2003, Pt Ii, Proceedings 2724:2168-2178.
10. Kosakovsky Pond, S., S. D. W. Frost, and S. V. Muse. 2000. HyPhy: hypothesis testing using phylogenies, Bioinformatics Advance Access published on October 27, 2004, doi:10.1093/bioinformatics/bti079.
11. Kullback, S., and R. Liebler. 1951. On information and sufficiency. Ann. Math. Stat. 22:79-86.
12. Lemmon, A. R., and M. C. Milinkovitch. 2002. The metapopulation genetic algorithm: an efficient solution for the problem of phylogeny estimation. Proc. Natl. Acad. Sci. USA 99: 10516-10521.
13. Lewis, P. O. 1998. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol. 15:277-283.
14. Messier, W., and C. B. Stewart. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151-154.
15. Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
16. Schwarz, G. 1978. Estimating the dimension of a model. Ann. Stat. 6:461-464.
17. Shen, J., and R. B. Heckendorn. 2004. Discrete branch length representations for genetic algorithms in phylogenetic search. Appl. Evol. Comput. 3005:94-103.
18. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
19. Sugiura, N. 1978. Further analysis of the data by Akaike's information criterion and the finite corrections. Commun. Stat. Theory Methods A7:13-26.
20. Whitley, D. 2001. An overview of evolutionary algorithms: practical issues and common pitfalls. J. Inf. Software Technol. 43:817-831.
21. Yang, Z. H. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.
22. Yang, Z. H., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
23. Yang, Z. H., R. Nielsen, N. Goldman, and A. M. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.