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Volumn 27, Issue 6, 2010, Pages 1327-1337

A simple multiallele model and its application to identifying preferred-unpreferred codons using polymorphism data

Author keywords

Codon usage; Multiallele models; Mutational bias; Natural selection; Transition matrix

Indexed keywords

AMINO ACID;

EID: 77952826597     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq023     Document Type: Article
Times cited : (34)

References (57)
  • 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
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
    • Akashi H, Gojobori T. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA. 99:3695-3700.
    • (2002) Proc Natl Acad Sci USA. , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 3
    • 0030903283 scopus 로고    scopus 로고
    • Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila
    • Akashi H, Schaeffer SW. 1997. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146:295-307.
    • (1997) Genetics , vol.146 , pp. 295-307
    • Akashi, H.1    Schaeffer, S.W.2
  • 4
    • 38849194141 scopus 로고    scopus 로고
    • Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
    • Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17:1755-1762.
    • (2007) Genome Res. , vol.17 , pp. 1755-1762
    • Andolfatto, P.1
  • 5
    • 0345730813 scopus 로고    scopus 로고
    • Effect of misoriented sites on neutrality tests with outgroup
    • Baudry E, Depaulis F. 2003. Effect of misoriented sites on neutrality tests with outgroup. Genetics 165:1619-1622.
    • (2003) Genetics , vol.165 , pp. 1619-1622
    • Baudry, E.1    Depaulis, F.2
  • 6
    • 44949129000 scopus 로고    scopus 로고
    • Assessing the evolutionary impact of amino acid mutations in the human genome
    • Boyko AR, Williamson SH, Indap AR, et al. (14 co-authors). 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 4:e1000083.
    • (2008) PLoS Genet. , vol.4
    • Boyko, A.R.1    Williamson, S.H.2    Indap, A.R.3
  • 7
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907.
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 8
    • 0035691964 scopus 로고    scopus 로고
    • Directional selection and the site-frequency spectrum
    • Bustamante CD, Wakeley J, Sawyer S, Hartl DL. 2001. Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
    • (2001) Genetics , vol.159 , pp. 1779-1788
    • Bustamante, C.D.1    Wakeley, J.2    Sawyer, S.3    Hartl, D.L.4
  • 9
    • 27844577664 scopus 로고    scopus 로고
    • Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila
    • Comeron JM, Guthrie TB. 2005. Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila. Mol Biol Evol. 22:2519-2530.
    • (2005) Mol Biol Evol. , vol.22 , pp. 2519-2530
    • Comeron, J.M.1    Guthrie, T.B.2
  • 10
    • 0036263105 scopus 로고    scopus 로고
    • Population, evolutionary and genomic consequences of interference selection
    • Comeron JM, Kreitman M. 2002. Population, evolutionary and genomic consequences of interference selection. Genetics 161:389-410.
    • (2002) Genetics , vol.161 , pp. 389-410
    • Comeron, J.M.1    Kreitman, M.2
  • 11
    • 37349011445 scopus 로고    scopus 로고
    • The Hill-Robertson effect: Evolutionary consequences of weak selection and linkage in finite populations
    • Comeron JM, Williford A, Kliman RM. 2008. The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100:19-31.
    • (2008) Heredity , vol.100 , pp. 19-31
    • Comeron, J.M.1    Williford, A.2    Kliman, R.M.3
  • 12
    • 33750021975 scopus 로고    scopus 로고
    • Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhab-ditis remanei
    • Cutter AD, Charlesworth B. 2006. Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhab-ditis remanei. Curr Biol. 16:2053-2057.
    • (2006) Curr Biol. , vol.16 , pp. 2053-2057
    • Cutter, A.D.1    Charlesworth, B.2
  • 13
    • 61349120804 scopus 로고    scopus 로고
    • The polymorphism frequency spectrum of finitely many sites under selection
    • Desai MM, Plotkin JB. 2008. The polymorphism frequency spectrum of finitely many sites under selection. Genetics 180:2175-2191.
    • (2008) Genetics , vol.180 , pp. 2175-2191
