Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

Genetics

Volumn 148, Issue 3, 1998, Pages 929-936

  Nielsen, Rasmus ^a,c   Yang, Ziheng ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CODON; DNA FLANKING REGION; ENVELOPE GENE; HUMAN IMMUNODEFICIENCY VIRUS 1; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; VIRUS GENE;

AMINO ACIDS; BINDING SITES; CODON; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; HIV ENVELOPE PROTEIN GP120; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; MUTAGENESIS, SITE-DIRECTED; PEPTIDE FRAGMENTS; SELECTION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0031972161     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (24)

1. BOENHOEFFER, S., E. C. HOLMES and M. A. NOWAK, 1995 Causes of HIV diversity. Nature 376: 125.
2. CUMMINGS, M. P., S. P. OTTO and J. WAKELEY, 1995 Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12: 814-822.
3. GILLESPIE, J. H., 1991 The causes of molecular evolution. Oxford University Press, Oxford.
4. GOLDMAN, N., and Z. YANG, 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
5. HOLMES, E. C., L. Q. ZHANG, P. SIMMONDS, C. A. LUDLAM and A. J. L. BROWN, 1992 Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. USA 89: 4835-4839.
6. HUGHES, A. L., and M. NEI, 1988 Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-70.
7. INA, Y., 1995 New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40: 190-226.
8. JONES, D. T., W. R. TAYLOR and J. M. THORNTON, 1992 The rapid generation of mutation data matrices from protein sequences. CABIOS 8: 275-282.
9. KIMURA, M., 1968 Evolutionary rate at the molecular level. Nature 217: 624-626.
10. LEE, Y. H., T. OTA and V. D. VACQUIER, 1995 Positive selection is a general phenonemon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12: 231-238.
11. LI, W.-H., C.-I. WU and C.-C. LUO, 1985 A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
12. MESSIER, W., and C.-B. STEWART, 1997 Episodic adaptive evolution of primate lysozymes. Nature 385: 151-154.
13. MINDELL, D. P., 1996 Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees. Proc. Natl. Acad. Sci. USA 93: 3284-3288.
14. NEI, M., and T. GOJOBORI, 1986 Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
15. NIELSEN, R., 1997 The ratio of replacement to silent divergence and tests of neutrality. J. Evol. Biol. 10: 217-231.
16. OHTA, T., 1973 Slightly deleterious mutant substitutions in evolution. Nature. 246: 96-98.
17. WILLEY, R. L., R. A.. RUTLEDGE, S. DIAS, T. FOLKS, T. THEODORE et al., 1986 Identification of conserved and divergent domains within the envelope gene of the acquired immunodeficiency syndrome virus. Proc. Natl. Acad. Sci. USA 83: 5038-5042.
18. YANG, Z., 1993 Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 39: 105-111.
19. YANG, Z., 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-314.
20. YANG, Z., 1995 A space-time process model for the evolution of DNA sequences. Genetics 139: 993-1005.
21. YANG, Z, 1997 Phylogenetic analysis by maximum likelihood (PAML), Version 1.3. University of California, Berkeley, California, USA.
22. YANG, Z., N. GOLDMAN and A. E. FRIDAY, 1994 Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Mol. Biol. Evol. 11: 316-324.
23. YAMAGUCHI, Y., and T. GOJOBORI, 1997 Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc. Natl. Acad. Sci. USA 94: 1264-1269.
24. YOKOYAMA, S., and R. YOKOYAMA, 1996 Adaptive evolution of photoreceptors and visual pigments in vertebrates. Ann. Rev. Ecol. Syst. 27: 543-567.