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Volumn 59, Issue 1, 2004, Pages 121-132

A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution

Author keywords

Codon model; ECP; EDN; Functional divergence; Globins; Maximum likelihood

Indexed keywords

ARTICLE; CODON; CONTROLLED STUDY; EOSINOPHIL; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC CODE; MOLECULAR MODEL; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRESSURE; PROTEIN FUNCTION;

EID: 3042842589     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2597-8     Document Type: Article
Times cited : (225)

References (53)
  • 1
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova M, Bielawski JP, 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
  • 2
    • 0036272936 scopus 로고    scopus 로고
    • Accuracy and power of Bayesian prediction of amino acid sites under positive selection
    • Anisimova M, Bielawski JP, 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
  • 3
    • 0036021702 scopus 로고    scopus 로고
    • Expansion of genome coding regions by acquisition of new genes
    • Betrán E, Long M (2002) Expansion of genome coding regions by acquisition of new genes. Genetica 115:65-80
    • (2002) Genetica , vol.115 , pp. 65-80
    • Betrán, E.1    Long, M.2
  • 4
    • 0037270595 scopus 로고    scopus 로고
    • Maximum likelihood methods for detecting adaptive evolution after gene duplication
    • Bielawski JP, Yang Z (2003) Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics 3:201-212
    • (2003) J Struct Funct Genomics , vol.3 , pp. 201-212
    • Bielawski, J.P.1    Yang, Z.2
  • 5
    • 0030970280 scopus 로고    scopus 로고
    • Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish
    • Chen L, DeVries AL, Cheng CH (1997) Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc Natl Acad Sci USA 94:3811-3816
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 3811-3816
    • Chen, L.1    DeVries, A.L.2    Cheng, C.H.3
  • 6
    • 0035895513 scopus 로고    scopus 로고
    • Gene number. What if there are only 30,000 human genes?
    • Claverie JM (2001) Gene number. What if there are only 30,000 human genes? Science 291:1255-1257
    • (2001) Science , vol.291 , pp. 1255-1257
    • Claverie, J.M.1
  • 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 JB, Bonville CA, Dyer KD, Rosenberg HF (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
    • 0025816675 scopus 로고
    • Duplication of the gamma-globin gene mediated by L1 long interspersed repetitive elements in an early ancestor of simian primates
    • Fitch DH, Bailey WJ, Tagle DA, Goodman M, Sieu L, Slightom JL (1991) Duplication of the gamma-globin gene mediated by L1 long interspersed repetitive elements in an early ancestor of simian primates. Proc Natl Acad Sci USA 88:7396-7400
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 7396-7400
    • Fitch, D.H.1    Bailey, W.J.2    Tagle, D.A.3    Goodman, M.4    Sieu, L.5    Slightom, J.L.6
  • 10
    • 0042573997 scopus 로고    scopus 로고
    • A codon-based model of host-specific selection in parasites, with an application to the influenza A virus
    • Forsberg R, Christiansen FB (2003) A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol Biol Evol 20:1252-1259
    • (2003) Mol Biol Evol , vol.20 , pp. 1252-1259
    • Forsberg, R.1    Christiansen, F.B.2
  • 11
    • 0036606898 scopus 로고    scopus 로고
    • Predicting functional divergence in protein evolution by site-specific rate shifts
    • Gaucher EA, Gu X, Miyamoto MM, Benner SA (2002) Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci 27:315-321
    • (2002) Trends Biochem Sci , vol.27 , pp. 315-321
    • Gaucher, E.A.1    Gu, X.2    Miyamoto, M.M.3    Benner, S.A.4
  • 12
    • 0036942922 scopus 로고    scopus 로고
    • The evolution of engrailed genes after duplication and speciation events
    • Gibert JM (2002) The evolution of engrailed genes after duplication and speciation events. Dev Genes Evol 212:307-318
    • (2002) Dev Genes Evol , vol.212 , pp. 307-318
    • Gibert, J.M.1
  • 13
    • 0028168856 scopus 로고
    • A codon based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, 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
  • 14
    • 0033360816 scopus 로고    scopus 로고
    • The genomic record of Humankind's evolutionary roots
    • Goodman M (1999) The genomic record of Humankind's evolutionary roots. Am J Hum Genet 64:31-39
    • (1999) Am J Hum Genet , vol.64 , pp. 31-39
    • Goodman, M.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
