메뉴 건너뛰기




Volumn 3, Issue 1-4, 2003, Pages 201-212

Maximum likelihood methods for detecting adaptive evolution after gene duplication

Author keywords

Codon model; ECP; EDN; Gene family; Maximum likelihood; Positive selection; Troponin C

Indexed keywords

EOSINOPHIL CATIONIC PROTEIN; EOSINOPHIL PROTEIN X; TROPONIN C;

EID: 0037270595     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1022642807731     Document Type: Review
Times cited : (149)

References (46)
  • 1
    • 0031682224 scopus 로고    scopus 로고
    • Evolution of the DAZ gene family suggests that Y-linked DAZ plays little, or a limited, role in spermatogenesis but underlines a recent African origin for human populations
    • Agulnik, A.I., Zharkikh, A., Boettger-Tong, H., Bourgeron, T., McElreavey, K. and Bishop, C.E. (1998) Evolution of the DAZ gene family suggests that Y-linked DAZ plays little, or a limited, role in spermatogenesis but underlines a recent African origin for human populations. Hum. Mol. Genet. 7, 1371-1377.
    • (1998) Hum. Mol. Genet. , vol.7 , pp. 1371-1377
    • Agulnik, A.I.1    Zharkikh, A.2    Boettger-Tong, H.3    Bourgeron, T.4    McElreavey, K.5    Bishop, C.E.6
  • 2
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova, M., Bielawski, J.P. and Yang, Z. (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18, 1585-1592.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 3
    • 0036272936 scopus 로고    scopus 로고
    • Accuracy and power of Bayesian prediction of amino acid sites under positive selection
    • Anisimova, M., Bielawski, J.P. and Yang, Z. (2002) Accuracy and power of Bayesian prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19, 950-958.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 950-958
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 4
    • 0035061474 scopus 로고    scopus 로고
    • Positive and negative selection in the DAZ gene family
    • Bielawski, J.P. and Yang, Z. (2000) Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18, 523-528.
    • (2000) Mol. Biol. Evol. , vol.18 , pp. 523-528
    • Bielawski, J.P.1    Yang, Z.2
  • 5
    • 0034625046 scopus 로고    scopus 로고
    • Rapid evolution of plant chitinases: Molecular targets of selection in plant-pathogen coevolution
    • Bishop, J.G., Dean, A.M. and Mitchell-Olds, T (2000) Rapid evolution of plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc. Natl. Acad. Sci. USA 97, 5322-5327.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 5322-5327
    • Bishop, J.G.1    Dean, A.M.2    Mitchell-Olds, T.3
  • 6
    • 0033028201 scopus 로고    scopus 로고
    • Parallel evolution of drug resistance in HIV: Failure of nonsynonymous/synonymous substitution rate ratio to detect selection
    • Crandall, K.A., Kelsey, C.R., Imanichi, H., Lane, H.C. and Salzman, N.P. (1999) Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16, 372-382.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 372-382
    • Crandall, K.A.1    Kelsey, C.R.2    Imanichi, H.3    Lane, H.C.4    Salzman, N.P.5
  • 7
    • 0032404137 scopus 로고    scopus 로고
    • Evolution of antiviral activity in the ribonuclease A gene superfamily: Evidence for a specific interaction between eosinophil-derived neurotoxin (EDN/RNase 2) and respiratory syncytial virus
    • Domachowske, J.B., Bonville, C.A., Dyer, K.D. and Rosenberg, H.F. (1998) Evolution of antiviral activity in the ribonuclease A gene superfamily: evidence for a specific interaction between eosinophil-derived neurotoxin (EDN/RNase 2) and respiratory syncytial virus. Nucleic Acids Res. 26, 5327-5332.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 5327-5332
    • Domachowske, J.B.1    Bonville, C.A.2    Dyer, K.D.3    Rosenberg, H.F.4
  • 8
    • 13044283060 scopus 로고    scopus 로고
    • Molecular genetics of ecological diversification: Duplication and rapid evolution of toxin genes of the venomous gastropod Conus
    • Duda, T.F. and Palumbi, S.R. (1999) Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc. Natl. Acad. Sci. USA 96, 6820-6823.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 6820-6823
    • Duda, T.F.1    Palumbi, S.R.2
  • 9
    • 0019255001 scopus 로고
    • Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background
    • Dykhuizen, D. and Hartl, D.L. (1980) Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics 96, 801-817.
    • (1980) Genetics , vol.96 , pp. 801-817
    • Dykhuizen, D.1    Hartl, D.L.2
  • 10
    • 0030007094 scopus 로고    scopus 로고
    • Large-scale search for genes on which positive selection may operate
    • Endo, T., Ikeo. K. and Gojobori, T. (1996) Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13, 685-690.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 685-690
    • Endo, T.1    Ikeo, K.2    Gojobori, T.3
  • 11
    • 0029031198 scopus 로고
    • The troponin complex and regulation of muscle contraction
    • Farah, C.S. and Reinach, F.C. (1995) The troponin complex and regulation of muscle contraction. FASEB J. 9, 755-767.
