To illustrate the distance-dependent decay of linkage disequilibrium, we adopted the method implemented by Shapiro et al.69. We used the core orthologs (1140 genes) that are present in one copy per genome in each of the 43 Legionella serogroups and species, and each unique allele was assigned a unique allele number. We then selected pairs of loci separated by increasing distance in the L. pneumophila reference genome. Neighboring loci on the same strand were excluded. Linkage disequilibrium between 2 pairs of loci was estimated using the D′A metric70, which provides a summary measure of linkage disequilibrium between those two loci.