    • Desai, M.M.1    Plotkin, J.B.2
  • 14
    • 0034754512 scopus 로고    scopus 로고
    • Likelihoods and simulation methods for a class of nonneutral population genetics models
    • Donnelly P, Nordborg M, Joyce P. 2001. Likelihoods and simulation methods for a class of nonneutral population genetics models. Genetics 159:853-867.
    • (2001) Genetics , vol.159 , pp. 853-867
    • Donnelly, P.1    Nordborg, M.2    Joyce, P.3
  • 15
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
    • Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA. 96:4482-4487.
    • (1999) Proc Natl Acad Sci USA. , vol.96 , pp. 4482-4487
    • Duret, L.1    Mouchiroud, D.2
  • 16
    • 33750971421 scopus 로고    scopus 로고
    • Non-equilibrium theory of the allele frequency spectrum
    • Evans SN, Shvets Y, Slatkin M. 2007. Non-equilibrium theory of the allele frequency spectrum. Theor Popul Biol. 71:109-119.
    • (2007) Theor Popul Biol. , vol.71 , pp. 109-119
    • Evans, S.N.1    Shvets, Y.2    Slatkin, M.3
  • 17
    • 0015310384 scopus 로고
    • The sampling theory of selectively neutral alleles
    • Ewens WJ. 1972. The sampling theory of selectively neutral alleles. Theor Popul Biol. 3:87-112.
    • (1972) Theor Popul Biol. , vol.3 , pp. 87-112
    • Ewens, W.J.1
  • 19
    • 0033880990 scopus 로고    scopus 로고
    • On the average coefficient of dominance of deleterious spontaneous mutations
    • Garcia-Dorado A, Caballero A. 2000. On the average coefficient of dominance of deleterious spontaneous mutations. Genetics 155:1991-2001.
    • (2000) Genetics , vol.155 , pp. 1991-2001
    • Garcia-Dorado, A.1    Caballero, A.2
  • 21
    • 34548452457 scopus 로고
    • Simulating probability distributions in the coalescent
    • Griffiths RC, Tavaré S. 1994. Simulating probability distributions in the coalescent. Theor Popul Biol. 46:131-159.
    • (1994) Theor Popul Biol. , vol.46 , pp. 131-159
    • Griffiths, R.1    Tavaré, S.2
  • 22
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings WK. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 23
    • 34547808850 scopus 로고    scopus 로고
    • Context dependence, ancestral misidentification, and spurious signatures of natural selection
    • Hernandez RD, Williamson SH, Bustamante CD. 2007. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol. 24:1792-1800.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1792-1800
    • Hernandez, R.D.1    Williamson, S.H.2    Bustamante, C.D.3
  • 24
    • 0013979181 scopus 로고
    • The effect of linkage on limits to artificial selection
    • Hill WG, Robertson A. 1966. The effect of linkage on limits to artificial selection. Genet Res. 8:269-294.
    • (1966) Genet Res. , vol.8 , pp. 269-294
    • Hill, W.G.1    Robertson, A.2
  • 25
    • 35048822011 scopus 로고    scopus 로고
    • Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data
    • Hutter S, Li H, Beisswanger S, De Lorenzo D, Stephan W. 2007. Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data. Genetics 177:469-480.
    • (2007) Genetics , vol.177 , pp. 469-480
    • Hutter, S.1    Li, H.2    Beisswanger, S.3    De Lorenzo, D.4    Stephan, W.5
  • 26
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 2:13-34.
    • (1985) Mol Biol Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 27
    • 0019869334 scopus 로고
    • The molecular basis of dominance
    • Kacser H, Burns JA. 1981. The molecular basis of dominance. Genetics 97:639-666.
    • (1981) Genetics , vol.97 , pp. 639-666
    • Kacser, H.1    Burns, J.A.2
  • 28
    • 58149496323 scopus 로고    scopus 로고
    • The effects of deleterious mutations on evolution in non-recombining genomes
    • Kaiser VB, Charlesworth B. 2009. The effects of deleterious mutations on evolution in non-recombining genomes. Trends Genet. 25:9-12.
    • (2009) Trends Genet. , vol.25 , pp. 9-12
    • Kaiser, V.B.1    Charlesworth, B.2
  • 29
    • 37249042614 scopus 로고    scopus 로고
    • Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
    • Keightley PD, Eyre-Walker A. 2007. Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177:2251-2261.
    • (2007) Genetics , vol.177 , pp. 2251-2261
