S. Altizer, R. Bartel, and B. Han, Animal Migration and Infectious Disease Risk, Science, vol.331, issue.6015, pp.296-302, 2011.
DOI : 10.1126/science.1194694

P. Tortosa, H. Pascalis, V. Guernier, E. Cardinale, L. Corre et al., Deciphering arboviral emergence within insular ecosystems, Infection, Genetics and Evolution, vol.12, issue.6, pp.1333-1342, 2012.
DOI : 10.1016/j.meegid.2012.03.024

URL : https://hal.archives-ouvertes.fr/hal-00842630

Z. Hubálek, AN ANNOTATED CHECKLIST OF PATHOGENIC MICROORGANISMS ASSOCIATED WITH MIGRATORY BIRDS, Journal of Wildlife Diseases, vol.40, issue.4, pp.639-59, 2004.
DOI : 10.7589/0090-3558-40.4.639

R. Webster, W. Bean, O. Gorman, T. Chambers, and Y. Kawaoka, Evolution and ecology of influenza A viruses, Microbiol Rev, vol.56, pp.152-179, 1992.

D. Stallknecht and S. Shane, Host range of avian influenza virus in free-living birds, Veterinary Research Communications, vol.3, issue.1, pp.125-141, 1988.
DOI : 10.1007/BF00362792

B. Olsen, V. Munster, A. Wallensten, J. Waldenström, A. Osterhaus et al., Global Patterns of Influenza A Virus in Wild Birds, Science, vol.312, issue.5772, pp.384-392, 2006.
DOI : 10.1126/science.1122438

D. Vijaykrishna, J. Bahl, S. Riley, L. Duan, J. Zhang et al., Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses, PLoS Pathogens, vol.14, issue.9, p.18818732, 2008.
DOI : 10.1371/journal.ppat.1000161.s004

G. Smith, J. Bahl, D. Vijaykrishna, J. Zhang, L. Poon et al., Dating the emergence of pandemic influenza viruses, Proceedings of the National Academy of Sciences, vol.106, issue.28, pp.11709-11712, 2009.
DOI : 10.1073/pnas.0904991106

T. Lam, J. Wang, Y. Shen, B. Zhou, L. Duan et al., The genesis and source of the H7N9 influenza viruses causing human infections in China, Nature, vol.5, issue.7470, pp.241-245, 2013.
DOI : 10.1093/bioinformatics/btq429

A. Arnal, M. Vittecoq, J. Pearce-duvet, M. Gauthier-clerc, T. Boulinier et al., Laridae: A neglected reservoir that could play a major role in avian influenza virus epidemiological dynamics, Critical Reviews in Microbiology, vol.47, issue.4, pp.1-12, 2014.
DOI : 10.1073/pnas.1212579109

URL : https://hal.archives-ouvertes.fr/hal-00935832

D. Danckwerts, C. Mcquaid, A. Jaeger, G. Mcgregor, R. Dwight et al., Biomass consumption by breeding seabirds in the western Indian Ocean: indirect interactions with fisheries and implications for management, ICES Journal of Marine Science, vol.71, issue.9, pp.2589-2598, 2014.
DOI : 10.1093/icesjms/fsu093

URL : https://hal.archives-ouvertes.fr/hal-01306712

I. Sinclair and O. Langrand, Birds of the Indian Ocean islands. Chamberlain. Struik Nature, 2003.

C. Feare, S. Jaquemet, L. Corre, and M. , ) in the western Indian Ocean with special reference to threats and trends, Ostrich, vol.78, issue.2, pp.423-434, 2007.
DOI : 10.2989/OSTRICH.2007.78.2.49.129

V. Friesen, T. Burg, and K. Mccoy, Mechanisms of population differentiation in seabirds, Molecular Ecology, vol.97, issue.9, pp.1765-85, 2007.
DOI : 10.1111/j.1365-294X.2006.03197.x

L. Corre, M. Jaeger, A. Pinet, P. Kappes, M. A. Weimerskirch et al., Tracking seabirds to identify potential Marine Protected Areas in the tropical western Indian Ocean, Biological Conservation, vol.156, pp.83-93, 2012.
DOI : 10.1016/j.biocon.2011.11.015

URL : https://hal.archives-ouvertes.fr/hal-00737237

C. Lebarbenchon, J. Brown, M. Luttrell, and D. Stallknecht, antibodies, Journal of Veterinary Diagnostic Investigation, vol.54, issue.1, pp.161-166, 2012.
DOI : 10.2307/2529310

URL : https://hal.archives-ouvertes.fr/hal-01483417

J. Pedersen, Hemagglutination-inhibition test for avian influenza virus subtype identification and the detection and quantification of serum antibodies to avian influenza viruses Avian influenza virus, 2008.

