Fig. 4.

The estimated substitution rate of the sampled M. bovis population. a The sampled (n = 9000, 10% burn-in removed) posterior distributions of the substitution rate estimated by BEAST analyses using different population models. Each analysis in BEAST was repeated 3 times and replicates plotted with the corresponding colour for the population model. b Pairwise comparisons of the posterior distributions resulting from analyses based upon different population models. Each boxplot summarises the distribution of differences produced by calculating the difference between 10,000 random samples of the posteriors being compared. The blue points represent the upper and lower bounds of distribution of differences. Outliers of the difference distributions are coloured in grey