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Volumn 63, Issue 3, 2014, Pages 309-321

Posterior predictive bayesian phylogenetic model selection

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

EID: 84898997868     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt068     Document Type: Article
Times cited : (46)

References (44)
  • 1
    • 0016355478 scopus 로고
    • A new look at statistical model identification
    • Akaike H. 1974. A new look at statistical model identification. IEEE Trans. Automat. Contr. 19:716-723.
    • (1974) IEEE Trans Automat. Contr. , vol.19 , pp. 716-723
    • Akaike, H.1
  • 2
    • 84859329829 scopus 로고    scopus 로고
    • Improved harmonic mean estimator for phylogenetic model evidence
    • Arima S., Tardella L. 2012. Improved harmonic mean estimator for phylogenetic model evidence. J. Comput. Biol. 19:418-438.
    • (2012) J. Comput. Biol. , vol.19 , pp. 418-438
    • Arima, S.1    Tardella, L.2
  • 3
    • 84865475040 scopus 로고    scopus 로고
    • Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
    • Baele G., Lemey P., Bedford T., Rambaut A., Suchard M.A., Alekseyenko A.V. 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    Lemey, P.2    Bedford, T.3    Rambaut, A.4    Suchard, M.A.5    Alekseyenko, A.V.6
  • 4
    • 0037819441 scopus 로고    scopus 로고
    • Widespread horizontal transfer of mitochondrial genes in flowering plants
    • Bergthorsson U., Adams K.L., Thomason B., Palmer J.D. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197-201.
    • (2003) Nature , vol.424 , pp. 197-201
    • Bergthorsson, U.1    Adams, K.L.2    Thomason, B.3    Palmer, J.D.4
  • 5
    • 0035986890 scopus 로고    scopus 로고
    • Bayesian model adequacy and choice in phylogenetics
    • Bollback J. 2002. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19:1171-1180.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1171-1180
    • Bollback, J.1
  • 6
    • 33645024781 scopus 로고    scopus 로고
    • Nielsen R., editor. Statistical methods in molecular evolution. New York: Springer Verlag.
    • Bollback J.P. 2005. Posterior mapping and predictive distributions. In: Nielsen R., editor. Statistical methods in molecular evolution. New York: Springer Verlag. pp. 439-462.
    • (2005) Posterior Mapping and Predictive Distributions , pp. 439-462
    • Bollback, J.P.1
  • 7
    • 60149104693 scopus 로고    scopus 로고
    • PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy
    • Brown J.M., ElDabaje R. 2009. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics 25:537-538.
    • (2009) Bioinformatics , vol.25 , pp. 537-538
    • Brown, J.M.1    Eldabaje, R.2
  • 8
    • 77649243408 scopus 로고    scopus 로고
    • When trees grow too long: Investigating the causes of highly inaccurate Bayesian branch-length estimates
    • Brown J.M., Hedtke S.M., Lemmon A.R., Lemmon E.M. 2010. When trees grow too long: Investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 59:145-161.
    • (2010) Syst. Biol. , vol.59 , pp. 145-161
    • Brown, J.M.1    Hedtke, S.M.2    Lemmon, A.R.3    Lemmon, E.M.4
  • 9
    • 24944440819 scopus 로고    scopus 로고
    • Bayesian criterion based model assessment for categorical data
    • Chen M.-H., Dey D., Ibrahim J. 2004. Bayesian criterion based model assessment for categorical data. Biometrika 91:45-63.
    • (2004) Biometrika , vol.91 , pp. 45-63
    • Chen, M.-H.1    Dey, D.2    Ibrahim, J.3
  • 11
    • 80051782566 scopus 로고    scopus 로고
    • A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases
    • Cummins C.A., McInerney J.O. 2011. A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Syst. Biol. 60:833-844.
    • (2011) Syst. Biol. , vol.60 , pp. 833-844
    • Cummins, C.A.1    McInerney, J.O.2
  • 12
    • 78650500247 scopus 로고    scopus 로고
    • Choosing among partition models in Bayesian phylogenetics
    • Fan Y., Wu R., Chen M.-H., Kuo L., Lewis P.O. 2011. Choosing among partition models in Bayesian phylogenetics. Mol. Biol. Evol. 28:523-532.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 523-532
    • Fan, Y.1    Wu, R.2    Chen, M.-H.3    Kuo, L.4    Lewis, P.O.5
  • 13
    • 3242701529 scopus 로고    scopus 로고
    • Modeling compositional heterogeneity
    • Foster P.G. 2004. Modeling compositional heterogeneity. Syst. Biol. 53:485-495.
    • (2004) Syst. Biol. , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 14
    • 42149143421 scopus 로고    scopus 로고
    • Marginal likelihood estimation via power posteriors
    • Friel N., Pettitt A.N. 2008. Marginal likelihood estimation via power posteriors. J. Roy. Stat. Soc. B 70:589-607.
    • (2008) J. Roy. Stat. Soc. , vol.B70 , pp. 589-607
    • Friel, N.1    Pettitt, A.N.2
  • 15
    • 0001135784 scopus 로고
    • Sampling and Bayes' inference in scientific modelling and robustness
    • In discussion of G E. P. Box paper entitled
    • Geisser S. 1980. In discussion of G. E. P. Box paper entitled: Sampling and Bayes' inference in scientific modelling and robustness. J. Roy. Stat. Soc. A 143:416-417.
    • (1980) J. Roy. Stat. Soc. , vol.A143 , pp. 416-417
    • Geisser, S.1
  • 17
    • 0002799511 scopus 로고    scopus 로고
    • Model choice: A minimum posterior predictive loss approach
    • Gelfand A.E., Ghosh S. 1998. Model choice: A minimum posterior predictive loss approach. Biometrika 85:1-11.
    • (1998) Biometrika , vol.85 , pp. 1-11
    • Gelfand, A.E.1    Ghosh, S.2
  • 18
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon, S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 19
    • 2442671519 scopus 로고    scopus 로고
