Fig. 3: P. falciparum population structure by geography in Mozambique.

Microhaplotypes from regions of 150–300 bp in length between long tandem repeats were reconstructed from whole genome sequences and used to test the geographic structure of P. falciparum parasites. a Distribution of the expected heterozygosity at the 8722 microhaplotype loci extracted from whole genome sequences. The y-axis represents the number of microhaplotype loci for a given expected heterozygosity. The red line marks the 75% percentile of the distribution; the 25% most diverse loci were considered for population structure analysis. b Chromosomal locations of the 155 most important microhaplotypes, which contribute to the geographic (North-Central-South) classification model. c Principal coordinates analysis with samples grouped into regions (North-Central-South; n = 1089), considering microhaplotypes at loci with expected heterozygosity in the top 25% percentile. d Principal coordinates analysis with samples grouped into regions considering the 155 top microhaplotypes, with an out-of-bag error rate of classification of 24.89%. e, f Complexity of infection (COI) for samples in different regions of Mozambique in 2015 (e) and 2018 (f), as indicated by the number of genetically distinct clones. Regional assignment of samples: North: C. Delgado; Central: Sofala, Tete, and Zambézia; South: Gaza, Inhambane, and Maputo.