P. Schmid-hempel and D. Ebert, On the evolutionary ecology of specific immune defence, Trends in Ecology & Evolution, vol.18, issue.1, pp.27-32, 2003.
DOI : 10.1016/S0169-5347(02)00013-7

T. Little, D. Hultmark, and A. Read, Invertebrate immunity and the limits of mechanistic immunology, Nature Immunology, vol.104, issue.7, 2005.
DOI : 10.1126/science.1091789

DOI : 10.2307/2411336

DOI : 10.1111/j.1558-5646.2009.00845.x

L. Lambrechts, C. Chevillon, R. Albright, B. Thaisomboonsuk, J. Richardson et al., Genetic specificity and potential for local adaptation between dengue viruses and mosquito vectors, BMC Evolutionary Biology, vol.9, issue.1, 2009.
DOI : 10.1186/1471-2148-9-160

L. Lambrechts, J. Halbert, P. Durand, L. Gouagna, and J. Koella, Host genotype by parasite genotype interactions underlying the resistance of anopheline mosquitoes to Plasmodium falciparum, Malaria Journal, vol.4, issue.1, pp.3-10, 2005.
DOI : 10.1186/1475-2875-4-3

P. Schmid-hempel, K. Puhr, N. Krüger, C. Reber, and R. Schmid-hempel, Dynamic and Genetic Consequences of Variation in Horizontal Transmission for a Microparasitic Infection, Evolution, vol.53, issue.2, pp.426-434, 1999.
DOI : 10.2307/2640779

H. Schulenburg and J. Ewbank, Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens, BMC Evol. Biol, vol.44, issue.9, 2004.
URL : https://hal.archives-ouvertes.fr/inserm-00096153

J. Webster and M. Woolhouse, Selection and Strain Specificity of Compatibility between Snail Intermediate Hosts and Their Parasitic Schistosomes, Evolution, vol.52, issue.6, 1998.
DOI : 10.2307/2411336

P. Luijckx, F. Ben-ami, L. Mouton, D. Pasquier, L. Ebert et al., Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions, Ecology Letters, vol.85, issue.2, pp.125-131, 2011.
DOI : 10.1111/j.1461-0248.2010.01561.x

URL : https://hal.archives-ouvertes.fr/hal-00698035

B. Lemaitre, J. Reichhart, and J. Hoffmann, Drosophila host defense: Differential induction of antimicrobial peptide genes after infection by various classes of microorganisms, Proc. Natl Acad, 1997.
DOI : 10.1073/pnas.94.26.14614

P. Schmid-hempel, Natural insect host-parasite systems show immune priming and specificity: puzzles to be solved, BioEssays, vol.14, issue.4, 2005.
DOI : 10.1002/bies.20282

L. Lambrechts, Dissecting the Genetic Architecture of Host???Pathogen Specificity, PLoS Pathogens, vol.11, issue.8, 2010.
DOI : 10.1371/journal.ppat.1001019

D. Wit, P. Mehrabi, R. Van-den-burg, H. Stergiopoulos, and I. , Fungal effector proteins: past, present and future, Molecular Plant Pathology, vol.44, issue.2, pp.735-747, 2009.
DOI : 10.1111/j.1364-3703.2009.00591.x

J. Ellis, P. Dodds, and G. Lawrence, Flax Rust Resistance Gene Specificity is Based on Direct Resistance-Avirulence Protein Interactions, Annual Review of Phytopathology, vol.45, issue.1, 2007.
DOI : 10.1146/annurev.phyto.45.062806.094331

S. Gilbert, Association of Malaria Parasite Population Structure, HLA, and Immunological Antagonism, Science, vol.279, issue.5354, pp.279-5354, 1998.
DOI : 10.1126/science.279.5354.1173

J. Kubinak, J. Ruff, C. Hyzer, P. Slev, and W. Potts, 2012 Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types, Proc. Natl Acad

J. Carpenter, J. Hadfield, J. Bangham, and F. Jiggins, 2012 Specific interactions between host and parasite genotypes do not act as a constraint on the evolution of antiviral resistance in Drosophila, Evolution, vol.66

A. Fleuriet, Polymorphism of the hereditary sigma virus in natural populations of Drosophila melanogaster, Genetics, vol.95, pp.459-465, 1980.

C. Harris, L. Lambrechts, F. Rousset, L. Abate, S. Nsango et al., Polymorphisms in Anopheles gambiae Immune Genes Associated with Natural Resistance to Plasmodium falciparum, PLoS Pathogens, vol.21, issue.9, p.1001112
DOI : 10.1371/journal.ppat.1001112.s004

Y. Mone, B. Gourbal, D. Duval, D. Pasquier, L. Kieffer-jaquinod et al., A Large Repertoire of Parasite Epitopes Matched by a Large Repertoire of Host Immune Receptors in an Invertebrate Host/Parasite Model, PLoS Neglected Tropical Diseases, vol.462, issue.Pt 3, p.813
DOI : 10.1371/journal.pntd.0000813.t004

URL : https://hal.archives-ouvertes.fr/halsde-00515823

E. Bernstein, A. Caudy, S. Hammond, G. Hannon, C. Dostert et al., Role for a bidentate ribonuclease in the initiation step of RNA interference, Essential function in vivo for Dicer-2 in host defense against RNA viruses in Drosophila, pp.363-366, 1335.

