Document Detail

Modeling compositional heterogeneity.
MedLine Citation:
PMID:  15503675     Owner:  NLM     Status:  MEDLINE    
Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.
Peter G Foster
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Systematic biology     Volume:  53     ISSN:  1063-5157     ISO Abbreviation:  Syst. Biol.     Publication Date:  2004 Jun 
Date Detail:
Created Date:  2004-10-26     Completed Date:  2004-12-21     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9302532     Medline TA:  Syst Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  485-95     Citation Subset:  IM    
Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
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MeSH Terms
Base Composition*
Bayes Theorem
Classification / methods*
Computer Simulation
Likelihood Functions
Markov Chains
Models, Genetic*
Monte Carlo Method

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