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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
1Department of Biology, University College London, Darwin Building, Gower Street, London, United Kingdom.
Molecular Biology and Evolution
|February 12, 2011
Summary
This study introduces a faster Bayesian dating method using Taylor expansion to approximate molecular clock likelihoods. Parameter transforms, especially arcsine, improve accuracy for relaxed clock models, aiding large phylogenetic analyses.
Area of Science:
- Evolutionary Biology
- Computational Biology
- Phylogenetics
Background:
- Estimating species divergence times is crucial for evolutionary studies.
- Molecular clocks, calibrated with fossil/geological data, are widely used.
- Bayesian methods integrate diverse data but face computational challenges with complex models.
Purpose of the Study:
- To develop a computationally efficient method for Bayesian divergence time estimation.
- To improve the speed of Markov chain Monte Carlo (MCMC) in phylogenetic dating.
- To explore parameter transforms for enhancing likelihood approximations in Bayesian analyses.
Main Methods:
- Utilized Taylor expansion to approximate the likelihood function during MCMC iterations.
- Investigated parameter transforms (square root, logarithm, arcsine) to improve approximation accuracy.
- Tested approximations under global and relaxed clock models.
Main Results:
- Taylor expansion significantly accelerates likelihood calculations in MCMC.
- Arcsine transform provided highly accurate approximations, especially for relaxed clock models.
- Approximation accuracy decreased under seriously violated global clock assumptions.
Conclusions:
- Approximate likelihood calculation via Taylor expansion with parameter transforms is a viable speed-up for Bayesian phylogenetic dating.
- The arcsine transform offers a robust improvement for relaxed clock models.
- This method shows promise for analyzing large datasets in molecular dating.
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