I. Sanchez-vargas, J. Scott, B. Poole-smith, A. Franz, V. Barbosa-solomieu et al., Dengue Virus Type 2 Infections of Aedes aegypti Are Modulated by the Mosquito's RNA Interference Pathway, PLoS Pathogens, vol.35, issue.2, 2009.
DOI : 10.1371/journal.ppat.1000299.t001

X. Wang, R. Aliyari, W. Li, H. Li, K. Kim et al., RNA Interference Directs Innate Immunity Against Viruses in Adult Drosophila, Science, vol.312, issue.5772, 2006.
DOI : 10.1126/science.1125694

D. Gubler, Dengue and dengue hemorrhagic fever, Clin. Microbiol. Rev, vol.11, pp.480-496, 1998.

W. Black, K. Bennett, N. Gorrochotegui-escalante, C. Barillas-mury, I. Fernandez-salas et al., Flavivirus Susceptibility in Aedes aegypti, Archives of Medical Research, vol.33, issue.4, pp.8-440900373, 2002.
DOI : 10.1016/S0188-4409(02)00373-9

M. Lynch and B. Walsh, Genetics and analysis of quantitative traits, 1998.

D. Martin, P. Lemey, M. Lott, V. Moulton, D. Posada et al., RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, 2010.
DOI : 10.1093/bioinformatics/btq467

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2-7, 2011.
DOI : 10.1093/molbev/msr121

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, 2009.
DOI : 10.1093/bioinformatics/btp187

M. Raymond and F. Rousset, GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism, Journal of Heredity, vol.86, issue.3, pp.248-249, 1995.
DOI : 10.1093/oxfordjournals.jhered.a111573

URL : https://hal.archives-ouvertes.fr/halsde-00186383

N. Li and M. Stephens, 2003 Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data, Genetics, vol.165, pp.2213-2233

J. Cornuet and G. Luikart, 1996 Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data, Genetics, vol.144, 2001.

S. Piry, G. Luikart, and J. Cornuet, Bottleneck: a computer program for detecting recent reduction in the effective population size using allele frequency data, 1999.

V. Nene, Genome Sequence of Aedes aegypti, a Major Arbovirus Vector, Science, vol.316, issue.5832, pp.1718-1723, 2007.
DOI : 10.1126/science.1138878

URL : https://hal.archives-ouvertes.fr/hal-00156214

D. Severson, J. Meece, D. Lovin, G. Saha, and I. Morlais, Linkage map organization of expressed sequence tags and sequence tagged sites in the mosquito, Aedes aegypti, Insect Molecular Biology, vol.85, issue.4, 2002.
DOI : 10.1017/S0016672399003791

R. Van-rij and E. Berezikov, Small RNAs and the control of transposons and viruses in Drosophila, Trends in Microbiology, vol.17, issue.4, 2009.
DOI : 10.1016/j.tim.2009.01.003

C. Khoo, J. Piper, I. Sanchez-vargas, K. Olson, and A. Franz, The RNA interference pathway affects midgut infection- and escape barriers for Sindbis virus in Aedes aegypti, BMC Microbiology, vol.10, issue.1, pp.130-140, 1471.
DOI : 10.1186/1471-2180-10-130

D. Obbard, K. Gordon, A. Buck, and F. Jiggins, The evolution of RNAi as a defence against viruses and transposable elements, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.20, issue.23, pp.99-115, 2009.
DOI : 10.1101/gad.1495506

D. Obbard, F. Jiggins, D. Halligan, and T. Little, Natural Selection Drives Extremely Rapid Evolution in Antiviral RNAi Genes, Current Biology, vol.16, issue.6, pp.580-585, 2006.
DOI : 10.1016/j.cub.2006.01.065

I. Yoon, 2012 Fine scale spatiotemporal clustering of dengue virus transmission in children and Aedes aegypti in rural Thai villages

L. Lambrechts and T. Scott, 2009 Mode of transmission and the evolution of arbovirus virulence in mosquito vectors, Proc. R. Soc. B, vol.276

L. Wilfert and P. Schmid-hempel, The genetic architecture of susceptibility to parasites, BMC Evolutionary Biology, vol.8, issue.1, 2008.
DOI : 10.1186/1471-2148-8-187

G. Yan, B. Christensen, and D. Severson, Comparisons of Genetic Variability and Genome Structure Among Mosquito Strains Selected for Refractoriness to a Malaria Parasite, Journal of Heredity, vol.88, issue.3, pp.187-194, 1997.
DOI : 10.1093/oxfordjournals.jhered.a023087

C. Zapata, C. Nunez, and T. Velasco, Distribution of nonrandom associations between pairs of protein loci along the third chromosome of Drosophila melanogaster, Genetics, vol.161, pp.1539-1550, 2002.

S. Mukherjee and K. Hanley, RNA interference modulates replication of dengue virus in Drosophila melanogaster cells, BMC Microbiology, vol.10, issue.1, p.127
DOI : 10.1186/1471-2180-10-127

R. Aliyari, Q. Wu, H. Li, X. Wang, F. Li et al., Mechanism of Induction and Suppression of Antiviral Immunity Directed by Virus-Derived Small RNAs in Drosophila, Cell Host & Microbe, vol.4, issue.4, pp.387-397, 2008.
DOI : 10.1016/j.chom.2008.09.001