R. Feachem, A. Phillips, J. Hwang, C. Cotter, B. Wielgosz et al., Shrinking the malaria map: progress and prospects, The Lancet, vol.376, issue.9752, pp.1566-1578, 2010.
DOI : 10.1016/S0140-6736(10)61270-6

P. Martens and L. Hall, Malaria on the Move: Human Population Movement and Malaria Transmission, Emerging Infectious Diseases, vol.6, issue.2, pp.103-109, 2000.
DOI : 10.3201/eid0602.000202

J. Cohen, D. Smith, C. Cotter, A. Ward, G. Yamey et al., Malaria resurgence: a systematic review and assessment of its causes, Malaria Journal, vol.11, issue.1
DOI : 10.1111/j.1365-2915.1993.tb00701.x

P. Corran, P. Coleman, E. Riley, and C. Drakeley, Serology: a robust indicator of malaria transmission intensity? Trends Parasitol, pp.575-582, 2007.

C. Drakeley and J. Cook, Chapter 5 Potential Contribution of Sero???Epidemiological Analysis for Monitoring Malaria Control and Elimination: Historical and Current Perspectives, Adv Parasitol, vol.69, pp.299-352, 2009.
DOI : 10.1016/S0065-308X(09)69005-9

A. Djimdé, O. Doumbo, J. Cortese, K. Kayentao, S. Doumbo et al., A Molecular Marker for Chloroquine-Resistant Falciparum Malaria, New England Journal of Medicine, vol.344, issue.4, pp.257-263, 2001.
DOI : 10.1056/NEJM200101253440403

N. Noranate, R. Durand, A. Tall, L. Marrama, A. Spiegel et al., Rapid Dissemination of Plasmodium falciparum Drug Resistance Despite Strictly Controlled Antimalarial Use, PLoS ONE, vol.2, issue.1, p.139, 2007.
DOI : 10.1371/journal.pone.0000139.s003

J. Wootton, X. Feng, M. Ferdig, R. Cooper, J. Mu et al., Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum, Nature, vol.91, issue.6895, pp.320-323, 2002.
DOI : 10.1086/320707

C. Chan, R. Spathis, D. Reiff, S. Mcgrath, R. Garruto et al., Diversity of Plasmodium falciparum Chloroquine Resistance Transporter (pfcrt) Exon 2 Haplotypes in the Pacific from 1959 to 1979, PLoS ONE, vol.1, issue.4, p.30213, 1959.
DOI : 10.1371/journal.pone.0030213.s001

S. Vinayak, M. Alam, R. Sem, N. Shah, A. Susanti et al., Multiple genetic backgrounds of the amplified Plasmodium falciparum multidrug resistance (pfmdr1) gene and selective sweep of 184F mutation in Cambodia, pp.1551-1560, 0201.

A. Mccollum, L. Basco, R. Tahar, V. Udhayakumar, and A. Escalante, Hitchhiking and Selective Sweeps of Plasmodium falciparum Sulfadoxine and Pyrimethamine Resistance Alleles in a Population from Central Africa, Antimicrobial Agents and Chemotherapy, vol.52, issue.11, pp.4089-4097, 2008.
DOI : 10.1128/AAC.00623-08

S. Nair, J. Williams, A. Brockman, L. Paiphun, M. Mayxay et al., A Selective Sweep Driven by Pyrimethamine Treatment in Southeast Asian Malaria Parasites, Molecular Biology and Evolution, vol.20, issue.9, pp.1526-1536, 2003.
DOI : 10.1093/molbev/msg162

B. Genton, I. Betuela, I. Felger, F. Al-yaman, R. Anders et al., Density and Exerts Selective Pressure on Parasite Populations in a Phase 1???2b Trial in Papua New Guinea, The Journal of Infectious Diseases, vol.185, issue.6, pp.820-827, 2002.
DOI : 10.1086/339342

C. Flück, S. Schoëpflin, T. Smith, B. Genton, M. Alpers et al., Effect of the malaria vaccine Combination B on merozoite surface antigen 2 diversity, Infection, Genetics and Evolution, vol.7, issue.1, pp.44-51, 2007.
DOI : 10.1016/j.meegid.2006.03.006

M. Nei, Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics, vol.89, pp.583-590, 1978.

R. Paul, I. Hackford, A. Brockman, C. Muller-graf, R. Price et al., Transmission intensity and Plasmodium falciparum diversity on the northwestern border of Thailand, Am J Trop Med Hyg, vol.58, pp.195-203, 1998.