    • (1995) FASEB J. , vol.9 , pp. 755-767
    • Farah, C.S.1    Reinach, F.C.2
  • 12
    • 0035029534 scopus 로고    scopus 로고
    • Maximum-likelihood phylogenetic analysis under a covarion-like model
    • Galtier, N. (2001) Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18, 866-873.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 866-873
    • Galtier, N.1
  • 13
    • 0031966661 scopus 로고    scopus 로고
    • The structural basis of molecular adaptation
    • Golding, G.B. and Dean, A.M. (1998) The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355-369.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 355-369
    • Golding, G.B.1    Dean, A.M.2
  • 14
    • 0028168856 scopus 로고
    • A codon based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman, N. and Yang, Z. (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
  • 15
    • 0032728408 scopus 로고    scopus 로고
    • Statistical methods for testing functional divergence after gene duplication
    • Gu, X. (1999) Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16, 1664-1674.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1664-1674
    • Gu, X.1
  • 16
    • 0035061686 scopus 로고    scopus 로고
    • Maximum-likelihood approach for gene family evolution under functional divergence
    • Gu, X. (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18, 453-464.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 453-464
    • Gu, X.1
  • 17
    • 0035148533 scopus 로고    scopus 로고
    • Evidence for positive selection in foot-and-mouth-disease virus genes from field isolates
    • Haydon, D.T., Bastos, A.D., Knowles, N.J. and Samuel, A.R. (2001) Evidence for positive selection in foot-and-mouth-disease virus genes from field isolates. Genetics 157, 151-154.
    • (2001) Genetics , vol.157 , pp. 151-154
    • Haydon, D.T.1    Bastos, A.D.2    Knowles, N.J.3    Samuel, A.R.4
  • 19
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    • Hughes, A.L. and Nei, M. (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335, 167-170.
    • (1988) Nature , vol.335 , pp. 167-170
    • Hughes, A.L.1    Nei, M.2
  • 21
    • 0004732896 scopus 로고    scopus 로고
    • Analysis of HIV-1 env gene reveals evidence for a low effective number in the viral population
    • Leigh Brown, A.J. (1997) Analysis of HIV-1 env gene reveals evidence for a low effective number in the viral population. Proc. Natl. Acad. Sci. USA 94, 1862-1865.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 1862-1865
    • Leigh Brown, A.J.1
  • 22
    • 0003070062 scopus 로고
    • Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy
    • (Eds., Otha, T. and Aoki, K.), Japan Scientific Press, Tokyo
    • Li, W.-H. (1985) Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy. In Population Genetics and Molecular Evolution (Eds., Otha, T. and Aoki, K.), Japan Scientific Press, Tokyo, pp. 333-352.
    • (1985) Population Genetics and Molecular Evolution , pp. 333-352
    • Li, W.-H.1
  • 23
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 24
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome
    • Muse, S.V. and Gaut, B.S. (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome. Mol. Biol. Evol. 11, 715-725.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-725
    • Muse, S.V.1    Gaut, B.S.2
  • 25
    • 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 Yang, Z. (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
  • 27
    • 0003101372 scopus 로고
    • Further simulation studies on evolution by gene duplication
    • Ohta, T. (1988a) Further simulation studies on evolution by gene duplication. Evolution 42, 375-386.
    • (1988) Evolution , vol.42 , pp. 375-386
    • Ohta, T.1
  • 28
    • 0003160625 scopus 로고
    • Multigene and supergene families
    • Ohta, T. (1988b) Multigene and supergene families. Oxf. Surv. Evol. Biol. 5, 41-65.
    • (1988) Oxf. Surv. Evol. Biol. , vol.5 , pp. 41-65
    • Ohta, T.1
  • 29
    • 0027327059 scopus 로고
    • Pattern of nucleotide substitution in growth hormone-prolactin gene family: A paradigm for evolution by gene duplication
    • Ohta, T. (1993) Pattern of nucleotide substitution in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication. Genetics 134: 1271-1276.
    • (1993) Genetics , vol.134 , pp. 1271-1276
    • Ohta, T.1
  • 30
    • 0028034301 scopus 로고
    • Further examples of evolution by gene duplication revealed through DNA sequence comparisons
    • Ohta, T. (1994) Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics 138, 1331-1337.
    • (1994) Genetics , vol.138 , pp. 1331-1337
    • Ohta, T.1
  • 31
    • 0030980281 scopus 로고    scopus 로고
    • Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo
    • Plikat, U., Nieselt-Struwe, K. and Meyerhans, A. (1997) Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo. J. Virol. 71, 4233-4240.
    • (1997) J. Virol. , vol.71 , pp. 4233-4240
