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African apes harbour at least six  Plasmodium  species of the subgenus  Laverania , one of which gave rise to human  Plasmodium falciparum . Here we use a selective amplification strategy to sequence the genome of chimpanzee parasites classified as  Plasmodium reichenowi  and  Plasmodium gaboni  based on the subgenomic fragments. Genome-wide analyses show that these parasites indeed represent distinct species, with no evidence of cross-species mating. Both  P. reichenowi  and  P. gaboni  are 10-fold more diverse than  P. falciparum , indicating a very recent origin of the human parasite. We also find a remarkable  Laverania -specific expansion of a multigene family involved in erythrocyte remodelling, and show that a short region on chromosome 4, which encodes two essential invasion genes, was horizontally transferred into a recent  P. falciparum  ancestor. Our results validate the selective amplification strategy for characterizing cryptic pathogen species, and reveal evolutionary events that likely predisposed the precursor of  P. falciparum  to colonize humans.

Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria