, World Malaria Report, 2008.

D. Fontenille and F. Simard, Unravelling complexities in human malaria transmission dynamics in Africa through a comprehensive knowledge of vector populations, Comp Immunol Microbiol Infect Dis, vol.27, pp.357-375, 2004.

O. Niaré, K. Markianos, J. Volz, F. Oduol, and A. Touré, Genetic loci affecting resistance to human malaria parasites in a West African mosquito vector population, Science, vol.298, pp.213-216, 2002.

M. M. Riehle, K. Markianos, O. Niaré, J. Xu, and J. Li, Natural malaria infection in Anopheles gambiae is regulated by a single genomic control region, Science, vol.312, pp.577-579, 2006.

D. M. Menge, D. Zhong, T. Guda, L. Gouagna, and J. Githure, Quantitative trait loci controlling refractoriness to Plasmodium falciparum in natural Anopheles gambiae mosquitoes from a malaria-endemic region in western Kenya, Genetics, vol.173, pp.235-241, 2006.

M. M. Riehle, K. Markianos, L. Lambrechts, A. Xia, and I. Sharakhov, 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, J. Xu, B. P. Lazzaro, S. M. Rottschaefer, and B. Coulibaly, Anopheles gambiae APL1 is a family of variable LRR proteins required for Rel1mediated protection from the malaria parasite, Plasmodium berghei, PLoS ONE, vol.3, p.3672, 2008.

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

T. Habtewold, M. Povelones, A. M. Blagborough, and G. K. Christophides, Transmission blocking immunity in the malaria non-vector mosquito Anopheles quadriannulatus species A, PLoS Pathog, vol.4, p.1000070, 2008.

M. A. Osta, G. K. Christophides, and F. C. Kafatos, Effects of mosquito genes on Plasmodium development, Science, vol.303, pp.2030-2032, 2004.

M. Fraiture, R. H. Baxter, S. Steinert, Y. Chelliah, and C. Frolet, Two mosquito LRR proteins function as complement control factors in the TEP1mediated killing of Plasmodium, Cell Host Microbe, vol.5, pp.273-284, 2009.

M. Povelones, R. M. Waterhouse, F. C. Kafatos, and G. K. Christophides, Leucinerich repeat protein complex activates mosquito complement in defense against Plasmodium parasites, Science, vol.324, pp.258-261, 2009.

T. J. Little and N. Cobbe, The evolution of immune-related genes from disease carrying mosquitoes: diversity in a peptidoglycan-and a thioester-recognizing protein, Insect Mol Biol, vol.14, pp.599-605, 2005.

D. J. Obbard, Y. M. Linton, F. M. Jiggins, G. Yan, and T. J. Little, Population genetics of Plasmodium resistance genes in Anopheles gambiae: no evidence for strong selection, Mol Ecol, vol.16, pp.3497-3510, 2007.

F. Simard, M. Licht, N. J. Besansky, and T. Lehmann, Polymorphism at the defensin gene in the Anopheles gambiae complex: testing different selection hypotheses, Infect Genet Evol, vol.7, pp.285-292, 2007.

M. A. Slotman, A. Parmakelis, J. C. Marshall, P. H. Awono-ambene, and C. Antonionkondjo, Patterns of selection in anti-malarial immune genes in malaria vectors: evidence for adaptive evolution in LRIM1 in Anopheles arabiensis, PLoS One, vol.2, p.793, 2007.

A. Cohuet, S. Krishnakumar, F. Simard, I. Morlais, and A. Koutsos, SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system, BMC Genomics, vol.9, p.227, 2008.

D. J. Obbard, D. M. Callister, F. M. Jiggins, D. C. Soares, and G. Yan, The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae, BMC Evol Biol, vol.8, p.274, 2008.

A. Parmakelis, M. A. Slotman, J. C. Marshall, P. H. Awono-ambene, and C. Antonionkondjio, The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex, BMC Evol Biol, vol.8, p.79, 2008.

T. Lehmann, J. C. Hume, M. Licht, C. S. Burns, and K. Wollenberg, Molecular evolution of immune genes in the malaria mosquito Anopheles gambiae, PLoS One, vol.4, p.4549, 2009.

D. J. Obbard, J. J. Welch, and T. J. Little, Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors, Malar J, vol.8, p.117, 2009.

S. Blandin, S. H. Shiao, L. F. Moita, C. J. Janse, and A. P. Waters, Complementlike protein TEP1 is a determinant of vectorial capacity in the malaria vector Anopheles gambiae, Cell, vol.116, pp.661-670, 2004.

Y. Dong, R. Aguilar, Z. Xi, E. Warr, and E. Mongin, Anopheles gambiae immune responses to human and rodent Plasmodium parasite species, PLoS Pathog, vol.2, p.52, 2006.

S. A. Blandin, R. Wang-sattler, M. Lamacchia, J. Gagneur, and G. Lycett, Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae, Science, vol.326, pp.147-150, 2009.

T. Lehmann and A. Diabate, The molecular forms of Anopheles gambiae: a phenotypic perspective, Infect Genet Evol, vol.8, pp.737-746, 2008.

R. R. Hudson and N. L. Kaplan, The coalescent process in models with selection and recombination, Genetics, vol.120, pp.831-840, 1988.

V. Castric, J. Bechsgaard, M. H. Schierup, and X. Vekemans, Repeated adaptive introgression at a gene under multiallelic balancing selection, PLoS Genet, vol.4, p.1000168, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00305315

J. H. Mcdonald and M. Kreitman, Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.351, pp.652-654, 1991.

S. I. Wright and B. Charlesworth, The HKA test revisited: a maximumlikelihood-ratio test of the standard neutral model, Genetics, vol.168, pp.1071-1076, 2004.

