메뉴 건너뛰기




Volumn 168, Issue 2, 2004, Pages 1041-1051

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; HLA SYSTEM; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS;

EID: 8544225780     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.031153     Document Type: Article
Times cited : (479)

References (41)
  • 1
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • ANISIMOVA, M., J. P. BIELAWSKI and Z. YANG, 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 bayes prediction of amino acid sites under positive selection
    • ANISIMOVA, M., J. P. BIELAWSKI and Z. YANG, 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
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 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
    • 0037884727 scopus 로고    scopus 로고
    • MHC studies in nonmodel vertebrates: What have we learned about natural selection in 15 years?
    • BERNATCHEZ, L., and C. LANDRY, 2003 MHC studies in nonmodel vertebrates: What have we learned about natural selection in 15 years? J. Evol. Biol. 16: 363-377.
    • (2003) J. Evol. Biol. , vol.16 , pp. 363-377
    • Bernatchez, L.1    Landry, C.2
  • 6
    • 0023187442 scopus 로고
    • The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens
    • BJORKMAN, P. J., S. A. SAFER, B. SAMRAOUI, W. S. BENNET, J. L. STROMINGER et al., 1987b The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329: 512-518.
    • (1987) Nature , vol.329 , pp. 512-518
    • Bjorkman, P.J.1    Safer, S.A.2    Samraoui, B.3    Bennet, W.S.4    Strominger, J.L.5
  • 7
    • 0032736987 scopus 로고    scopus 로고
    • Positive selection on the H3 hemagglutinin gene of human influenza virus A
    • BUSH, R. M., W. M. FITCH, C. A. BENDER and N. J. COX, 1999 Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol. Biol. Evol. 16: 1457-1465.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1457-1465
    • Bush, R.M.1    Fitch, W.M.2    Bender, C.A.3    Cox, N.J.4
  • 8
    • 0000926206 scopus 로고
    • On the distribution of the likelihood ratio
    • CHERNOFF, H., 1954 On the distribution of the likelihood ratio. Ann. Math. Stat. 25: 573-578.
    • (1954) Ann. Math. Stat. , vol.25 , pp. 573-578
    • Chernoff, H.1
  • 9
    • 0842326022 scopus 로고    scopus 로고
    • Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes
    • CHOISY, M., C. H. WOELK, J. F. GUEGAN and D. L. ROBERTSON, 2004 Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J. Virol. 78: 1962-1970.
    • (2004) J. Virol. , vol.78 , pp. 1962-1970
    • Choisy, M.1    Woelk, C.H.2    Guegan, J.F.3    Robertson, D.L.4
  • 10
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • FITCH, W. M., 1971 Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20: 406-416.
    • (1971) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 11
    • 0030750055 scopus 로고    scopus 로고
    • Long term trends in the evolution of H(3) HA1 human influenza type A
    • FITCH, W. M., R. M. BUSH, C. A. BENDER and N. J. COX, 1997 Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl. Acad. Sci. USA 94: 7712-7718.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7712-7718
    • Fitch, W.M.1    Bush, R.M.2    Bender, C.A.3    Cox, N.J.4
  • 12
    • 0028168856 scopus 로고
    • Acodon-based model of nucleotide substitution for protein-coding DNA sequences
    • GOLDMAN, N., and Z. YANG, 1994 Acodon-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
  • 13
    • 0002329356 scopus 로고
    • Minimum mutation fits to a given tree
    • HARTIGAN, J. A., 1973 Minimum mutation fits to a given tree. Biometrics 29: 53-65.
    • (1973) Biometrics , vol.29 , pp. 53-65
    • Hartigan, J.A.1
  • 14
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • KIMURA, M., 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 15
    • 0036075245 scopus 로고    scopus 로고
    • Tracking adaptive evolutionary events in genomic sequences
    • REVIEWS1018
    • LIBERLES, D. A., and M. L. WAYNE, 2002 Tracking adaptive evolutionary events in genomic sequences. Genome Biol. 3: REVIEWS1018.
    • (2002) Genome Biol. , vol.3
    • Liberles, D.A.1    Wayne, M.L.2
  • 17
    • 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
  • 18
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • NEI, M., and T. GOJOBORI, 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 19
    • 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
  • 20
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • SAITOU, N., and M. NEI, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 21
