The Annals of Applied Probability

Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny

Elchanan Mossel and Eric Vigoda

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Markov chain Monte Carlo algorithms play a key role in the Bayesian approach to phylogenetic inference. In this paper, we present the first theoretical work analyzing the rate of convergence of several Markov chains widely used in phylogenetic inference. We analyze simple, realistic examples where these Markov chains fail to converge quickly. In particular, the data studied are generated from a pair of trees, under a standard evolutionary model. We prove that many of the popular Markov chains take exponentially long to reach their stationary distribution. Our construction is pertinent since it is well known that phylogenetic trees for genes may differ within a single organism. Our results shed a cautionary light on phylogenetic analysis using Bayesian inference and highlight future directions for potential theoretical work.

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Ann. Appl. Probab., Volume 16, Number 4 (2006), 2215-2234.

First available in Project Euclid: 17 January 2007

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Primary: 60J10: Markov chains (discrete-time Markov processes on discrete state spaces) 92D15: Problems related to evolution

Markov chain Monte Carlo phylogeny tree space


Mossel, Elchanan; Vigoda, Eric. Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny. Ann. Appl. Probab. 16 (2006), no. 4, 2215--2234. doi:10.1214/105051600000000538.

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