Over the past 10 years, comparative genomics studies have been piecing together the ways in which individual bacterial genomes are related to larger taxonomic groups. Because bacteria are very diverse and every taxon has unique aspects to its ecology and genetics, this work has been mostly an empirical effort, aimed at estimating some of the basic parameters of evolution. Here, we characterized the genus level pan-genome, species-wide core genome and deciphered features of the natural history of Legionella based on comparative analyses of 43 genomes, encompassing all those that commonly or rarely cause human disease6.