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Volumn 60, Issue 1, 2011, Pages 60-73

Quantifying the impact of dependent evolution among sites in phylogenetic inference

Author keywords

continuous time Markov model; distance methods; Independence; maximum likelihood; parsimony

Indexed keywords

DNA; MYOGLOBIN; PROTEIN; RNA;

EID: 79952147429     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq074     Document Type: Article
Times cited : (26)

References (37)
  • 1
    • 58449116673 scopus 로고    scopus 로고
    • Investigating protein-coding sequence evolution with probabilistic substitution models
    • Anisimova M., Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic substitution models. Mol. Biol. Evol. 26:255-271.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 255-271
    • Anisimova, M.1    Kosiol, C.2
  • 2
    • 0035427382 scopus 로고    scopus 로고
    • How to guarantee optimal stability for most representative structures in the protein data bank
    • Bastolla U., Farwer J., Knapp E. W., Vendruscolo M. 2001. How to guarantee optimal stability for most representative structures in the protein data bank. Proteins. 44:79-96.
    • (2001) Proteins , vol.44 , pp. 79-96
    • Bastolla, U.1    Farwer, J.2    Knapp, E.W.3    Vendruscolo, M.4
  • 4
    • 34547809931 scopus 로고    scopus 로고
    • Quantifying the impact of protein tertiary structure on molecular evolution
    • DOI 10.1093/molbev/msm097
    • Choi S. C., Hobolth A., Robinson D. M., Kishino H., Thorne J. L. 2007. Quantifying the impact of protein tertiary structure on molecular evolution. Mol. Biol. Evol. 24:1769-1782. (Pubitemid 47236697)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1769-1782
    • Choi, S.C.1    Hobolth, A.2    Robinson, D.M.3    Kishino, H.4    Thorne, J.L.5
  • 5
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-411.
    • (1978) Syst. Zool. , vol.27 , pp. 401-411
    • Felsenstein, J.1
  • 6
    • 0030034795 scopus 로고    scopus 로고
    • A Hidden Markov Model approach to variation among sites in rate of evolution
    • Felsenstein J., Churchill G. A. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104. (Pubitemid 26012458)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.1 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 7
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N., Thorne J., Jones D. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics. 149:445-458.
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.2    Jones, D.3
  • 8
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N., Yang Z. 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
  • 9
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • Huelsenbeck J. P., Hillis D. M. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
    • (1993) Syst. Biol. , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 10
    • 0033139150 scopus 로고    scopus 로고
    • Effect of nonindependent substitution on phylogenetic accuracy
    • Huelsenbeck J. P., Nielsen R. 1999. Effect of non-independent substitution on phylogenetic accuracy. Syst. Biol. 48:317-328. (Pubitemid 129493669)
    • (1999) Systematic Biology , vol.48 , Issue.2 , pp. 317-328
    • Huelsenbeck, J.P.1    Nielsen, R.2
  • 11
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • DOI 10.1006/jmbi.1999.2583
    • Jones D. 1999. Genthreader: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287:797-815. (Pubitemid 29176514)
    • (1999) Journal of Molecular Biology , vol.287 , Issue.4 , pp. 797-815
    • Jones, D.T.1
  • 12
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones D. T., Taylor W. R., Thornton J. M. 1992. A new approach to protein fold recognition. Nature. 358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 13
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro H. N, editor, San Diego CA: Academic Press
    • Jukes T. H., Cantor C. R. 1969. Evolution of protein molecules. In: Munro H. N, editor. Mammalian protein metabolism. San Diego (CA): Academic Press. p. 21-123.
    • (1969) Mammalian Protein Metabolism , pp. 21-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 14
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • DOI 10.1007/BF01731581
    • 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. (Pubitemid 11166431)
    • (1980) Journal of Molecular Evolution , vol.16 , Issue.2 , pp. 111-120
    • Kimura, M.1
  • 16
    • 0031014702 scopus 로고    scopus 로고
    • Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element
    • Mathews, D. H., Banerjee A., Luan D., Eickbush T., Turner D. 1997. Secondary structure model of the rna recognized by the reverse transcriptase from the r2 retrotransposable element. RNA. 3:1-16. (Pubitemid 27030245)
