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Volumn 29, Issue 16, 2013, Pages 1970-1979

Bayesian evolutionary model testing in the phylogenomics era: Matching model complexity with computational efficiency

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CODON; GENOMICS; METHODOLOGY; MITOCHONDRIAL GENOME; PHYLOGENY; STATISTICAL MODEL; PROCEDURES;

EID: 84880992494     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt340     Document Type: Article
Times cited : (73)

References (43)
  • 1
    • 84555188616 scopus 로고    scopus 로고
    • BEAGLE: An application programming interface and highperformance computing library for statistical phylogenetics
    • Ayres, D.L. et al. (2012) BEAGLE: an application programming interface and highperformance computing library for statistical phylogenetics. Syst. Biol., 61, 170-173.
    • (2012) Syst. Biol. , vol.61 , pp. 170-173
    • Ayres, D.L.1
  • 2
    • 79957510431 scopus 로고    scopus 로고
    • Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes
    • Baele, G. et al. (2011) Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. BMC Evol. Biol., 11, 145.
    • (2011) BMC Evol. Biol , vol.11 , pp. 145
    • Baele, G.1
  • 3
    • 84865475040 scopus 로고    scopus 로고
    • Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
    • Baele, G. et al. (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol., 29, 2157-2167.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 2157-2167
    • Baele, G.1
  • 4
    • 84877663836 scopus 로고    scopus 로고
    • Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics
    • Baele, G. et al. (2013a) Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol., 30, 239-243.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 239-243
    • Baele, G.1
  • 5
    • 84874534890 scopus 로고    scopus 로고
    • Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution
    • Baele, G. et al. (2013b) Make the most of your samples: bayes factor estimators for high-dimensional models of sequence evolution. BMC Bioinformatics, 14, 85.
    • (2013) BMC Bioinformatics , vol.14 , pp. 85
    • Baele, G.1
  • 6
    • 34447253826 scopus 로고    scopus 로고
    • Accounting for gene rate heterogeneity in phylogenetic inference
    • Bevan, R.B. et al. (2007) Accounting for gene rate heterogeneity in phylogenetic inference. Syst. Biol., 56, 194-205.
    • (2007) Syst. Biol. , vol.56 , pp. 194-205
    • Bevan, R.B.1
  • 7
    • 12044257391 scopus 로고
    • Partitioning and combining data in phylogenetic analysis
    • Bull, J.J. et al. (1993) Partitioning and combining data in phylogenetic analysis. Syst. Biol., 42, 384-397.
    • (1993) Syst. Biol. , vol.42 , pp. 384-397
    • Bull, J.J.1
  • 8
    • 84880467251 scopus 로고    scopus 로고
    • Graph hierarchies for phylogeography
    • Cybis, G.B. et al. (2013) Graph hierarchies for phylogeography. Phil. Trans. R. Soc. B, Biol. Sci., 368, 20120206.
    • (2013) Phil. Trans. R. Soc. B, Biol. Sci. , vol.368 , pp. 20120206
    • Cybis, G.B.1
  • 9
    • 33344465800 scopus 로고    scopus 로고
    • Relaxed phylogenetics and dating with confidence
    • Drummond, A.J. et al. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol., 4, e88.
    • (2006) PLoS Biol. , vol.4
    • Drummond, A.J.1
  • 10
    • 77956488734 scopus 로고    scopus 로고
    • Bayesian random local clocks, or one rate to rule them all
    • Drummond, A.J. and Suchard, M.A. (2010) Bayesian random local clocks, or one rate to rule them all. BMC Biology, 8, 114.
    • (2010) BMC Biology , vol.8 , pp. 114
    • Drummond, A.J.1    Suchard, M.A.2
  • 11
    • 84864530626 scopus 로고    scopus 로고
    • Bayesian phylogenetics with BEAUti and the BEAST 1.7
    • Drummond, A.J. et al. (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol., 29, 1969-1973.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1969-1973
    • Drummond, A.J.1
  • 12
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsuc, F. et al. (2005) Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet, 6, 361-375.
    • (2005) Nat. Rev. Genet , vol.6 , pp. 361-375
    • Delsuc, F.1
  • 13
    • 79955417630 scopus 로고    scopus 로고
    • Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: Efficient hypothesis testing through hierarchical phylogenetic models
