On the Use of Bootstrapped Topologies in Coalescent-Based Bayesian MCMC Inference: A Comparison of Estimation and Computational Efficiencies

Coalescent-based Bayesian Markov chain Monte Carlo (MCMC) inference generates estimates of evolutionary parameters and their posterior probability distributions. As the number of sequences increases, the length of time taken to complete an MCMC analysis increases as well. Here, we investigate an approach to distribute the MCMC analysis across a cluster of computers. To do this, we use bootstrapped topologies as fixed genealogies, perform a single MCMC analysis on each genealogy without topological rearrangements, and pool the results across all MCMC analyses. We show, through simulations, that although the standard MCMC performs better than the bootstrap-MCMC at estimating the effective population size (scaled by mutation rate), the bootstrap-MCMC returns better estimates of growth rates. Additionally, we find that our bootstrap-MCMC analyses are, on average, 37 times faster for equivalent effective sample sizes.