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Volumn 21, Issue 7, 2004, Pages 1350-1360

The genomic rate of adaptive amino acid substitution in Drosophila

Author keywords

Adaptive evolution; Amino acid substitutions; Drosophila; McDonald Kreitman test

Indexed keywords

ADAPTATION; AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; CODON; DROSOPHILA; DROSOPHILA SIMULANS; DROSOPHILA YAKUBA; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN;

EID: 3042544623     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh134     Document Type: Article
Times cited : (174)

References (54)
  • 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
    • 0029985179 scopus 로고    scopus 로고
    • Molecular evolution between Drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster
    • -. 1996. Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144:1297-1307.
    • (1996) Genetics , vol.144 , pp. 1297-1307
  • 3
    • 0032953881 scopus 로고    scopus 로고
    • Inferring the fitness effects of DNA mutations from polymorphism and divergence data: Statistical power to detect directional selection under stationarity and free recombination
    • -. 1999. Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics 151:221-238.
    • (1999) Genetics , vol.151 , pp. 221-238
  • 4
    • 0030903283 scopus 로고    scopus 로고
    • Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila
    • Akashi, H., and S. W. Schaeffer. 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
  • 5
    • 0035546073 scopus 로고    scopus 로고
    • Adaptive hitchhiking effects on genome variability
    • Andolfatto, P. 2001. Adaptive hitchhiking effects on genome variability. Curr. Opin. Genet. Dev. 11:635-641.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 635-641
    • Andolfatto, P.1
  • 6
    • 0033828706 scopus 로고    scopus 로고
    • A genome-wide departure from the standard neutral model in natural populations of Drosophila
    • Andolfatto, P., and M. Przeworski. 2000. A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156:257-268.
    • (2000) Genetics , vol.156 , pp. 257-268
    • Andolfatto, P.1    Przeworski, M.2
  • 7
    • 0034012339 scopus 로고    scopus 로고
    • Estimating multilocus linkage disequilibria
    • Barton, N. H. 2000. Estimating multilocus linkage disequilibria. Heredity 84:373-389.
    • (2000) Heredity , vol.84 , pp. 373-389
    • Barton, N.H.1
  • 8
    • 0034938613 scopus 로고    scopus 로고
    • The frequency distribution of nucleotide variation in Drosophila simulans
    • Begun, D. 2001. The frequency distribution of nucleotide variation in Drosophila simulans. Mol. Biol. Evol. 18:1343-1352.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1343-1352
    • Begun, D.1
  • 9
    • 0026529344 scopus 로고
    • Levels of naturally occuring DNA polymorphism correlate with recombination rates in D. melanogaster
    • Begun, D. J., and C. F. Aquadro. 1992. Levels of naturally occuring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356:519-520.
    • (1992) Nature , vol.356 , pp. 519-520
    • Begun, D.J.1    Aquadro, C.F.2
  • 10
    • 0028348142 scopus 로고
    • Neutralism and selectionism face up to DNA data
    • Brookfield, J. J. Y., and P. M. Sharp. 1994. Neutralism and selectionism face up to DNA data. Trends Genet. 10:109-111.
    • (1994) Trends Genet. , vol.10 , pp. 109-111
    • Brookfield, J.J.Y.1    Sharp, P.M.2
  • 12
    • 0032991552 scopus 로고    scopus 로고
    • Characterization of single-nucleotide polymorphisms in coding regions of human genes
    • 17 co-authors
    • Cargill, M., D. Altshuler, J. Irel et al. (17 co-authors). 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22:231-238.
    • (1999) Nat. Genet. , vol.22 , pp. 231-238
    • Cargill, M.1    Altshuler, D.2    Irel, J.3
  • 13
    • 0017809894 scopus 로고
    • Statistical studies on protein polymorphism in natural population. II. Gene differentiation between populations
    • Chakraborty, R., P. A. Fuerst, and M. Nei. 1978. Statistical studies on protein polymorphism in natural population. II. Gene differentiation between populations. Genetics 88: 367-390.
    • (1978) Genetics , vol.88 , pp. 367-390
    • Chakraborty, R.1    Fuerst, P.A.2    Nei, M.3
  • 14
    • 0028222304 scopus 로고
    • The effect of background selection against deleterious mutations on weakly selected, linked variants
    • Charlesworth, B. 1994. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63:213-227.
    • (1994) Genet. Res. , vol.63 , pp. 213-227
    • Charlesworth, B.1
  • 16
    • 0036961560 scopus 로고    scopus 로고
    • Changing effective population size and the McDonald-Kreitman test
    • Eyre-Walker, A. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics 162:2017-2024.
    • (2002) Genetics , vol.162 , pp. 2017-2024
    • Eyre-Walker, A.1
  • 17
    • 0036900082 scopus 로고    scopus 로고
    • Quantifying the slightly deleterious mutation model of molecular evolution