    • Plikat, U.1    Nieselt-Struwe, K.2    Meyerhans, A.3
  • 32
    • 0032931263 scopus 로고    scopus 로고
    • Rapid evolution of primate sperm protein: Relaxation of functional constraint or positive Darwinian selection?
    • Rooney, A.P. and Zhang, J. (1999) Rapid evolution of primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Mol. Biol. Evol. 16, 706-710.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 706-710
    • Rooney, A.P.1    Zhang, J.2
  • 33
    • 0033507441 scopus 로고    scopus 로고
    • Eosinophils, riobnucleases and host defence: Solving the puzzle
    • Rosenberg, H.F. and Domachowske, J.B. (1999) Eosinophils, riobnucleases and host defence: solving the puzzle. Immunol. Res. 20, 261-274.
    • (1999) Immunol. Res. , vol.20 , pp. 261-274
    • Rosenberg, H.F.1    Domachowske, J.B.2
  • 34
    • 0029041577 scopus 로고
    • Rapid evolution of a unique family of primate ribonuclease genes
    • Rosenberg, H.F., Dyer, K.D., Tiffany, H.L. and Gonzalez, M. (1995) Rapid evolution of a unique family of primate ribonuclease genes. Nature Genet. 10, 219-223.
    • (1995) Nature Genet. , vol.10 , pp. 219-223
    • Rosenberg, H.F.1    Dyer, K.D.2    Tiffany, H.L.3    Gonzalez, M.4
  • 35
    • 0032953315 scopus 로고    scopus 로고
    • Molecular evolution of the COX7A gene family in primates
    • Schmidt, T.R., Goodman, M. and Grossman, L.I. (1999) Molecular evolution of the COX7A gene family in primates. Mol. Biol. Evol. 16, 619-626.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 619-626
    • Schmidt, T.R.1    Goodman, M.2    Grossman, L.I.3
  • 36
    • 1842328059 scopus 로고    scopus 로고
    • In search of molecular Darwinism
    • Sharp, P.M. (1997) In search of molecular Darwinism. Nature 385, 401-404.
    • (1997) Nature , vol.385 , pp. 401-404
    • Sharp, P.M.1
  • 37
    • 0035957018 scopus 로고    scopus 로고
    • Positive Darwinian selection in the evolution of mammalian female reproductive proteins
    • Swanson, W.J., Yang, Z., Wolfner, M.F. and Aquadro, C.F. (2001) Positive Darwinian selection in the evolution of mammalian female reproductive proteins. Proc. Natl. Acad. Sci. USA 98, 2509-2514.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 2509-2514
    • Swanson, W.J.1    Yang, Z.2    Wolfner, M.F.3    Aquadro, C.F.4
  • 38
    • 0030844231 scopus 로고    scopus 로고
    • Nucleotide sequence evolution at the kappa-casein locus: Evidence for positive selection within the family Bovidae
    • Ward, T.J., Honeycutt, R.L. and Derr, J.N. (1997) Nucleotide sequence evolution at the kappa-casein locus: evidence for positive selection within the family Bovidae. Genetics 147, 1863-1872.
    • (1997) Genetics , vol.147 , pp. 1863-1872
    • Ward, T.J.1    Honeycutt, R.L.2    Derr, J.N.3
  • 39
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analyses by maximum likelihood
    • Yang, Z. (1997) PAML: a program package for phylogenetic analyses by maximum likelihood. Cabios 13, 555-556.
    • (1997) Cabios , vol.13 , pp. 555-556
    • Yang, Z.1
  • 40
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z. (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
    • Yang, Z.1
  • 41
    • 0001050687 scopus 로고    scopus 로고
    • Adaptive molecular evolution
    • (Eds., Balding, D.J., Bishop, M. and Cannings, C.), Wiley & Sons, New York, NY
    • Yang, Z. (2001) Adaptive molecular evolution. In Handbook of Statistical Genetics (Eds., Balding, D.J., Bishop, M. and Cannings, C.), Wiley & Sons, New York, NY, pp. 327-350.
    • (2001) Handbook of Statistical Genetics , pp. 327-350
    • Yang, Z.1
  • 42
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang, Z. and Nielsen, R. (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
  • 43
    • 0036134765 scopus 로고    scopus 로고
    • Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    • Yang, Z. and Swanson, W.J. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol., 19, 49-57.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 49-57
    • Yang, Z.1    Swanson, W.J.2
  • 44
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., Nielsen, R., Goldman, N. and A.-M.K. Pederson, W.J. (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    Pederson, A.-M.K.W.J.4
  • 45
    • 0032737463 scopus 로고    scopus 로고
    • Genealogical evidence for positive selection in the nef gene of HIV-1
    • Zanotto, P.M. de A., Kallas. E.G., de Souza, R.F. and Holmes, E.C. (1999) Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153, 1077-1089.
    • (1999) Genetics , vol.153 , pp. 1077-1089
    • De Zanotto, P.M.A.1    Kallas, E.G.2    De Souza, R.F.3    Holmes, E.C.4
  • 46
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • Zhang, J., Rosenburg, H.F. and Nei, M. (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95, 3708-3713.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3708-3713
    • Zhang, J.1    Rosenburg, H.F.2    Nei, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.