Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations
Fig 2
Phylogenetic tree constructed from P. knowlesi mitochondrial sequences for the 60 whole genome sequenced samples and 54 published others [6] sourced from human, M. nemestrina (Mn) and M. fascicularis (Mf) samples.
The mitochondrial genotype groups defined here are cross-referenced to the nuclear genotypes in Fig 1A (pentagons in the outer ring, missing pentagons relate to the 54 samples with only mitochondrial sequence data [6]). Samples sourced from the different macaques are highlighted in the tree branches. The tree shows three main subpopulations: (i) two clades including Peninsular Malaysia (Peninsular nuclear genotype, Cluster 3, purple) and Borneo Malaysia (mix of Mf-Pk and Mn-Pk nuclear genotypes, Cluster 1 and 2, red) presenting a very similar mitochondrial haplotype; (ii) the majority of the samples with a Mn-Pk nuclear genotype together with the only sequence obtained from a Mn sample (Cluster 2, green); (iii) samples with a Mf-Pk nuclear genotype (Cluster 1, blue). These clusters are consistent with microsatellite-based trees [12]. The presence of monkey samples spread throughout the tree indicates that none of the mitochondrial genotypes groups are human-specific, consistent with microsatellite-based analysis [9]. Black arrows indicate the presence of samples with mismatched nuclear and mitochondrial subtypes.