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

DOI10.1214/105051600000000538MaRDI QIDQ997424zbMATH OpenOpenAlexFDO

Authors Elchanan Mossel, Eric Vigoda

Publication date 6 August 2007

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

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

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)

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.

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Cites work

• scientific article; zbMATH DE number 3366301 (Why is no real title available?)
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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
• The combinatorics of discrete time-trees: theory and open problems
• An adjacent-swap Markov chain on coalescent trees
• Convergence rate of Markov chain methods for genomic motif discovery
• An extended model for phylogenetic maximum likelihood based on discrete morphological characters

Describes a project that uses

Uses Software

• MrBayes

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