Population genomics reveals the expansion of highly inbred Plasmodium vivax lineages in the main malaria hotspot of Brazil (original) (raw)
Fig 3
Linkage disequilibrium and population substructure of the Mâncio Lima population of Plasmodium vivax in northwestern Brazil.
(A) Linkage disequilibrium (LD) decay with increasing distance between pairs of SNPs along the chromosome. The horizontal dotted line indicates the background level of LD in the population, given by the median _r_2 between pairs of SNPs from different chromosomes. Note that median _r_2 values approach the background level within approximately 1.5 kb. (B) Empirical distribution of percent genetic distances (percentage of SNP mismatches among all SNPs genotyped in each sample pair [30], shown as blue bars) compared with that expected under random assortment of alleles in a panmictic population (continuous orange line). Note the greater variance of the empirical distribution, which is more spread out along the x axis than the expected distribution. (C) Empirical distance to nearest distribution (distribution of genetic distances between each parasite and its nearest neighbor [31], shown as blue bars) compared with that expected under random assortment of alleles in a panmictic population (continuous orange line). Note that the empirical distribution is bimodal, with the short-distance distribution to the left corresponding to pairwise comparisons within clusters of highly related parasites. (D) Ratio of observed (_V_D) to expected (_V_E) variances of the distributions shown in panel B as a test for genome-wide LD; under panmixia, _V_D/_V_E is expected to be equal to 1 [32]. See main text for details.