Not so different after all: A comparison of methods for detecting amino acid sites under selection

Molecular Biology and Evolution

Volumn 22, Issue 5, 2005, Pages 1208-1222

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

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Codon substitution models; Parallel algorithms; Positive and negative selection; Substitution rates

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID SUBSTITUTION; ARTICLE; BAYES THEOREM; ENVELOPE GENE; HUMAN IMMUNODEFICIENCY VIRUS 1; MATHEMATICAL ANALYSIS; MAXIMUM LIKELIHOOD METHOD; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; STRUCTURAL GENE;

AMINO ACIDS; CODON; EVOLUTION, MOLECULAR; GENES, POL; HIV ENVELOPE PROTEIN GP120; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; PHYLOGENY; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 17744396121     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi105     Document Type: Article

References (57)

1. Anisimova, M., J. P. Bielawski, and Z. Yang. 2001. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18(8):1585-1592.
2. _. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19(6):950-958.
3. Comeron, J. M. 1995. A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J. Mol. Evol. 41:1152-1159.
4. Deng, H. W., and Y. X. Fu. 1996. The effects of variable mutation rates across sites on the phylogenetic estimation of effective population size or mutation rate of DNA sequences. Genetics 144:1271-1281.
5. Durrett, R. 2005. Mathematical flaws in Suzuki and Gojobori's test for selection. Mol. Biol. Evol. (in press).
6. Fay, J. C., and C. I. Wu. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
7. Felsenstein, J. 1981. Evolutionary trees from DNA-sequences - a maximum-likelihood approach. J. Mol. Evol. 17:368-376.
8. Fitzgibbon, J., R. Howell, T. Schwartzer, D. Gocke, and D. Dubin. 1991. In vivo prevalence of azidothymidine (AZT) resistance mutations in an AIDS patient before and after AZT therapy. AIDS Res. Hum. Retroviruses 7(3):265-269.
9. Fu, Y. X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925.
10. Fu, Y. X., and W. H. Li. 1993a. Maximum-likelihood-estimation of population parameters. Genetics 134:1261-1270.
11. _. 1993b. Statistical tests of neutrality of mutations. Genetics 133:693-709.
12. Goldman, N., and Z. H. Yang. 1994. Codon-based model of nucleotide substitution for protein-coding DNA-sequences. Mol. Biol. Evol. 11:725-736.
13. Green, D. M., and J. A. Swets. 1966. Signal detection theory and psychophysics. John Wiley and Sons, New York.
14. Huelsenbeck, J. P., and K. A. Dyer. 2004. Bayesian estimation of positively selected sites. J. Mol. Evol. 58:661-672.
15. Huelsenbeck, J. P., B. Larget, and M. E. Alfaro. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21(6):1123-1133.
16. Kosakovsky Pond, S. L., and S. D. W. Frost. 2005a. A simple hierarchical approach to modeling distributions of substitution rates. Mol. Biol. Evol. 22(2):223-234.
17. Kosakovsky Pond S. L., and S. D. W. Frost. 2005b. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. Advance Access published February 15, 2005, doi:10.1093/ bioinformatics/bti320.
18. Kosakovsky Pond, S. L., and S. V. Muse. 2005. Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. (in press).
19. Kosakovsky Pond, S. L., S. D. W. Frost, and S. V. Muse. 2005. HyPhy: hypothesis testing using phytogenies. Bioinform 21:676-679.
20. Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
21. Larder, B., and S. Kemp. 1989. Multiple mutations in HIV-1 reverse transcriptase confer high-level resistance to zidovudine (AZT). Science 246(4934):1155-1158.
22. Leitner, T., and J. Albert. 1999. The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc. Natl. Acad. Sci. USA 96:10752-10757.
23. Leitner, T., S. Kumar, and J. Albert. 1997. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71:4761-4770.
24. Li, W. H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
25. Li, W. H., C. I. Wu, and C. C. Luo. 1985. A new method for estimatingsynonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
26. Misawa, K., and F. Tajima. 1997. Estimation of the amount of DNA polymorphism when the neutral mutation rate varies among sites. Genetics 147:1959-1964.
27. Muse, S. V. 1999. Modeling the molecular evolution of HIV sequences. Pp. 122-152 in K. A. Crandall, ed. The evolution of HIV. The Johns Hopkins University Press, Baltimore, Md.
28. 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.
29. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
30. Nielsen, R. 1997. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst. Biol. 46(2):346-353.
31. _. 2002. Mapping mutations on phytogenies. Syst. Biol. 51(5):729-739.
32. Nielsen, R., and J. Huelsenbeck. 2002. Detecting positively selected amino acid sites using posterior predictive p-values. Pac. Symp. Biocomput. 7:576-588.
33. Nielsen, R., and Z. H. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
34. Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48:612-622.
35. Pamilo, P., and N. O. Bianchi. 1993. Evolution of the zfx and zfy genes - rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281.
36. Pupko, T., I. Pe'er, R. Shamir, and D. Graur. 2000. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol. 17:890-896.
37. Rodriguez, F., J. L. Oliver, A. Marin, and J. R. Medina. 1990. The general stochastic-model of nucleotide substitution. J. Theor. Biol. 142:485-501.
38. Saitou, N., and M. Nei. 1987. The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
39. Sankoff, D. 1975. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28:35-42.
40. Sorhannus, U. 2003. The effect of positive selection on a sexual reproduction gene in Thalassiosira weissflogii (Bacillariophyta): results obtained from maximum-likelihood and parsimony-based methods. Mol. Biol. Evol. 20:1326-1328.
41. Suzuki, Y. 2004. New methods for detecting positive selection at single amino acid sites. J. Mol. Evol. 59:11-19.
42. Suzuki, Y., and T. Gojobori. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315-1328.
43. Suzuki, Y., and M. Nei. 2001. Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 18:2179-2185.
44. _. 2002. Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 19(11):1865-1869.
45. _. 2004. False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol. Biol. Evol. 21(5):914-921.
46. Tajima, F. 1989. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
47. _. 1996. The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics 143:1457-1465.
48. Tamura, K., and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
49. Tavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
50. Winters, M., and T. Merigan. 2001. Variants other than aspartic acid at codon 69 of the human immunodeficiency virus type 1 reverse transcriptase gene affect susceptibility to nucleoside analogs. Antimicrob. Agents Chemother. 45(8):2276-2279.
51. Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168(2):1041-1051.
52. Yang, Z. 2000. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51:423-432.
53. Yang, Z., S. Kumar, and M. Nei. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
54. Yang, Z., and W. Swanson. 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19(1):49-57.
55. Yang, Z. H. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
56. Yang, Z. H., and R. Nielsen. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.
57. 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.