, France. 3 Program in Genomics, Boston Children's Hospital, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA. 4 Centre National de Recherche et de Formation sur le Paludisme, 1487 Avenue de l'Oubritenga, 01 BP 2208 Ouagadougou, Burkina Faso. 5 Malaria Research and Training Centre, Faculty of Medicine and Dentistry, CNRS Unit of Hosts, Vectors and Pathogens, vol.75015, 1500.

D. M. Menge, D. Zhong, T. Guda, L. C. Gouagna, J. I. Githure et al., Quantitative Trait Loci Controlling Refractoriness to Plasmodium falciparum in Natural Anopheles gambiae from a Malaria Endemic Region in Western Kenya, Genetics, vol.173, issue.1, pp.235-276, 2006.

M. M. Riehle, K. Markianos, L. Lambrechts, A. Xia, I. Sharakhov et al., A major genetic locus controlling natural Plasmodium falciparum infection is shared by East and West African Anopheles gambiae, Malar J, vol.6, p.87, 2007.

M. M. Riehle, K. Markianos, O. Niaré, J. Xu, J. Li et al., Natural malaria infection in Anopheles gambiae is regulated by a single genomic control region, Science, vol.312, pp.577-586, 2006.

F. H. Collins, R. K. Sakai, K. D. Vernick, S. Paskewitz, D. C. Seeley et al., Genetic selection of a Plasmodium-refractory strain of the malaria vector Anopheles gambiae, Science, vol.234, issue.4776, pp.607-617, 1986.

S. J. Dunstan, K. A. Rockett, N. Quyen, Y. Y. Teo, C. Q. Thai et al., Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese, Genes and immunity, vol.13, pp.503-511, 2012.

M. Jallow, Y. Y. Teo, K. S. Small, K. A. Rockett, P. Deloukas et al., Genomewide and fine-resolution association analysis of malaria in West Africa, Nature genetics, vol.41, pp.657-65, 2009.

D. Van-tyne, D. J. Park, S. F. Schaffner, D. E. Neafsey, E. Angelino et al., Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum, PLoS genetics, vol.7, p.1001383, 2011.

C. Harris, L. Lambrechts, F. Rousset, L. Abate, S. E. Nsango et al., Polymorphisms in Anopheles gambiae immune genes associated with natural resistance to Plasmodium falciparum, PLoS Pathog, vol.6, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02011022

A. A. Horton, Y. Lee, C. A. Coulibaly, V. K. Rashbrook, A. J. Cornel et al., Identification of three single nucleotide polymorphisms in Anopheles gambiae immune signaling genes that are associated with natural Plasmodium falciparum infection, Malaria journal, vol.9, p.160, 2010.

D. E. Neafsey, M. Lawniczak, D. J. Park, S. N. Redmond, M. B. Coulibaly et al., SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes, Science, vol.330, pp.514-521, 2010.

J. E. Crawford, E. Bischoff, T. Garnier, A. Gneme, K. Eiglmeier et al., Evidence for population-specific positive selection on immune genes of Anopheles gambiae, vol.3, pp.1505-1524, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-02008329

C. S. Wilding, D. Weetman, K. Steen, and M. J. Donnelly, High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooledtemplate sequencing: implications for high-throughput genotyping protocols, BMC genomics, vol.10, p.320, 2009.

E. G. King, S. J. Macdonald, and A. D. Long, Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits, Genetics, vol.191, pp.935-984, 2012.

E. G. King, C. M. Merkes, C. L. Mcneil, S. R. Hoofer, S. Sen et al., Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource, Genome research, vol.22, pp.1558-66, 2012.

K. L. Svenson, D. M. Gatti, W. Valdar, C. E. Welsh, R. Cheng et al., Highresolution genetic mapping using the Mouse Diversity outbred population, Genetics, vol.190, pp.437-484, 2012.

W. Valdar, L. C. Solberg, D. Gauguier, S. Burnett, P. Klenerman et al., Genome-wide genetic association of complex traits in heterogeneous stock mice, Nature genetics, vol.38, pp.879-87, 2006.

J. Hastbacka, A. De-la-chapelle, I. Kaitila, P. Sistonen, A. Weaver et al., Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland, Nature genetics, vol.2, issue.3, pp.204-215, 1992.

A. Kong, G. Masson, M. L. Frigge, A. Gylfason, P. Zusmanovich et al., Detection of sharing by descent, long-range phasing and haplotype imputation, Nature genetics, vol.40, issue.9, pp.1068-75, 2008.

M. Boehnke, Limits of resolution of genetic linkage studies: implications for the positional cloning of human disease genes, Am J Hum Genet, vol.55, pp.379-90, 1994.

R. A. Holt, G. M. Subramanian, A. Halpern, G. G. Sutton, R. Charlab et al., The genome sequence of the malaria mosquito Anopheles gambiae, Science, vol.298, pp.129-178, 2002.

G. Christophides, E. Zdobnov, C. Blass, P. T. Brey, F. H. Collins et al., Immunity-related genes and gene families in Anopheles gambiae, Science, vol.159, pp.159-65, 2002.