    • Edo-Matas, D. et al. (2011) Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models. Mol. Biol. Evol., 28, 1605-1616.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 1605-1616
    • Edo-Matas, D.1
  • 14
    • 0038518196 scopus 로고    scopus 로고
    • Phylogenomics: Intersection of evolution and genomics
    • Eisen, J.A. and Fraser, C.M. (2003) Phylogenomics: intersection of evolution and genomics. Science, 300, 1706-1707.
    • (2003) Science , vol.300 , pp. 1706-1707
    • Eisen, J.A.1    Fraser, C.M.2
  • 15
    • 0242318326 scopus 로고    scopus 로고
    • Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes
    • Faith, J.J. and Pollock, D.D. (2003) Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics, 165, 735-745.
    • (2003) Genetics , vol.165 , pp. 735-745
    • Faith, J.J.1    Pollock, D.D.2
  • 16
    • 42149143421 scopus 로고    scopus 로고
    • Marginal likelihood estimation via power posteriors
    • Friel, N. and Petitt, A.N. (2008) Marginal likelihood estimation via power posteriors. J. R. Stat. Soc. B., 70, 589-607.
    • (2008) J. R. Stat. Soc. B. , vol.70 , pp. 589-607
    • Friel, N.1    Petitt, A.N.2
  • 17
    • 48049107322 scopus 로고    scopus 로고
    • The conditioned reconstructed process
    • Gernhard, T. (2008) The conditioned reconstructed process. J. Theor. Biol., 253, 769-778.
    • (2008) J. Theor. Biol. , vol.253 , pp. 769-778
    • Gernhard, T.1
  • 18
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein coding DNA sequences
    • Goldman, N. and Yang, Z.H. (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.H.2
  • 19
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M. et al. (1985) Dating of 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
  • 20
    • 33645850710 scopus 로고    scopus 로고
    • Phylogenomics: The beginning of incongruence?
    • Jeffroy, O. et al. (2006) Phylogenomics: the beginning of incongruence? Trends Genet., 22, 225-231.
    • (2006) Trends Genet. , vol.22 , pp. 225-231
    • Jeffroy, O.1
  • 21
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro, H.M. (ed.), Academic Press, New York
    • Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In: Munro, H.M. (ed.) Mammalian protein metabolism. Academic Press, New York, pp. 21-132.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 22
    • 27844569825 scopus 로고    scopus 로고
    • Site-to-site variation of synonymous substitution rates
    • Kosakovsky Pond, S.L. and Muse, S. (2005) Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol., 22, 2375-2385.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 2375-2385
    • Kosakovsky Pond, S.L.1    Muse, S.2
  • 23
    • 84862928655 scopus 로고    scopus 로고
    • Statistics and truth in phylogenomics
    • Kumar, S. et al. (2012) Statistics and truth in phylogenomics. Mol. Biol. Evol., 29, 457-472.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 457-472
    • Kumar, S.1
  • 24
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • Lartillot, N. and Philippe, H. (2006) Computing Bayes factors using thermodynamic integration. Syst. Biol., 55, 195-207.
    • (2006) Syst. Biol. , vol.55 , pp. 195-207
    • Lartillot, N.1    Philippe, H.2
  • 25
    • 84870797333 scopus 로고    scopus 로고
    • A counting renaissance: Combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
    • Lemey, P. et al. (2012) A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinformatics, 28, 3248-3256.
    • (2012) Bioinformatics , vol.28 , pp. 3248-3256
    • Lemey, P.1
  • 26
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and non-synonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse, S.V. and Gaut, B.S. (1994) A likelihood approach for comparing synonymous and non-synonymous 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
  • 27
    • 38349192060 scopus 로고    scopus 로고
    • Strong variations of mitochondrial mutation rate across mammals - The longevity hypothesis
    • Nabholz, B. et al. (2008) Strong variations of mitochondrial mutation rate across mammals - the longevity hypothesis. Mol. Biol. Evol., 25, 120-130.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 120-130
