Fig. 3

Bayesian phylogeny and population dynamics of CC5 and CC8. Bayesian maximum clade credibility time-calibrated phylogeny of CC5 (a) and CC8 (b) based on non-recombining regions of the core genome. Divergence date (median estimate with 95% highest posterior density dates in brackets) is indicated in blue on the tree. Bayesian skygrowth plot showing changes in effective population size (Ne) over time of CC5 (c) and CC8 (d). Median is represented by a black line and 95% confidence intervals are in blue