We tested for clade-specific signatures of positive selection using PAML30, and identified 10 core genes (FDR p-value < 0.05) in Clade 1 compared to the other clades. These genes had no known relationship to Legionella virulence or interactions with each other based on searching the STRING database31. Clade 2 had the highest number of genes under positive selection (362 genes) followed by Clade 3 (170 genes) (Supplementary Table 4a,c,e). Eight genes total were under positive selection in all 3 clades sans Clade 4. Ninety-seven core genes showed evidence of positive selection in both Clades 2 and 3. T4SS protein IcmL was under positive selection in both Clades 2 and 3, while IcmC and IcmG were under positive selection only in Clade 3. Similarly, the T2SS protein LspJ was under selection only in Clade 3, while LspD was under selection only in Clade 2. There were 272 and 78 clade-specific core genes under selection in Clades 2 and 3, respectively.