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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)

Main Article

Figure 5

Plasmodium knowlesi cluster 3 clinical isolates forming genomic subpopulations that co-occur locally, Peninsular Malaysia. A) Principal component analysis of the 28 cluster 3 P. knowlesi clinical isolates from Peninsular Malaysia, showing clustering into 3 groups: subclusters A (15 isolates), B (10 isolates), and C (3 isolates). The assignment of all samples to these 3 subclusters is completely consistent with their placement in the within-cluster 3 branching of the neighbor-joining tree based o

Figure 5. Plasmodium knowlesi cluster 3 clinical isolates forming genomic subpopulations that co-occur locally, Peninsular Malaysia. A) Principal component analysis of the 28 cluster 3 P. knowlesi clinical isolates from Peninsular Malaysia, showing clustering into 3 groups: subclusters A (15 isolates), B (10 isolates), and C (3 isolates). The assignment of all samples to these 3 subclusters is completely consistent with their placement in the within-cluster 3 branching of the neighbor-joining tree based on the pairwise distance matrix (Figure 2, panel A). The first principal component accounts for 10.5% of overall variation and separated subcluster 3 from the others, whereas the second principal component accounts for 6.5% of overall variation and separated subclusters A and B. B). Each of the cluster 3 P. knowlesi subclusters was detected at multiple sites within peninsular Malaysia (points shown at each of the 5 sampling sites show individual infections with colors for the different subclusters as in panel A). The site with most samples had all 3 subclusters co-occurring locally. C) Genomewide scan of diversity shows that the subcluster C samples are virtually identical in large parts of the genome, whereas subclusters A and B are both highly diverse throughout the genome, with only a few genomic regions showing lower diversity in subcluster B compared with A (in chromosomes 2, 7, 12, and 13). D) Genomewide scan of differentiation between subclusters A and B by sliding window between-population fixation index analysis shows peaks of differentiation corresponding to regions with differences in diversity. Most notable is a large region of chromosome 12 having many windows with between-population fixation index values >0.2 and containing some individual single-nucleotide polymorphisms with fixed differences (Appendix 1 Figure 2).

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Page updated: June 25, 2020
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