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A biologist’s guide to Bayesian phylogenetic analysis

Abstract

Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software for running sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC) sampling, the diagnosis of an MCMC run, and ways of summarizing the MCMC sample. We discuss the specification of the prior, the choice of the substitution model and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software packages and recommend appropriate applications.

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Fig. 1: Bayesian analysis of a two-parameter phylogenetic example.
Fig. 2: Trace plots and histograms for d and κ from sampling a posterior distribution using efficient and inefficient MCMC chains.

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Acknowledgements

This work was supported by Biotechnology and Biological Sciences Research Council (UK) grant BB/N000609/1. F.F.N. was supported by a Royal Society and British Academy Newton International Fellowship (UK) grant number NF140338.

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F.F.N. conceived the idea. F.F.N., M.d.R. and Z.Y. wrote the paper.

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Correspondence to Fabrícia F. Nascimento or Ziheng Yang.

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Nascimento, F.F., Reis, M.d. & Yang, Z. A biologist’s guide to Bayesian phylogenetic analysis. Nat Ecol Evol 1, 1446–1454 (2017). https://doi.org/10.1038/s41559-017-0280-x

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