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. 2017 Sep 18;13(9):e1007008. doi: 10.1371/journal.pgen.1007008

Fig 1. Whole genome population structure and evidence of genetic exchange in chromosome 8.

Fig 1

A) Neighbour joining tree constructed using 1,632,024 genome-wide SNPs across the 60 P. knowlesi (Pk) samples. The tree shows two levels of resolution involved in the clustering of genotypes. The first level differentiates Peninsular Malaysia samples (Cluster 3, purple) from the Malaysian-Borneo host-related Pk genotypes (Cluster 1, M. fascicularis macaques (Mf-Pk), blue; Cluster 2, M. nemestrina macaques (Mn-Pk), green). The second level differentiates within Cluster 1, where Mf-Pk genotypes fall in subgroups from Betong (light blue) and from Kapit (dark blue). Samples from Sarikei have been highlighted using orange arrows. B) Allele frequency differences between Betong and Kapit regional subgroups of the Mf-Pk genotype in chromosome 8 SNPs using the population differentiation measure FST. There is high differentiation (FST > 0.4) in several regions across chromosome 8 (0.85-1Mb, 1.2Mb-1.35Mb, and 1.6–1.7Mb), and these signals overlap with strong evidence of recent positive selection, measured by the average XP-EHH calculated in 1kbp windows (red trace above). C) Haplotype plots for all samples (y-axis) at common SNP positions (MAF >5%, x-axis) highlighting the regions with abnormally high FST values (0.85-1Mb, 1.2Mb-1.35Mb, and 1.6–1.7Mb), as well as the low Fst region spanning from 0.1 to 0.2Mb for comparison. The black arrows indicate samples with the Mf-Pk genotype from Betong present with a Mn-Pk Cluster 2-like haplotype. These patterns are indicative of genetic exchange between the Mf-Pk and Mn-Pk genotype clusters, which is supported by the neighbour joining trees included in D). Missing calls are coloured in black and mixed calls are coloured in yellow. D) Neighbour joining trees constructed using SNPs in each of the regions in C). The trees show clear clustering of Mf-Pk Betong samples with the Mn-Pk genotype cluster in the genetic regions of abnormal FST (2nd, 3rd and 4th trees) compared to the 1st tree where only sample DIM2 presents introgression.