On the Diversity of Malaria Parasites in African Apes and the Origin of Plasmodium falciparum from Bonobos Sabrina Krief 1. , Ananias A. Escalante 2. *, M. Andreina Pacheco 2 , Lawrence Mugisha 3 , Claudine Andre ´ 4 , Michel Halbwax 5 , Anne Fischer 5¤ , Jean-Michel Krief 6 , John M. Kasenene 7 , Mike Crandfield 8 , Omar E. Cornejo 9 , Jean-Marc Chavatte 10 , Clara Lin 11 , Franck Letourneur 12 , Anne Charlotte Gru ¨ ner 11,12 , Thomas F. McCutchan 13 , Laurent Re ´ nia 11,12 , Georges Snounou 10,11,14,15,16 * 1 UMR 7206-USM 104, Eco-Anthropologie et Ethnobiologie, Muse ´ um National d’Histoire Naturelle, Paris, France, 2 School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America, 3 Chimpanzee Sanctuary & Wildlife Conservation Trust (CSWCT), Entebbe, Uganda, 4 Lola Ya Bonobo Bonobo Sanctuary, ‘‘Petites Chutes de la Lukaya’’, Kimwenza–Mont Ngafula, Kinshasa, Democratic Republic of Congo, 5 Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 6 Projet pour la Conservation des Grands Singes, Paris, France, 7 Department of Botany, Makerere University, Kampala, Uganda; Makerere University Biological Field Station, Fort Portal, Uganda, 8 Research and Conservation Program, The Maryland Zoo in Baltimore, Baltimore, Maryland, United States of America, 9 Emory University, Program in Population Biology, Ecology, and Evolution, Atlanta, Georgia, United States of America, 10 USM0307, Parasitologie Compare ´ e et Mode ` les Expe ´ rimentaux, Muse ´ um National d’Histoire Naturelle, Paris, France, 11 Laboratory of Malaria Immunobiology, Singapore Immunology Network, Agency for Science Technology and Research (A*STAR), Biopolis, Singapore, 12 Institut Cochin, Universite ´ Paris Descartes, CNRS (UMR 8104), Paris, France; INSERM U567, Paris, France, 13 Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, Maryland, United States of America, 14 INSERM UMR S 945, Paris, France, 15 Universite ´ Pierre & Marie Curie, Faculte ´ de Me ´decine Pitie ´ -Salpe ˆtrie `re, Paris, France, 16 Department of Microbiology, National University of Singapore, Singapore Abstract The origin of Plasmodium falciparum, the etiological agent of the most dangerous forms of human malaria, remains controversial. Although investigations of homologous parasites in African Apes are crucial to resolve this issue, studies have been restricted to a chimpanzee parasite related to P. falciparum, P. reichenowi, for which a single isolate was available until very recently. Using PCR amplification, we detected Plasmodium parasites in blood samples from 18 of 91 individuals of the genus Pan, including six chimpanzees (three Pan troglodytes troglodytes, three Pan t. schweinfurthii) and twelve bonobos (Pan paniscus). We obtained sequences of the parasites’ mitochondrial genomes and/or from two nuclear genes from 14 samples. In addition to P. reichenowi, three other hitherto unknown lineages were found in the chimpanzees. One is related to P. vivax and two to P. falciparum that are likely to belong to distinct species. In the bonobos we found P. falciparum parasites whose mitochondrial genomes indicated that they were distinct from those present in humans, and another parasite lineage related to P. malariae. Phylogenetic analyses based on this diverse set of Plasmodium parasites in African Apes shed new light on the evolutionary history of P. falciparum. The data suggested that P. falciparum did not originate from P. reichenowi of chimpanzees (Pan troglodytes), but rather evolved in bonobos (Pan paniscus), from which it subsequently colonized humans by a host-switch. Finally, our data and that of others indicated that chimpanzees and bonobos maintain malaria parasites, to which humans are susceptible, a factor of some relevance to the renewed efforts to eradicate malaria. Citation: Krief S, Escalante AA, Pacheco MA, Mugisha L, Andre ´ C, et al. (2010) On the Diversity of Malaria Parasites in African Apes and the Origin of Plasmodium falciparum from Bonobos. PLoS Pathog 6(2): e1000765. doi:10.1371/journal.ppat.1000765 Editor: L. David Sibley, Washington University School of Medicine, United States of America Received September 4, 2009; Accepted January 13, 2010; Published February 12, 2010 This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Funding: This study was financially supported by the Museum National d’Histoire Naturelle (Paris, France), the Fyssen Foundation and a Leakey grant to SK. AAE was supported by an R01 grant (GM080586) from the US National Institutes of Health. The US NIH intramural program supported TFM. LR, ACG, CL and GS were supported by INSERM and the Agency for Science, Technology and Research (A*STAR), Singapore. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: Ananias.Escalante@asu.edu (AAE); georges.snounou@upmc.fr or gsnounou@gmail.com (GS) . These authors contributed equally to this work. ¤ Current address: African Insect Science for Food and Health, Nairobi, Kenya Introduction Malaria infections have influenced the development of human civilizations, and have shaped the genetic make-up of current human populations. There are four globally distributed Plasmo- dium protozoan parasites that are responsible for malaria in humans (P. falciparum, P. vivax, P. malariae and P. ovale). Molecular phylogenetic analyses have demonstrated that these four parasites are not monophyletic [1,2], indicating that they independently colonised hominids [3–6]. The timing of their appearance in Homo sapiens, however, remains unresolved. This is of some importance to current efforts to control malaria, because it will affect how observed patterns of genetic diversity in the parasite populations are interpreted. For example, several evolutionary genetic approaches rely on reliable phylogenetic information to detect putative adaptive genetic variation, thereby identifying genes that might be involved in pathogenesis or in the evasion of host immune responses. Addressing these issues is a PLoS Pathogens | www.plospathogens.org 1 February 2010 | Volume 6 | Issue 2 | e1000765