    • Keightley, P.D.1    Eyre-Walker, A.2
  • 30
    • 67650064592 scopus 로고    scopus 로고
    • Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
    • Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML. 2009. Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res. 19:1195-1201.
    • (2009) Genome Res. , vol.19 , pp. 1195-1201
    • Keightley, P.D.1    Trivedi, U.2    Thomson, M.3    Oliver, F.4    Kumar, S.5    Blaxter, M.L.6
  • 31
    • 0014494672 scopus 로고
    • The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations
    • Kimura M. 1969. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61:893-903.
    • (1969) Genetics , vol.61 , pp. 893-903
    • Kimura, M.1
  • 32
    • 75949146309 scopus 로고
    • The number of alleles that can be maintained in a finite population
    • Kimura M, Crow JF. 1964. The number of alleles that can be maintained in a finite population. Genetics 49:725-738.
    • (1964) Genetics , vol.49 , pp. 725-738
    • Kimura, M.1    Crow, J.F.2
  • 33
    • 0032829163 scopus 로고    scopus 로고
    • Recent selection on synonymous codon usage in Drosophila
    • Kliman RM. 1999. Recent selection on synonymous codon usage in Drosophila. J Mol Evol. 49:343-351.
    • (1999) J Mol Evol. , vol.49 , pp. 343-351
    • Kliman, R.M.1
  • 34
    • 0023064998 scopus 로고
    • Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons
    • Li WH. 1987. Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J Mol Evol. 24:337-345.
    • (1987) J Mol Evol. , vol.24 , pp. 337-345
    • Li, W.H.1
  • 35
    • 43149124400 scopus 로고    scopus 로고
    • A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana
    • Llopart A, Mabille A, Peters-Hall JR, Comeron JM, Kliman RM. 2008. A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana. J Mol Evol. 66:224-231.
    • (2008) J Mol Evol. , vol.66 , pp. 224-231
    • Llopart, A.1    Mabille, A.2    Peters-Hall, J.R.3    Comeron, J.M.4    Kliman, R.M.5
  • 36
    • 1142302213 scopus 로고    scopus 로고
    • Selection on codon usage in Drosophila americana
    • Maside X, Lee AW, Charlesworth B. 2004. Selection on codon usage in Drosophila americana. Curr Biol. 14:150-154.
    • (2004) Curr Biol. , vol.14 , pp. 150-154
    • Maside, X.1    Lee, A.W.2    Charlesworth, B.3
  • 37
    • 0034099647 scopus 로고    scopus 로고
    • The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation
    • McVean GA, Charlesworth B. 2000. The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155:929-944.
    • (2000) Genetics , vol.155 , pp. 929-944
    • McVean, G.A.1    Charlesworth, B.2
  • 38
    • 0035157374 scopus 로고    scopus 로고
    • Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila
    • McVean GA, Vieira J. 2001. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157:245-257.
    • (2001) Genetics , vol.157 , pp. 245-257
    • McVean, G.A.1    Vieira, J.2
  • 39
    • 0032749124 scopus 로고    scopus 로고
    • A population genetic model for the evolution of synonymous codon usage: Patterns and predictions
    • McVean GAT, Charlesworth B. 1999. A population genetic model for the evolution of synonymous codon usage: patterns and predictions. Genet Res. 74:145-158.
    • (1999) Genet Res. , vol.74 , pp. 145-158
    • McVean, G.A.T.1    Charlesworth, B.2
  • 41
    • 70350170130 scopus 로고    scopus 로고
    • Modeling multiallelic selection using a Moran model
    • Muirhead CA, Wakeley J. 2009. Modeling multiallelic selection using a Moran model. Genetics 182:1141-1157.
    • (2009) Genetics , vol.182 , pp. 1141-1157
    • Muirhead, C.A.1    Wakeley, J.2
  • 42
    • 33845898825 scopus 로고    scopus 로고
    • Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila
    • Nielsen R, Bauer DuMont VL, Hubisz MJ, Aquadro CF. 2007. Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila. Mol Biol Evol. 24:228-235.
    • (2007) Mol Biol Evol. , vol.24 , pp. 228-235
    • Nielsen, R.1    Bauer Dumont, V.L.2    Hubisz, M.J.3    Aquadro, C.F.4
  • 43
    • 24744465216 scopus 로고    scopus 로고
    • Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation
    • Ometto L, Glinka S, De Lorenzo D, Stephan W. 2005. Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol Biol Evol. 22:2119-2130.
