All genes families with at least three members in each of Clades 1 to 3 were clustered using UPGMA. Each resulting tree was tested using the imonophyletic command of the R ape package42 and also using TOPD/FMTS (Version 3.3), where the former was implemented to determine if genes from the same clade formed monophyletic groups and the latter to check whether the topology of each of the accessory genes agrees with the topology of the Legionella species phylogenetic tree. For families that failed the screen, ML phylogenies were computed using RAxML38 and visually inspected for evidence of inter-clade gene movement.