    • Bayesian phylogenetic model selection using reversible jump markov chain monte carlo
    • Huelsenbeck J.P., Larget B., Alfaro M.E. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123-1133.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1123-1133
    • Huelsenbeck, J.P.1    Larget, B.2    Alfaro, M.E.3
  • 20
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 21
    • 0035638096 scopus 로고    scopus 로고
    • Criterion-based methods for Bayesian model assessment
    • Ibrahim J., Chen M., Sinha D. 2001. Criterion-based methods for Bayesian model assessment. Stat. Sinica 11:419-443.
    • (2001) Stat. Sinica , vol.11 , pp. 419-443
    • Ibrahim, J.1    Chen, M.2    Sinha, D.3
  • 22
    • 0000732090 scopus 로고
    • In: Munro H.N., editor., Mammalian protein metabolism.NewYork Academic Press.
    • Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N., editor., Mammalian protein metabolism.NewYork:Academic Press. pp. 21-132.
    • (1969) Evolution of Protein Molecules , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 23
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • 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.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 24
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N., Lepage T., Blanquart S. 2009. PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 25
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • Lartillot N., Phillippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195-207.
    • (2006) Syst. Biol. , vol.55 , pp. 195-207
    • Lartillot, N.1    Phillippe, H.2
  • 26
  • 27
    • 72049096137 scopus 로고    scopus 로고
    • Cryptic failure of partitioned Bayesian phylogenetic analyses: Lost in the land of long trees
    • Marshall D.C. 2010. Cryptic failure of partitioned Bayesian phylogenetic analyses: Lost in the land of long trees. Syst. Biol. 59:108-117.
    • (2010) Syst. Biol. , vol.59 , pp. 108-117
    • Marshall, D.C.1
  • 28
    • 0003078723 scopus 로고
    • Approximate Bayesian inference with theweighted likelihood bootstrap (with discussion)
    • Newton M.A., Raftery A.E. 1994. Approximate Bayesian inference with theweighted likelihood bootstrap (with discussion). J.Roy. Stat. Soc. B 56:3-48.
    • (1994) J.Roy. Stat. Soc. , vol.B56 , pp. 3-48
    • Newton, M.A.1    Raftery, A.E.2
  • 30
    • 45849154165 scopus 로고    scopus 로고
    • JModelTest: Phylogenetic model averaging
    • Posada D. 2008. jModelTest: Phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 31
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada D., Crandall K.A. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 32
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A., Grassly N.C. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 33
    • 84859893546 scopus 로고    scopus 로고
    • Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference
    • Rannala B., Zhu T., Yang Z. 2011. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.
    • (2011) Mol. Biol. Evol. , vol.29 , pp. 325-335
    • Rannala, B.1    Zhu, T.2    Yang, Z.3
  • 34
    • 78649389370 scopus 로고    scopus 로고
    • Assessment of substitution model adequacy using frequentist and Bayesian methods
    • Ripplinger J., Sullivan J. 2010. Assessment of substitution model adequacy using frequentist and Bayesian methods. Mol. Biol. Evol. 27:2790-2803.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 2790-2803
    • Ripplinger, J.1    Sullivan, J.2
  • 36
    • 85006545436 scopus 로고
    • Estimating the dimension of a model
    • Schwarz G.E. 1978. Estimating the dimension of a model. Ann. Statist. 6:461-464.
    • (1978) Ann. Statist. , vol.6 , pp. 461-464
    • Schwarz, G.E.1
  • 37
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • 379-423
    • Shannon C.E. 1948. A mathematical theory of communication. AT&T Tech. J. 27:379-423, 623-656.
    • (1948) AT&T Tech. J. , vol.27 , pp. 623-656
    • Shannon, C.E.1
  • 38
    • 0034983646 scopus 로고    scopus 로고
    • Bayesian selection of continuous-Time Markov chain evolutionary models
    • Suchard M., Weiss R., Sinsheimer J. 2001. Bayesian selection of continuous-Time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001-1013.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1001-1013
    • Suchard, M.1    Weiss, R.2    Sinsheimer, J.3
  • 41
    • 84870859470 scopus 로고    scopus 로고
    • Probing the monophyly of the directly opposite flagellar apparatus group in Chlorophyceae using data from five genes
    • Tippery N.P., Fǔcikova K., Lewis P.O., Lewis L.A. 2012. Probing the monophyly of the directly opposite flagellar apparatus group in Chlorophyceae using data from five genes. J. Phycol. 48:1482-1493.
    • (2012) J. Phycol. , vol.48 , pp. 1482-1493
    • Tippery, N.P.1    Fǔcikova, K.2    Lewis, P.O.3    Lewis, L.A.4
  • 42
    • 0001972601 scopus 로고
    • The large-sample distribution of the likelihood ratio for testing composite hypotheses
    • Wilks S.S. 1938. The large-sample distribution of the likelihood ratio for testing composite hypotheses. Ann. Statist. 9:60-62.
    • (1938) Ann. Statist. , vol.9 , pp. 60-62
    • Wilks, S.S.1
  • 43
    • 79951566251 scopus 로고    scopus 로고
    • Improvingmarginal likelihood estimation for Bayesian phylogenetic model selection
    • Xie W., Lewis P.O., Fan Y., Kuo L., Chen M.-H. 2011. Improvingmarginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60:150-160.
    • (2011) Syst. Biol. , vol.60 , pp. 150-160
    • Xie, W.1    Lewis, P.O.2    Fan, Y.3    Kuo, L.4    Chen, M.-H.5


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