R. Development and C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2012.

C. Lebarbenchon, A. Jaeger, M. Bastien, L. Corre, M. Dellagi et al., Absence of Coronaviruses, Paramyxoviruses, and Influenza A Viruses in Seabirds in the Southwestern Indian Ocean, Journal of Wildlife Diseases, vol.49, issue.4, pp.1056-1059, 2013.
DOI : 10.7589/2012-09-227

URL : https://hal.archives-ouvertes.fr/hal-01274592

E. Spackman, D. Senne, T. Myers, L. Bulaga, L. Garber et al., Development of a Real-Time Reverse Transcriptase PCR Assay for Type A Influenza Virus and the Avian H5 and H7 Hemagglutinin Subtypes, Journal of Clinical Microbiology, vol.40, issue.9, pp.3256-3260, 2002.
DOI : 10.1128/JCM.40.9.3256-3260.2002

K. Tsukamoto, H. Ashizawa, K. Nakanishi, N. Kaji, K. Suzuki et al., Subtyping of Avian Influenza Viruses H1 to H15 on the Basis of Hemagglutinin Genes by PCR Assay and Molecular Determination of Pathogenic Potential, Journal of Clinical Microbiology, vol.46, issue.9, pp.3048-3055, 2008.
DOI : 10.1128/JCM.02386-07

K. Vandalen, T. Anderson, M. Killian, J. Pedersen, A. Franklin et al., Increased detection of influenza A H16 in the United States, Archives of Virology, vol.14, issue.10, pp.1981-1984, 2008.
DOI : 10.1007/s00705-008-0213-8

M. Lee, P. Chang, J. Shien, M. Cheng, and H. Shieh, Identification and subtyping of avian influenza viruses by reverse transcription-PCR, Journal of Virological Methods, vol.97, issue.1-2, pp.13-22, 2001.
DOI : 10.1016/S0166-0934(01)00301-9

B. Qiu, W. Liu, S. Hu, Y. Tang, and X. Liu, A reverse transcription-PCR for subtyping of the neuraminidase of avian influenza viruses, Journal of Virological Methods, vol.155, issue.2, pp.193-198, 2009.
DOI : 10.1016/j.jviromet.2008.10.001

Y. Bao, P. Bolotov, D. Dernovoy, B. Kiryutin, L. Zaslavsky et al., The Influenza Virus Resource at the National Center for Biotechnology Information, Journal of Virology, vol.82, issue.2, pp.596-601, 2008.
DOI : 10.1128/JVI.02005-07

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-328, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, pp.214-17996036, 2007.
DOI : 10.1186/1471-2148-7-214

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2247476

J. Bahl, D. Vijaykrishna, E. Holmes, G. Smith, and Y. Guan, Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts, Virology, vol.390, issue.2, pp.289-97, 2009.
DOI : 10.1016/j.virol.2009.05.002

C. Lebarbenchon and D. Stallknecht, Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin, Virology Journal, vol.8, issue.1, p.21711553, 2011.
DOI : 10.1371/journal.ppat.1001081

B. Shapiro, A. Rambaut, and A. Drummond, Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences, Molecular Biology and Evolution, vol.23, issue.1, pp.7-9, 2006.
DOI : 10.1093/molbev/msj021

A. Drummond, A. Rambaut, B. Shapiro, and O. Pybus, Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences, Molecular Biology and Evolution, vol.22, issue.5, pp.1185-92, 2005.
DOI : 10.1093/molbev/msi103

W. Becker, The isolation and classification of Tern virus: Influenza Virus A/Tern/South Africa/1961, Journal of Hygiene, vol.62, issue.03, pp.309-320, 1961.
DOI : 10.1016/0042-6822(56)90056-3

J. Mackenzie, E. Edwards, R. Holmes, and V. Hinshaw, ISOLATION OF ORTHO- AND PARAMYXOVIRUSES FROM WILD BIRDS IN WESTERN AUSTRALIA, AND THE CHARACTERIZATION OF NOVEL INFLUENZA A VIRUSES, Australian Journal of Experimental Biology and Medical Science, vol.62, issue.1, pp.89-99, 1984.
DOI : 10.1038/icb.1984.9

C. Röhm, N. Zhou, J. Süss, J. Mackenzie, and R. Webster, Characterization of a Novel Influenza Hemagglutinin, H15: Criteria for Determination of Influenza A Subtypes, Virology, vol.217, issue.2, pp.508-524, 1996.
DOI : 10.1006/viro.1996.0145

