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Volumn 11, Issue 9, 1996, Pages 367-372

Among-site rate variation and its impact on phylogenetic analyses

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY RATE; PHYLOGENY; SPECIATION;

EID: 0030451420     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/0169-5347(96)10041-0     Document Type: Review
Times cited : (1011)

References (47)
  • 1
    • 0014092973 scopus 로고
    • A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome casa model case
    • Fitch, W.M. and Margoliash, E. (1967) A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome casa model case, Biochem. Genet. 1, 65-71
    • (1967) Biochem. Genet. , vol.1 , pp. 65-71
    • Fitch, W.M.1    Margoliash, E.2
  • 2
    • 0001434413 scopus 로고
    • On the topography of the genetic fine structure
    • Benzer, S. (1961) On the topography of the genetic fine structure, Genetics 47, 403-415
    • (1961) Genetics , vol.47 , pp. 403-415
    • Benzer, S.1
  • 3
    • 0001952402 scopus 로고
    • Evolution of DNA sequences
    • (MacIntyre, J., ed.), Plenum Press
    • Li, W-H., Wu, C-I. and Luo, C-C. (1985) Evolution of DNA sequences, in Molecular Evolutionary Genetics (MacIntyre, J., ed.), pp. 1-94, Plenum Press
    • (1985) Molecular Evolutionary Genetics , pp. 1-94
    • Li, W.-H.1    Wu, C.-I.2    Luo, C.-C.3
  • 4
    • 0015219691 scopus 로고
    • Fitting discrete probability distributions to evolutionary events
    • Uzzell, T. and Corbin, K.W. (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
  • 5
    • 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
  • 6
    • 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
  • 7
    • 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
  • 8
    • 0025061094 scopus 로고
    • Limitations of the evolutionary parsimony method of phylogenetic analysis
    • Jin, L. and Nei, N. (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis, Mol Biol Evol. 7, 82-102
    • (1990) Mol Biol Evol. , vol.7 , pp. 82-102
    • Jin, L.1    Nei, N.2
  • 9
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura, K. and Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol. 10, 512-526
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 10
    • 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
  • 11
    • 0028230202 scopus 로고
    • Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites
    • Rzhetsky, A. and Nei, M. (1994) Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites, J. Mol. Evol. 38, 295-299
    • (1994) J. Mol. Evol. , vol.38 , pp. 295-299
    • Rzhetsky, A.1    Nei, M.2
  • 12
    • 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 Kumar, S. (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
  • 13
    • 0014680905 scopus 로고
    • Non-darwinian evolution
    • King, J.L. and Jukes, T.H. (1969) Non-darwinian evolution, Science 164, 788-798
    • (1969) Science , vol.164 , pp. 788-798
    • King, J.L.1    Jukes, T.H.2
  • 14
    • 0022376704 scopus 로고
    • Dating the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating 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
  • 15
    • 0024359678 scopus 로고
    • Rates of molecular evolution and the function of nucleotide positions free to vary
    • Palumbi, S.R. (1989) Rates of molecular evolution and the function of nucleotide positions free to vary, J. Mol. Evol. 29, 180-187
    • (1989) J. Mol. Evol. , vol.29 , pp. 180-187
    • Palumbi, S.R.1
  • 16
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
    • Gu, X., Fu, Y-X. and Li, W-H. (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
  • 17
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • Yang, Z. (1995) A space-time process model for the evolution of DNA sequences, Genetics 139, 993-1005
    • (1995) Genetics , vol.139 , pp. 993-1005
    • Yang, Z.1
  • 18
    • 0027428406 scopus 로고
    • Toward a more accurate time scale for the human mitochondrial DNA tree
    • Hasegawa, M. et al. (1993) Toward a more accurate time scale for the human mitochondrial DNA tree, J. Mol. Evol. 37, 347-354
    • (1993) J. Mol. Evol. , vol.37 , pp. 347-354
    • Hasegawa, M.1
  • 19
