Response to Yang et al.: Problems with Bayesian methods of detecting positive selection at the DNA sequence level

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 36, 2009, Pages

  Nozawa, Masafumi ^a   Suzuki, Yoshiyuki ^a,b   Nei, Masatoshi ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RHODOPSIN;

ACCURACY; AMINO ACID SUBSTITUTION; BAYES THEOREM; CODON; COMPUTER SIMULATION; DNA SEQUENCE; FISHER EXACT TEST; GENE IDENTIFICATION; GENETIC LINE; GENETIC SELECTION; HUMAN; LETTER; NONHUMAN; PARSIMONY ANALYSIS; PRIORITY JOURNAL; PROTEIN FUNCTION;

EID: 70349308387     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0906089106     Document Type: Letter

References (7)

1. Yang Z, Nielsen R, Goldman N (2009) In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA, 10.1073/pnas0904550106.
2. 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.
3. Bakewell MA, Shi P, Zhang J (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104:7489-7494. (Pubitemid 47185933)
4. Zhang J, Kumar S, Nei M (1997) Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol Biol Evol 14:1335-1338.
5. Suzuki Y (2008) False-positive results obtained from the branch-site test of positive selection. Genes Genet Syst 83:331-338.
6. King JL, Jukes TH (1969) Non-Darwinian evolution. Science 164:788-798.
7. Yokoyama S, Tada T, Zhang H, Britt L (2008) Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci USA 105:13480-13485.