    • Eyre-Walker, A., P. D. Keightley, N. G. C. Smith, and D. Gaffney. 2002. Quantifying the slightly deleterious mutation model of molecular evolution. Mol. Biol. Evol. 19:2142-2149.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 2142-2149
    • Eyre-Walker, A.1    Keightley, P.D.2    Smith, N.G.C.3    Gaffney, D.4
  • 18
    • 0034924997 scopus 로고    scopus 로고
    • Positive and negative selection on the human genome
    • Fay, J. C., G. J. Wycoff, 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    Wycoff, G.J.2    Wu, C.-I.3
  • 19
    • 0037186608 scopus 로고    scopus 로고
    • Testing the neutral theory of molecular evolution with genomic data from Drosophila
    • -. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415:1024-1026.
    • (2002) Nature , vol.415 , pp. 1024-1026
  • 20
    • 0035546129 scopus 로고    scopus 로고
    • The neutral theory in the genomic era
    • Fay, J. C., and C. I. Wu. 2001. The neutral theory in the genomic era. Curr. Opin. Genet. Dev. 11:642-6.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 642-646
    • Fay, J.C.1    Wu, C.I.2
  • 21
    • 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
  • 22
    • 33646226097 scopus 로고
    • Linkage disequilibrium in finite populations
    • Hill, W. G., and A. Robertson. 1968. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38:226-231.
    • (1968) Theor. Appl. Genet. , vol.38 , pp. 226-231
    • Hill, W.G.1    Robertson, A.2
  • 23
    • 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
  • 24
    • 0033927343 scopus 로고    scopus 로고
    • Joint effects of genetic hitchhiking and background selection on neutral variation
    • Kim, Y., and W. Stephan. 2000. Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155:1415-1427.
    • (2000) Genetics , vol.155 , pp. 1415-1427
    • Kim, Y.1    Stephan, W.2
  • 25
    • 0038192127 scopus 로고    scopus 로고
    • Selective sweeps in the presence of interference among partially linked loci
    • -. 2003. Selective sweeps in the presence of interference among partially linked loci. Genetics 164:389-398.
    • (2003) Genetics , vol.164 , pp. 389-398
  • 27
    • 0015220547 scopus 로고
    • Protein polymorphisn as a phase of molecular evolution
    • Kimura, M., and T. Ohta. 1971. Protein polymorphisn as a phase of molecular evolution. Nature 229:467-469.
    • (1971) Nature , vol.229 , pp. 467-469
    • Kimura, M.1    Ohta, T.2
  • 28
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., C. D. Gelatt, and M. P. Vecchi. 1983. Optimization by simulated annealing. Science 220:671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 29
    • 0032829163 scopus 로고    scopus 로고
    • Recent selection on synonymous codon usage in Drosophila
    • Kliman, R. 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.1
  • 30
    • 0029200909 scopus 로고
    • Molecular evidence for natural selection
    • Kreitman, M., and H. Akashi. 1995. Molecular evidence for natural selection. Annu. Rev. Ecol. Syst. 26:403-422.
    • (1995) Annu. Rev. Ecol. Syst. , vol.26 , pp. 403-422
    • Kreitman, M.1    Akashi, H.2
  • 31
    • 0036948339 scopus 로고    scopus 로고
    • Directions in evolutionary biology
    • Lewontin, R. C. 2002. Directions in evolutionary biology. Annu. Rev. Genet. 36:1-18.
    • (2002) Annu. Rev. Genet. , vol.36 , pp. 1-18
    • Lewontin, R.C.1
  • 32
    • 0033178244 scopus 로고    scopus 로고
    • Paleo-demography of the Drosophila melanogaster subgroup: Application of the maximum likelihood method
    • Li, Y. J., Y. Satta, and N. Takahata. 1999. Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method. Genes Genet. Syst. 74:117-127.
    • (1999) Genes Genet. Syst. , vol.74 , pp. 117-127
    • Li, Y.J.1    Satta, Y.2    Takahata, N.3
  • 34
    • 0026428610 scopus 로고
    • Adaptive evolution at the Adh locus in Drosophila
    • McDonald, J. H., and M. Kreitman. 1991. Adaptive evolution at the Adh locus in Drosophila. Nature 351:652-654.
    • (1991) Nature , vol.351 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 35
    • 0035157374 scopus 로고    scopus 로고
    • Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila
    • McVean, G., and J. Vieira. 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.1    Vieira, J.2
  • 37
    • 0030034357 scopus 로고    scopus 로고
    • Intraspecific nuclear DNA variation in Drosophila
    • Moriyama, E. N., and J. R. Powell. 1996. Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13:261-277.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 261-277
    • Moriyama, E.N.1    Powell, J.R.2
  • 38
    • 0031770039 scopus 로고    scopus 로고
    • DNA variability and recombination rates at X-linked loci in humans
    • Nachman, M. W., V. L. Bauer, S. L. Crowell, and C. F. Aquadro. 1998. DNA variability and recombination rates at X-linked loci in humans. Genetics 150:1133-1141.
    • (1998) Genetics , vol.150 , pp. 1133-1141
    • Nachman, M.W.1    Bauer, V.L.2    Crowell, S.L.3    Aquadro, C.F.4
