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Volumn 165, Issue 3, 2003, Pages 1587-1597

The Problem of Counting Sites in the Estimation of the Synonymous and Nonsynonymous Substitution Rates: Implications for the Correlation between the Synonymous Substitution Rate and Codon Usage Bias

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CALCULATION; CODON USAGE; CORRELATION ANALYSIS; DNA BASE COMPOSITION; DROSOPHILA; GOLDMAN YANG METHOD; MAMMAL; MOLECULAR EVOLUTION; MUTATION RATE; MUTATIONAL OPPORTUNITY; NONHUMAN; NONSYNONYMOUS SUBSTITUTION RATE; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; SYNONYMOUS SUBSTITUTION RATE;

EID: 0346991738     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (73)

References (38)
  • 1
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogasler: Natural selection and translational accuracy
    • AKASHI, H., 1994 Synonymous codon usage in Drosophila melanogasler: natural selection and translational accuracy. Genetics 136: 927-935.
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 2
    • 0029082357 scopus 로고
    • Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure
    • BERG, O. G., and M. MARTELIUS, 1995 Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure. J. Mol. Evol. 41: 449-456.
    • (1995) J. Mol. Evol. , vol.41 , pp. 449-456
    • Berg, O.G.1    Martelius, M.2
  • 3
    • 0027428828 scopus 로고
    • Silent substitutions in mammalian genomes and their evolutionary implications
    • BERNARD G., D. MOUCHROUD and C. GAUTHIER, 1993 Silent substitutions in mammalian genomes and their evolutionary implications. J. Mol. Evol. 37: 583-589.
    • (1993) J. Mol. Evol. , vol.37 , pp. 583-589
    • Bernard, G.1    Mouchroud, D.2    Gauthier, C.3
  • 4
    • 0037108764 scopus 로고    scopus 로고
    • Linkage limits the power of natural selection in Drosophila
    • BETANCOUR, A. J., and D. C. PRESGRAVES, 2002 Linkage limits the power of natural selection in Drosophila. Proc. Natl. Acad. Sci. USA 99: 13616-13620.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 13616-13620
    • Betancour, A.J.1    Presgraves, D.C.2
  • 5
    • 0033762460 scopus 로고    scopus 로고
    • Rates of nucleotide substitution and mammalian nuclear gene evolution: Approximate and maximum-likelihood methods lead to different conclusions
    • BIELAWSKI, J. P., K. A. DUNN and Z. YANG, 2000 Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156: 1299-1308.
    • (2000) Genetics , vol.156 , pp. 1299-1308
    • Bielawski, J.P.1    Dunn, K.A.2    Yang, Z.3
  • 6
    • 0026005922 scopus 로고
    • Use of the method of generalized least squares in reconstructing phylogenies from sequence data
    • BULMER, M., 1991 Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Mol. Biol. vol. 8: 868-883.
    • (1991) Mol. Biol. , vol.8 , pp. 868-883
    • Bulmer, M.1
  • 7
    • 0025779286 scopus 로고
    • Synonymous substition rates in mammalian genes: Implications for the molecular clock and the relationships of mammalian orders
    • BULMER, M., K. H. WOLFE and P. M. SHARP, 1991 Synonymous substition rates in mammalian genes: implications for the molecular clock and the relationships of mammalian orders. Proc. Natl. Acad. Sci. USA 88: 5974-5978.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 5974-5978
    • Bulmer, M.1    Wolfe, K.H.2    Sharp, P.M.3
  • 8
    • 0029563023 scopus 로고
    • A method for estimating the numbers of synonymous and nonsynonymons substitutions per site
    • COMERON, J., 1995 A method for estimating the numbers of synonymous and nonsynonymons substitutions per site. J. Mol. Evol. 41: 1152-1159.
    • (1995) J. Mol. Evol. , vol.41 , pp. 1152-1159
    • Comeron, J.1
  • 9
    • 0035155844 scopus 로고    scopus 로고
    • Substitution rates in Drosophila nuclear genes: Implications for translational selection
    • DUNN, K. A., J. P. BIELAWSKI and Z. YANG, 2001 Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 157: 295-305.
    • (2001) Genetics , vol.157 , pp. 295-305
