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Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC).

Joëlle Barido-Sottani1, Orlando Schwery2,3,4, Rachel C M Warnock5

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Summary

This study explains how Markov chain Monte Carlo (MCMC) methods are used in Bayesian phylogenetic inference, especially for complex models like the fossilized birth-death (FBD) model. It offers strategies for diagnosing and troubleshooting MCMC convergence issues in phylogenetic analyses.

Keywords:
BEAST2Bayesian phylogenetic inferenceMCMCMrBayesfossilized birth-deathphylogenetic inference softwaretotal-evidencetroubleshooting

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Statistical Modeling

Background:

  • Phylogenetic tree estimation is complex, requiring evaluation of evolutionary models and parameters.
  • Modern methods incorporate fossil data and advanced statistical techniques.
  • Markov chain Monte Carlo (MCMC) is crucial for Bayesian phylogenetic inference but presents interpretation challenges.

Purpose of the Study:

  • To provide an overview of MCMC in Bayesian phylogenetic inference.
  • To emphasize its application in complex hierarchical models, such as the fossilized birth-death (FBD) model.
  • To offer strategies for diagnosing and troubleshooting MCMC convergence issues.

Main Methods:

  • Overview of MCMC application in Bayesian phylogenetic inference.
  • Focus on complex hierarchical models, including the fossilized birth-death (FBD) model.
  • Discussion of strategies for diagnosing MCMC problems and convergence issues.

Main Results:

  • MCMC is a leading method for approximating posterior distributions in Bayesian phylogenetic inference.
  • Strategies for improving MCMC performance by adjusting study design, models, priors, and software features are discussed.
  • Unique challenges of incorporating fossil data are addressed.

Conclusions:

  • Effective use of MCMC in phylogenetic inference requires careful attention to model complexity and parameter estimation.
  • Troubleshooting MCMC convergence issues is critical for reliable phylogenetic results.
  • Incorporating fossil data presents specific challenges that can be overcome with appropriate strategies.