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Volumn 22, Issue 4, 2005, Pages 1107-1118

Bayes empirical Bayes inference of amino acid sites under positive selection

Author keywords

Bayes empirical Bayes; Codon substitution models; Positive selection

Indexed keywords

AMINO ACID;

EID: 16344378246     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi097     Document Type: Article
Times cited : (1865)

References (39)
  • 1
    • 0034897709 scopus 로고    scopus 로고
    • The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites
    • Anisimova, M., J. P. Bielawski, and Z. Yang. 2001. The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. 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 Bayes prediction of amino acid sites under positive selection
    • -. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19:950-958.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 950-958
  • 3
    • 0042208362 scopus 로고    scopus 로고
    • Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    • Anisimova, M., R. Nielsen, and Z. Yang. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236.
    • (2003) Genetics , vol.164 , pp. 1229-1236
    • Anisimova, M.1    Nielsen, R.2    Yang, Z.3
  • 4
    • 0035061474 scopus 로고    scopus 로고
    • Positive and negative selection in the DAZ gene family
    • Bielawski, J. P., and Z. Yang. 2001. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18:523-529.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 523-529
    • Bielawski, J.P.1    Yang, Z.2
  • 5
    • 3042842589 scopus 로고    scopus 로고
    • A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    • -. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J. Mol. Evol. 59:121-132.
    • (2004) J. Mol. Evol. , vol.59 , pp. 121-132
  • 6
    • 0034625046 scopus 로고    scopus 로고
    • Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution
    • Bishop, J. G., A. M. Dean, and T. Mitchell-Olds. 2000. Rapid evolution in 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
  • 8
    • 0000365503 scopus 로고
    • Approaches for empirical Bayes confidence intervals
    • Carlin, B. P., and A. E. Gelfand. 1990. Approaches for empirical Bayes confidence intervals. J. Am. Stat. Assoc. 85:105-114.
    • (1990) J. Am. Stat. Assoc. , vol.85 , pp. 105-114
    • Carlin, B.P.1    Gelfand, A.E.2
  • 10
    • 3242811414 scopus 로고    scopus 로고
    • Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates
    • Filip, L. C., and N. I. Mundy. 2004. Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates. Mol. Biol. Evol. 21:1504-1511.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1504-1511
    • Filip, L.C.1    Mundy, N.I.2
  • 11
    • 0035057075 scopus 로고    scopus 로고
    • Molecular evolution of transferrin: Evidence for positive selection in salmonids
    • Ford, M. J. 2001. Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 18:639-647.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 639-647
    • Ford, M.J.1
  • 12
    • 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., and F. B. Christiansen. 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
  • 13
    • 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
  • 14
    • 4444357279 scopus 로고    scopus 로고
    • Modeling the site-specific variation of selection patterns along lineages
    • Guindon, S., A. G. Rodrigo, K. A. Dyer, and J. P. Huelsenbeck. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc. Natl. Acad. Sci. USA 101:12957-12962.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12957-12962
    • Guindon, S.1    Rodrigo, A.G.2    Dyer, K.A.3    Huelsenbeck, J.P.4
  • 15
    • 0035148533 scopus 로고    scopus 로고
    • Evidence for positive selection in foot-and-mouth-disease virus capsid genes from field isolates
    • Haydon, D. T., A. D. Bastos, N. J. Knowles, and A. R. Samuel. 2001. Evidence for positive selection in foot-and-mouth-disease virus capsid genes from field isolates. Genetics 157:7-15.
    • (2001) Genetics , vol.157 , pp. 7-15
    • Haydon, D.T.1    Bastos, A.D.2    Knowles, N.J.3    Samuel, A.R.4
  • 16
    • 2942656772 scopus 로고    scopus 로고
    • Bayesian estimation of positively selected sites
    • Huelsenbeck, J. P., and K. A. Dyer. 2004. Bayesian estimation of positively selected sites. J. Mol. Evol. 58:661-672.
    • (2004) J. Mol. Evol. , vol.58 , pp. 661-672
    • Huelsenbeck, J.P.1    Dyer, K.A.2
  • 18
    • 84950461861 scopus 로고
    • Empirical Bayes confidence intervals based on bootstrap samples
    • Laird, N. M., and T. A. Louis. 1987. Empirical Bayes confidence intervals based on bootstrap samples. J. Amer. Stat. Assoc. 82:739-750.
    • (1987) J. Amer. Stat. Assoc. , vol.82 , pp. 739-750
    • Laird, N.M.1    Louis, T.A.2
  • 19
    • 4744358984 scopus 로고    scopus 로고
    • Species specificity in rodent pheromone receptor repertoires
    • Lane, R. P., J. Young, T. Newman, and B. J. Trask. 2004. Species specificity in rodent pheromone receptor repertoires. Genome Res. 14:603-608.
    • (2004) Genome Res. , vol.14 , pp. 603-608
