메뉴 건너뛰기




Volumn 15, Issue 12, 1998, Pages 1600-1611

Models of amino acid substitution and applications to mitochondrial protein evolution

Author keywords

Amino acid substitution; Mammals; Maximum likelihood; Mitochondrial DNA; Protein evolution

Indexed keywords

MITOCHONDRIAL DNA;

EID: 0031792828     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025888     Document Type: Article
Times cited : (324)

References (46)
  • 1
    • 0003243559 scopus 로고
    • MOLPHY: Programs for molecular phylogenetics, I. - PROTML: maximum likelihood inference of protein phylogeny
    • ADACHI, J., and M. HASEGAWA. 1992. MOLPHY: programs for molecular phylogenetics, I. - PROTML: maximum likelihood inference of protein phylogeny. Comput. Sci. Monogr. 27:1-77.
    • (1992) Comput. Sci. Monogr. , vol.27 , pp. 1-77
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 0002367729 scopus 로고    scopus 로고
    • MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
    • _. 1996a. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.
    • (1996) Comput. Sci. Monogr. , vol.28 , pp. 1-150
  • 3
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • _. 1996b. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459-468.
    • (1996) J. Mol. Evol. , vol.42 , pp. 459-468
  • 4
    • 0022358402 scopus 로고
    • Evolutionary trees from nucleic acid and protein sequences
    • BISHOP, M. J., and A. E. FRIDAY. 1985. Evolutionary trees from nucleic acid and protein sequences. Proc. R. Soc. Lond. B. Biol. Sci. 226:271-302.
    • (1985) Proc. R. Soc. Lond. B. Biol. Sci. , vol.226 , pp. 271-302
    • Bishop, M.J.1    Friday, A.E.2
  • 5
    • 0005723678 scopus 로고
    • Tetropad relationships: The molecular evidence
    • C. PATTERSON, ed. Cambridge University Press, Cambridge, England
    • _. 1987. Tetropad relationships: the molecular evidence. Pp. 123-139 in C. PATTERSON, ed. Molecules and morphology in evolution: conflict or compromise? Cambridge University Press, Cambridge, England.
    • (1987) Molecules and Morphology in Evolution: Conflict or Compromise? , pp. 123-139
  • 6
    • 0028941917 scopus 로고
    • Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications
    • BROWN, J. R., and W. F. DOOLITTLE. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 92: 2441-2445.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 2441-2445
    • Brown, J.R.1    Doolittle, W.F.2
  • 7
    • 0028172520 scopus 로고
    • Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
    • CAO, Y., J. ADACHI, A. JANKE, S. PAABO, and M. HASEGAWA. 1994a. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 39:519-527.
    • (1994) J. Mol. Evol. , vol.39 , pp. 519-527
    • Cao, Y.1    Adachi, J.2    Janke, A.3    Paabo, S.4    Hasegawa, M.5
  • 8
    • 0028362463 scopus 로고
    • Phylogenetic place of guinea pigs: No support of the rodent polyphyly hypothesis from maximum likelihood analyses of multiple protein sequences
    • CAO, Y., J. ADACHI, T. YANO, and M. HASEGAWA. 1994b. Phylogenetic place of guinea pigs: no support of the rodent polyphyly hypothesis from maximum likelihood analyses of multiple protein sequences. Mol. Biol. Evol. 11:593-604.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 593-604
    • Cao, Y.1    Adachi, J.2    Yano, T.3    Hasegawa, M.4
  • 10
    • 0019829486 scopus 로고
    • Simulation of protein evolution by random fixation of allowed codons
    • COATES, M., and S. STONE. 1981. Simulation of protein evolution by random fixation of allowed codons. J. Mol. Evol. 17:311-328.
    • (1981) J. Mol. Evol. , vol.17 , pp. 311-328
    • Coates, M.1    Stone, S.2
  • 11
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • National Biomedical Research Foundation, Washington, D.C.
    • DAYHOFF, M. O., R. M. SCHWARTZ, and B. C. ORCUTT. 1978. A model of evolutionary change in proteins. Pp. 345-352 in Atlas of protein sequence and structure. Vol. 5, Suppl. 3. National Biomedical Research Foundation, Washington, D.C.
    • (1978) Atlas of Protein Sequence and Structure , vol.5 , Issue.3 SUPPL. , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 12
    • 3643115136 scopus 로고