    • 0029970097 scopus 로고    scopus 로고
    • Maximum likelihood models for combined analyses of multiple sequence data
    • in press
    • Yang, Z. Maximum likelihood models for combined analyses of multiple sequence data, J. Mol Evol. (in press)
    • J. Mol Evol.
    • Yang, Z.1
  • 20
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • Felsenstein, J. and Churchill, G.A. (1996) A hidden Markov model approach to variation among sites in rate of evolution, Mol. Biol. Evol. 13, 93-104
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 21
    • 0029930086 scopus 로고    scopus 로고
    • Modeling nucleotide evolution: A heterogeneous rate analysis
    • Kelly, C. and Rice, J. (1996) Modeling nucleotide evolution: a heterogeneous rate analysis, Math. Biosci. 133, 85-109
    • (1996) Math. Biosci. , vol.133 , pp. 85-109
    • Kelly, C.1    Rice, J.2
  • 22
    • 0028807391 scopus 로고
    • Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmontine rodents
    • Sullivan, J, Holsinger, K.E. and Simon, C. (1995) Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmontine rodents, Mol. Biol. Evol. 12, 988-1001
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 988-1001
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 23
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation
    • Yang, Z., Goldman, N. and Friday, A.E. (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
  • 24
    • 0029880314 scopus 로고    scopus 로고
    • The effect of topology on estimation of among-site rate variation
    • Sullivan, J., Holsinger, K.E. and Simon, C. (1996) The effect of topology on estimation of among-site rate variation, J. Mol. Evol. 42, 308-312
    • (1996) J. Mol. Evol. , vol.42 , pp. 308-312
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 25
    • 0029120814 scopus 로고
    • Mixed model analysis of DNA sequence evolution
    • Yang, Z. and Wang, T. (1995) Mixed model analysis of DNA sequence evolution, Biometrics 51, 552-561
    • (1995) Biometrics , vol.51 , pp. 552-561
    • Yang, Z.1    Wang, T.2
  • 26
    • 0030008961 scopus 로고    scopus 로고
    • Evolution of the hedgehog gene family
    • Kumar, S., Balczarek, K.A. and Lai, Z-C. (1996) Evolution of the hedgehog gene family, Genetics 142, 965-972
    • (1996) Genetics , vol.142 , pp. 965-972
    • Kumar, S.1    Balczarek, K.A.2    Lai, Z.-C.3
  • 27
    • 0029067458 scopus 로고
    • Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
    • Yang, Z. (1995) Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites, J. Mol. Evol. 40, 689-697
    • (1995) J. Mol. Evol. , vol.40 , pp. 689-697
    • Yang, Z.1
  • 28
    • 0029960344 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates
    • Kumar, S. (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates, Genetics 143, 537-548
    • (1996) Genetics , vol.143 , pp. 537-548
    • Kumar, S.1
  • 29
    • 0008114066 scopus 로고
    • Rates of molecular evolution
    • Gillespie, J.H. (1986) Rates of molecular evolution, Annu. Rev. Ecol. Syst. 17, 637-665
    • (1986) Annu. Rev. Ecol. Syst. , vol.17 , pp. 637-665
    • Gillespie, J.H.1
  • 30
    • 0029039263 scopus 로고
    • Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites
    • Adachi, J. and Hasegawa, M. (1995) Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites, J. Mol. Evol. 40, 622-628
    • (1995) J. Mol. Evol. , vol.40 , pp. 622-628
    • Adachi, J.1    Hasegawa, M.2
  • 31
    • 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
  • 32
    • 0001062055 scopus 로고    scopus 로고
    • The excess of transitions among nucleotide substitutions: New methods of estimating transition bias underscore its significance
    • Wakeley, J. (1996) The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance, Trends Ecol. Evol. 11, 158-163
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 158-163
    • Wakeley, J.1
  • 33
    • 0029469716 scopus 로고
    • Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
    • Yang, Z., Goldman, N. and Friday, A.E. (1995) Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem, Syst. Biol. 44, 384-399
    • (1995) Syst. Biol. , vol.44 , pp. 384-399
    • Yang, Z.1    Goldman, N.2    Friday, A.E.3
