Extended Data Fig. 2: Haplotype structure at the pfcrt (left panel) and pfaat1 (right panel) regions.

Haplotype relationships were based on Identity-by-Descent of genome segments encompassing 25 kb on either side of each gene (see methods). Haplotypes joined by lines indicate >90% IBD. Each point depicts an isolate with point colors representing the years from which they were sampled. Square points represent complex infections and circles represent monoclonals. MOI, multiplicity of infection.