N. J. Besansky, J. Krzywinski, T. Lehmann, F. Simard, and M. Kern, Semipermeable species boundaries between Anopheles gambiae and Anopheles arabiensis: evidence from multilocus DNA sequence variation, Proc Natl Acad Sci U S A, vol.100, pp.10818-10823, 2003.

A. Parmakelis, M. Moustaka, N. Poulakakis, C. Louis, and M. A. Slotman, Anopheles immune genes and amino acid sites evolving under the effect of positive selection, PLoS One, vol.5, p.8885, 2010.

A. D. Kern, C. D. Jones, and D. J. Begun, Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex, Genetics, vol.167, pp.725-735, 2004.

B. P. Lazzaro, Elevated polymorphism and divergence in the class C scavenger receptors of Drosophila melanogaster and D. simulans, Genetics, vol.169, pp.2023-2034, 2005.

Y. Yamaguchi-kabata, M. K. Shimada, Y. Hayakawa, S. Minoshima, and R. Chakraborty, Distribution and effects of nonsense polymorphisms in human genes, PLoS One, vol.3, p.3393, 2008.

M. Coluzzi, A. Sabatini, V. Petrarca, D. Deco, and M. A. , Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex, Trans R Soc Trop Med Hyg, vol.73, pp.483-497, 1979.

J. R. Powell, V. Petrarca, A. Della-torre, A. Caccone, and M. Coluzzi, Population structure, speciation, and introgression in the Anopheles gambiae complex, Parassitologia, vol.41, pp.101-113, 1999.

Y. T. Touré, V. Petrarca, S. F. Traoré, A. Coulibaly, and H. M. Maiga, The distribution and inversion polymorphism of chromosomally recognized taxa of the Anopheles gambiae complex in Mali, West Africa. Parassitologia, vol.40, pp.477-511, 1998.

M. Smith, J. Haigh, and J. , The hitch-hiking effect of a favourable gene, Genet Res, vol.23, pp.23-35, 1974.

J. M. Braverman, R. R. Hudson, N. L. Kaplan, C. H. Langley, and W. Stephan, The hitchhiking effect on the site frequency spectrum of DNA polymorphisms, Genetics, vol.140, pp.783-796, 1995.

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

Y. X. Fu and W. H. Li, Statistical tests of the neutrality of mutations, Genetics, vol.133, pp.693-709, 1993.

K. Zeng, S. Mano, S. Shi, and C. I. Wu, Comparisons of site-and haplotypefrequency methods for detecting positive selection, Mol Biol Evol, vol.24, pp.1562-1574, 2007.

B. J. White, M. Lawniczak, C. Cheng, M. B. Coulibaly, and M. D. Wilson, Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium, Proc Natl Acad Sci, vol.108, pp.244-249, 2011.

T. L. Turner, M. W. Hahn, and S. V. Nuzhdin, Genomic islands of speciation in Anopheles gambiae, PLoS Biol, vol.3, p.285, 2005.

T. L. Turner and M. W. Hahn, Locus-and population-specific selection and differentiation between incipient species of Anopheles gambiae, Mol Biol Evol, vol.24, pp.2132-2138, 2007.

E. A. Levashina, L. F. Moita, S. Blandin, G. Vriend, and M. Lagueux, Conserved role of a complement-like protein in phagocytosis revealed by dsRNA knockout in cultured cells of the mosquito, Anopheles gambiae. Cell, vol.104, pp.709-718, 2001.

W. J. Ewens, Sampling theory of selectively neutral alleles, Theor Pop Biol, vol.3, pp.87-112, 1972.

R. R. Hudson, D. D. Boos, and N. L. Kaplan, A statistical test for detecting geographic subdivision, Mol Biol Evol, vol.9, pp.138-151, 1992.

R. A. Holt, G. M. Subramanian, A. Halpern, G. G. Sutton, and R. Charlab, The genome sequence of the malaria mosquito Anopheles gambiae, Science, vol.298, pp.129-149, 2002.

G. Favia, A. Lanfrancotti, L. Spanos, I. Sidén-kiamos, and C. Louis, Molecular characterization of ribosomal DNA polymorphisms discriminating among chromosomal forms of Anopheles gambiae s.s, Insect Mol Biol, vol.10, pp.19-23, 2001.

B. J. White, F. Santolamazza, L. Kamau, M. Pombi, and O. Grushko, Molecular karyotyping of the 2La inversion in Anopheles gambiae, Am J Trop Med Hyg, vol.76, pp.334-339, 2007.

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, pp.1451-1452, 2009.

R. R. Hudson, Generating samples under a Wright-Fisher neutral model, Bioinformatics, vol.18, pp.337-338, 2002.
DOI : 10.1093/bioinformatics/18.2.337
URL : https://academic.oup.com/bioinformatics/article-pdf/18/2/337/606095/180337.pdf

R. R. Hudson, M. Slatkin, and W. P. Maddison, Estimation of levels of gene flow from DNA sequence data, Genetics, vol.132, pp.583-589, 1992.

S. Kumar, K. Tamura, and M. Nei, MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment, Briefings in Bioinformatics, vol.5, pp.150-163, 2004.
DOI : 10.1093/bib/5.2.150
URL : https://academic.oup.com/bib/article-pdf/5/2/150/9731818/150.pdf