Bayesian estimation of positively selected sites

Journal of Molecular Evolution

Volumn 58, Issue 6, 2004, Pages 661-672

  Huelsenbeck, John P ^a   Dyer, Kelly A ^b  

^a University of California at San Diego   (United States)

^b UNIVERSITY OF ROCHESTER   (United States)

Author keywords

Bayesian estimation; Codon model; Hierarchical Bayes; Markov chain Monte Carlo

Indexed keywords

BETA GLOBIN; DNA;

ARTICLE; BAYES THEOREM; CODON; DATA ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; SUBSTITUTION REACTION;

ANIMALS; BAYES THEOREM; CODON; EVOLUTION, MOLECULAR; GLOBINS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; SELECTION (GENETICS); VERTEBRATES;

VERTEBRATA;

EID: 2942656772     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2588-9     Document Type: Article

References (17)

1. Berger JO (1985) Statistical decision theory and Bayesian analysis. Springer-Verlag, New York
2. Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368-376
3. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725-736
4. Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109
5. Huelsenbeck JH, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755
6. Hughes A, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals over-dominant selection. Nature 335:167-170
7. Larget B, Simon D (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750-759
8. Lee YH, Ota T, Vaquier V (1995) Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol Biol Evol 12:231-238
9. Messier W, Stewart CB (1997) Episodic adaptive evolution of primate lysozymes. Nature 385:151-154
10. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equations of state calculations by fast computing machines. J Chem Phys 21:1087-1091
11. Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol Biol Evol 11:715-724
12. Nielsen R (1997) The ratio of replacement to silent divergence and tests of neutrality. J Evol Biol 10:217-231
13. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
14. Ronquist F, Huelsenbeck JP (2003) MrBayes version 3.0: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
15. Tierney L (1994) Markov chains for exploring posterior distributions. Ann Stat 22:1701-1762
16. Yang Z, Nielsen R, Goldman N, Pedersen A (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
17. Yokoyama S, Yokoyama R (1996) Evolution of photoreceptor cells and visual pigments. Annu Rev Ecol Syst 27:543-567