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

DOI10.1214/105051600000000538zbMATH Open1121.60078arXivq-bio/0505002OpenAlexW1963972906MaRDI QIDQ997424FDOQ997424

Authors: Elchanan Mossel, Eric Vigoda 

Publication date: 6 August 2007

Published in: The Annals of Applied Probability (Search for Journal in Brave)

Abstract: 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.

Full work available at URL: https://arxiv.org/abs/q-bio/0505002

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zbMATH Keywords

Markov chain Monte Carlotree spacephylogeny

Mathematics Subject Classification ID

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

Cites Work

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Cited In (14)

• Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph
• Experiments with the site frequency spectrum
• Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
• Geometric ergodicity of a Metropolis-Hastings algorithm for Bayesian inference of phylogenetic branch lengths
• MCMC for imbalanced categorical data
• Parallel hierarchical sampling: a general-purpose interacting Markov chains Monte Carlo algorithm
• Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference
• Bayesian inference in molecular phylogenetics
• Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths
• Bayesian phylogenetic inference using a combinatorial sequential Monte Carlo method
• An adjacent-swap Markov chain on coalescent trees
• The combinatorics of discrete time-trees: theory and open problems
• Convergence rate of Markov chain methods for genomic motif discovery
• An extended model for phylogenetic maximum likelihood based on discrete morphological characters

Uses Software

• MrBayes

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