Contigs from assembled shotgun data were annotated for genes and RNA features using the PROKKA pipeline20. The average number of protein-coding genes across the genus was around 3,200 (Supplementary Table 1). Predicted genes were classified as either core or accessory within the Legionella genus pan-genome using OrthoMCL21. Genus phylogeny of whole genome data was inferred using maximum likelihood (ML) phylogeny of the concatenated progressiveMAUVE alignment22 of 759,392 nucleotides of the 1140 protein-coding genes (Fig. 1), the ML phylogeny of the concatenated alignment of 299,244 amino acid residues of the 1140 translated core genes (Supplementary Figure 1), and a ClonalFrame nucleotide-based phylogenetic analysis23. The latter has the advantage of removing most recombinant regions of the DNA alignment from consideration. All three approaches yielded similar phylogenetic tree topologies from which four clades were defined (Fig. 1): Clade 1 (red) contained only Lp strains, Clade 2 (green) contained eight Legionella species: L. birminghamensis, L. erythra, L. nautarum, L. maceachernii, L. micdadei, L. jordanis, L. jamestowniensis and L. brunensis; Clade 3 (blue) nine Legionella species: L. cincinnatiensis, L. longbeachae NSW150, L. dumoffii, L. cherii, L. wadsworthii, L. bozemanii 1, L. bozemanii 2, L. tucsonensis and L. anisa, and Clade 4 only L. rowbothamii. Lp strains were a monophyletic group based on the whole genome phylogeny (Fig. 2).