R. Paul, A. Brockman, R. Price, C. Luxemburger, N. White et al., Genetic analysis of Plasmodium falciparum infections on the north-western border of Thailand, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.93, issue.6, pp.587-593, 1999.
DOI : 10.1016/S0035-9203(99)90057-3

T. Anderson, B. Haubold, J. Williams, J. Estrada-franco, L. Richardson et al., Microsatellite Markers Reveal a Spectrum of Population Structures in the Malaria Parasite Plasmodium falciparum, Molecular Biology and Evolution, vol.17, issue.10, pp.1467-1482, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026247

M. Iwagami, P. Rivera, E. Villacorte, A. Escueta, T. Hatabu et al., Genetic diversity and population structure of Plasmodium falciparum in the Philippines, Malaria Journal, vol.8, issue.1, p.96, 2009.
DOI : 10.1186/1475-2875-8-96

S. Campino, S. Auburn, K. Kivinen, I. Zongo, J. Ouedraogo et al., Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay, PLoS ONE, vol.94, issue.6, p.20251, 2011.
DOI : 10.1371/journal.pone.0020251.s006

S. Schoepflin, F. Valsangiacomo, E. Lin, B. Kiniboro, I. Mueller et al., Comparison of Plasmodium falciparum allelic frequency distribution in different endemic settings by high-resolution genotyping, Malaria Journal, vol.8, issue.1, p.250, 2009.
DOI : 10.1186/1475-2875-8-250

T. Pumpaibool, C. Arnathau, P. Durand, N. Kanchanakhan, N. Siripoon et al., Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country, Malaria Journal, vol.8, issue.1, p.155, 2009.
DOI : 10.1186/1475-2875-8-155

V. Mobegi, K. Loua, A. Ahouidi, J. Satoguina, D. Nwakanma et al., Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa, Malaria Journal, vol.11, issue.1, p.223, 2012.
DOI : 10.1017/S0031182000080665

R. Paul, M. Packer, M. Walmsley, M. Lagog, L. Ranford-cartwright et al., Mating patterns in malaria parasite populations of Papua New Guinea, Science, vol.269, issue.5231, pp.1709-1711, 1995.
DOI : 10.1126/science.7569897

R. Paul and K. Day, Mating Patterns of Plasmodium falciparum, Parasitology Today, vol.14, issue.5, pp.197-202, 1998.
DOI : 10.1016/S0169-4758(98)01226-5

H. Bogreau, F. Renaud, H. Bouchiba, P. Durand, S. Assi et al., Genetic diversity and structure of African Plasmodium falciparum populations in urban and rural areas, AmJTrop Med Hyg, vol.74, pp.953-959, 2006.

S. Rebaudet, H. Bogreau, R. Silaï, J. Lepere, L. Bertaux et al., and Elimination of Malaria, Comoros Archipelago, Emerging Infectious Diseases, vol.16, issue.11, pp.1686-1694, 2010.
DOI : 10.3201/eid1611.100694

S. Wright, The Interpretation of Population Structure by F-Statistics with Special Regard to Systems of Mating, Evolution, vol.19, issue.3, pp.395-420, 1965.
DOI : 10.2307/2406450

B. Weir and C. Cockerham, Estimating F-Statistics for the Analysis of Population Structure, Evolution, vol.38, issue.6, pp.1358-1370, 1984.
DOI : 10.2307/2408641

A. Tatem, D. Smith, P. Gething, C. Kabaria, R. Snow et al., Ranking of elimination feasibility between malaria-endemic countries, The Lancet, vol.376, issue.9752, pp.1579-1591, 2010.
DOI : 10.1016/S0140-6736(10)61301-3

J. Cohen, B. Moonen, R. Snow, and D. Smith, How absolute is zero? An evaluation of historical and current definitions of malaria elimination, Malaria Journal, vol.9, issue.1, p.213, 2010.
DOI : 10.1186/1475-2875-9-213

B. Carteron, D. Morvan, and F. Rodhain, The question of endemic malaria in Republic of Djibouti (in French) Med Trop (Mars), pp.299-304, 1978.

