. Mosquito-taxonomic-inventoy, http://mosquito-taxonomic-inventory. info. Accessed 1, 2016.

P. Barraud, . India, and X. Part, The genus Aedes (sens. lat.) and the classification of the subgenus, Descriptions of the Indian species of Aedes (Aedimorphus), Aedes (Ochlerotatus), and Aedes (Banksinella), with notes on Aedes (Stegomyia) uariegatus, pp.653-69, 1928.

Y. Huang, Contributions to the mosquito fauna of Southeast Asia. XIV. The subgenus Stegomyia of Aedes in Southeast Asia I -The scutellaris group of species, Contrib Am Ent Inst, vol.9, pp.1-109, 1972.

K. Tanaka, K. Mizusawa, and E. Saugstad, A revision of the adult and larval mosquitoes of Japan (including the Ryukyu Archipelago and the Ogasawara Islands) and Korea (Diptera: Culicidae), Contributions of the American Entomological Institute, pp.1-987, 1979.

L. Rueda, Pictorial keys for the identification of mosquitoes (Diptera: Culicidae) associated with dengue virus transmission. Walter Reed army inst. of research, 2004.

W. Hawley, The biology of Aedes albopictus, J Am Mosq Control Assoc Suppl, vol.1, pp.1-39, 1988.

Y. Huang, Medical Entomology Studies -XI. The subgenus Stegomyia of Aedes in the Oriental region with keys to the species (Diptera: Culicidae), Medical Entomology Project Report, 1979.

D. Mclain, K. Rai, and M. Fraser, Intraspecific and interspecific variation in the sequence and abundance of highly repeated DNA among mosquitoes of the Aedes albopictus subgroup, Heredity, vol.58, issue.3, pp.373-81, 1987.
DOI : 10.1038/hdy.1987.65

E. Patsoula, A. Samanidou-voyadjoglou, G. Spanakos, J. Kremastinou, G. Nasioulas et al., Molecular and Morphological Characterization of <I>Aedes albopictus</I> in Northwestern Greece and Differentiation from <I>Aedes cretinus</I> and <I>Aedes aegypti</I>, Journal of Medical Entomology, vol.43, issue.1, pp.40-54, 2006.
DOI : 10.1603/0022-2585(2006)043[0040:MAMCOA]2.0.CO;2

A. Rani, A. Sharma, R. Rajagopal, T. Adak, and R. Bhatnagar, Bacterial diversity analysis of larvae and adult midgut micro-flora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector, BMC Microbiology, vol.9, issue.1, p.96, 2009.
DOI : 10.1186/1471-2180-9-96

G. Gimonneau, M. Tchioffo, L. Abate, A. Boissière, P. Awono-ambéné et al., Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages, Infection, Genetics and Evolution, vol.28, pp.715-739, 2014.
DOI : 10.1016/j.meegid.2014.09.029

URL : https://hal.archives-ouvertes.fr/hal-01546167

E. Muturi, C. Kim, J. Bara, E. Bach, and M. Siddappaji, Culex pipiens and Culex restuans mosquitoes harbor distinct microbiota dominated by few bacterial taxa, Parasites & Vectors, vol.20, issue.1, p.18, 2016.
DOI : 10.1371/journal.pone.0127704

D. Duguma, R. , P. Kaufman, M. Hall, M. Neufeld et al., Bacterial Communities Associated with Culex Mosquito Larvae and Two Emergent Aquatic Plants of Bioremediation Importance, PLoS ONE, vol.93, issue.8, p.72522, 2013.
DOI : 10.1371/journal.pone.0072522.s002

G. Minard, P. Mavingui, and C. Moro, Diversity and function of bacterial microbiota in the mosquito holobiont, Parasites & Vectors, vol.6, issue.1, p.146, 2013.
DOI : 10.1007/s00253-010-2449-y

P. Engel and N. Moran, The gut microbiota of insects ??? diversity in structure and function, FEMS Microbiology Reviews, vol.37, issue.5, pp.699-735, 2013.
DOI : 10.1111/1574-6976.12025

M. Shapira, Gut Microbiotas and Host Evolution: Scaling Up Symbiosis, Trends in Ecology & Evolution, vol.31, issue.7, pp.539-588, 2016.
DOI : 10.1016/j.tree.2016.03.006

P. Kittayapong, K. Baisley, R. Sharpe, V. Baimai, O. Neill et al., Maternal transmission efficiency of Wolbachia superinfections in Aedes albopictus populations in Thailand., The American Journal of Tropical Medicine and Hygiene, vol.66, issue.1, pp.103-110, 2002.
DOI : 10.4269/ajtmh.2002.66.103

