Fig. 3

Non-reference allele frequency (NRAF) computed for samples belonging to the first three sampling intervals. a NRAF trajectories over time within the kelch13 resistance locus. Colored lines indicate the progression of the allele frequency of non-synonymous substitutions located within kelch13 and having frequency greater than 5% in at least one of the collection eras depicted in this graph (2001–2004, 2008, and 2011–2012) and all other kelch13 mutations not meeting this criterion (blue line). The dashed line represents the percentage of samples with at least one non-synonymous substitution in kelch13. b NRAF trajectories over time outside the kelch13 gene. Gray lines show the frequency of 100 alleles randomly chosen from all SNPs detected in the dataset. The red line represents the frequency of C580Y across the first three collection intervals. Black lines indicate the frequency of what we designate as the “C580Y-like” set: alleles absent in the earliest collection phases (2001–2004, 2008) but with NRAF higher than 5% in 2011–2012