    • Relation of protein evolution to tertiary structure
    • EPSTEIN, C. J. 1964. Relation of protein evolution to tertiary structure. Nature 203:1350-1352.
    • (1964) Nature , vol.203 , pp. 1350-1352
    • Epstein, C.J.1
  • 13
    • 0014214038 scopus 로고
    • Non-randomness of amino-acid changes in the evolution of homologous proteins
    • _. 1967. Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature 215:355-359.
    • (1967) Nature , vol.215 , pp. 355-359
  • 14
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 16
    • 0021070935 scopus 로고
    • Codon substitution in evolution and the "saturation" of synonymous changes
    • GOJOBORI, T. 1983. Codon substitution in evolution and the "saturation" of synonymous changes. Genetics 105:1011-1027.
    • (1983) Genetics , vol.105 , pp. 1011-1027
    • Gojobori, T.1
  • 17
    • 0021003230 scopus 로고
    • Estimates of DNA and protein sequence divergence: An examination of some assumptions
    • GOLDING, G. B. 1983. Estimates of DNA and protein sequence divergence: an examination of some assumptions. Mol. Biol. Evol. 1:125-142.
    • (1983) Mol. Biol. Evol. , vol.1 , pp. 125-142
    • Golding, G.B.1
  • 18
    • 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
  • 20
    • 0027463557 scopus 로고
    • Ribosomal RNA trees misleading?
    • HASEGAWA, M., and T. HASHIMOTO. 1993. Ribosomal RNA trees misleading? Nature 361:23.
    • (1993) Nature , vol.361 , pp. 23
    • Hasegawa, M.1    Hashimoto, T.2
  • 21
    • 0029976676 scopus 로고    scopus 로고
    • Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1α/Tu and 2/G
    • HASHIMOTO, T., and M. HASEGAWA. 1996. Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1α/Tu and 2/G. Adv. Biophys. 32:73-120.
    • (1996) Adv. Biophys. , vol.32 , pp. 73-120
    • Hashimoto, T.1    Hasegawa, M.2
  • 22
    • 0024358140 scopus 로고
    • Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
    • IWABE, N., K. KUMA, M. HASEGAWA, S. OSAWA, and T. MIYATA. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:9355-9359.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 9355-9359
    • Iwabe, N.1    Kuma, K.2    Hasegawa, M.3    Osawa, S.4    Miyata, T.5
  • 23
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 24
    • 0016627084 scopus 로고
    • A model for the evolution of the proteins
    • JORRÉ, R. P., and N. CURNOW. 1975. A model for the evolution of the proteins. Biochemie 57:1141-1146.
    • (1975) Biochemie , vol.57 , pp. 1141-1146
    • Jorré, R.P.1    Curnow, N.2
  • 26
    • 0025181359 scopus 로고
    • Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
    • KISHINO, H., T. MIYATA, and M. HASEGAWA. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
    • (1990) J. Mol. Evol. , vol.31 , pp. 151-160
    • Kishino, H.1    Miyata, T.2    Hasegawa, M.3
  • 27
    • 0014368775 scopus 로고
    • Formal analysis of protein sequences. II. Method for structural studies of homologous proteins and amino acid substitutions in cytochrome c
    • KRZYWICKI, A., and P. P. SLONIMSKI. 1968. Formal analysis of protein sequences. II. Method for structural studies of homologous proteins and amino acid substitutions in cytochrome c. J. Theor. Biol. 21:305-330.
    • (1968) J. Theor. Biol. , vol.21 , pp. 305-330
    • Krzywicki, A.1    Slonimski, P.P.2
  • 28
    • 0015505473 scopus 로고
    • Repeating sequences and gene duplication in proteins
    • MACLACHLAN, A. D. 1972. Repeating sequences and gene duplication in proteins. J. Mol. Evol. 64:417-437.
    • (1972) J. Mol. Evol. , vol.64 , pp. 417-437
    • Maclachlan, A.D.1
  • 29
    • 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
  • 30
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to chloroplast genome
    • MUSE, S. V., and B. S. GAUT. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to 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
  • 31
    • 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
  • 32
    • 0026808975 scopus 로고
    • Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA
    • REEVES, J. H. 1992. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J. Mol. Evol. 35:17-31.
