| Phylogenetic MCMC algorithms are misleading on mixtures of trees. | |
| | |
MedLine Citation:
|
PMID: 16195459 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
Markov chain Monte Carlo (MCMC) algorithms play a critical role in the Bayesian approach to phylogenetic inference. We present a theoretical analysis of the rate of convergence of many of the widely used Markov chains. For N characters generated from a uniform mixture of two trees, we prove that the Markov chains take an exponentially long (in N) number of iterations to converge to the posterior distribution. Nevertheless, the likelihood plots for sample runs of the Markov chains deceivingly suggest that the chains converge rapidly to a unique tree. Our results rely on novel mathematical understanding of the log-likelihood function on the space of phylogenetic trees. The practical implications of our work are that Bayesian MCMC methods can be misleading when the data are generated from a mixture of trees. Thus, in cases of data containing potentially conflicting phylogenetic signals, phylogenetic reconstruction should be performed separately on each signal. |
| | |
Authors:
|
Elchanan Mossel; Eric Vigoda |
Related Documents
:
|
12689349 - Gapcoder automates the use of indel characters in phylogenetic analysis. 19961329 - Bayesian phylogenetics and its influence on insect systematics. 18378469 - The first mistletoes: origins of aerial parasitism in santalales. 20461159 - A decision tree model for the prediction of homodimer folding mechanism. 2223159 - Phylogeny and molecular evolution in primates. 20525339 - Evolution of nectarivory in phyllostomid bats (phyllostomidae gray, 1825, chiroptera: m... 17281049 - A web-based wavelet application to reduce one dimensional physiological data with infre... 17185279 - Using supervised principal components analysis to assess multiple pollutant effects. 21495209 - Pollen and seed dispersal inferred from seedling genotypes: the bayesian revolution has... |
Publication Detail:
|
Type: Journal Article; Research Support, U.S. Gov't, Non-P.H.S. |
Journal Detail:
|
Title: Science (New York, N.Y.) Volume: 309 ISSN: 1095-9203 ISO Abbreviation: Science Publication Date: 2005 Sep |
Date Detail:
|
Created Date: 2005-09-30 Completed Date: 2005-10-07 Revised Date: 2007-03-19 |
Medline Journal Info:
|
Nlm Unique ID: 0404511 Medline TA: Science Country: United States |
Other Details:
|
Languages: eng Pagination: 2207-9 Citation Subset: IM |
Affiliation:
|
Department of Statistics, University of California at Berkeley, Berkeley, CA 94720, USA. mossel@stat.berkeley.edu. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Algorithms* Bayes Theorem* Likelihood Functions Markov Chains* Mathematics Monte Carlo Method* Phylogeny* |
| Comments/Corrections | |
Comment In:
|
Science. 2006 Apr 21;312(5772):367; author reply 367
[PMID:
16627724
]
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Preindustrial to modern interdecadal variability in coral reef pH.
Next Document: Dynamic paternity allocation as a function of male plumage color in barn swallows.