E. Fox, E. Abbate, M. Leef, E. Mikhail, Y. Said-salah et al., Malaria in the Djibouti Republic. Results of a serologic survey in Ambouli](in French, Med Trop (Mars), vol.49, pp.159-160, 1989.

E. Fox, J. Bouloumie, J. Olson, D. Tible, M. Lluberas et al., [Plasmodium falciparum travels by train from Ethiopia to Djibouti](in French) Med Trop (Mars), pp.51185-189, 1991.

S. Manguin, P. Carnevale, J. Mouchet, M. Coosemans, J. Julvez et al., Biodiversity of Malaria in the World, p.140, 2008.

B. Khaireh, S. Briolant, A. Pascual, M. Mokrane, V. Machault et al., Plasmodium vivax and Plasmodium falciparum infections in the Republic of Djibouti: evaluation of their prevalence and potential determinants, Malaria Journal, vol.11, issue.1, p.395, 2012.
DOI : 10.1186/1475-2875-10-173
URL : https://hal.archives-ouvertes.fr/inserm-00773588

L. Ollivier, R. Nevin, H. Darar, J. Bougã¨re, M. Saleh et al., Malaria in the Republic of Djibouti, 1998-2009, Malaria in the Republic of Djibouti, pp.554-559, 1998.
DOI : 10.4269/ajtmh.2011.11-0122

C. Rogier, B. Pradines, H. Bogreau, J. Koeck, and M. Kamil, Malaria Epidemic and Drug Resistance, Djibouti, Emerging Infectious Diseases, vol.11, issue.2, pp.317-321, 2005.
DOI : 10.3201/eid1102.040108

T. Ministère, Rapport d'activité semestriel, 2008.

A. Noor, M. Mohamed, C. Mugyenyi, M. Osman, H. Guessod et al., Establishing the extent of malaria transmission and challenges facing pre-elimination in the Republic of Djibouti, BMC Infectious Diseases, vol.8, issue.1, p.121, 2011.
DOI : 10.1186/1475-2875-8-287

J. Officiel-de-la-république-de-djibout, Décret n°2010-0038/PR/ MEFPCP portant publication des résultats du 2ème Recensement Général de la Population et de l, 2010.

J. Kublin, F. Dzinjalamala, D. Kamwendo, E. Malkin, J. Cortese et al., Malaria, The Journal of Infectious Diseases, vol.185, issue.3, pp.380-388, 2002.
DOI : 10.1086/338566

S. Nair, A. Brockman, L. Paiphun, F. Nosten, and T. Anderson, Rapid genotyping of loci involved in antifolate drug resistance in Plasmodium falciparum by primer extension, International Journal for Parasitology, vol.32, issue.7, pp.852-858, 2002.
DOI : 10.1016/S0020-7519(02)00033-4

K. Belkhir, P. Borsa, L. Chikhi, L. Raufaste, and F. Bonhomme, [GENETIX 4.05, Windows software for population genetics] [in French]; 2012

J. Goudet, FSTAT (version 2.9.3.2), a program to estimate and test population genetics parameters
DOI : 10.1093/oxfordjournals.jhered.a111627
URL : http://jhered.oxfordjournals.org/cgi/content/short/86/6/485

J. Benzécri, L'analyse des données / leçons sur l'analyse factorielle et la reconnaissance des formes et travaux. France: Dunod, 1982.