    • (1997) RNA , vol.3 , Issue.1 , pp. 1-16
    • Mathews, D.H.1    Banerjee, A.R.2    Luan, D.D.3    Eickbush, T.H.4    Turner, D.H.5
  • 18
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • DOI 10.1006/jmbi.1999.2700
    • Mathews D. H., Sabina J., Zuker M., Turner D. H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:911-940. (Pubitemid 29248642)
    • (1999) Journal of Molecular Biology , vol.288 , Issue.5 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 19
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse S. V., Gaut B. S. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724. (Pubitemid 24274880)
    • (1994) Molecular Biology and Evolution , vol.11 , Issue.5 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 20
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R., Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:929-93.
    • (1998) Genetics , vol.148 , pp. 929-993
    • Nielsen, R.1    Yang, Z.2
  • 22
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • Robinson D. F., Foulds L. R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147. (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 24
    • 15544374861 scopus 로고    scopus 로고
    • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    • DOI 10.1016/j.gene.2004.12.011
    • Rodrigue N., Lartillot N., Bryant D., Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene. 347:207-217. (Pubitemid 40403760)
    • (2005) Gene , vol.347 , Issue.2 SPEC. ISSUE , pp. 207-217
    • Rodrigue, N.1    Lartillot, N.2    Bryant, D.3    Philippe, H.4
  • 25
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N., Nei M. 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
  • 26
    • 0028512129 scopus 로고
    • A stochastic model and the evolution of autocorrelated dna sequences
    • Schöniger M., von Haeseler A. 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
  • 28
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems on the analysis of DNA sequences
    • Tavaré S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lectures in Mathematics in the Life Sciences 17:57-86.
    • (1986) Lectures in Mathematics in the Life Sciences , vol.17 , pp. 57-86
    • Tavaré, S.1
  • 30
    • 0028136449 scopus 로고
    • Maximum likelihood with multiparameter models of substitution
    • DOI 10.1007/BF00160273
    • Tillier E. R. M. 1994. Maximum likelihood with multiparameter models of substitution. J. Mol. Evol. 39:409-417. (Pubitemid 24307741)
    • (1994) Journal of Molecular Evolution , vol.39 , Issue.4 , pp. 409-417
    • Tillier, E.R.M.1
  • 31
    • 0028874337 scopus 로고
    • Neighbor joining and maximum likelihood with rna sequences: Addressing the interdependence of sites
    • Tillier E. R. M., Collins A. 1995. Neighbor joining and maximum likelihood with rna sequences: addressing the interdependence of sites. Mol. Biol. Evol. 12:7-15.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 7-15
    • Tillier, E.R.M.1    Collins, A.2
  • 32
    • 0000171351 scopus 로고    scopus 로고
    • Pairwise contact potentials are unsuitable for protein folding
    • DOI 10.1063/1.477748, PII S0021960698502474
    • Vendruscolo M., Domany E. 1998. Pairwise contact potentials are unsuitable for protein folding. J. Chem. Phys. 109:11101-11108. (Pubitemid 128675160)
    • (1998) Journal of Chemical Physics , vol.109 , Issue.24 , pp. 11101-11108
    • Vendruscolo, M.1    Domany, E.2
  • 33
    • 0033628817 scopus 로고    scopus 로고
    • Protein folding using contact maps
    • Vendruscolo M., Domany E. 2000. Protein folding using contact maps. Vitam. Horm. 58:171-212.
    • (2000) Vitam. Horm , vol.58 , pp. 171-212
    • Vendruscolo, M.1    Domany, E.2
  • 34
    • 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. (Pubitemid 23352619)
    • (1993) Molecular Biology and Evolution , vol.10 , Issue.6 , pp. 1396-1401
    • Yang, Z.1
  • 35
    • 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. (Pubitemid 24283346)
    • (1994) Journal of Molecular Evolution , vol.39 , Issue.3 , pp. 306-314
    • Yang, Z.1
  • 36
    • 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
  • 37
    • 33748080427 scopus 로고    scopus 로고
    • Dependence among sites in RNA evolution
    • DOI 10.1093/molbev/msl015
    • Yu J., Thorne J. L. 2006. Dependence among sites in RNA evolution. Mol. Biol. Evol. 23:1525-1537. (Pubitemid 44297411)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.8 , pp. 1525-1537
    • Yu, J.1    Thorne, J.L.2


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