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Volumn 16, Issue 12, 1999, Pages 1664-1674

Statistical methods for testing functional divergence after gene duplication

Author keywords

Functional divergence; Gene duplication; Gene family evolution; Hidden Markov model; Site specific profile

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; GENE CLUSTER; GENE DUPLICATION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; PROBABILITY; STATISTICAL ANALYSIS; STOCHASTIC MODEL;

EID: 0032728408     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026080     Document Type: Article
Times cited : (402)

References (37)
  • 1
    • 0031897589 scopus 로고    scopus 로고
    • Predicting functions from protein sequences - Where are the bottlenecks?
    • BORK, P., and E. V. KOONIN. 1998. Predicting functions from protein sequences - where are the bottlenecks? Nat. Genet. 18:313-318.
    • (1998) Nat. Genet. , vol.18 , pp. 313-318
    • Bork, P.1    Koonin, E.V.2
  • 2
    • 0344432269 scopus 로고    scopus 로고
    • Parsimonious counting of mutations and estimating mutation rate heterogeneity within a DNA sequence
    • M. K. UYENOYAMA and A. VON HAESELER, eds. Duke University Publications Group, Durham, N.C.
    • DENG, H. W., and Y. X. FU. 1998. Parsimonious counting of mutations and estimating mutation rate heterogeneity within a DNA sequence. Pp. 64-71 in M. K. UYENOYAMA and A. VON HAESELER, eds. Proceedings of the Trinational Workshop on Molecular Evolution. Duke University Publications Group, Durham, N.C.
    • (1998) Proceedings of the Trinational Workshop on Molecular Evolution , pp. 64-71
    • Deng, H.W.1    Fu, Y.X.2
  • 4
    • 0031976258 scopus 로고    scopus 로고
    • Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
    • EISEN, J. A. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8:163-167.
    • (1998) Genome Res. , vol.8 , pp. 163-167
    • Eisen, J.A.1
  • 5
    • 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
  • 6
    • 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
  • 7
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • FITCH, W. M., and E. MARKOWITZ. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-593.
    • (1970) Biochem. Genet. , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 8
    • 0030249746 scopus 로고    scopus 로고
    • The coevolution of gene family trees
    • FRYXELL, K. J. 1996. The coevolution of gene family trees. Trends Genet. 12:364-369.
    • (1996) Trends Genet. , vol.12 , pp. 364-369
    • Fryxell, K.J.1
  • 9
    • 0031966661 scopus 로고    scopus 로고
    • The structural basis of molecular adaptation
    • GOLDING, G. B., and A. M. DEAN. 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
  • 10
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
    • GU, X., Y. X. Fu, and W. H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 546-557
    • Gu, X.1    Fu, Y.X.2    Li, W.H.3
  • 11
    • 7344256125 scopus 로고    scopus 로고
    • Direct mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria
    • GU, X., D. HEWETT-EMMETT, and W. H. LI. 1998. Direct mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102/103: 383-391.
    • (1998) Genetica , vol.102-103 , pp. 383-391
    • Gu, X.1    Hewett-Emmett, D.2    Li, W.H.3
  • 12
    • 0026911443 scopus 로고
    • Higher rates of amino acid substitution in rodents than in humans
    • GU, X., and W. H. LI. 1992. Higher rates of amino acid substitution in rodents than in humans. Mol. Phylogenet. Evol. 1:211-214.
    • (1992) Mol. Phylogenet. Evol. , vol.1 , pp. 211-214
    • Gu, X.1    Li, W.H.2
  • 13
    • 0028943946 scopus 로고
    • The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
    • _. 1995. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J. Mol. Evol. 40:464-473.
    • (1995) J. Mol. Evol. , vol.40 , pp. 464-473
  • 14
    • 0029900516 scopus 로고    scopus 로고
    • A general additive distance with time-reversibility and rate variation among nucleotide sites
    • _. 1996. A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc. Natl. Acad. Sci. USA 93:4671-4676.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 4671-4676
  • 15