    • (1992) J. Mol. Evol. , vol.35 , pp. 17-31
    • Reeves, J.H.1
  • 33
    • 0028512129 scopus 로고
    • A stochastic model and the evolution of autocorrelated DNA sequences
    • SCHÖNIGER, M., and A. VON HAESELER. 1994. A stochastic model and the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 3:240-247.
    • (1994) Mol. Phylogenet. Evol. , vol.3 , pp. 240-247
    • Schöniger, M.1    Von Haeseler, A.2
  • 34
    • 0013965569 scopus 로고
    • Relations between chemical structures and biological activity in peptides
    • SNEATH, P. H. A. 1966. Relations between chemical structures and biological activity in peptides. J. Theor. Biol. 12:157-195.
    • (1966) J. Theor. Biol. , vol.12 , pp. 157-195
    • Sneath, P.H.A.1
  • 35
    • 0022591495 scopus 로고
    • The classification of amino acid conservation
    • TAYLOR, W. R. 1986. The classification of amino acid conservation. J. Theor. Biol. 119:205-218.
    • (1986) J. Theor. Biol. , vol.119 , pp. 205-218
    • Taylor, W.R.1
  • 36
    • 0029985399 scopus 로고    scopus 로고
    • Combining protein evolution and secondary structure
    • THORNE, J. L., N. GOLDMAN, and D. T. JONES. 1996. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:666-673.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 666-673
    • Thorne, J.L.1    Goldman, N.2    Jones, D.T.3
  • 37
    • 0015219691 scopus 로고
    • Fitting discrete probability distributions to evolutionary events
    • UZZELL, T., and K. W. CORBIN. 1971. Fitting discrete probability distributions to evolutionary events. Science 172: 1089-1096.
    • (1971) Science , vol.172 , pp. 1089-1096
    • Uzzell, T.1    Corbin, K.W.2
  • 38
    • 0028297534 scopus 로고
    • Substitution rate variation among sites and the estimation of transition bias
    • WAKELEY, J. 1994. Substitution rate variation among sites and the estimation of transition bias. Mol. Biol. Evol. 11:436-442.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 436-442
    • Wakeley, J.1
  • 39
    • 0022006915 scopus 로고
    • On the PAM matrix model of protein evolution
    • WILBUR, W. J. 1985. On the PAM matrix model of protein evolution. Mol. Biol. Evol. 2:434-447.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 434-447
    • Wilbur, W.J.1
  • 40
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • YANG, Z. 1994a. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
    • (1994) J. Mol. Evol. , vol.39 , pp. 105-111
    • Yang, Z.1
  • 41
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • _. 1994b. 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
  • 42
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation
    • YANG, Z., N. GOLDMAN, and A. E. FRIDAY. 1994. Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Mol. Biol. Evol. 11: 316-324.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.E.3
  • 43
    • 0029892459 scopus 로고    scopus 로고
    • Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
    • YANG, Z., and S. KUMAR. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13: 650-659.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 650-659
    • Yang, Z.1    Kumar, S.2
  • 44
    • 0028961933 scopus 로고
    • On the use of nucleic acid sequences to infer early branchings in the tree of life
    • YANG, Z., and D. ROBERTS. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12:451-458.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 451-458
    • Yang, Z.1    Roberts, D.2
  • 45
    • 0028108336 scopus 로고
    • Estimation of evolutionary distances between nucleotide sequences
    • ZHARKIKH, A. 1994. Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol. 39:315-329.
    • (1994) J. Mol. Evol. , vol.39 , pp. 315-329
    • Zharkikh, A.1
  • 46
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence in proteins
    • V. BRYSON and H. J. VOGEL, eds. Academic Press, New York
    • ZUCKERKANDL, E., and L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pp. 97-116 in V. BRYSON and H. J. VOGEL, eds. Evolving genes and proteins. Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 97-116
    • Zuckerkandl, E.1    Pauling, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.