Scan for allele frequency divergence among 11 populations sampled across West Africa. (A) Mean FST scores for all pairwise site by site comparisons plotted for each SNP across the genome (the overall genome wide mean FST was 0.007). The arrow shows the locus with highest mean FST value (FST = 0.18 for an intergenic SNP at position 1,383,344 of chromosome 9 adjacent to the gdv1 gene PF3D7_09035400). Table 2 lists this and three other genomic regions that each contained at least three SNPs with mean FST > 0.05 and at least one SNP with mean FST > 0.1 (with <15 kb between adjacent SNPs having these high values). (B) Zoomed in view of FST values of the SNPs in the most highly differentiated region on chromosome 9, with the highest FST SNPs spanning the region between gdv1 and gexp22. (C) Geographical allele frequency distribution of chromosome 9 SNP at position 1383344, with pie charts showing the reference 3D7-type allele (red), and the alternate allele (blue). Allele frequency distributions for the highest FST SNP in each of the other three high FST windows are shown in Supplementary Fig. S2.