Genes under positive selection were identified using codeml as implemented in PAML, version 4.830. All gene clusters previously identified as having undergone recombination under any of the 3 intragenic recombination methods (described above) were removed for this analysis. We implemented the branch-site test268 to identify genes under positive selection in each of the clades compared to other Legionella clades. For each core gene, the likelihood of a model that does not allow positive selection (null model) was compared to a model that allows positive selection (alternative model) using a Likelihood Ratio Test (LRT)68. One degree of freedom was used to calculate p-values, and correction for multiple testing was performed using the Benjamini and Hochberg method at a significance level of 0.05 implemented in the software Q-value67.