Suzanne E. Hocking, Paul C.S. Divis, Khamisah A. Kadir, Balbir Singh, and David J. Conway
Figure 7. Scan for evidence of genomic regions affected by recent positive directional selection in Plasmodium knowlesi in Peninsular Malaysia, using the standardized integrated haplotype score |iHS| index. Examination of the ranges of extended haplotype homozygosity for individual single-nucleotide polymorphisms (SNPs) with high |iHS| values identified 4 distinct genomic windows of extended haplotypes (Appendix 2 Datasheet 3). Two of these (in chromosomes 1 and 9) spanned across SICAvar and kir genes, which were masked from SNP calling, whereas the other 2 did not include SICAvar or kir genes but covered ≈28 kb on chromosome 7 and ≈315 kb on chromosome 12. The large region on chromosome 12 is a merged window, consisting of 4 high |iHS| core SNPs with overlapping windows of extended haplotype homozygosity, and coincides with the region of chromosome 12 that has the highest genomic divergence between cluster 3 population subclusters A and B (Figure 5, panel D).