Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax
Fig 4
Principal component analysis of the population structure of P. vivax in the New World.
Panel A shows results using the complete data set of 94,122 SNPs; panel B shows results obtained with a set of 37 segregating SNPs included in a previously described P. vivax barcode [49]; and panel C shows results obtained with a hypothetical barcode comprising the 100 SNPs yielding the highest average Wright’s fixation index FST values in pairwise comparisons of New World P. vivax populations. The SNPs used in the analysis shown in panel C are listed in S5 Table. Samples are colored according to their geographic origin as shown in Fig 1. The percentage contributions of each principal component (C1, C2, and C3) to overall variance were as follows: panel A, C1 = 22.27%, C2 = 14.15%, and C3 = 8.15%; panel B, C1 = 19.93%, C2 = 12.03%, and C3 = 11.42%; and panel C, C1 = 21.36%, C2 = 10.93%, and C3 = 9.33%.