J. Brown, M. Luttrell, R. Berghaus, W. Kistler, S. Keeler et al., PREVALENCE OF ANTIBODIES TO TYPE A INFLUENZA VIRUS IN WILD AVIAN SPECIES USING TWO SEROLOGIC ASSAYS, Journal of Wildlife Diseases, vol.46, issue.3, pp.896-911, 2010.
DOI : 10.7589/0090-3558-46.3.896

C. Feare, E. Gill, H. Carty, and V. Ayrton, Habitat use by Seychelles sooty terns Sterna fuscata and implications for colony management, Biological Conservation, vol.81, issue.1-2, pp.69-76, 1997.
DOI : 10.1016/S0006-3207(96)00114-0

J. Del-hoyo, A. Elliott, and J. Sargatal, Handbook of the Birds of the World, Hoatzin to Auks. Barcelona: Lynx Edicions, 1996.

J. Verhagen, F. Majoor, P. Lexmond, O. Vuong, G. Kasemir et al., Epidemiology of Influenza A Virus among Black-headed Gulls, the Netherlands, 2006???2010, Emerging Infectious Diseases, vol.20, issue.1, pp.138-179, 2006.
DOI : 10.3201/eid2001.130984

M. Wille, G. Robertson, H. Whitney, M. Bishop, J. Runstadler et al., Extensive Geographic Mosaicism in Avian Influenza Viruses from Gulls in the Northern Hemisphere, PLoS ONE, vol.24, issue.6, p.21697989, 2011.
DOI : 10.1371/journal.pone.0020664.s014

G. Sharp, Y. Kawaoka, D. Jones, W. Bean, S. Pryor et al., Coinfection of wild ducks by influenza A viruses: distribution patterns and biological significance, J Virol, vol.71, pp.6128-6163, 1997.

T. Hatchette, D. Walker, C. Johnson, A. Baker, S. Pryor et al., Influenza A viruses in feral Canadian ducks: extensive reassortment in nature, Journal of General Virology, vol.85, issue.8, pp.2327-2364, 2004.
DOI : 10.1099/vir.0.79878-0

V. Dugan, R. Chen, D. Spiro, N. Sengamalay, J. Zaborsky et al., The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds, PLoS Pathogens, vol.14, issue.5, p.18516303, 2008.
DOI : 10.1371/journal.ppat.1000076.s009

C. Lebarbenchon, S. Sreevatsan, T. Lefèvre, M. Yang, M. Ramakrishnan et al., Reassortant influenza A viruses in wild duck populations: effects on viral shedding and persistence in water, Proceedings of the Royal Society B: Biological Sciences, vol.54, issue.1 Suppl, pp.3967-75, 2012.
DOI : 10.1637/8760-033109-Reg.1

E. Jourdain, M. Gauthier-clerc, D. Bicout, and P. Sabatier, Bird Migration Routes and Risk for Pathogen Dispersion into Western Mediterranean Wetlands, Emerging Infectious Diseases, vol.13, issue.3, pp.365-72, 2007.
DOI : 10.3201/eid1303.060301

S. Krauss, D. Stallknecht, N. Negovetich, L. Niles, R. Webby et al., Coincident ruddy turnstone migration and horseshoe crab spawning creates an ecological 'hot spot' for influenza viruses, Proceedings of the Royal Society B: Biological Sciences, vol.15, issue.6, pp.3373-3382, 2010.
DOI : 10.3201/eid1506.080981

Y. Huang, G. Robertson, D. Ojkic, H. Whitney, and A. Lang, Diverse inter-continental and host lineage reassortant avian influenza A viruses in pelagic seabirds, Infection, Genetics and Evolution, vol.22, p.24462905, 2014.
DOI : 10.1016/j.meegid.2014.01.014

Y. Huang, M. Wille, J. Benkaroun, H. Munro, A. Bond et al., Perpetuation and reassortment of gull influenza A viruses in Atlantic North America, Virology, vol.456, issue.457, pp.456-457, 2014.
DOI : 10.1016/j.virol.2014.04.009

G. Cumming, A. Caron, C. Abolnik, G. Cattoli, L. Bruinzeel et al., The Ecology of Influenza A Viruses in Wild Birds in Southern Africa, EcoHealth, vol.13, issue.1, p.21516374, 2011.
DOI : 10.1007/s10393-011-0684-z

N. Gaidet, A. Caron, J. Cappelle, G. Cumming, G. Balança et al., Understanding the ecological drivers of avian influenza virus infection in wildfowl: a continental-scale study across Africa, Proceedings of the Royal Society B: Biological Sciences, vol.26, issue.35, pp.1131-1172, 2012.
DOI : 10.1016/j.vaccine.2008.06.027

