MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Abstract

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

Changes in phytophagous insect host ranges following the invasion of their community: Long‐term data for fruit flies

“…The best‐fit models were GTR + G for matk and GTR + I + G for rbcl . The phylogeny was then reconstructed with MrBayes v3.2 (Ronquist et al., 2012), with each gene defined as a distinct partition of the combined alignment, due to their different models of evolution. Two runs with four Markov chains each were conducted simultaneously for 5,000,000 generations, and variations in likelihood scores were examined graphically with Tracer v1.5 (available from http://tree.bio.ed.ac.uk/software/tracer/).…”

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

“…This model was used to produce maximum‐likelihood (ML) and Bayesian phylogenetic trees. The Bayesian analysis was performed in MrBayes 3.2.6 (Ronquist et al., 2012) using a Markov Chain Monte Carlo (MCMC) method sampled every 100 generations for a total of 5,350,000 generations. A 50% majority rule consensus tree was generated after a burn in of the first 25% of sampled generations.…”

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

“…Individual gene trees for this analysis were estimated using MrBayes (v.3.2; Ronquist et al. 2012). To test the impact of the discordance parameter (alpha), independent analyses were run using alpha = 1, alpha = 10, and alpha = 1000.…”