R. Team, R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, p.24, 2012.

E. Feil, B. Li, D. Aanensen, W. Hanage, and B. Spratt, eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data, Journal of Bacteriology, vol.186, issue.5, pp.1518-1530, 2004.
DOI : 10.1128/JB.186.5.1518-1530.2004

A. Francisco, M. Bugalho, M. Ramirez, and J. Carriço, Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach, BMC Bioinformatics, vol.10, issue.1, p.152, 2009.
DOI : 10.1186/1471-2105-10-152

A. Francisco, C. Vaz, P. Monteiro, J. Melo-cristino, M. Ramirez et al., PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods, BMC Bioinformatics, vol.13, issue.1, p.87, 2012.
DOI : 10.1093/oxfordjournals.molbev.a026082

S. Rich, R. Hudson, and F. Ayala, Plasmodium falciparum antigenic diversity: Evidence of clonal population structure, Proceedings of the National Academy of Sciences, vol.94, issue.24, pp.13040-13045, 1997.
DOI : 10.1073/pnas.94.24.13040

L. Urdaneta, A. Lal, C. Barnabe, B. Oury, I. Goldman et al., Evidence for clonal propagation in natural isolates of Plasmodium falciparum from Venezuela, Proceedings of the National Academy of Sciences, vol.98, issue.12, pp.6725-6729, 2001.
DOI : 10.1073/pnas.111144998

M. Tibayrenc and F. Ayala, The clonal theory of parasitic protozoa: 12 years on, Trends in Parasitology, vol.18, issue.9, pp.405-410, 2002.
DOI : 10.1016/S1471-4922(02)02357-7

C. Gauthier and M. Tibayrenc, Population structure of malaria parasites: The driving epidemiological forces, Acta Tropica, vol.94, issue.3, pp.241-250, 2005.
DOI : 10.1016/j.actatropica.2005.04.001

F. Razakandrainibe, P. Durand, J. Koella, D. Meeus, T. Rousset et al., "Clonal" population structure of the malaria agent Plasmodium falciparum in high-infection regions, Proceedings of the National Academy of Sciences, vol.102, issue.48, pp.17388-17393, 2005.
DOI : 10.1073/pnas.0508871102
URL : https://hal.archives-ouvertes.fr/halsde-00325183

Z. Annan, P. Durand, F. Ayala, C. Arnathau, P. Awono-ambene et al., Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus, Proceedings of the National Academy of Sciences, vol.104, issue.19, pp.7987-7992, 2007.
DOI : 10.1073/pnas.0702715104

D. Echeverry, S. Nair, L. Osorio, S. Menon, C. Murillo et al., Long term persistence of clonal malaria parasite Plasmodium falciparum lineages in the Colombian Pacific region, BMC Genetics, vol.14, issue.1, 2013.
DOI : 10.1186/1471-2156-14-2

A. Arez, G. Snounou, J. Pinto, C. Sousa, D. Modiano et al., A clonal Plasmodium falciparum population in an isolated outbreak of malaria in the Republic of Cabo Verde, Parasitology, vol.118, issue.4, pp.347-355, 1999.
DOI : 10.1017/S0031182099003972

K. Laserson, I. Petralanda, R. Almera, R. Barker, . Jr et al., Malaria among Yanomami Amerindians, The Journal of Infectious Diseases, vol.180, issue.6, pp.2081-2085, 1999.
DOI : 10.1086/315144

S. Griffing, T. Mixson-hayden, S. Sridaran, M. Alam, A. Mccollum et al., South American Plasmodium falciparum after the Malaria Eradication Era: Clonal Population Expansion and Survival of the Fittest Hybrids, PLoS ONE, vol.54, issue.9, p.23486, 2011.
DOI : 10.1371/journal.pone.0023486.t003

P. Hunter and M. Gaston, Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity, J Clin Microbiol, vol.26, pp.2465-2466, 1988.

A. Manjurano, L. Okell, T. Lukindo, H. Reyburn, R. Olomi et al., Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania, Malaria Journal, vol.10, issue.1, p.370, 2011.
DOI : 10.1186/1475-2875-9-244

M. Bruce, A. Macheso, A. Mcconnachie, and M. Molyneux, Comparative population structure of Plasmodium malariae and Plasmodium falciparum under different transmission settings in Malawi, Malaria Journal, vol.10, issue.1, p.38, 2011.
DOI : 10.1017/S0031182097001145

M. Vafa, M. Troye-blomberg, J. Anchang, and A. Garcia, Multiplicity of Plasmodium falciparum infection in asymptomatic children in Senegal: relation to transmission, age and erythrocyte variants, Malaria Journal, vol.7, issue.1, p.17, 2008.
DOI : 10.1186/1475-2875-7-17

P. Daubersies, S. Sallenave-sales, S. Magne, J. Trape, H. Contamin et al., Rapid turnover of Plasmodium falciparum populations in asymptomatic individuals living in a high transmission area, Am J Trop Med Hyg, vol.54, pp.18-26, 1996.

