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Volumn 20, Issue 8, 2003, Pages 1231-1239

Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA

Author keywords

dN dS; Maximum likelihood; Mitochondrial DNA; Neutral theory; Positive selection; Selection coefficients

Indexed keywords

MITOCHONDRIAL DNA; VIRUS DNA;

EID: 0042354654     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg147     Document Type: Article
Times cited : (129)

References (33)
  • 1
    • 0032736987 scopus 로고    scopus 로고
    • Positive selection on the H3 hemagglutinin gene of human influenza virus A
    • Bush, R. M., W. M. Fitch, C. A. Bender, and N. J. Cox. 1999. Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol. Biol. Evol. 16:1457-1465.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1457-1465
    • Bush, R.M.1    Fitch, W.M.2    Bender, C.A.3    Cox, N.J.4
  • 3
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
    • Halpern, A. L., and W. J. Bruno. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol. 15:910-917.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 4
    • 0034924997 scopus 로고    scopus 로고
    • Positive and negative selection on the human genome
    • Fay, J. C., G. J. Wyckoff, and C.-I. Wu. 2001. Positive and negative selection on the human genome. Genetics 158:1227-1234.
    • (2001) Genetics , vol.158 , pp. 1227-1234
    • Fay, J.C.1    Wyckoff, G.J.2    Wu, C.-I.3
  • 5
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 6
    • 0001122789 scopus 로고
    • The distribution of gene ratios for rare mutations
    • Fisher, R. A. 1930a. The distribution of gene ratios for rare mutations. Proc. R. Soc. Edinb. Sect. B 50:204-219.
    • (1930) Proc. R. Soc. Edinb. Sect. B , vol.50 , pp. 204-219
    • Fisher, R.A.1
  • 9
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 10
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • P. H. Harvey and L. Partridge, eds. Oxford University Press, New York
    • Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pp. 1-44 in P. H. Harvey and L. Partridge, eds. Oxford surveys in evolutionary biology. Vol. 7. Oxford University Press, New York.
    • (1990) Oxford Surveys in Evolutionary Biology , vol.7 , pp. 1-44
    • Hudson, R.R.1
  • 11
    • 0023339852 scopus 로고
    • A test of neutral molecular evolution based on nucleotide data
    • Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
    • (1987) Genetics , vol.116 , pp. 153-159
    • Hudson, R.R.1    Kreitman, M.2    Aguadé, M.3
  • 12
    • 0028072361 scopus 로고
    • The distribution of mutation effects of viability in Drosophila melanogaster
    • Keightley, P. D. 1994. The distribution of mutation effects of viability in Drosophila melanogaster. Genetics 138:1315-1322.
    • (1994) Genetics , vol.138 , pp. 1315-1322
    • Keightley, P.D.1
  • 13
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura, M. 1962. On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
    • (1962) Genetics , vol.47 , pp. 713-719
    • Kimura, M.1
  • 14
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • -. 1968. Evolutionary rate at the molecular level. Nature 217:624-626.
    • (1968) Nature , vol.217 , pp. 624-626
  • 15
    • 0042545546 scopus 로고
    • Model of effectively neutral mutations in which selective constraint is incorporated
    • -. 1979. Model of effectively neutral mutations in which selective constraint is incorporated. Proc. Natl. Acad. Sci. USA 75:1934-1937.
    • (1979) Proc. Natl. Acad. Sci. USA , vol.75 , pp. 1934-1937
  • 18
    • 78651159254 scopus 로고
    • The genetic structure of natural populations of Drosophila melanogaster. I. Spontaneous mutation rate of polygenes controlling viability
    • Mukai, T. 1964. The genetic structure of natural populations of Drosophila melanogaster. I. Spontaneous mutation rate of polygenes controlling viability. Genetics 50:1-19.
    • (1964) Genetics , vol.50 , pp. 1-19
    • Mukai, T.1
  • 19
    • 0015405272 scopus 로고
    • Mutation rate and dominance of genes affecting viability in Drosophila melanogaster
    • Mukai, T., S. I. Chigusa, L. E. Metler, and J. F. Crow. 1972. Mutation rate and dominance of genes affecting viability in Drosophila melanogaster. Genetics 72:333-355.
    • (1972) Genetics , vol.72 , pp. 333-355
    • Mukai, T.1    Chigusa, S.I.2    Metler, L.E.3    Crow, J.F.4
  • 20
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to chloroplast genome
    • Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to chloroplast genome. Mol. Biol. Evol. 11:715-724.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 22
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 24
    • 0015722319 scopus 로고
    • Slightly deleterious mutant substitutions in evolution
    • Ohta, T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98.
    • (1973) Nature , vol.246 , pp. 96-98
    • Ohta, T.1
  • 25
    • 0027020232 scopus 로고
    • The nearly neutral theory of molecular evolution
    • -. 1992. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23:263-286.
    • (1992) Annu. Rev. Ecol. Syst. , vol.23 , pp. 263-286
  • 26
    • 0026460082 scopus 로고
    • Population genetics of polymorphism and divergence
    • Sawyer, S., and D. Hartl. 1992. Population genetics of polymorphism and divergence. Genetics 132:1161-1176.
    • (1992) Genetics , vol.132 , pp. 1161-1176
    • Sawyer, S.1    Hartl, D.2
  • 27
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 28
    • 0033995286 scopus 로고    scopus 로고
    • Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes
    • Yamaguchi-Kabata, Y., and T. Gojobori. 2000. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J. Virol. 74:4335-4350.
    • (2000) J. Virol. , vol.74 , pp. 4335-4350
    • Yamaguchi-Kabata, Y.1    Gojobori, T.2
  • 29
    • 0033692959 scopus 로고    scopus 로고
    • Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A
    • 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.
    • (2000) J. Mol. Evol. , vol.51 , pp. 423-432
    • Yang, Z.1
  • 30
    • 0035221557 scopus 로고    scopus 로고
    • Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene
    • -. 2001. Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pacific Symp. Biocomp. 2001:226-237.
    • (2001) Pacific Symp. Biocomp. , vol.2001 , pp. 226-237
  • 31
    • 0036270185 scopus 로고    scopus 로고
    • Codon substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang, Z., and R. Nielsen. 2002. Codon substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 32
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for variable selection pressure at amino acid sites
    • Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000. Codon-substitution models for variable selection pressure at amino acid sites. Genetics 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.K.4
  • 33
    • 0033933640 scopus 로고    scopus 로고
    • Estimation of primate speciation dates using local molecular clocks
    • Yoder, A. D., and Z. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1081-1090
    • Yoder, A.D.1    Yang, Z.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.