An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics

Syst Biol. 2020 Jan 1;69(1):155-183. doi: 10.1093/sysbio/syz028.

Abstract

We describe an "embarrassingly parallel" method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo (SMC), based on recent advances in the SMC literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed SMC by reviewing and comparing with other computational Bayesian phylogenetic methods, in particular, different marginal likelihood estimation methods. Unlike previous SMC methods in phylogenetics, our annealed method can utilize standard Markov chain Monte Carlo (MCMC) tree moves and hence benefit from the large inventory of such moves available in the literature. Consequently, the annealed SMC method should be relatively easy to incorporate into existing phylogenetic software packages based on MCMC algorithms. We illustrate our method using simulation studies and real data analysis.

Keywords: Marginal likelihood; Sequential Monte Carlo; phylogenetics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Bayes Theorem
  • Classification / methods*
  • Monte Carlo Method
  • Phylogeny*
  • Software