H. Hopkins, A. Talisuna, C. Whitty, and S. Staedke, Impact of home-based management of malaria on health outcomes in Africa: a systematic review of the evidence, Malaria Journal, vol.6, issue.1, p.134, 2007.
DOI : 10.1186/1475-2875-6-134

A. Yeshiwondim, S. Gopal, A. Hailemariam, D. Dengela, and H. Patel, Spatial analysis of malaria incidence at the village level in areas with unstable transmission in Ethiopia, International Journal of Health Geographics, vol.8, issue.1, p.5, 2009.
DOI : 10.1186/1476-072X-8-5

. Shargieeb, . Ngondij, . Gravespm, . Getachewa, . Hwangj et al., Rapid increase in ownership and use of long-lasting insecticidal nets and decrease in prevalence of malaria in three regional States of ethiopia, JT r o pM e d2010, p.12, 0201.

T. Ministère, Rapport d'activité semestriel, p.22, 2008.

T. Gebru-woldearegai, A. Hailu, M. Grobusch, and J. Kun, Molecular surveillance of mutations in dihydrofolate reductase and dihydropteroate synthase genes of Plasmodium falciparum in Ethiopia, Am J Trop Med Hyg, vol.73, pp.1131-1134, 2005.

M. Schunk, W. Kumma, I. Miranda, M. Osman, S. Roewer et al., High prevalence of drug-resistance mutations in Plasmodium falciparum and Plasmodium vivax in southern Ethiopia, Malaria Journal, vol.5, issue.1, p.54, 2006.
DOI : 10.1186/1475-2875-5-54

P. Mula, A. Fernàndez-martinez, D. Lucio, A. Ramos, J. Reyes et al., Detection of high levels of mutations involved in anti-malarial drug resistance in Plasmodium falciparum and Plasmodium vivax at a rural hospital in southern Ethiopia, Malaria Journal, vol.10, issue.1, p.214, 2011.
DOI : 10.1179/136485905X75395

S. Chenet, K. Schneider, L. Villegas, and A. Escalante, Local population structure of Plasmodium: impact on malaria control and elimination, Malaria Journal, vol.11, issue.1
DOI : 10.1073/pnas.0508871102

S. Griffing, G. Viana, T. Mixson-hayden, S. Sridaran, M. Alam et al., Historical Shifts in Brazilian P. falciparum Population Structure and Drug Resistance Alleles, PLoS ONE, vol.95, issue.3, p.58984, 2013.
DOI : 10.1371/journal.pone.0058984.t005

R. Daniels, H. Chang, P. Séne, D. Park, D. Neafsey et al., Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal, PLoS ONE, vol.170, issue.4, p.60780, 2013.
DOI : 10.1371/journal.pone.0060780.s010

A. Vardo-zalik, G. Zhou, D. Zhong, Y. Afrane, A. Githeko et al., Alterations in Plasmodium falciparum Genetic Structure Two Years after Increased Malaria Control Efforts in Western Kenya, American Journal of Tropical Medicine and Hygiene, vol.88, issue.1, pp.29-36, 2013.
DOI : 10.4269/ajtmh.2012.12-0308

T. Anthony, D. Conway, J. Cox-singh, A. Matusop, S. Ratnam et al., in a Region of Declining Endemicity, The Journal of Infectious Diseases, vol.191, issue.9, pp.1558-1564, 2005.
DOI : 10.1086/429338

S. Nkhoma, S. Nair, S. Saai, E. Ashley, R. Mcgready et al., Population genetic correlates of declining transmission in a human pathogen, Molecular Ecology, vol.38, issue.Suppl. 1, pp.273-285, 2013.
DOI : 10.1111/mec.12099