D. ?l-of, heating for 5 min at 94 °C, 30 s at 94 °C, 30 s at 53 °C, and 30 s at 52 °C for nested PCR, and 1 min at 72 °C for 40 cycles and a final 10-min extension at 72 °C. Ldh7 and Ldh8 were used for sequencing, p.1

A. Escalante and F. Ayala, Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences., Proceedings of the National Academy of Sciences, vol.91, issue.24, pp.11373-11377, 1994.
DOI : 10.1073/pnas.91.24.11373

A. Escalante and F. Ayala, Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes., Proceedings of the National Academy of Sciences, vol.92, issue.13, pp.5793-5797, 1995.
DOI : 10.1073/pnas.92.13.5793

A. Escalante, E. Barrio, and F. Ayala, Evolutionary origin of human and primate malarias: Evidence from the circumsporozoite protein gene, Mol Biol Evol, vol.12, pp.616-626, 1995.

D. Fiore, A. Disotell, T. Gagneux, P. Ayala, and F. , Primate Parasite Ecology. The Dynamics and Study of Host-Parasite Relationships, pp.141-182, 2009.

A. Escalante, D. Freeland, W. Collins, and A. Lal, The evolution of primate malaria parasites based on the gene encoding cytochrome b from the linear mitochondrial genome, Proceedings of the National Academy of Sciences, vol.95, issue.14, pp.8124-8129, 1998.
DOI : 10.1073/pnas.95.14.8124

S. Hagner, B. Misof, W. Maier, and H. Kampen, Bayesian analysis of new and old malaria parasite DNA sequence data demonstrates the need for more phylogenetic signal to clarify the descent of Plasmodium falciparum, Parasitology Research, vol.96, issue.3, pp.493-503, 2007.
DOI : 10.1007/s00436-007-0499-6

S. Perkins and J. Schall, A Molecular Phylogeny of Malarial Parasites Recovered from Cytochrome b Gene Sequences, The Journal of Parasitology, vol.88, issue.5, pp.972-978, 2002.
DOI : 10.2307/3285540

S. Rich, M. Licht, R. Hudson, and F. Ayala, Malaria's Eve: Evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum, Proceedings of the National Academy of Sciences, vol.95, issue.8, pp.4425-4430, 1998.
DOI : 10.1073/pnas.95.8.4425

S. Rich and F. Ayala, Population structure and recent evolution of Plasmodium falciparum, Proceedings of the National Academy of Sciences, vol.97, issue.13, pp.6994-7001, 2000.
DOI : 10.1073/pnas.97.13.6994

F. Ayala and S. Rich, Genetic variation and the recent worldwide expansion of Plasmodium falciparum, Gene, vol.261, issue.1, pp.161-170, 2000.
DOI : 10.1016/S0378-1119(00)00478-9

S. Volkman, Recent Origin of Plasmodium falciparum from a Single Progenitor, Science, vol.293, issue.5529, pp.482-484, 2001.
DOI : 10.1126/science.1059878

S. Tishkoff, Haplotype Diversity and Linkage Disequilibrium at Human G6PD: Recent Origin of Alleles That Confer Malarial Resistance, Science, vol.293, issue.5529, pp.455-462, 2001.
DOI : 10.1126/science.1061573

D. Hartl, The paradoxical population genetics of Plasmodium falciparum, Trends in Parasitology, vol.18, issue.6, pp.266-272, 2002.
DOI : 10.1016/S1471-4922(02)02268-7

S. Tishkoff and B. Verrelli, Infectious Disease and Host-Pathogen Evolution, Dronamraju KR, pp.113-140, 2004.

A. Escalante, O. Cornejo, A. Rojas, V. Udhayakumar, and A. Lal, Assessing the effect of natural selection in malaria parasites, Trends in Parasitology, vol.20, issue.8, pp.388-395, 2004.
DOI : 10.1016/j.pt.2004.06.002

