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Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon
Nicolas Rodrigue1, Hervé Philippe, Nicolas Lartillot
1Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, C.P. 6821, Succ. Centre-ville, Montréal, Québec Canada. nicolas.rodrigue@umontreal.ca
Bioinformatics (Oxford, England)
|November 16, 2007
Summary
This study introduces a new uniformization technique for mapping evolutionary character state changes on phylogenetic trees, improving efficiency for codon substitution models.
Area of Science:
- Evolutionary biology
- Computational phylogenetics
- Molecular evolution
Background:
- Mapping character state changes on phylogenetic trees is crucial for evolutionary studies.
- Existing probabilistic methods struggle with specific evolutionary models, like codon substitution models.
Purpose of the Study:
- To develop a general method for generating evolutionary character state mappings.
- To improve the efficiency of phylogenetic analyses using codon substitution models.
Main Methods:
- A uniformization technique is employed to generate realizations of Markovian substitution processes.
- The method is integrated into a data augmentation-based Markov chain Monte Carlo sampler.
- This approach approximates posterior distributions for codon substitution models.
Main Results:
- The new method is applicable to a broad range of evolutionary models.
- The developed Markov chain Monte Carlo sampler significantly outperforms conventional pruning-based samplers.
- Decorrelation times between posterior draws are reduced by a factor of 20 or more.
Conclusions:
- The uniformization technique offers a more efficient approach for phylogenetic inference.
- This method enhances the study of molecular evolution, particularly for codon-level processes.
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