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Volume 26, Number 8—August 2020
Research

Population Genomic Structure and Recent Evolution of Plasmodium knowlesi, Peninsular Malaysia

Suzanne E. Hocking, Paul C.S. Divis, Khamisah A. Kadir, Balbir Singh, and David J. ConwayComments to Author 
Author affiliations: London School of Hygiene and Tropical Medicine Department of Infection Biology, London, UK (S.E. Hocking, D.J. Conway); Universiti Sarawak Malaysia Malaria Research Centre, Kota Samarahan, Malaysia (P.C.S. Divis, K.A. Kadir, B. Singh, D.J. Conway)

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Figure 4

Genomewide between-population fixation index (FST) scan of divergence between Plasmodium knowlesi in Peninsular Malaysia sampled in this study (cluster 3) and the major subpopulations previously sampled in Malaysian Borneo (clusters 1 and 2). All single-nucleotide polymorphisms (SNPs) with overall allele frequencies >10% were included, and the solid points show values for analysis windows containing 500 consecutive SNPs, centered by the midpoint of each sequential window and overlapping by 25

Figure 4. Genomewide between-population fixation index (FST) scan of divergence between Plasmodium knowlesi in Peninsular Malaysia sampled in this study (cluster 3) and the major subpopulations previously sampled in Malaysian Borneo (clusters 1 and 2). All single-nucleotide polymorphisms (SNPs) with overall allele frequencies >10% were included, and the solid points show values for analysis windows containing 500 consecutive SNPs, centered by the midpoint of each sequential window and overlapping by 250 SNPs. The red dashed line on each plot shows the genomewide mean value for all analyzed SNPs across the genome. A) The level of divergence between cluster 3 in Peninsular Malaysia and cluster 1 in Malaysian Borneo does not differ greatly throughout the genome (mean FST value 0.32). B) Divergence between cluster 3 in Peninsular Malaysia and cluster 2 in Malaysian Borneo is slightly higher (mean FST value 0.42) and shows more heterogeneity between genomic regions because of mosaic structure of diversity in cluster 2 (as explained by panel C). C) Divergence between clusters 1 and 2 in Malaysian Borneo, showing marked heterogeneity across the genome that explains most of the moderate heterogeneity shown in panel B, attributable to a mosaic structure of diversity within cluster 2, as previously reported (16).

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