M. Martin, J. Rayner, P. Gagneux, J. Barnwell, and A. Varki, Evolution of human-chimpanzee differences in malaria susceptibility: Relationship to human genetic loss of N-glycolylneuraminic acid, Proceedings of the National Academy of Sciences, vol.102, issue.36, pp.12819-12824, 2005.
DOI : 10.1073/pnas.0503819102

A. Varki and P. Gagneux, Human-specific evolution of sialic acid targets: Explaining the malignant malaria mystery?, Proceedings of the National Academy of Sciences, vol.106, issue.35, pp.14739-14740, 2009.
DOI : 10.1073/pnas.0908196106

S. Rich, The origin of malignant malaria, Proceedings of the National Academy of Sciences, vol.106, issue.35, pp.14902-14907, 2009.
DOI : 10.1073/pnas.0907740106

B. Singh, A large focus of naturally acquired Plasmodium knowlesi infections in human beings, The Lancet, vol.363, issue.9414, pp.1017-1024, 2004.
DOI : 10.1016/S0140-6736(04)15836-4

S. Jongwutiwes, C. Putaporntip, T. Iwasaki, T. Sata, and H. Kanbara, Malaria in Human, Thailand, Emerging Infectious Diseases, vol.10, issue.12, pp.2211-2213, 2004.
DOI : 10.3201/eid1012.040293

I. Vythilingam, Natural transmission of Plasmodium knowlesi to humans by Anopheles latens in Sarawak, Malaysia, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.100, issue.11, pp.1087-1088, 2006.
DOI : 10.1016/j.trstmh.2006.02.006

A. Kantele, H. Marti, I. Felger, D. Müller, and T. Jokiranta, Monkey Malaria in a European Traveler Returning from Malaysia, Emerging Infectious Diseases, vol.14, issue.9, pp.1434-1436, 2008.
DOI : 10.3201/eid1409.080170

L. Duval, Chimpanzee Malaria Parasites Related to Plasmodium ovale in Africa, PLoS ONE, vol.17, issue.5, p.5520, 2009.
DOI : 10.1371/journal.pone.0005520.t005

T. Hayakawa, R. Culleton, H. Otani, T. Horii, and K. Tanabe, Big Bang in the Evolution of Extant Malaria Parasites, Molecular Biology and Evolution, vol.25, issue.10, pp.2233-2239, 2008.
DOI : 10.1093/molbev/msn171

T. Hayakawa, Identification of Plasmodium malariae, a Human Malaria Parasite, in Imported Chimpanzees, PLoS ONE, vol.25, issue.10, p.7412, 2009.
DOI : 10.1371/journal.pone.0007412.g002

B. Ollomo, A New Malaria Agent in African Hominids, PLoS Pathogens, vol.21, issue.5, p.1000446, 2009.
DOI : 10.1371/journal.ppat.1000446.s006

S. Mharakurwa, C. Simoloka, P. Thuma, C. Shiff, and D. Sullivan, PCR detection of Plasmodium falciparum in human urine and saliva samples, Malaria Journal, vol.5, issue.1, p.103, 2006.
DOI : 10.1186/1475-2875-5-103

D. Nwakanma, DNA in Saliva, Blood, and Urine, The Journal of Infectious Diseases, vol.199, issue.11, pp.1567-1574, 2009.
DOI : 10.1086/598856

F. Prugnolle, African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum, Proceedings of the National Academy of Sciences, vol.107, issue.4, pp.1458-1463, 2010.
DOI : 10.1073/pnas.0914440107

S. Krief, On the Diversity of Malaria Parasites in African Apes and the Origin of Plasmodium falciparum from Bonobos, PLoS Pathogens, vol.16, issue.2, p.1000765, 2010.
DOI : 10.1371/journal.ppat.1000765.s002

A. Yoder, M. Cartmill, M. Ruvolo, K. Smith, and R. Vilgalys, Ancient single origin for Malagasy primates., Proceedings of the National Academy of Sciences, vol.93, issue.10, pp.5122-5126, 1996.
DOI : 10.1073/pnas.93.10.5122

A. Matsui, F. Rakotondraparany, I. Munechika, M. Hasegawa, and S. Horai, Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs, Gene, vol.441, issue.1-2, pp.53-66, 2009.
DOI : 10.1016/j.gene.2008.08.024

G. Coatney, W. Collins, M. Warren, and P. Contacos, The Primate malarias (illustrated). (US Government Printing Office, 1971.