    • 0032568590 scopus 로고    scopus 로고
    • Evolutionary distances under stationary and nonstationary models of nucleotide substitutions
    • _. 1998. Evolutionary distances under stationary and nonstationary models of nucleotide substitutions. Proc. Natl. Acad. Sci. USA 95:5899-5905.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5899-5905
  • 16
    • 0030734575 scopus 로고    scopus 로고
    • A simple method for estimating the parameter of substitution rate variation among sites
    • GU, X., and J. ZHANG. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol. Biol. Evol. 14:1106-1113.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1106-1113
    • Gu, X.1    Zhang, J.2
  • 19
    • 0028342845 scopus 로고
    • The evolution of functionally novel proteins after gene duplication
    • HUGHES, A. L. 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
    • 0016087667 scopus 로고
    • On some principles governing molecular evolution
    • KIMURA, M., and T. OHTA. 1974. On some principles governing molecular evolution. Proc. Natl. Acad. Sci. USA 71: 2848-2852.
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 2848-2852
    • Kimura, M.1    Ohta, T.2
  • 22
    • 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
  • 23
    • 0002402035 scopus 로고
    • Evolution of duplicated genes
    • M. NEI and R. K. KOEHN, eds. Sinauer, Sunderland, Mass.
    • LI, W. H. 1983. Evolution of duplicated genes. Pp. 14-37 in M. NEI and R. K. KOEHN, eds. Evolution of genes and proteins. Sinauer, Sunderland, Mass.
    • (1983) Evolution of Genes and Proteins , pp. 14-37
    • Li, W.H.1
  • 24
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer, Sunderland, Mass.
    • _. 1997. Molecular evolution. Sinauer, Sunderland, Mass.
    • (1997) Molecular Evolution
  • 25
    • 0027284770 scopus 로고
    • Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse
    • LUNDIN, L. G. 1993 Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1-19.
    • (1993) Genomics , vol.16 , pp. 1-19
    • Lundin, L.G.1
  • 26
    • 0028922906 scopus 로고
    • Testing the covarion hypothesis of molecular evolution
    • MIYAMOTO, M. M., and W. M. FITCH. 1995. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12:503-513.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 503-513
    • Miyamoto, M.M.1    Fitch, W.M.2
  • 28
    • 0030791307 scopus 로고    scopus 로고
    • Evolution by the birth-and-death process in multigene families of the vertebrate immune systems
    • NEI, M., X. GU, and T. SITNIKOVA. 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune systems. Proc. Natl. Acad. Sci. USA 94: 7799-7806.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7799-7806
    • Nei, M.1    Gu, X.2    Sitnikova, T.3
  • 31
    • 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
  • 32
    • 0031022113 scopus 로고    scopus 로고
    • Vertebrate evolution by interspecific hybridisation - Are we polyploid?
    • SPRING, J. 1997. Vertebrate evolution by interspecific hybridisation - are we polyploid? FEBS Lett. 400:2-8.
    • (1997) FEBS Lett. , vol.400 , pp. 2-8
    • Spring, J.1
  • 33
    • 0015219691 scopus 로고
    • Fitting discrete probability distribution to evolutionary events
    • UZZEL, T, and K. W. CORBIN. 1971. Fitting discrete probability distribution to evolutionary events. Science 172:1089-1096.
    • (1971) Science , vol.172 , pp. 1089-1096
    • Uzzel, T.1    Corbin, K.W.2
  • 34
    • 0027496790 scopus 로고
    • Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA
    • WAKELEY, J. 1993 Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
    • (1993) J. Mol. Evol. , vol.37 , pp. 613-623
    • Wakeley, J.1
  • 35
    • 0000378875 scopus 로고
    • Evidence for higher rates of nucleotide substitution in rodents than in human
    • WU, C. I., and W. H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in human. Proc. Natl. Acad. Sci. USA 82:1741-1745.
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 1741-1745
    • Wu, C.I.1    Li, W.H.2
  • 36
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • YANG, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 37
    • 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.