S. Valanne, J. Wang, and M. Rämet, The Drosophila Toll signaling pathway, Journal of immunology, vol.186, pp.649-56, 1950.

L. S. Garver, A. C. Bahia, S. Das, J. A. Souza-neto, J. Shiao et al., Anopheles Imd pathway factors and effectors in infection intensity-dependent antiPlasmodium action, PLoS pathogens, vol.8, p.1002737, 2012.

C. Mitri, J. Jacques, I. Thiery, M. M. Riehle, J. Xu et al., Fine pathogen discrimination within the APL1 gene family protects Anopheles gambiae against human and rodent malaria species, PLoS pathogens, vol.5, p.1000576, 2009.

S. Tauszig, E. Jouanguy, J. A. Hoffmann, and J. L. Imler, Toll-related receptors and the control of antimicrobial peptide expression in Drosophila, Proceedings of the National Academy of Sciences of the United States of America, vol.97, pp.10520-10525, 2000.

M. Nakamoto, R. H. Moy, J. Xu, S. Bambina, A. Yasunaga et al., Virus recognition by Toll-7 activates antiviral autophagy in Drosophila, Immunity, vol.36, pp.658-67, 2012.

J. L. Ramirez and G. Dimopoulos, The Toll immune signaling pathway control conserved anti-dengue defenses across diverse Ae. aegypti strains and against multiple dengue virus serotypes, Developmental and comparative immunology, vol.34, pp.625-634, 2010.

S. W. Shin, G. Bian, and A. S. Raikhel, Toll5A and Spz1C, are involved in toll antifungal immune signaling in the mosquito Aedes aegypti, The Journal of biological chemistry, vol.281, pp.39388-95, 2006.

Y. Goltsev, G. L. Rezende, K. Vranizan, G. Lanzaro, D. Valle et al., Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo, Developmental biology, vol.330, pp.462-70, 2009.

O. Marinotti, E. Calvo, Q. K. Nguyen, S. Dissanayake, J. Ribeiro et al., Genome-wide analysis of gene expression in adult Anopheles gambiae, Insect molecular biology, vol.15, pp.1-12, 2006.

A. M. Mendes, P. H. Awono-ambene, S. E. Nsango, A. Cohuet, D. Fontenille et al., Infection intensity-dependent responses of Anopheles gambiae to the African malaria parasite Plasmodium falciparum, Infection and immunity, vol.79, pp.4708-4723, 2011.

M. M. Riehle, W. M. Guelbeogo, A. Gneme, K. Eiglmeier, I. Holm et al., A cryptic subgroup of Anopheles gambiae is highly susceptible to human malaria parasites, Science, vol.331, pp.596-604, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01971785

F. Rousset and . Genepop, 007: a complete re-implementation of the genepop software for Windows and Linux, Molecular Ecology Resources, vol.8, pp.103-109, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00366752

S. Kumar, K. Tamura, I. B. Jakobsen, and M. Nei, MEGA2: molecular evolutionary genetics analysis software, Bioinformatics, vol.17, issue.12, pp.1244-1249, 2001.

T. Ponnudurai, A. H. Lensen, A. D. Leeuwenberg, and J. H. Meuwissen, Cultivation of fertile Plasmodium falciparum gametocytes in semi-automated systems. 1. Static cultures, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.76, pp.812-820, 1982.

V. L. Singer, L. J. Jones, S. T. Yue, and R. P. Haugland, Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation, Anal Biochem, vol.249, issue.2, pp.228-266, 1997.

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome biology, vol.10, p.25, 2009.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009.

S. Qanbari, T. M. Strom, G. Haberer, S. Weigend, . Gheyas-aa et al., Simianer H: A High Resolution Genome-Wide Scan for Significant Selective Sweeps: An Application to Pooled Sequence Data in Laying Chickens PLoS ONE, vol.7, p.49525, 2012.

M. Reimers and V. J. Carey, Bioconductor: an open source framework for bioinformatics and computational biology, Methods Enzymol, vol.411, pp.119-153, 2006.

S. Purcell, B. Neale, K. Todd-brown, L. Thomas, M. Ferreira et al., PLINK: a tool set for whole-genome association and population-based linkage analyses, American journal of human genetics, vol.81, pp.559-75, 2007.

C. Schlotterer, R. Tobler, R. Kofler, and V. Nolte, Sequencing pools of individualsmining genome-wide polymorphism data without big funding, Nature reviews Genetics, vol.15, issue.11, pp.749-63, 2014.

W. Mclaren, B. Pritchard, D. Rios, Y. Chen, P. Flicek et al., Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor, Bioinformatics, vol.26, pp.2069-70, 2010.

K. Megy, S. J. Emrich, D. Lawson, D. Campbell, E. Dialynas et al., VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics, Nucleic acids research, vol.40, pp.729-763, 2012.

R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling et al., Bioconductor: open software development for computational biology and bioinformatics, Genome biology, vol.5, p.80, 2004.

N. F. Lobo, D. M. Sangaré, A. A. Regier, K. R. Reidenbach, D. A. Bretz et al., Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion, Malaria journal, vol.9, p.293, 2010.

R. A. Fisher, Statistical Methods for Research Workers, 1954.