C. Lebarbenchon, C. Chang, V. Grandhomme, M. Dietrich, Y. Kayser et al., Avian Influenza Circulation in the Camargue (South of France) During the 2006???07 Season, Avian Diseases, vol.54, issue.s1, pp.446-449, 2010.
DOI : 10.1637/8665-022509-ResNote.1

N. Gaidet, S. Newman, W. Hagemeijer, T. Dodman, J. Cappelle et al., Duck Migration and Past Influenza A (H5N1) Outbreak Areas, Emerging Infectious Diseases, vol.14, issue.7, pp.1164-1166, 2008.
DOI : 10.3201/eid1407.071477

C. Lebarbenchon, Maladies infectieuses et écosystèmes: écologie des virus influenza aviaires en Camargue, 2008.

N. Gaidet, O. E. Mamy, A. Cappelle, J. Caron, A. Cumming et al., Investigating Avian Influenza Infection Hotspots in Old-World Shorebirds, PLoS ONE, vol.7, issue.9, p.23029383, 2012.
DOI : 10.1371/journal.pone.0046049.s007

V. Munster, C. Baas, P. Lexmond, J. Waldenström, A. Wallensten et al., Spatial, Temporal, and Species Variation in Prevalence of Influenza A Viruses in Wild Migratory Birds, PLoS Pathogens, vol.33, issue.5, pp.61-17500589, 2007.
DOI : 10.1371/journal.ppat.0030061.st002

B. Wilcox, G. Knutsen, J. Berdeen, V. Goekjian, R. Poulson et al., Influenza-A Viruses in Ducks in Northwestern Minnesota: Fine Scale Spatial and Temporal Variation in Prevalence and Subtype Diversity, PLoS ONE, vol.51, issue.5, p.21931636, 2011.
DOI : 10.1371/journal.pone.0024010.s003

C. Lebarbenchon, C. Chang, M. Gauthier-clerc, F. Thomas, F. Renaud et al., H9N2 avian influenza virus in a Mediterranean gull, Journal of Molecular and Genetic Medicine, vol.03, issue.01, pp.121-124, 2008.
DOI : 10.4172/1747-0862.1000023

URL : https://hal.archives-ouvertes.fr/pasteur-00457884

M. Jackwood and D. Stallknecht, Molecular Epidemiologic Studies on North American H9 Avian Influenza Virus Isolates from Waterfowl and Shorebirds, Avian Diseases, vol.51, issue.s1, pp.448-50, 2007.
DOI : 10.1637/7536-032706R.1

K. Li, K. Xu, J. Peiris, L. Poon, K. Yu et al., Characterization of H9 Subtype Influenza Viruses from the Ducks of Southern China: a Candidate for the Next Influenza Pandemic in Humans?, Journal of Virology, vol.77, issue.12, pp.6988-6994, 2003.
DOI : 10.1128/JVI.77.12.6988-6994.2003

Y. Guan, K. Shortridge, S. Krauss, and R. Webster, Molecular characterization of H9N2 influenza viruses: Were they the donors of the "internal" genes of H5N1 viruses in Hong Kong?, Proceedings of the National Academy of Sciences, vol.96, issue.16, pp.9363-9367, 1999.
DOI : 10.1073/pnas.96.16.9363

M. Peiris, K. Yuen, C. Leung, K. Chan, P. Ip et al., Human infection with influenza H9N2, The Lancet, vol.354, issue.9182, pp.916-923, 1999.
DOI : 10.1016/S0140-6736(99)03311-5

K. Shanmuganatham, M. Feeroz, L. Jones-engel, G. Smith, M. Fourment et al., Antigenic and Molecular Characterization of Avian Influenza A(H9N2) Viruses, Bangladesh, Emerging Infectious Diseases, vol.19, issue.9, pp.1393-1402, 2013.
DOI : 10.3201/eid1909.130336

N. Negovetich, M. Feeroz, L. Jones-engel, D. Walker, S. Alam et al., Live Bird Markets of Bangladesh: H9N2 Viruses and the Near Absence of Highly Pathogenic H5N1 Influenza, PLoS ONE, vol.81, issue.4, p.21541296, 2011.
DOI : 10.1371/journal.pone.0019311.t004

C. Tosh, S. Nagarajan, P. Behera, K. Rajukumar, K. Purohit et al., Genetic analysis of H9N2 avian influenza viruses isolated from India, Archives of Virology, vol.81, issue.1, pp.1433-1442, 2008.
DOI : 10.1007/s00705-008-0131-9

A. Jaeger, R. Summers, C. Lebarbenchon, C. Larose, L. Corre et al., Geolocation reveals migration patterns of a superabundant tropical seabird species, the sooty tern Onychoprion fuscatus, from a breeding colony on Bird Island, Seychelles