Performance of standard and stochastic branch-site models for detecting positive selection among coding sequences

Molecular Biology and Evolution

Volumn 31, Issue 2, 2014, Pages 484-495

  Lu, Ashley ^a,b   Guindon, Stéphane ^a,c  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

^c LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRANCH SITE MODEL; CLADISTICS; CODON; GENE FREQUENCY; GENETIC SELECTION; GENETIC VARIABILITY; NATURAL SELECTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SIMULATION; STOCHASTIC MODEL;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; OPEN READING FRAMES; SELECTION, GENETIC; SENSITIVITY AND SPECIFICITY;

EID: 84893152258     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst198     Document Type: Article

References (23)

1. Anisimova M, Bielawski J, Yang Z. 2001. The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Mol Biol Evol. 18:1585-1592.
2. Anisimova M, Yang Z. 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol. 24:1219-1228.
3. Fletcher W, Yang Z. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol. 27:2257-2267.
4. Gascuel O, Guindon S. 2007. Modelling the variability of evolutionary processes. In: Gascuel O, Steel M, editors. Reconstructing evolution: new mathematical and computational advances. Oxford: Oxford University Press. p. 65-99.
5. Gharib WH, Robinson-Rechavi M. 2013. The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol. 30: 1675-1686.
6. Guindon S, Rodrigo A, Dyer K, Huelsenbeck J. 2004. Modeling the sitespecific variation of selection patterns along lineages. Proc Natl Acad Sci USA 101:12957-12962.
7. Kosakovsky Pond S, Frost S. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22:1208-1222.
8. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K. 2011. A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol. 28:3033-3043.
9. Massingham T, Goldman N. 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753-1762.
10. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Pond SLK. 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 8:e1002764.
11. Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and application to the HIV-1 envelope gene. Genetics 148:929-936.
12. Nozawa M, Suzuki Y, Nei M. 2009. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA 106:6700-6705.
13. Self S, Liang K. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J Am Stat Assoc. 82:605-610.
14. Shan H, Zahn L, Guindon S, Wall P, Kong H, Ma H, DePamphilis C, Leebens-Mack J. 2009. Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Mol Biol Evol. 26:2229-2244.
15. Suzuki Y. 2008. False-positive results obtained from the branch-site test of positive selection. Genes Genet Syst. 83:331-338.
16. Yang Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 15: 568-573.
17. Yang Z. 2006. Computational molecular evolution. Vol. 284. Oxford: Oxford University Press.
18. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
19. Yang Z, dos Reis M. 2011. Statistical properties of the branch-site test of positive selection. Mol Biol Evol. 28:1217-1228.
20. Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 19:908-917.
21. Yang Z, Swanson W, Vacquier V. 2000. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites.Mol Biol Evol. 17:1446-1455.
22. Yang Z, Wong W, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22: 1107-1118.
23. 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.