Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

Systematic Biology

Volumn 65, Issue 2, 2016, Pages 250-264

  Baele, Guy ^a   Lemey, Philippe ^a   Suchard, Marc A ^b,c  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bayes factor; Bayesian inference; coalescent model; marginal likelihood; MCMC; phylogenetics; Working distribution

Indexed keywords

BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; MOLECULAR EVOLUTION; PHYLOGENY; PROCEDURES;

BAYES THEOREM; CLASSIFICATION; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY;

EID: 84966589392     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syv083     Document Type: Article

References (39)

1. Arima S., Tardella L. 2012. Improved harmonic mean estimator for phylogenetic model evidence. J. Comp. Biol. 19:418-438.
2. Baele G., Lemey P. 2013. Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. Bioinformatics 29:1970-1979.
3. Baele G., Lemey P. 2014. Bayesian model selection in phylogenetics and genealogy-based population genetics. In Bernardo J. M., Bayarri M. J., Berger J. O., editors. Bayesian phylogenetics: methods, computational algorithms, and applications. Boca Raton, Florida: Chapman & Hall/CRC Mathematical & Computational Biology. pp. 55-90.
4. 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.
5. Baele G., Lemey P., Vansteelandt S. 2013a. Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution. BMC Bioinformatics 14:85.
6. Baele G., Li W.L.S., Drummond A.J., Suchard M.A., Lemey P. 2013b. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol. Biol. Evol. 30:239-243.
7. Bielejec F., Lemey P., Baele G., Rambaut A., Suchard M.A. 2014. BUSS: a parallel beast/beagle utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics 15:133.
8. Drummond A.J., Suchard M.A., Xie D., Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29:1969-1973.
9. 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.
10. Faria N.R., Rambaut A., Suchard M.A., Baele G., Bedford T., Ward M.J., Tatem A.J., Sousa J.D., Arinaminpathy N., Pépin J., Posada D., Peeters M., Pybus O.G., Lemey P. 2014. The early spread and epidemic ignition of hiv-1 in human populations. Science 346:56-61.
11. Friel N., Petitt A.N. 2008. Marginal likelihood estimation via power posteriors. J. R. Stat. Soc. B 70:589-607.
12. Gelman A., Meng X.-L. 1998. Simulating normalizing constants: from importance sampling to bridge sampling to path sampling. Stat. Sci. 13:163-185.
13. Gill M.S., Lemey P., Faria N.R., Rambaut A., Shapiro B., Suchard M.A. 2013. Improving bayesian population dynamics inference: a coalescent-based model formultiple loci. Mol. Biol.Evol. 30:713-724.
14. Gray R.R., Tatem A.J., Johnson J.A., Alekseyenko A.V., Pybus O.G., Suchard M.A., Salemi M. 2011. Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant staphylococcus aureus st239 genome-wide data within a Bayesian framework.Mol. Biol. Evol. 28:1593-1603.
15. Hasegawa M., Kishino H., Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial dna. J. Mol. Evol. 22:160-174.
16. Holder M.T., Lewis P.O., Swofford D.L., Bryant D. 2014. Variable tree topology stepping-stone marginal likelihood estimation. In: Chen M.-H., Kuo L., Lewis P.O., editors. Bayesian phylogenetics: methods, algorithms, and applications. Vol. 1.NewYork: Chapman & Hall/CRC. pp. 95-111.
17. 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.
18. Jeffreys H. 1935. Some tests of significance treated by theory of probability. In: Proceedings of the Cambridge Philosophical Society vol. 31. pp. 203-222.
19. Lartillot N., Philippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195-207.
20. Lepage T., Bryant D., Philippe H., Lartillot N. 2007. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24:2669-2680.
21. Minin V.M., Bloomquist E.W., Suchard M.A. 2008. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25:1459-1471.
22. Murphy K.P. 2007. Conjugate bayesian analysis of the gaussian distribution. Technical Report University of British Columbia.
23. Newton M.A., Raftery A.E. 1994. Approximating Bayesian inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B 56:3-48.
24. Rodrigo A.G., Felsenstein J. 1999. Coalescent approaches to hiv population genetics. In: Crandall, K.A. editor, The Evolution of HIV. Baltimore, Maryland: Johns Hopkins University Press. pp. 233-272.
25. Rodrigue N., Philippe H., Lartillot N. 2006. Assessing siteinterdependent phylogenetic models of sequence evolution. Mol. Biol. Evol. 23:1762-1775.
26. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. 2012. Mrbayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61:539-542.
27. Shapiro B., Rambaut A., Drummond A.J. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 23:7-9.
28. Sheather S.J. 2004. Density estimation. Stat. Sci. 19:588-597.
29. SilvermanB.W. 1986. The kernel method for univariate data. In: Density estimation for statistics and data analysis. London: Chapman & Hall/CRC, pp. 34-72
30. Sinsheimer J.S., Lake J.A., Little R.J. 1996. Bayesian hypothesis testing of four-taxon topologies using molecular sequence data. Biometrics 52:193-210.
31. Steel M.A. 2005. Should phylogenetic models be trying to fit an elephant? Trends Genet. 21:307-309.
32. Suchard M.A., Weiss R.E., Sinsheimer J.S. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001-1013.
33. Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of dna sequences. In: Waterman M.S., editor. Some mathematical questions in biology: DNA sequence analysis. Providence, RI: American Mathematical Society, pp. 57-86.
34. Vrancken B., Rambaut A., Suchard M.A., Drummond A.J., Baele G., Derdelinckx I., Wijngaerden E.V., Vandamme A.-M., Laethem K.V., and Lemey P. 2014. The genealogical population dynamics of hiv-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comp. Biol. 10:e1003505.
35. Worobey, M., M. Gemmel, D. E. Teuwen, T. Haselkorn, K. Kunstman, M. Bunce, J. J. Muyembe, J. M. M. Kabongo, R. M. Kalengayi, E. V. Marck, M. Thomas, P. Gilbert, and S. M. Wolinsky. 2008. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.Nature 455:661-665.
36. Xie W., Lewis P.O., Fan Y., Kuo L., Chen M.H. 2011 Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60, 150-160
37. Yang Z., Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
38. Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367-372.
39. Zhu T., Korber B.T., Nahmias A.J., Hooper E., Shaper P.M., Ho D.D. 1998. An african HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 391:594-597.