  • 34
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang, Z. (1994) Estimating the pattern of nucleotide substitution, J. Mol. Evol. 39, 105-111
    • (1994) J. Mol. Evol. , vol.39 , pp. 105-111
    • Yang, Z.1
  • 35
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
    • Tateno, Y., Takezaki, N. and Nei, M. (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site, Mol. Biol. Evol. 11, 261-277
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 261-277
    • Tateno, Y.1    Takezaki, N.2    Nei, M.3
  • 36
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner, M.K. and Felsenstein, J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol. Biol. Evol. 11, 459-468
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 37
    • 0028887457 scopus 로고
    • Success of maximum likelihood phylogeny inference in the four-taxon case
    • Gaut, B.S. and Lewis, P.O. (1995) Success of maximum likelihood phylogeny inference in the four-taxon case, Mol. Biol. Evol. 12, 152-162
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 152-162
    • Gaut, B.S.1    Lewis, P.O.2
  • 38
    • 11944268967 scopus 로고
    • The performance of phylogenetic methods in simulation
    • Huelsenbeck, J.P. (1995) The performance of phylogenetic methods in simulation, Syst. Biol. 44, 17-48
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.P.1
  • 39
    • 0029935637 scopus 로고    scopus 로고
    • Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
    • Lockhart, P.J. et al. (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis, Proc. Natl. Acad. Sci. U. S. A. 93, 1930-1934
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 1930-1934
    • Lockhart, P.J.1
  • 40
    • 84963028421 scopus 로고
    • A successive approximations approach to character weighting
    • Farris, J.S. (1969) A successive approximations approach to character weighting, Syst. Zool. 18, 374-385
    • (1969) Syst. Zool. , vol.18 , pp. 374-385
    • Farris, J.S.1
  • 41
    • 0025274493 scopus 로고
    • Phylogenetic determination using dynamically weighted parsimony method
    • Williams, P.L. and Fitch, P.M. (1990) Phylogenetic determination using dynamically weighted parsimony method, Methods Enzymol. 183, 615-626
    • (1990) Methods Enzymol. , vol.183 , pp. 615-626
    • Williams, P.L.1    Fitch, P.M.2
  • 42
    • 0029097280 scopus 로고
    • The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters
    • Berterolle, G. and Slatkin, M. (1995) The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters, Mol. Biol. Evol 12, 887-892
    • (1995) Mol. Biol. Evol , vol.12 , pp. 887-892
    • Berterolle, G.1    Slatkin, M.2
  • 43
    • 0030056912 scopus 로고    scopus 로고
    • The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism
    • Aris-Brosou, S. and Excoffier, L. (1996) The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism, Mol. Biol. Evol. 13, 494-504
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 494-504
    • Aris-Brosou, S.1    Excoffier, L.2
  • 44
    • 0042057558 scopus 로고    scopus 로고
    • The performance of phylogenetic methods for a well-supported phylogeny
    • in press
    • Huelsenbeck, J.P., Cunningham, C.W. and Graybeal, A. The performance of phylogenetic methods for a well-supported phylogeny, Syst. Biol. (in press)
    • Syst. Biol.
    • Huelsenbeck, J.P.1    Cunningham, C.W.2    Graybeal, A.3
  • 45
    • 0029091043 scopus 로고
    • Estimating substitution rates in ribosomal RNA genes
    • Rzhetsky. R. (1995) Estimating substitution rates in ribosomal RNA genes, Genetics 141, 771-783
    • (1995) Genetics , vol.141 , pp. 771-783
    • Rzhetsky, R.1
  • 46
    • 0028805929 scopus 로고
    • Molecular evolution of the hepatitis b virus genome
    • Yang, Z., Lauder, I.J. and Lin, H.J. (1995) Molecular evolution of the hepatitis B virus genome, J. Mol. Evol. 41, 587-596
    • (1995) J. Mol. Evol. , vol.41 , pp. 587-596
    • Yang, Z.1    Lauder, I.J.2    Lin, H.J.3
  • 47
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D.T., Taylor, W.R. and Thornton, J.M. (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


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