    • Dunn, K.A.1    Bielawski, J.P.2    Yang, Z.3
  • 10
    • 0029027991 scopus 로고
    • Synonymous substitution rates in enterobacteria
    • EYRE-WALKER, A., and M. BULMER, 1995 Synonymous substitution rates in enterobacteria. Genetics 140: 1407-1412.
    • (1995) Genetics , vol.140 , pp. 1407-1412
    • Eyre-Walker, A.1    Bulmer, M.2
  • 11
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding sequences
    • GOLDMAN, N., and Z. YANG, 1994 A codon-based model of nucleotide substitution for protein-coding sequences. Mol. Biol. Evol. 11: 725-736.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 12
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • HASEGAWA, M., H. KISHINO and T. YANO, 1985 Dating of 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
  • 13
    • 0028906291 scopus 로고
    • New methods for estimating the numbers of synonynous and non-synonymous substitutions
    • INA, Y., 1995 New methods for estimating the numbers of synonynous and non-synonymous substitutions. J. Mol. Evol. 40: 190-226.
    • (1995) J. Mol. Evol. , vol.40 , pp. 190-226
    • Ina, Y.1
  • 14
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • edited by N. H. Munro. Academic Press, New York
    • JUKES, T. H., and C. R. CANTOR, 1969 Evolution of protein molecules, pp. 121-123 in Mammalian Protein Metabolism, edited by N. H. MUNRO. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 121-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 15
    • 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
  • 17
    • 0036094963 scopus 로고    scopus 로고
    • Molecular evolution of nuclear genes in Cupressacea, a group of conifers
    • KUSUMI, J., Y. TSUMURA, H. YOSHIMURA and H. TACHIDA, 2002 Molecular evolution of nuclear genes in Cupressacea, a group of conifers. Mol. Biol. Evol. 19: 736-747.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 736-747
    • Kusumi, J.1    Tsumura, Y.2    Yoshimura, H.3    Tachida, H.4
  • 18
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and non-synonymous substitution
    • LI, W.-H., 1993 Unbiased estimation of the rates of synonymous and non-synonymous substitution. J. Mol. Evol. 36: 96-99.
    • (1993) J. Mol. Evol , vol.36 , pp. 96-99
    • Li, W.-H.1
  • 19
    • 0022005270 scopus 로고
    • A new method of estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • LI, W.-H., C.-I WU and C.-C. LUO, 1985 A new method of estimating synonymous and nonsynonymous rates of nucleotide substitution 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    Luo, C.-C.2
  • 20
    • 0019134329 scopus 로고
    • Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitution from homologous sequences and its application
    • MIYATA, T., and T. YASUNAGA, 1980 Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitution from homologous sequences and its application. J. Mol. Evol. 16: 23-26.
    • (1980) J. Mol. Evol. , vol.16 , pp. 23-26
    • Miyata, T.1    Yasunaga, T.2
  • 21
    • 0027153966 scopus 로고
    • Codon usage bias and base composition of nuclear genes of Drosophila
    • MORIYAMA, E. N., and D. L. HARTL, 1993 Codon usage bias and base composition of nuclear genes of Drosophila. Genetics 134: 847-858.
    • (1993) Genetics , vol.134 , pp. 847-858
    • Moriyama, E.N.1    Hartl, D.L.2
  • 22
    • 0030054305 scopus 로고    scopus 로고
    • Estimating the synonymous and nonsynonymous substitution rates
    • MUSE, S. V., 1996 Estimating the synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 13: 105-114.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 105-114
    • Muse, S.V.1
  • 23
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide rates, with application to the chloroplast genome
    • MUSE, S. V., and B. S. GAUT, 1994 A likelihood approach for comparing synonymous and nonsynonymous nucleotide rates, with application to the 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
  • 24
    • 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
  • 25
    • 0027533924 scopus 로고