D. Taylor, Parasitologic and immunologic studies of experimental Plasmodium falciparum infection in nonsplenectomized chimpanzees, 1985.

J. Rodhain and R. Dellaert, Contribution a l etude de Plasmodium schwetzi E. Brumpt (2eme note) Transmission de Plasmodium schwetzi a l'homme, Ann Soc Belg Med Trop, vol.35, pp.757-775, 1955.

P. Contacos, Transmission of Plasmodium schwetzi from the chimpanzee to man by mosquito bite, Am J Trop Med Hyg, vol.19, pp.190-195, 1970.

R. Carter and K. Mendis, Evolutionary and Historical Aspects of the Burden of Malaria, Clinical Microbiology Reviews, vol.15, issue.4, pp.564-594, 2002.
DOI : 10.1128/CMR.15.4.564-594.2002

F. Ayala, A. Escalante, and S. Rich, Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum, Parassitologia, vol.41, pp.55-68, 1999.

W. Collins and G. Jeffery, Plasmodium malariae: Parasite and Disease, Clinical Microbiology Reviews, vol.20, issue.4, pp.579-592, 2007.
DOI : 10.1128/CMR.00027-07
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176047

R. Bray, Studies on malaria in chimpanzees. VI. Laverania falciparum, Am J Trop Med Hyg, vol.7, pp.20-24, 1958.

R. Bray, The Malaria Parasites of Anthropoid Apes, The Journal of Parasitology, vol.49, issue.6, pp.888-891, 1963.
DOI : 10.2307/3275713

T. Macfie, E. Nerrienet, N. De-groot, R. Bontrop, and N. Mundy, Patterns of Diversity in HIV-Related Loci among Subspecies of Chimpanzee: Concordance at CCR5 and Differences at CXCR4 and CX3CR1, Molecular Biology and Evolution, vol.26, issue.4, pp.719-727, 2009.
DOI : 10.1093/molbev/msp016

S. Calattini, Detection and molecular characterization of foamy viruses in Central African chimpanzees of the Pan troglodytes troglodytes and Pan troglodytes vellerosus subspecies, Journal of Medical Primatology, vol.9, issue.2, pp.59-66, 2006.
DOI : 10.1093/jhered/92.4.371

L. Duval, Multiple host-switching of Haemosporidia parasites in bats, Malaria Journal, vol.6, issue.1, p.157, 2007.
DOI : 10.1186/1475-2875-6-157

Y. Rumpler, Comparing chromosomal and mitochondrial phylogenies of sportive lemurs (Genus Lepilemur, Primates), Chromosome Research, vol.12, issue.1???3, pp.1143-1158, 2008.
DOI : 10.1007/s10577-008-1265-z

M. Hajibabaei, G. Singer, P. Hebert, and D. Hickey, DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics, Trends in Genetics, vol.23, issue.4, pp.167-172, 2007.
DOI : 10.1016/j.tig.2007.02.001

E. Martinsen, S. Perkins, and J. Schall, A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches, Molecular Phylogenetics and Evolution, vol.47, issue.1, pp.261-273, 2008.
DOI : 10.1016/j.ympev.2007.11.012

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

X. Xia and Z. Xie, DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution, Journal of Heredity, vol.92, issue.4, pp.371-373, 2001.
DOI : 10.1093/jhered/92.4.371

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

D. Zwickl, Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, 2006.

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985.
DOI : 10.1007/BF02101694

J. Huelsenbeck and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, issue.8, pp.754-755, 2001.
DOI : 10.1093/bioinformatics/17.8.754