Since ClonalFrame revealed that recombination has been a major factor in Legionella species evolution, we investigated how genetic variation is apportioned across species using BAPS40 and ChromoPainter + fineSTRUCTURE41. Both methods establish genetically differentiated groups and infer possible admixture occurring among those groups. As input, we used the 759,392 nucleotide MAUVE alignment based on conserved blocks of all 43 genomes. BAPS estimated the presence of 15 populations (Fig. 5) at the finest hierarchical level (within the Lp species), while ChromoPainter + fineSTRUCTURE assigned individual Legionella genomes to 21 populations (Fig. 6).