Haplotypes from isolates belonging to each of the separate lineages were tested for linkage disequilibrium using the index of association (IA), rBarD and the 4-gamete test.

To check differences between lineages were not resulting from different numbers of isolates, 2 subsets were made from BdGPL. Subset 1 consisted of isolates VC1, AP15 and JEL423. Subset 2 consisted of subset 1, ETH4 and MODS27. For each isolate subset, the total length (in nucleotides) of all haplotypes and the total number of loci with ≥2 alleles is given. Over 30% of the BdGPL haplotypes from any of the subsets were in significant disequilibrium, whilst only 11% of the haplotypes in BdCH and 16% of the haplotypes in BdCAPE were in disequilibrium, suggesting these populations are recombining more than the clonal BdGPL. The numbers of variable sites per locus are also shown, demonstrating all lineages to be as likely to have arisen from out-crossing.