    • 0025110837 scopus 로고
    • Structure and chromosome localization of the human eosinophil-derived neurotoxin and eosinophil cationic protein genes: Evidence for intronless coding sequences in the ribonuclease gene superfamily
    • Hamann KJ, Ten RM, Loegering DA, Jenkins RB, Heise MT, Schad CR, Pease LR, Gleich GJ, Barker RL (1990) Structure and chromosome localization of the human eosinophil-derived neurotoxin and eosinophil cationic protein genes: Evidence for intronless coding sequences in the ribonuclease gene superfamily. Genomics 7:535-546
    • (1990) Genomics , vol.7 , pp. 535-546
    • Hamann, K.J.1    Ten, R.M.2    Loegering, D.A.3    Jenkins, R.B.4    Heise, M.T.5    Schad, C.R.6    Pease, L.R.7    Gleich, G.J.8    Barker, R.L.9
  • 18
    • 0037103621 scopus 로고    scopus 로고
    • Shh-Bmp2 signalling module and the evolutionary origin and diversification of feathers
    • Harris MP, Fallon JF, Prum RO (2002) Shh-Bmp2 signalling module and the evolutionary origin and diversification of feathers. J Exp Zool 294:160-176
    • (2002) J Exp Zool , vol.294 , pp. 160-176
    • Harris, M.P.1    Fallon, J.F.2    Prum, R.O.3
  • 19
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T (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
  • 20
    • 0028342845 scopus 로고
    • The evolution of functionally novel proteins after gene duplication
    • Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B Biol Sci 256:119-124
    • (1994) Proc R Soc Lond B Biol Sci , vol.256 , pp. 119-124
    • Hughes, A.L.1
  • 21
    • 0036716752 scopus 로고    scopus 로고
    • Adaptive evolution after gene duplication
    • Hughes AL (2002) Adaptive evolution after gene duplication. Trends Genet 18:433-434
    • (2002) Trends Genet , vol.18 , pp. 433-434
    • Hughes, A.L.1
  • 23
    • 0035807886 scopus 로고    scopus 로고
    • A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins
    • Knudsen B, Miyamoto MM (2001) A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci USA 98:14512-14517
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14512-14517
    • Knudsen, B.1    Miyamoto, M.M.2
  • 24
    • 0024025049 scopus 로고
    • Evolutionary and developmental aspects of two hemoglobin beta-chain genes (epsilon M and beta M) of opossum
    • Koop BF, Goodman M (1988) Evolutionary and developmental aspects of two hemoglobin beta-chain genes (epsilon M and beta M) of opossum. Proc Natl Acad Sci USA 85:3893-3897
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 3893-3897
    • Koop, B.F.1    Goodman, M.2
  • 25
    • 0003070062 scopus 로고
    • Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy
    • Otha T, Aoki K (eds) Japan Scientific Press, Tokyo
    • Li W-H (1985) Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy. In: Otha T, Aoki K (eds) Population genetics and molecular evolution. Japan Scientific Press, Tokyo, pp 333-352
    • (1985) Population Genetics and Molecular Evolution , pp. 333-352
    • Li, W.-H.1
  • 26
    • 0035546224 scopus 로고    scopus 로고
    • Evolution of novel genes
    • Long M (2001) Evolution of novel genes. Curr Opin Genet Dev 11:673-680
    • (2001) Curr Opin Genet Dev , vol.11 , pp. 673-680
    • Long, M.1
  • 27
    • 0027905006 scopus 로고
    • Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila
    • Long M, Langley CH (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260:91-95
    • (1993) Science , vol.260 , pp. 91-95
    • Long, M.1    Langley, C.H.2
  • 28
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS (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
  • 29
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate gene preservation by subfunctionalization
    • Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473
    • (2000) Genetics , vol.154 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 30
    • 0034799277 scopus 로고    scopus 로고
    • Analyzing gene function after duplication
    • Massingham T, Davies LJ, Lio P (2001) Analyzing gene function after duplication. Bioessays 23:873-876
    • (2001) Bioessays , vol.23 , pp. 873-876
    • Massingham, T.1    Davies, L.J.2    Lio, P.3
  • 32
    • 0033144664 scopus 로고    scopus 로고
    • Molecular phytogeny of ateline new world monkeys (Platyrrhini, atelinae) based on gamma-globin gene sequences: Evidence that brachyteles is the sister group of lagothrix
    • Meireles CM, Czelusniak J, Schneider MP, Muniz JA, Brigido MC, Ferreira HS, Goodman M (1999) Molecular phytogeny of ateline new world monkeys (Platyrrhini, atelinae) based on gamma-globin gene sequences: evidence that brachyteles is the sister group of lagothrix. Mol Phylogenet Evol 12:10-30