    • Evolution of Zfx and Zfy genes-rates and interdependence between the genes
    • PAMILO, P., and N. O. BIANCHI, 1993 Evolution of 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
  • 27
    • 0023274170 scopus 로고
    • The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias
    • SHARP, P. M., and W.-H. LI, 1987 The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 4: 222-230.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 222-230
    • Sharp, P.M.1    Li, W.-H.2
  • 28
    • 0024591558 scopus 로고
    • On the rate of DNA sequence evolution in Drosophila
    • SHARP, P. M., and W.-H. LI, 1989 On the rate of DNA sequence evolution in Drosophila. J. Mol. Evol. 28: 398-402.
    • (1989) J. Mol. Evol. , vol.28 , pp. 398-402
    • Sharp, P.M.1    Li, W.-H.2
  • 29
    • 85054231438 scopus 로고
    • Selective use of termination and variation in codon choice
    • edited by D. L. Hatfield, B. J. Lee, and R. M. Pirtle. CRC Press, Boca Raton, FL
    • SHARP, P. M., C. J. BURGESS, A. T. LLOYD and K. J. MITCHELL, 1992 Selective use of termination and variation in codon choice, pp. 397-425 in Transfer RNA in Protein Synthesis, edited by D. L. HATFIELD, B. J. LEE, and R. M. PIRTLE. CRC Press, Boca Raton, FL.
    • (1992) Transfer RNA in Protein Synthesis , pp. 397-425
    • Sharp, P.M.1    Burgess, C.J.2    Lloyd, A.T.3    Mitchell, K.J.4
  • 30
    • 0032714307 scopus 로고    scopus 로고
    • The effect of tandem substitutions on the correlation between synonymous and non-synonymous rates in rodents
    • SMITH, N. G. C., and L. D. HURST, 1999 The effect of tandem substitutions on the correlation between synonymous and non-synonymous rates in rodents. Genetics 153: 1395-1402.
    • (1999) Genetics , vol.153 , pp. 1395-1402
    • Smith, N.G.C.1    Hurst, L.D.2
  • 31
    • 0034750390 scopus 로고    scopus 로고
    • Nucleotide substitution rate estimation in enterobacteria: Approximate and maximum-likelihood methods lead to similar conclusions
    • SMITH, N. G. C., and A. EYRE-WALKER, 2001 Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions. Mol. Biol. Evol. 18: 2124-2126.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2124-2126
    • Smith, N.G.C.1    Eyre-Walker, A.2
  • 32
    • 0021716351 scopus 로고
    • Estimation of evolutionary distances between nucleotide sequences
    • TAJIMA, F., and M. NEI, 1984 Estimation of evolutionary distances between nucleotide sequences. Mol. Biol. Evol. 1: 269-285.
    • (1984) Mol. Biol. Evol. , vol.1 , pp. 269-285
    • Tajima, F.1    Nei, M.2
  • 33
    • 0026711010 scopus 로고
    • Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases
    • TAMURA, K., 1992 Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol. Biol. Evol. 9: 678-687.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 678-687
    • Tamura, K.1
  • 34
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • TAMURA, K., and M. NEI, 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 35
    • 0024497416 scopus 로고
    • Mutation rates differ among regions of the mammalian genome
    • WOLFE, K. H., P. M. SHARP and W.-H. LI, 1989 Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
    • (1989) Nature , vol.337 , pp. 283-285
    • Wolfe, K.H.1    Sharp, P.M.2    Li, W.-H.3
  • 36
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • WRIGHT, F., 1990 The 'effective number of codons' used in a gene. Gene 87: 23-29.
    • (1990) Gene. , vol.87 , pp. 23-29
    • Wright, F.1
  • 37
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 38
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence in proteins
    • edited by V. Bryson and H. J. Vogel. Academic Press, New York
    • ZUCKERKANDL, E., and L. PAULING, 1965 Evolutionary divergence and convergence in proteins, pp. 97-166 in Evolving Genes and proteins, edited by V. BRYSON and H. J. VOGEL. Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 97-166
    • Zuckerkandl, E.1    Pauling, L.2


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