Quantifying MCMC exploration of phylogenetic tree space

Systematic Biology

Volumn 64, Issue 3, 2015, Pages 472-491

  Whidden, Chris ^a   Matsen, Frederick A ^a  

^a USA   (United States)

Author keywords

Markov chain Monte Carlo; phylogenetic methods; subtree prune and regraft; topological peaks; tree space

Indexed keywords

ARCHAEON; BACTERIUM; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; EUKARYOTE; GENETICS; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; PROCEDURES;

ARCHAEA; BACTERIA; BAYES THEOREM; CLASSIFICATION; EUKARYOTA; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY;

EID: 84929590793     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syv006     Document Type: Article

References (56)

1. Aldous D.J. 2000. Mixing time for a Markov chain on cladograms. Combin. Probab. Comput. 9:191-204.
2. Allen B.L., Steel M. 2001. Subtree transfer operations and their induced metrics on evolutionary trees. Ann. Comb. 5:1-15.
3. Beiko R.G., Keith J.M., Harlow T.J., Ragan M.A. 2006. Searching for convergence in phylogenetic Markov chain Monte Carlo. Syst. Biol. 55:553-565.
4. BordewichM.,Semple C. 2005.Onthecomputationalcomplexity of the rooted subtree prune and regraft distance. Ann. Comb. 8:409-423.
5. Bouckaert R., Heled J., Kühnert D., Vaughan T., Wu C.-H., Xie D., Suchard M.A., Rambaut A., Drummond A.J. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10:e1003537.
6. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
7. 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.
8. Garey J.R., Near T.J., Nonnemacher M.R., Nadler S.A. 1996. Molecular evidence for Acanthocephala as a subtaxon of Rotifera. J. Mol. Evol. 43:287-292.
9. Gelman A., Rubin D.B. 1992. Inference from iterative simulation using multiple sequences. Statist. Sci. 7:457-472.
10. Geweke J. 1991. Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments. In: Bernardo J.M., Berger J.O., DawidA.P., SmithA.F.M., editors, Bayesian statistics 4. Oxford, UK: Clarendon Press, pp. 169-193.
11. Geyer C.J. 1992. Practical Markov chain Monte Carlo. Statist. Sci. 7: 473-483.
12. Hasegawa M., Kishino H., Yano T.-a. 1985. Dating of human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
13. Hastings W.K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
14. Hedges S.B., Moberg K.D., Maxson L.R. 1990. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol. Biol. Evol. 7: 607-633.
15. Hein J., Jiang T., Wang L., Zhang K. 1996. On the complexity of comparing evolutionary trees. Discrete Appl. Math. 71:153-169.
16. Henk D.A., Weir A., Blackwell M. 2003. Laboulbeniopsis termitarius, an ectoparasite of termites newly recognized as a member of the Laboulbeniomycetes. Mycologia 95:561-564.
17. Hickey G., Dehne F., Rau-Chaplin A., Blouin C. 2008. SPR distance computation for unrooted trees. Evol. Bioinformatics 4:17-27.
18. Hillis D.M., Heath T.A., John K.S. 2005. Analysis and visualization of tree space. Syst. Biol. 54:471-482.
19. Höhna S., Defoin-Platel M., Drummond A. J. 2008. Clock-constrained tree proposal operators in Bayesian phylogenetic inference. In: BioInformatics and BioEngineering, 2008. BIBE 2008. 8th IEEE International Conference on IEEE. pp. 1-7.
20. Höhna S., Drummond A.J. 2012. Guided tree topology proposals for Bayesian phylogenetic inference. Syst. Biol. 61:1-11.
21. Huelsenbeck J.P., Ané C., Larget B., Ronquist F. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Syst. Biol. 57:406-419.
22. Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
23. Ingram A.L., Doyle J.J. 2004. Is Eragrostis (Poaceae) monophyletic? insights from nuclear and plastid sequence data. Syst. Botany 29:545-552.
24. Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N., editor.Mammalian protein metabolism, III.NewYork: Academic Press. pp. 21-132.
25. Kroken S., Taylor J.W. 2000. Phylogenetic species, reproductive mode, and specificity of the green alga Trebouxia forming lichens with the fungal genus letharia. Bryologist 103:645-660.
