Figure 3 | Scientific Reports

Figure 3

From: Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

Figure 3

Mean Rsb index scores of SNPs across the P. falciparum genome over all pairwise comparisons of 11 local populations in West Africa. This index of the relative rate of breakdown of haplotype homozygosity is used here to identify loci with the most substantial differences in extended haplotypes among the populations, as this may indicate local differences in recent selection. All population pairwise Rsb values were determined for 35,228 SNPs, and the mean score for all pairwise comparisons was calculated from the absolute score magnitudes (Supplementary Datafile S2). The top nine genomic windows each had at least three SNPS with a mean Rsb > 3 and at least one SNP with a mean Rsb > 5: (a) chromosome (chr) 6 coordinates 852–860 kb covering 4 genes (PF3D7_0620400-0620700), (b) chr 6 coordinates 1174–1253 kb covering 17 genes (PF3D7_0628400-0630000 including the merozoite surface protein gene msp10), (c) chr 7 coordinates 385–467 kb covering 19 genes (PF3D7_0708500-0710200 including the chloroquine resistance gene crt), (d) chr 8 coordinates 523–549 kb covering 7 genes (PF3D7_0810200-0810800 including the antifolate resistance gene dhps), (e) chr 8 coordinates 678–691 kb covering 5 genes (PF3D7_0813900-0814300), (f) chr 9 coordinates 1167–1176 kb covering 3 genes (PF3D7_0929200-0929400 including the merozoite invasion-related gene RhopH2), (g) chr 10 coordinates 237–269 kb covering 10 genes (PF3D7_0929200-0929400), (h) chr 10 coordinates 1352–1360 kb covering 3 genes (PF3D7_0929200-0929400), (i) chr 14 coordinates 3018–3027 kb covering 3 genes (PF3D7_1474000-1474200).