    • Nabholz, B.1
  • 28
    • 0003078723 scopus 로고
    • Approximating Bayesian inference with the weigthed likelihood bootstrap
    • Newton, M.A. and Raftery, A.E. (1994) Approximating Bayesian inference with the weigthed likelihood bootstrap. J. R. Stat. Soc. B, 56, 3-48.
    • (1994) J. R. Stat. Soc. B , vol.56 , pp. 3-48
    • Newton, M.A.1    Raftery, A.E.2
  • 29
    • 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 Yang, Z.H. (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.H.2
  • 30
    • 1642341403 scopus 로고    scopus 로고
    • Bayesian phylogenetic analysis of combined data
    • Nylander, J.A. et al. (2004) Bayesian phylogenetic analysis of combined data. Syst. Biol., 53, 47-67.
    • (2004) Syst. Biol. , vol.53 , pp. 47-67
    • Nylander, J.A.1
  • 31
    • 0031950474 scopus 로고    scopus 로고
    • Asymmetrical directional mutation pressure in the mitochondrial genome of mammals
    • Reyes, A. et al. (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol., 15, 957-966.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 957-966
    • Reyes, A.1
  • 32
    • 58449095670 scopus 로고    scopus 로고
    • Bayesian comparisons of codon substitution models
    • Rodrigue, N. et al. (2008) Bayesian comparisons of codon substitution models. Genetics, 180, 1579-1591.
    • (2008) Genetics , vol.180 , pp. 1579-1591
    • Rodrigue, N.1
  • 33
    • 81855168357 scopus 로고    scopus 로고
    • Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection
    • Rubinstein, N.D. et al. (2011) Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection. Mol. Biol. Evol., 28, 3297-3308.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 3297-3308
    • Rubinstein, N.D.1
  • 34
    • 28944450584 scopus 로고    scopus 로고
    • Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    • Shapiro, B. et al. (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol., 23, 7-9.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 7-9
    • Shapiro, B.1
  • 35
    • 65649118549 scopus 로고    scopus 로고
    • Many-core algorithms for statistical phylogenetics
    • Suchard, M.A. and Rambaut, A. (2009) Many-core algorithms for statistical phylogenetics. Bioinformatic, 25, 1370-1376.
    • (2009) Bioinformatic , vol.25 , pp. 1370-1376
    • Suchard, M.A.1    Rambaut, A.2
  • 36
    • 0242404116 scopus 로고    scopus 로고
    • Hierarchical phylogenetic models for analyzing multipartite sequence data
    • Suchard, M.A. et al. (2003) Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol., 52, 649-664.
    • (2003) Syst. Biol. , vol.52 , pp. 649-664
    • Suchard, M.A.1
  • 37
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Waterman, M.S. (ed.), AmericanMathematical Society, Providence (RI)
    • Tavaré, S. (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. In: Waterman, M.S. (ed.) Some Mathematical Questions in Biology: DNA Sequence Analysis. AmericanMathematical Society, Providence (RI), pp. 57-86.
    • (1986) Some Mathematical Questions in Biology: DNA Sequence Analysis , pp. 57-86
    • Tavaré, S.1
  • 38
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne, J.L. et al. (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol., 15, 1647-1657.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1647-1657
    • Thorne, J.L.1
  • 40
    • 79951566251 scopus 로고    scopus 로고
    • Improving marginal likelihood estimation for Bayesian phylogenetic model selection
    • Xie, W. et al. (2011) Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol., 60, 150-160.
    • (2011) Syst. Biol. , vol.60 , pp. 150-160
    • Xie, W.1
  • 41
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Yang, Z. (1996a) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol., 11, 367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
    • Yang, Z.1
  • 42
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang, Z. (1996b) Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol., 42, 587-596.
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1
  • 43
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol., 15, 568-573.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 568-573
    • Yang, Z.1


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