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Volume 26, Number 8—August 2020

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)

Main Article

Figure 2

Genomewide analysis of diversity in Plasmodium knowlesi clinical samples from Peninsular Malaysia compared with samples from elsewhere. A) Neighbor-joining tree based on a pairwise genetic distance matrix between individual P. knowlesi infection samples for the 28 new clinical samples from Peninsular Malaysia (shown in red), 5 previously sequenced laboratory isolates (shown in orange), most of which were originally isolated from Peninsular Malaysia many years ago (15), and 74 samples from Malays

Figure 2. Genomewide analysis of diversity in Plasmodium knowlesi clinical samples from Peninsular Malaysia compared with samples from elsewhere. A) Neighbor-joining tree based on a pairwise genetic distance matrix between individual P. knowlesi infection samples for the 28 new clinical samples from Peninsular Malaysia (shown in red), 5 previously sequenced laboratory isolates (shown in orange), most of which were originally isolated from Peninsular Malaysia many years ago (15), and 74 samples from Malaysian Borneo that grouped into separate subpopulation clusters (cluster 1 shown in blue, cluster 2 in green) (15,16,23). All the clinical isolate samples from Peninsular Malaysia grouped into cluster 3 together with the laboratory isolates. The distance matrix is based on the proportion of all single-nucleotide polymorphisms (SNPs) showing differences between each infection sample (scale bar shows branch length for 0.5% of SNPs differing); most reads within each infection sample determine the allele scored for each SNP. B) Genomewide scan of nucleotide diversity (π) for P. knowlesi among the clinical isolates in Peninsular Malaysia (cluster 3, shown in red), compared with diversity observed in the subpopulations in Malaysian Borneo (clusters 1 and 2). The sliding window plot shows values of nucleotide diversity for nonoverlapping windows of 50 kb in each of the 14 chromosomes.

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