21del genotype results in relation to PGG2 phylogeny. A simplified phylogenetic tree of PGG2 lineages shows that the 21del mutation is seen only within the Haarlem and LCC lineages indicating that they share a recent common ancestor. Results also suggest frequent gene conversion and recombination events, particularly between the Haarlem groups. Each mutational type is shown in colour and indicates the number of PPE38/71 genes present and the genotype (WT = wildtype, ie lacking the 21del mutation). Green (a): 21 bp deletion (21del) in PPE71, both genes retained; Blue (b): Recombination between PPE38/71 with PPE71 deletion; Yellow (c): Gene conversion leading to deletion of PPE71 and duplication of PPE38; Grey (d); Recombination between PPE38/71 with PPE38 deletion. The "Haarlem-like" lineages (F6 and F7) could not be included in the analysis because the 3' end of PPE38, including the region homologous to PPE71 21del, has been deleted due to an IS6110-associated deletion event [see additional file 2, S11 and S12].