Correlation between the losses of regions of difference (RDs) and single nucleotide polymorphism (SNP)-based evolution of Bordetella pertussis . RDs which were variable across 42 B. pertussis isolates from unique SNP profiles (SP) were plotted against the evolution of B. pertussis as determined previously by SNP typing. Grey boxes indicate the presence of a gene whereas white boxes indicate the absence of a gene. In total 16 genes were variable, representing 10 RDs. Genes representing RDs which were present in all strains were not included in this Figure. Roman numerals represent B. pertussis clusters determined by SNP typing  and ‘UC’ denotes isolates that were not assigned to a specific SNP cluster.