    • (2005) Mol Biol Evol. , vol.22 , pp. 2119-2130
    • Ometto, L.1    Glinka, S.2    De Lorenzo, D.3    Stephan, W.4
  • 44
    • 0033573925 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in Drosophila and mammalian genomes
    • Petrov DA, Hartl DL. 1999. Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci USA. 96:1475-1479.
    • (1999) Proc Natl Acad Sci USA. , vol.96 , pp. 1475-1479
    • Petrov, D.A.1    Hartl, D.L.2
  • 46
    • 0026460082 scopus 로고
    • Population genetics of polymorphism and divergence
    • Sawyer SA, Hartl DL. 1992. Population genetics of polymorphism and divergence. Genetics. 132:1161-1176.
    • (1992) Genetics. , vol.132 , pp. 1161-1176
    • Sawyer, S.A.1    Hartl, D.L.2
  • 47
    • 33847781444 scopus 로고    scopus 로고
    • Adaptive genic evolution in the Drosophila genomes
    • Shapiro JA, Huang W, Zhang C, et al. (13 co-authors). 2007. Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci USA. 104:2271-2276.
    • (2007) Proc Natl Acad Sci USA. , vol.104 , pp. 2271-2276
    • Shapiro, J.A.1    Huang, W.2    Zhang, C.3
  • 49
    • 0024116811 scopus 로고
    • Silent" sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons
    • Shields DC, Sharp PM, Higgins DG, Wright F. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol. 5:704-716.
    • (1988) Mol Biol Evol. , vol.5 , pp. 704-716
    • Shields, D.C.1    Sharp, P.M.2    Higgins, D.G.3    Wright, F.4
  • 50
    • 15544387147 scopus 로고    scopus 로고
    • Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster
    • Singh ND, Arndt PF, Petrov DA. 2005. Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics 169:709-722.
    • (2005) Genetics , vol.169 , pp. 709-722
    • Singh, N.D.1    Arndt, P.F.2    Petrov, D.A.3
  • 51
    • 0344585415 scopus 로고    scopus 로고
    • Ancestral inference in population genetics models with selection
    • Stephens M, Donnelly P. 2003. Ancestral inference in population genetics models with selection. Aust N Z J Stat. 45:395-430.
    • (2003) Aust N Z J Stat. , vol.45 , pp. 395-430
    • Stephens, M.1    Donnelly, P.2
  • 52
    • 0033939003 scopus 로고    scopus 로고
    • Molecular evolution in a multisite nearly neutral mutation model
    • Tachida H. 2000. Molecular evolution in a multisite nearly neutral mutation model. J Mol Evol. 50:69-81.
    • (2000) J Mol Evol. , vol.50 , pp. 69-81
    • Tachida, H.1
  • 53
    • 38649096895 scopus 로고    scopus 로고
    • Codon usage in twelve species of Drosophila
    • Vicario S, Moriyama EN, Powell JR. 2007. Codon usage in twelve species of Drosophila. BMC Evol Biol. 7:226. Watterson GA. 1977. Heterosis or neutrality? Genetics 85:789-814.
    • (2007) BMC Evol Biol. , vol.7 , Issue.226 , pp. 789-814
    • Vicario, S.1    Moriyama, E.N.2    Powell, J.R.3
  • 55
    • 0002920493 scopus 로고
    • Adaptation and selection
    • Jepson G Simpson G, Mayr E, editors Princeton (NJ): Princeton University Press
    • Wright S. 1949. Adaptation and selection. In: Jepson G Simpson G, Mayr E, editors. Genetics, palaeontology, and evolution. Princeton (NJ): Princeton University Press. p. 365-389.
    • (1949) Genetics, Palaeontology, and Evolution , pp. 365-389
    • Wright, S.1
  • 56
    • 70649090279 scopus 로고    scopus 로고
    • Estimating selection intensity on synonymous codon usage in a non-equilibrium population
    • Zeng K, Charlesworth B. 2009. Estimating selection intensity on synonymous codon usage in a non-equilibrium population. Genetics 183:651-662.
    • (2009) Genetics , vol.183 , pp. 651-662
    • Zeng, K.1    Charlesworth, B.2
  • 57
    • 76749119389 scopus 로고    scopus 로고
    • Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila mela-nogaster
    • Advance Access published December 30 2009 doi: 10.1007/s00239-009-9314-6
    • Zeng K, Charlesworth B. 2010. Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila mela-nogaster. J Mol Evol. Advance Access published December 30, 2009, doi: 10.1007/s00239-009-9314-6.
    • (2010) J Mol Evol
    • Zeng, K.1    Charlesworth, B.2


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