K. Zouache, F. Raharimalala, V. Raquin, V. Tran-van, L. Raveloson et al., Bacterial diversity of field-caught mosquitoes, Aedes albopictus and Aedes aegypti, from different geographic regions of Madagascar, FEMS Microbiology Ecology, vol.75, issue.3, pp.377-89, 2011.
DOI : 10.1111/j.1574-6941.2010.01012.x

URL : https://hal.archives-ouvertes.fr/halsde-00724643

A. De-albuquerque, T. Magalhães, and C. Ayres, High prevalence and lack of diversity of Wolbachia pipientis in Aedes albopictus populations from Northeast Brazil, Mem??rias do Instituto Oswaldo Cruz, vol.265, issue.6, pp.773-779, 2011.
DOI : 10.1098/rspb.1998.0324

K. Bourtzis, S. Dobson, Z. Xi, J. Rasgon, M. Calvitti et al., Harnessing mosquito???Wolbachia symbiosis for vector and disease control, Acta Tropica, vol.132
DOI : 10.1016/j.actatropica.2013.11.004

G. Minard, F. Tran, A. Dubost, V. Tran-van, P. Mavingui et al., Pyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study, Frontiers in Cellular and Infection Microbiology, vol.4, p.59, 2014.
DOI : 10.1111/j.1365-294X.2012.05759.x

G. Minard, F. Tran, V. Van, C. Goubert, C. Bellet et al., French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives, Frontiers in Microbiology, vol.13, issue.29, p.970, 2015.
DOI : 10.1111/j.1462-2920.2011.02448.x

S. Dobson, E. Marsland, and W. Rattanadechakul, Mutualistic Wolbachia infection in Aedes albopictus: accelerating cytoplasmic drive, Genetics, vol.160, pp.1087-94, 2002.

S. Bordenstein, O. Hara, F. Werren, and J. , Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia, Nature, vol.51, issue.6821, pp.707-717, 2001.
DOI : 10.1111/j.1558-5646.1997.tb03663.x

J. Rasgon, C. Gamston, and X. Ren, Survival of Wolbachia pipientis in Cell-Free Medium, Applied and Environmental Microbiology, vol.72, issue.11, pp.6934-6941, 2006.
DOI : 10.1128/AEM.01673-06

R. Brucker and S. Bordenstein, The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia, Science, vol.107, issue.1, pp.667-676, 2013.
DOI : 10.1038/hdy.2010.157

J. Kenney and A. Brault, The Role of Environmental, Virological and Vector Interactions in Dictating Biological Transmission of Arthropod-Borne Viruses by Mosquitoes, Adv. Virus Res, vol.89, pp.39-83, 2014.
DOI : 10.1016/B978-0-12-800172-1.00002-1

N. Forrester, L. Coffey, and S. Weaver, Arboviral Bottlenecks and Challenges to Maintaining Diversity and Fitness during Mosquito Transmission, Viruses, vol.6, issue.10, pp.3991-4004, 2014.
DOI : 10.1371/journal.pone.0001168

N. Jupatanakul, S. Sim, and G. Dimopoulos, The Insect Microbiome Modulates Vector Competence for Arboviruses, Viruses, vol.3, issue.11, pp.4294-313, 2014.
DOI : 10.1016/j.mib.2011.12.012

K. Takano, N. Nguyen, B. Nguyen, T. Sunahara, M. Yasunami et al., Partial mitochondrial DNA sequences suggest the existence of a cryptic species within the Leucosphyrus group of the genus Anopheles (Diptera: Culicidae), forest malaria vectors, in northern Vietnam, Parasites & Vectors, vol.3, issue.1, p.41, 2010.
DOI : 10.1186/1756-3305-3-41

H. Cuong, N. Vu, B. Cazelles, M. Boni, K. Thai et al., Spatiotemporal Dynamics of Dengue Epidemics, Southern Vietnam, Emerging Infectious Diseases, vol.19, issue.6, pp.945-53, 2013.
DOI : 10.3201/eid1906.121323

J. Rasgon, A. Cornel, and T. Scott, Evolutionary history of a mosquito endosymbiont revealed through mitochondrial hitchhiking, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1395, pp.1603-1614, 2006.
DOI : 10.1098/rspb.1998.0324

C. Atyame, F. Delsuc, N. Pasteur, M. Weill, and O. Duron, Diversification of Wolbachia Endosymbiont in the Culex pipiens Mosquito, Molecular Biology and Evolution, vol.28, issue.10, pp.2761-72, 2011.
DOI : 10.1093/molbev/msr083

