Fig. 5

Signatures of selection of C580Y-like SNPs. a Distribution of linkage disequilibrium (r) between mutant kelch13 and other SNPs, binned according to the 2011–2012 NRAF (interval left-closed, right-open). Boxplots in black depict the distribution of C580Y-like SNPs. The boxplots in blue depict the distribution of controls (SNPs with comparable NRAF in 2011–2012 but exhibiting non-zero NRAF in the earlier collection phases). Box boundaries represent the first and third quartiles and the length of whiskers corresponds to 1.5 times the interquartile range. P values indicate significantly different distributions of C580Y-like and control SNPs (Wilcoxon test). b Comparison of the distribution of non-normalized iHS (integrated haplotype score) values for C580Y-like SNPs and control SNPs. Lower iHS values indicate a stronger signature of selection. P values indicate significantly different iHS distributions for C580Y-like versus control SNPs (Wilcoxon test). c Comparison of the kelch13 allelic richness of association between C580Y-like SNPs (black) and control SNPs (blue). Each graph shows the distribution of richness for SNPs with NRAF (2011–2012) within the same quartiles defined for iHS and LD boxplots; quartiles are indicated on the top of each graph. Horizontal axes indicate the number of distinct kelch13 mutations co-occurring with each SNP (richness). Vertical axes indicate the percentage of SNPs. Controls consist of SNPs with 2011–2012 NRAF within the same quartile as candidate SNPs. P values on the top of the graph indicate significantly different distributions between C580Y-like and control SNPs (Wilcoxon test). The C580Y-like SNPs with NRAF less than 8% generally exhibit association with fewer kelch13 alleles than control SNPs, indicating they may be more likely to be products of genetic hitchhiking than C580Y-like SNPs with higher NRAF