  • 39
    • 0031267307 scopus 로고    scopus 로고
    • The mean and variance of the number of segregating sites since the last hitchhiking event
    • Perlitz, M., and W. Stephan. 1997. The mean and variance of the number of segregating sites since the last hitchhiking event. J. Math. Biol. 36:1-23.
    • (1997) J. Math. Biol. , vol.36 , pp. 1-23
    • Perlitz, M.1    Stephan, W.2
  • 40
    • 0030861159 scopus 로고    scopus 로고
    • Evolution of codon usage bias in Drosophila
    • Powell, J. R., and E. N. Moriyama. 1997. Evolution of codon usage bias in Drosophila. Proc. Natl. Acad. Sci. USA 94:7784-7790.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7784-7790
    • Powell, J.R.1    Moriyama, E.N.2
  • 41
    • 0032972599 scopus 로고    scopus 로고
    • DnaSP version 3: An integrated program for molecular population genetics and molecular evolution analysis
    • Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
    • (1999) Bioinformatics , vol.15 , pp. 174-175
    • Rozas, J.1    Rozas, R.2
  • 42
    • 0026460082 scopus 로고
    • Population genetics of polymorphism and divergence
    • Sawyer, S. A., and D. L. Hartl. 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
  • 43
    • 0024116811 scopus 로고
    • "Silent" sites in Drosophila are not neutral: Evidence of selection among synonymous codons
    • Shields, D. C., P. M. Sharp, D. G. Higgins, and F. Wright. 1988. "Silent" sites in Drosophila 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
  • 44
    • 0019996130 scopus 로고
    • Correlations between heterozygosity and evolutionary rate of proteins
    • Skibinski, D. O. F., and R. D. Ward. 1982. Correlations between heterozygosity and evolutionary rate of proteins. Nature 298:490-492.
    • (1982) Nature , vol.298 , pp. 490-492
    • Skibinski, D.O.F.1    Ward, R.D.2
  • 45
    • 0037186564 scopus 로고    scopus 로고
    • Adaptive protein evolution in Drosophila
    • Smith, N. G. C., and A. Eyre-Walker. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024.
    • (2002) Nature , vol.415 , pp. 1022-1024
    • Smith, N.G.C.1    Eyre-Walker, A.2
  • 46
    • 0029096510 scopus 로고
    • An improved method for estimating the rate of fixation of favourable mutations based on DNA polymorphism data
    • Stephan, W. 1995. An improved method for estimating the rate of fixation of favourable mutations based on DNA polymorphism data. Mol. Biol. Evol. 12:959-962.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 959-962
    • Stephan, W.1
  • 47
    • 3042684874 scopus 로고    scopus 로고
    • Recent applications of diffusion theory to population genetics
    • M. Slatkin and M. Veuille, eds. Oxford University Press, Oxford, UK
    • Stephan, W., and Y. Kim. 2002. Recent applications of diffusion theory to population genetics. Pp. 72-93 in M. Slatkin and M. Veuille, eds. Modern developments in theoretical population genetics, the legacy of Gustave Malecot. Oxford University Press, Oxford, UK.
    • (2002) Modern Developments in Theoretical Population Genetics, the Legacy of Gustave Malecot , pp. 72-93
    • Stephan, W.1    Kim, Y.2
  • 48
    • 0013272874 scopus 로고    scopus 로고
    • Pre-speciation coalescence and the effective size of ancestral populations
    • M. Slatkin and M. Veuille, eds. Oxford University Press, Oxford, UK
    • Takahata, N., and Y. Satta. 2002. Pre-speciation coalescence and the effective size of ancestral populations. Pp. 52-71 in M. Slatkin and M. Veuille, eds. Modern developments in theoretical population genetics, the legacy of Gustave Malecot. Oxford University Press, Oxford, UK.
    • (2002) Modern Developments in Theoretical Population Genetics, the Legacy of Gustave Malecot , pp. 52-71
    • Takahata, N.1    Satta, Y.2
  • 49
    • 0036743513 scopus 로고    scopus 로고
    • Testing models of selection and demography in Drosophila simulans
    • Wall, J. D., P. Andolfatto, and M. Przeworski. 2002. Testing models of selection and demography in Drosophila simulans. Genetics 162:203-216.
    • (2002) Genetics , vol.162 , pp. 203-216
    • Wall, J.D.1    Andolfatto, P.2    Przeworski, M.3
  • 50
    • 0027235978 scopus 로고
    • Analysis of a genetic hitch-hiking model, and its application to DNA polymorphism data from Drosophila melanogaster
    • Wiehe, T., and W. Stephan. 1993. Analysis of a genetic hitch-hiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol. Biol. Evol. 10:842-854.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 842-854
    • Wiehe, T.1    Stephan, W.2
  • 52
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. 1994. 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
    • Yang, Z.1
  • 54
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., R. Nielsen, N. Goldman, and A. M. Pedersen. 2000. Codon-substitution models for heterogeneous 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.4


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