Fig. 5.—

Acquisition and loss of the clade 5 PaLoc via homologous recombination. In A⁻B⁻ clade 5 strains, the phylogenies of cdu2 (A) and cdu1 (B) genes upstream of the PaLoc are distinct from other clade 5 strains, with the exception of WA12. The genes seen in these strains are more closely related to those of clades 1–4, suggesting that the PaLoc was lost via homologous recombination with a nontoxigenic strain from one of these clades. In the A⁺B⁺ clade 5 strains, the same is seen with the cdd1 gene (C), suggesting these strains gained cdd1 along with the PaLoc via homologous recombination with a toxigenic strain from another clade, whereas the phylogeny of cdd2 (D) remains relatively consistent throughout clade 5. L033 is not included in the trees for cdu2 and cdu1 as these genes are not present in this strain. Strain labels are shown in supplementary figure S3, Supplementary Material online.