The comparative population genetics of and .

are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 and 15 genomes. We find that is seven-times more diverse than in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that has acquired more of its diversity by recombination than . We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that has a higher effective population size than ; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in . The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald-Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.