    • Lane, R.P.1    Young, J.2    Newman, T.3    Trask, B.J.4
  • 20
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes
    • Li, W.-H., C.-I. Wu, and C.-C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions 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    Wu, C.-I.2    Luo, C.-C.3
  • 21
    • 0018415510 scopus 로고
    • Two types of amino acid substitutions in protein evolution
    • Miyata, T., S. Miyazawa, and T. Yasunaga. 1979. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:219-236.
    • (1979) J. Mol. Evol. , vol.12 , pp. 219-236
    • Miyata, T.1    Miyazawa, S.2    Yasunaga, T.3
  • 22
    • 0036739297 scopus 로고    scopus 로고
    • Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana
    • Mondragon-Palomino, M., B. C. Meyers, R. W. Michelmore, and B. S. Gaut. 2002. Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 12:1305-1315.
    • (2002) Genome Res. , vol.12 , pp. 1305-1315
    • Mondragon-Palomino, M.1    Meyers, B.C.2    Michelmore, R.W.3    Gaut, B.S.4
  • 23
    • 84950432453 scopus 로고
    • Parametric empirical Bayes inference: Theory and applications
    • Morris, C. 1983. Parametric empirical Bayes inference: theory and applications. J. Am. Stat. Assoc. 78:47-65.
    • (1983) J. Am. Stat. Assoc. , vol.78 , pp. 47-65
    • Morris, C.1
  • 24
    • 3242789545 scopus 로고    scopus 로고
    • Differential selection of genes of cucumber mosaic virus subgroups
    • Moury, B. 2004. Differential selection of genes of cucumber mosaic virus subgroups. Mol. Biol. Evol. 21:1602-1611.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1602-1611
    • Moury, B.1
  • 25
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution 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
  • 26
    • 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 Z. Yang. 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
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki, Y., and T. Gojobori. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315-1328.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 28
    • 0036855372 scopus 로고    scopus 로고
    • Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
    • Suzuki, Y., and M. Nei. 2002. Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 19:1865-1869.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1865-1869
    • Suzuki, Y.1    Nei, M.2
  • 29
    • 1942533483 scopus 로고    scopus 로고
    • False-positive selection identified by ML-based methods: Examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus
    • -. 2004. False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol. Biol. Evol. 21:914-921.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 914-921
  • 30
    • 0035957018 scopus 로고    scopus 로고
    • Positive Darwinian selection in the evolution of mammalian female reproductive proteins
    • Swanson, W. J., Z. Yang, M. F. Wolfner, and C. F. Aquadro. 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
  • 32
    • 0036297139 scopus 로고    scopus 로고
    • Phylogenetic evidence for adaptive evolution of dengue viruses in nature
    • Twiddy, S. S., C. H. Woelk, and E. C. Holmes. 2002. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J. Gen. Virol. 83:1679-1689.
    • (2002) J. Gen. Virol. , vol.83 , pp. 1679-1689
    • Twiddy, S.S.1    Woelk, C.H.2    Holmes, E.C.3
  • 33
    • 8544225780 scopus 로고    scopus 로고
    • Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    • Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051.
    • (2004) Genetics , vol.168 , pp. 1041-1051
    • Wong, W.S.W.1    Yang, Z.2    Goldman, N.3    Nielsen, R.4
  • 34
    • 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. (http://abacus.gene.ucl. ac.uk/software/paml.html).
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 35
    • 0033692959 scopus 로고    scopus 로고
    • Maximum likelihood estimation on large phytogenies and analysis of adaptive evolution in human influenza virus A
    • -. 2000. Maximum likelihood estimation on large phytogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51:423-432.
    • (2000) J. Mol. Evol. , vol.51 , pp. 423-432
  • 36
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang, Z., and R. Nielsen. 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
  • 37
    • 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. K. 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.K.4
  • 38
    • 0036134765 scopus 로고    scopus 로고
    • Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    • Yang, Z., and W. J. Swanson. 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
  • 39
    • 0032737463 scopus 로고    scopus 로고
    • Genealogical evidence for positive selection in the nef gene of HIV-1
    • Zanotto, P. M., E. G. Kallas, R. F. Souza, and E. C. Holmes. 1999. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153:1077-1089.
    • (1999) Genetics , vol.153 , pp. 1077-1089
    • Zanotto, P.M.1    Kallas, E.G.2    Souza, R.F.3    Holmes, E.C.4


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