We also estimated recombination based on a MAUVE alignment of all 43 Legionella genomes (759,392 bp): ρ/θ was estimated at 0.562 (95% credibility interval of 0.31–0.911) and the r/m value was 6.941 (95% credibility interval of 3.693–11.255) (Supplementary Figure 2). These values are not directly comparable to the values based on the intraspecific alignment, which is larger and covers more diverse regions of the conserved core genome, but they suggest recombination may be similarly important in other Legionella species.