Bacterial species are diverse in population structure, some being quite clonal (e.g., Mycobacterium tuberculosis)37 while others show high levels of recombination (e.g., Neisseria gonorrhoeae and Legionella spp.)141623. Recombination in a bacterial species is predicted to result in linkage disequilibrium, decaying as the distance between loci in the genome increases38. Similar to the acquisition of accessory genes by HGT, homologous recombination is potentially a way for bacterial species to share fitness gains under environmental selection pressure39. We measured linkage disequilibrium between alleles of core genes in the genus and found strong linkage up to ~20 kb, which tailed off to background levels after 100 kb (Fig. 3a,b). Levels of linkage disequilibrium decay fell somewhere between that seen for Chlamydia trachomatis and E. coli, suggesting that significant levels of homologous recombination occur between core genes. Using three classic substitution analysis methods (PHI, NSS and Maximum-Chi2) implemented for detecting intragenic homologous recombination, 119 core genes showed significant evidence for recombination (FDR corrected p-value <0.1) in at least one method (Supplementary Table 7a–c).