E. Dumas, C. Atyame, C. Malcolm, L. Goff, G. Unal et al., mosquito complex, Insect Molecular Biology, vol.265, issue.6, pp.800-809, 2016.
DOI : 10.1098/rspb.1998.0324

G. Hurst and F. Jiggins, Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts, Proceedings of the Royal Society B: Biological Sciences, vol.261, issue.1360, pp.1525-1559, 2005.
DOI : 10.1098/rspb.1995.0117

X. Sun, X. J. Cook, J. Feng, G. Huang, and D. , Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachiaon host mtDNA evolution and diversity, BMC Evolutionary Biology, vol.141, issue.1, p.86, 2011.
DOI : 10.1093/bioinformatics/btp187

S. Ritter, S. Michalski, J. Settele, M. Wiemers, Z. Fric et al., Wolbachia Infections Mimic Cryptic Speciation in Two Parasitic Butterfly Species, Phengaris teleius and P. nausithous (Lepidoptera: Lycaenidae), PLoS ONE, vol.11, issue.11
DOI : 10.1371/journal.pone.0078107.s005

I. Vaz-moreira, O. Nunes, and C. Manaia, Diversity and Antibiotic Resistance Patterns of Sphingomonadaceae Isolates from Drinking Water, Applied and Environmental Microbiology, vol.77, issue.16, pp.5697-706, 2011.
DOI : 10.1128/AEM.00579-11

A. Ashton, Advances in Sphingomonadaceae research and application, Atlanta: ScholarlyEditions, vol.2012

S. Derycke, D. Meester, N. Rigaux, A. Creer, S. Bik et al., complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability, Molecular Ecology, vol.64, issue.9, pp.2093-110, 2016.
DOI : 10.1093/bioinformatics/btt593

S. Sirivanakarn, The Female cibarial armature of new world Culex, subgenus Melanoconion and related subgenera with notes on this character in subgenera Culex, Lutzia and Neoculex and genera Galindomyia and Deinocerites. Medical entomology project report, 1978.

F. Raharimalala, L. Ravaomanarivo, P. Ravelonandro, L. Rafarasoa, K. Zouache et al., Biogeography of the two major arbovirus mosquito vectors, Aedes aegypti and Aedes albopictus (Diptera, Culicidae), in Madagascar, Parasites & Vectors, vol.5, issue.1, p.56, 2012.
DOI : 10.1186/1756-3305-5-56

URL : https://hal.archives-ouvertes.fr/pasteur-00700521

Y. Higa, T. Toma, Y. Tsuda, and I. Miyagi, A multiplex PCR-based molecular identification of five morphologically related, medically important subgenus Stegomyia mosquitoes from the genus Aedes (Diptera: Culicidae) found in the Ryukyu Archipelago, Japan Jpn J Infect Dis, vol.63, pp.312-318, 2010.

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-225, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00705187

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1453, 2009.
DOI : 10.1093/bioinformatics/btp187

D. Darriba, G. Taboada, R. Doallo, and D. Posada, jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, p.772, 2012.
DOI : 10.1109/TAC.1974.1100705

F. Ronquist, M. Teslenko, P. Van-der-mark, D. Ayres, A. Darling et al., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-581, 2012.
DOI : 10.1093/sysbio/sys029

W. Zhou, F. Rousset, O. Neil, and S. , Phylogeny and PCR-based classification of Wolbachia strains using wsp gene sequences, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1395, pp.509-524, 1998.
DOI : 10.1098/rspb.1998.0324

M. Cardinale, L. Brusetti, P. Quatrini, S. Borin, A. Puglia et al., Comparison of Different Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Complex Bacterial Communities, Applied and Environmental Microbiology, vol.70, issue.10, pp.6147-56, 2004.
DOI : 10.1128/AEM.70.10.6147-6156.2004

A. Ramette, Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities, Applied and Environmental Microbiology, vol.75, issue.8, pp.2495-505, 2009.
DOI : 10.1128/AEM.02409-08

A. Masella, A. Bartram, J. Truszkowski, D. Brown, and J. Neufeld, PANDAseq: paired-end assembler for illumina sequences, BMC Bioinformatics, vol.13, issue.1, p.31, 2012.
DOI : 10.1093/bioinformatics/btl158

P. Schloss, S. Westcott, T. Ryabin, J. Hall, M. Hartmann et al., Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities, Applied and Environmental Microbiology, vol.75, issue.23
DOI : 10.1128/AEM.01541-09

Q. Wang, G. Garrity, J. Tiedje, and J. Cole, Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy, Applied and Environmental Microbiology, vol.73, issue.16
DOI : 10.1128/AEM.00062-07