The ChromoPainter algorithm was applied to the genome-wide haplotype data using the linkage model41 to elucidate the population structure of Legionella. A recombination map file was created by specifying a uniform recombination rate per-site per-generation using a Perl script called makeuniformrecfile.pl. a preprocessing tool provided in ChromoPainter (http://www.paintmychromosomes.com). The output from ChromoPainter analysis is a co-ancestry matrix that summarizes the recombination-derived DNA imports and their donors across the 43 Legionella genomes. The fineSTRUCTURE algorithm uses the ChromoPainter generated co-ancestry matrix and performs model-based clustering using the Bayesian MCMC approach to explore population structure41. FineSTRUCTURE was run at a total of 400,000 iterations; the first 200,000 iterations were discarded as MCMC burn in. The thin interval was specified as 100.