To detect homologous intragenic recombination in the core gene clusters, we implemented the following three methods: (1) Pairwise Homoplasy Index (PHI); (2) Neighbor Similarity Score (NSS); and (3) Maximum2 using the PhiPack package66. For PHI, a window size of 50 nucleotides was used. For Maximum2, a fixed window size of two thirds of the number of polymorphic sites was used. P-values were estimated by employing 1,000 permutations for the three methods. Correction for multiple testing was performed using the Benjamini & Hochberg method implemented in the software Q-value67.