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Human specific <jats:italic>P. vivax<\/jats:italic> has evolved from a single ancestor that originated from a parasite of African apes. Although previous studies have proposed phylogenetic trees positioning <jats:italic>P. vivax<\/jats:italic> (the common ancestor of human and African ape <jats:italic>P. vivax<\/jats:italic>) within the assemblages of Asian primate parasites, its position has not yet been robustly confirmed. We determined nearly complete apicoplast genome sequences from seven Asian primate parasites, <jats:italic>Plasmodium cynomolgi<\/jats:italic> (strains Ceylonensis and Berok), <jats:italic>P. knowlesi P. fragile<\/jats:italic>, <jats:italic>P. fieldi<\/jats:italic>, <jats:italic>P. simiovale, P. hylobati<\/jats:italic>, <jats:italic>P. inui<\/jats:italic>, and an African primate parasite, <jats:italic>P. gonderi<\/jats:italic>, that infects African guenon. Phylogenetic relationships of the <jats:italic>Plasmodium<\/jats:italic> species were analyzed using newly and previously determined apicoplast genome sequences. Multigene maximum likelihood analysis of 30 protein coding genes did not position <jats:italic>P. vivax<\/jats:italic> within the Asian primate parasite clade but positioned it basal to the clade, after the branching of an African guenon parasite, <jats:italic>P. gonderi<\/jats:italic>. The result does not contradict with the emerging notion that <jats:italic>P. vivax<\/jats:italic> phylogenetically originated from Africa. The result is also supported by phylogenetic analyses performed using massive nuclear genome data of seven primate <jats:italic>Plasmodium<\/jats:italic> species.<\/jats:p>","DOI":"10.1038\/s41598-019-43831-1","type":"journal-article","created":{"date-parts":[[2019,5,13]],"date-time":"2019-05-13T22:03:33Z","timestamp":1557785013000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Apicoplast phylogeny reveals the position of Plasmodium vivax basal to the Asian primate malaria parasite clade"],"prefix":"10.1038","volume":"9","author":[{"given":"Nobuko","family":"Arisue","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetsuo","family":"Hashimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoru","family":"Kawai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hajime","family":"Honma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keitaro","family":"Kume","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshihiro","family":"Horii","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,5,13]]},"reference":[{"key":"43831_CR1","unstructured":"Levin, N. 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