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Volumn 17, Issue 1, 2000, Pages 32-43

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

Author keywords

Adaptive evolution; Approximate methods; Maximum likelihood; Molecular evolution; Nonsynonymous rate; Positive selection; Synonymous rate

Indexed keywords

ARTICLE; CODON; COMPUTER SIMULATION; DNA SEQUENCE; EVOLUTION; GENE FREQUENCY; HUMAN; INTERMETHOD COMPARISON; MAXIMUM LIKELIHOOD METHOD; MODEL; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE;

EID: 0033979433     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026236     Document Type: Article
Times cited : (1359)

References (40)
  • 1
    • 0028797897 scopus 로고
    • Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA
    • AKASHI, H. 1995. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139:1067-1076.
    • (1995) Genetics , vol.139 , pp. 1067-1076
    • Akashi, H.1
  • 2
    • 0029563023 scopus 로고
    • A method for estimating the numbers of synonymous and nonsynonymous substitutions per site
    • COMERON, J. M. 1995. A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J. Mol. Evol. 41:1152-1159.
    • (1995) J. Mol. Evol. , vol.41 , pp. 1152-1159
    • Comeron, J.M.1
  • 3
    • 0030992836 scopus 로고    scopus 로고
    • Rhodopsin evolution in the dark
    • CRANDALL, K. A., and D. M. HILLIS. 1997. Rhodopsin evolution in the dark. Nature 387:667-668.
    • (1997) Nature , vol.387 , pp. 667-668
    • Crandall, K.A.1    Hillis, D.M.2
  • 4
    • 0033611501 scopus 로고    scopus 로고
    • High genomic deleterious mutation rates in hominoids
    • EYRE-WALKER, A., and P. D. KEIGHTLEY. 1999. High genomic deleterious mutation rates in hominoids. Nature 397:344-347.
    • (1999) Nature , vol.397 , pp. 344-347
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 6
    • 0021070935 scopus 로고
    • Codon substitution in evolution and the "saturation" of synonymous changes
    • GOJOBORI, T. 1983. Codon substitution in evolution and the "saturation" of synonymous changes. Genetics 105:1011-1027.
    • (1983) Genetics , vol.105 , pp. 1011-1027
    • Gojobori, T.1
  • 7
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
    • (1993) J. Mol. Evol. , vol.36 , pp. 182-198
    • Goldman, N.1
  • 8
    • 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
    • 0022376704 scopus 로고
    • Dating the human-ape splitting by a molecular clock of mitochondrial DNA
    • HASEGAWA, M., H. KISHINO, and T. YANO. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 11
    • 0028906291 scopus 로고
    • New methods for estimating the numbers of synonymous and nonsynonymous substitutions
    • INA, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40:190-226.
    • (1995) J. Mol. Evol. , vol.40 , pp. 190-226
    • Ina, Y.1
  • 12
    • 21444438444 scopus 로고    scopus 로고
    • Pattern of synonymous and nonsynonymous substitutions: An indicator of mechanisms of molecular evolution
    • _. 1996. Pattern of synonymous and nonsynonymous substitutions: an indicator of mechanisms of molecular evolution. J. Genet. 75:91-115.
    • (1996) J. Genet. , vol.75 , pp. 91-115
  • 13
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H. N. MUNRO, ed. Academic Press, New York
    • JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 14
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 15
  • 16
    • 0028900746 scopus 로고
    • Positive selection is a general phenomenon in the evolution of abalone sperm lysin
    • LEE, Y. H., T. OTA, and V. D. VACQUIER. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12:231-238.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 231-238
    • Lee, Y.H.1    Ota, T.2    Vacquier, V.D.3
  • 17
    • 0024488925 scopus 로고
    • Inferring the number of evolutionary events from DNA coding sequence differences
    • LEWONTIN, R. 1989. Inferring the number of evolutionary events from DNA coding sequence differences. Mol. Biol. Evol. 6:15-32.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 15-32
    • Lewontin, R.1
  • 18
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and nonsynonymous substitution
    • LI, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
    • (1993) J. Mol. Evol. , vol.36 , pp. 96-99
    • Li, W.-H.1
  • 19
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer, Sunderland, Mass.
    • . 1997. Molecular evolution. Sinauer, Sunderland, Mass.
    • (1997) Molecular Evolution
  • 20
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and non-synonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes
    • LI, W.-H., C.-I. WU, and C.C. LUO. 1985. A new method for estimating synonymous and non-synonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 150-174
    • Li, W.-H.1    Wu, C.-I.2    Luo, C.C.3
  • 21
    • 0031033277 scopus 로고    scopus 로고
    • Episodic adaptive evolution of primate lysozymes
    • MESSIER, W., and C.-B. STEWART. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151-154.
    • (1997) Nature , vol.385 , pp. 151-154
    • Messier, W.1    Stewart, C.-B.2
  • 22
    • 0019134329 scopus 로고
    • Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applications
    • MIYATA, T., and T. YASUNAGA. 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applications. J. Mol. Evol. 16: 23-36.
    • (1980) J. Mol. Evol. , vol.16 , pp. 23-36
    • Miyata, T.1    Yasunaga, T.2
  • 23
    • 0030845166 scopus 로고    scopus 로고
    • Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes
    • MORIYAMA, E. N., and J. R. POWELL. 1997. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45:378-391.
    • (1997) J. Mol. Evol. , vol.45 , pp. 378-391
    • Moriyama, E.N.1    Powell, J.R.2
  • 24
    • 0030054305 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates
    • MUSE, S. V. 1996. Estimating synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 13:105-114.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 105-114
    • Muse, S.V.1
  • 25
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, will: Application to chloroplast genome
    • MUSE, S. V., and B. S. GAUT. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, will: 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
  • 26
    • 0022507362 scopus 로고
    • Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions
    • NEI, M., and T. GOJOBORI. 1986. Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 27
    • 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
  • 28
    • 0028955455 scopus 로고
    • Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory
    • OHTA, T. 1995. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 4056-63.
    • (1995) J. Mol. Evol. , vol.40 , pp. 56-63
    • Ohta, T.1
  • 29
    • 0028286120 scopus 로고
    • Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site
    • OTA, T., and M. NEI. 1994. Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Mol. Biol. Evol. 11:613-619.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 613-619
    • Ota, T.1    Nei, M.2
  • 30
    • 0027533924 scopus 로고
    • Evolution of the Zfx and Zfy genes - Rates and interdependence between the genes
    • 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.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 271-281
    • Pamilo, P.1    Bianchi, N.O.2
  • 31
    • 0031880125 scopus 로고    scopus 로고
    • A codon-based model designed to describe lentiviral evolution
    • PEDERSEN, A.-M. K., C. WIUF, and F. B. CHRISTIANSEN. 1998. A codon-based model designed to describe lentiviral evolution. Mol. Biol. Evol. 15:1069-1081.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1069-1081
    • Pedersen, A.-M.K.1    Wiuf, C.2    Christiansen, F.B.3
  • 34
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
    • TATENO, Y., N. TAKEZAKI, and M. NEI. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 261-277
    • Tateno, Y.1    Takezaki, N.2    Nei, M.3
  • 35
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • YANG, Z. 1994a. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
    • (1994) J. Mol. Evol. , vol.39 , pp. 105-111
    • Yang, Z.1
  • 36
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • _. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
  • 37
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • _. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 568-573
  • 39
    • 0031960185 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous rate variation in nuclear genes of mammals
    • YANG, Z., and R. NIELSEN. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46:409-418.
    • (1998) J. Mol. Evol. , vol.46 , pp. 409-418
    • Yang, Z.1    Nielsen, R.2
  • 40
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • YANG, Z., R. NIELSEN, and M. HASEGAWA. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Hasegawa, M.3


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