Fig. 5. Transmission dynamics of sublineage SL1: Evidence of local expansion after global spread.

(A) Each point summarizes the relative risk that a pair of isolates has an MRCA within a defined time frame and between different spatial scales (within the same country, within the same continent, or within different continents), relative to the risk that a pair of isolates from countries separated by >1000 km has an MRCA in the same range (set as the reference value, “ref”). Error bars represent the 95% CIs, based on 100 bootstrap time-calibrated trees. (B) Proportion of pairs of isolates within the same country (France) sharing an MRCA of 5 or less years in function of the spatial distance within and between administrative departments (shown in the map). The green line indicates the mean proportion of genetically close strains regardless of the geographical location. (C) Relative risk for a pair of isolates to share an MRCA of 5 or less years when (left) both are coming from Paris compared to when coming from another department (P = 0.43) and (right) when coming from the same department in France, except Paris, compared to when coming from different departments (P < 0.001, see Materials and Methods for details).