Fig. 1: Population structure of P. malariae isolates (n = 157) using 131,601 high-quality filtered SNPs. | Nature Communications

Fig. 1: Population structure of P. malariae isolates (n = 157) using 131,601 high-quality filtered SNPs.

From: Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility

Fig. 1

A Maximum-likelihood tree calculated using IQTREE with ModelFinder (GTR + F + R4 model), ultrafast bootstrap and sh-aLRT test both to 1000 replicates. Bootstrap scores >50 annotated with a black circle, and branches coloured by isolate continent. The region (separating the African continent into subregions) is annotated using the outer circular track where each isolate has a corresponding bar on the outer circle coloured to the region of origin. C Africa = Central Africa, E&S Africa = Eastern and Southern Africa, N Africa = Northern Africa, SAM = South America, W Africa = Western Africa. B Principal component analysis (PCA) of 157 isolates based on a Manhattan distance matrix, isolates coloured by region. C Admixture prediction of ancestral populations (K) per sample, visualised using 2 ancestral populations, which had the lowest cross-validation (CV) error score, and using 4 ancestral populations. The CV error score for K = 4 was higher, however this is used only to visualise preliminary segregation of African isolates and is not the most likely ancestral pattern. Isolates ordered according to the country of origin and grouped into regional population groups. Admixture analysis used only with countries that had > 5 isolates, (141 total isolates). Each bar represents an isolate which is coloured to reflect the percentage accordance with each predicted ancestral population.

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