26. Kruskal J.B. 1964a. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29:1-27.
27. Kruskal J.B. 1964b. Nonmetric multidimensional scaling: a numerical method. Psychometrika 29:115-129.
28. Lakner C., Van Der Mark P., Huelsenbeck J.P., Larget B., Ronquist F. 2008. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Syst. Biol. 57:86-103.
29. Larget B. 2013. The estimation of tree posterior probabilities using conditional clade probability distributions. Syst. Biol. 62: 501-511.
30. Lewis P.O., Holder M.T., Holsinger K.E. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241-253.
31. Lovász L. 1993. Random walks on graphs: a survey. Combinatorics, Paul Erdös is Eighty 2:1-46.
32. Matsen F.A. 2006. A geometric approach to tree shape statistics. Syst. Biol. 55:652-661.
33. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., Teller E. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087.
34. Mossel E., Vigoda E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209.
35. Mossel E., Vigoda E. 2006. Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny. Ann. Appl. Probab. 16:2215-2234.
36. Raftery A.E., Lewis S. 1992. Howmany iterations in the Gibbs sampler. Bayesian Statistics 4:763-773.
37. Robinson D.F., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
38. Ronquist F., Huelsenbeck J., Teslenko M. 2011. Draft MrBayes version 3.2 manual: tutorials and model summaries. Distributed with the software from http://brahms.biology.rochester. edu/software.html.
39. Ronquist F., Larget B., Huelsenbeck J.P., Kadane J.B., Simon D., van der Mark P. 2006. Comment on "phylogenetic MCMC algorithms are misleading on mixtures of trees". Science 312:367-367.
40. 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.
41. Rossman A.Y., McKemy J.M., Pardo-Schultheiss R.A., Schroers H.-J. 2001. Molecular studies of the Bionectriaceae using large subunit rDNA sequences. Mycologia 93:100-110.
42. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-2504.
43. Štefankovic D., Vigoda E. 2011. Fast convergence of Markov chain Monte Carlo algorithms for phylogenetic reconstruction with homogeneous data on closely related species. SIAM J. Discrete Math. 25:1194-1211.
44. Suchard M.A., B.D. Redelings. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22: 2047-2048.
45. Suh S.-O., Blackwell M. 1999. Molecular phylogeny of the cleistothecial fungi placed in Cephalothecaceae and Pseudeurotiaceae.Mycologia 91:836-848.
46. Szöllosi G.J., Rosikiewicz W., Boussau B., Tannier E., Daubin V. 2013. Efficient exploration of the space of reconciled gene trees. Syst. Biol. 62:901-912.
47. Tierney L. 1994. Markov chains for exploring posterior distributions. Ann. Statist. 22:1701-1728.
48. VenablesW.N., Ripley B.D. 2002. Modern applied statistics (Fourth S., editor) New York: Springer.
49. West D. 1979. Updating mean and variance estimates: an improved method. Communi. ACM 22:532-535.
50. Whidden C., Beiko R.G., Zeh N. 2010. Fast FPT algorithms for computing rooted agreement forests: theory and experiments. In: (Festa P., editor.) Experimental algorithms, vol. 6049 of Lecture Notes in Computer Science. Berlin Heidelberg: Springer. pp. 141-153.
51. Whidden C., Beiko R.G., Zeh N. 2013. Fixed-Parameter algorithms for maximum agreement forests. SIAM J. Comput. 42:1431-1466.
52. Whidden C., Zeh N. 2009. A unifying view on approximation and FPT of agreement forests. In: Proceedings of the 9th International Workshop, WABI 2009 vol. 5724 of Lecture Notes in Bioinformatics. Berlin, Germany: Springer Berlin Heidelberg. pp. 390-401.
53. Whidden C., Zeh N., Beiko R.G. 2014. Supertrees based on the subtree prune-and-regraft distance. Syst. Biol. 63:566-581.
54. Yang Z., Yoder A.D. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cutelooking mouse lemur species. Syst. Biol. 52:705-716.
55. Yoder A.D., Yang Z. 2004. Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol. Ecol. 13:757-773.
56. Zhang N., Blackwell M. 2001. Molecular phylogeny of dogwood anthracnose fungus (Discula destructiva) and the Diaporthales. Mycologia 93:355-365.