    • (1999) Mol Phylogenet Evol , vol.12 , pp. 10-30
    • Meireles, C.M.1    Czelusniak, J.2    Schneider, M.P.3    Muniz, J.A.4    Brigido, M.C.5    Ferreira, H.S.6    Goodman, M.7
  • 33
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome
    • Muse SV, Gaut BS (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
  • 34
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, 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
  • 35
    • 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
  • 36
    • 0033219469 scopus 로고    scopus 로고
    • Molecular phytogeny of Old World monkeys (Cercopithecidae) as inferred from gamma-globin DNA sequences
    • Page SL, Chiu Ch, Goodman M (1999) Molecular phytogeny of Old World monkeys (Cercopithecidae) as inferred from gamma-globin DNA sequences. Mol Phylogenet Evol 13:348-359
    • (1999) Mol Phylogenet Evol , vol.13 , pp. 348-359
    • Page, S.L.1    Chiu, Ch.2    Goodman, M.3
  • 37
    • 0018860147 scopus 로고
    • Regulation of oxygen affinity of mammalian haemoglobins
    • Perutz MF, Imai K (1980) Regulation of oxygen affinity of mammalian haemoglobins. J Mol Biol 136:183-191
    • (1980) J Mol Biol , vol.136 , pp. 183-191
    • Perutz, M.F.1    Imai, K.2
  • 38
    • 0026326815 scopus 로고
    • The recruitment of crystallins: New functions precede gene duplication
    • Piatigorsky J, Wistow G (1991) The recruitment of crystallins: new functions precede gene duplication. Science 252:1078-1079
    • (1991) Science , vol.252 , pp. 1078-1079
    • Piatigorsky, J.1    Wistow, G.2
  • 39
    • 0026698858 scopus 로고
    • Molecular adaptation of hemoglobin function in mammals
    • Poyart C, Wajcman H, Kister J (1992) Molecular adaptation of hemoglobin function in mammals. Respir Physiol 90:3-17
    • (1992) Respir Physiol , vol.90 , pp. 3-17
    • Poyart, C.1    Wajcman, H.2    Kister, J.3
  • 40
    • 0033507441 scopus 로고    scopus 로고
    • Eosinophils, riobnucleases and host defence: Solving the puzzle
    • Rosenberg HF, Domachowske JB (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
  • 41
    • 0036730253 scopus 로고    scopus 로고
    • Testing for differences in rates-across-sites distributions in phylogenetic subtrees
    • Susko E, Inagaki Y, Field C, Holder ME, Roger AJ (2002) Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol Biol Evol 19:1514-1523
    • (2002) Mol Biol Evol , vol.19 , pp. 1514-1523
    • Susko, E.1    Inagaki, Y.2    Field, C.3    Holder, M.E.4    Roger, A.J.5
  • 43
    • 0035368224 scopus 로고    scopus 로고
    • Genome duplication, divergent resolution and speciation
    • Taylor J, Van de Peer Y, Meyer A (2001) Genome duplication, divergent resolution and speciation. Trends Genet 17:299-301
    • (2001) Trends Genet , vol.17 , pp. 299-301
    • Taylor, J.1    Van De Peer, Y.2    Meyer, A.3
  • 45
    • 0036439421 scopus 로고    scopus 로고
    • Gene co-option in physiological and morphological evolution
    • True JR, Carrol SB (2002) Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18:53-80
    • (2002) Annu Rev Cell Dev Biol , vol.18 , pp. 53-80
    • True, J.R.1    Carrol, S.B.2
  • 46
    • 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
  • 47
    • 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. Appl Biosci 13:555-556
    • (1997) Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 48
    • 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
  • 49
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evolut 15:496-503
    • (2000) Trends Ecol Evolut , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 50
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang Z, 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
  • 51
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen A-MK (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.K.4
  • 52
    • 0037117541 scopus 로고    scopus 로고
    • Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates
    • Zhang J, Rosenberg HF (2002) Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc Natl Acad Sci USA 99:5486-5491
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5486-5491
    • Zhang, J.1    Rosenberg, H.F.2
  • 53
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • Zhang J, Rosenberg HF, 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    Rosenberg, H.F.2    Nei, M.3


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