    • 84907319426 scopus 로고
    • Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions
    • SELF, S., and K.-Y. LIANG, 1987 Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82: 605-610.
    • (1987) J. Am. Stat. Assoc. , vol.82 , pp. 605-610
    • Self, S.1    Liang, K.-Y.2
  • 22
    • 67649345185 scopus 로고
    • An improved Bonferroni procedure for multiple tests of significance
    • SIMES, R. J., 1986 An improved Bonferroni procedure for multiple tests of significance. Biometrika 73: 751-754.
    • (1986) Biometrika , vol.73 , pp. 751-754
    • Simes, R.J.1
  • 23
    • 0041571680 scopus 로고    scopus 로고
    • The effect of positive selection on a sexual reproduction gene in Thalassiosira weissflogii (Bacillariophyta): Results obtained from maximum-likelihood and parsimony-based methods
    • SORHANNUS, U., 2003 The effect of positive selection on a sexual reproduction gene in Thalassiosira weissflogii (Bacillariophyta): results obtained from maximum-likelihood and parsimony-based methods. Mol. Biol. Evol. 20: 1326-1328.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1326-1328
    • Sorhannus, U.1
  • 25
    • 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
  • 26
    • 0035215112 scopus 로고    scopus 로고
    • Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites
    • SUZUKI, Y., and M. NEI, 2001 Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 18: 2179-2185.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2179-2185
    • Suzuki, Y.1    Nei, M.2
  • 27
    • 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
  • 28
    • 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
    • SUZUKI, Y., and M. NEI, 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
    • Suzuki, Y.1    Nei, M.2
  • 29
    • 0034904729 scopus 로고    scopus 로고
    • ADAPTSITE: Detecting natural selection at single amino acid sites
    • SUZUKI, Y., T. GOJOBORI and M. NEI, 2001 ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics 17: 660-661.
    • (2001) Bioinformatics , vol.17 , pp. 660-661
    • Suzuki, Y.1    Gojobori, T.2    Nei, M.3
  • 30
    • 85047700164 scopus 로고    scopus 로고
    • The rapid evolution of reproductive proteins
    • SWANSON, W. J., and V. D. VACQUIER, 2002 The rapid evolution of reproductive proteins. Nat. Rev. Genet. 3: 137-144.
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 137-144
    • Swanson, W.J.1    Vacquier, V.D.2
  • 31
    • 0037230001 scopus 로고    scopus 로고
    • Pervasive adaptive evolution in mammalian fertilization proteins
    • SWANSON, W. J., R. NIELSEN and Q. YANG, 2003 Pervasive adaptive evolution in mammalian fertilization proteins. Mol. Biol. Evol. 20: 18-20.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 18-20
    • Swanson, W.J.1    Nielsen, R.2    Yang, Q.3
  • 32
    • 0033995286 scopus 로고    scopus 로고
    • Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes
    • YAMAGUCHI-KABATA, Y., and T. GOJOBORI, 2000 Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J. Virol. 74: 4335-4350.
    • (2000) J. Virol. , vol.74 , pp. 4335-4350
    • Yamaguchi-Kabata, Y.1    Gojobori, T.2
  • 33
    • 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.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 34
    • 0033692959 scopus 로고    scopus 로고
    • Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A
    • YANG, Z., 2000a Maximum likelihood estimation on large phylogenies 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
    • Yang, Z.1
  • 36
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • YANG, Z., and J. P. BIELAWSKI, 2000 Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15: 496-503.
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 37
    • 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
  • 38
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • YANG, Z., S. KUMAR and M. NEI, 1995 A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141: 1641-1650.
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 39
    • 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
  • 40
    • 0031025677 scopus 로고    scopus 로고
    • Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods
    • ZHANG, J., and M. NEI, 1997 Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J. Mol. Evol. 44: S139-S146.
    • (1997) J. Mol. Evol. , vol.44
    • Zhang, J.1    Nei, M.2
  • 41
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • ZHANG, J., H. F. ROSENBERG and M. NEI, 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.