Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax

Abstract

AbstractPlasmodium vivaxis the most prevalent and widespread human malaria parasite, with almost three billion people living at risk of infection. With the discovery of its closest genetic relatives in African great apes (Plasmodium vivax-like), the origin ofP. vivaxhas been proposed to be located in the sub-Saharan African area. However, the limited number of genetic markers and samples investigated questioned the robustness of this result. Here, we examined the population genomic variation of 447 humanP. vivaxstrains and 19 apeP. vivax-likestrains originating from 24 different countries across the world. We identified 2,005,455 high quality single-nucleotide polymorphism loci allowing us to conduct an extensive characterization to date ofP. vivaxworldwide genetic variation. Phylogenetic relationships between human and apePlasmodiumrevealed thatP. vivaxis a sister clade ofP. vivax-like, not included within the radiation ofP. vivax-like. By investigating a variety of aspects ofP. vivaxvariation, we identified several striking geographical patterns in summary statistics as function of increasing geographic distance from Southeast Asia, suggesting thatP. vivaxmay derived from serial founder effects from a single origin located in Asia.