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.1333-1339, 2012.
DOI : 10.1016/j.meegid.2012.03.024

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

N. Myers, R. Mittermeier, C. Mittermeier, G. Da-fonseca, and J. Kent, Biodiversity hotspots for conservation priorities, Nature, vol.401, issue.6772, pp.853-858, 2000.
DOI : 10.1038/32761

S. Goodman, S. Puechmaille, N. Friedli-weyeneth, J. Gerlach, and M. Ruedi, Phylogeny of the Emballonurini (Emballonuridae) with descriptions of a new genus and species from Madagascar, Journal of Mammalogy, vol.93, issue.6, pp.1440-1455, 2012.
DOI : 10.1111/j.1365-294X.2008.03994.x

E. Lagadec, Y. Gomard, V. Guernier, M. Dietrich, and H. Pascalis, spp. in Bats, Madagascar and Union of the Comoros, Emerging Infectious Diseases, vol.18, issue.10, pp.1696-1698, 2012.
DOI : 10.3201/eid1810.111898

URL : https://hal.archives-ouvertes.fr/hal-01285454

D. Wilkinson, S. Temmam, C. Lebarbenchon, E. Lagadec, and J. Chotte, Identification of novel paramyxoviruses in insectivorous bats of the Southwest Indian Ocean, Virus Research, vol.170, issue.1-2, pp.159-163, 2012.
DOI : 10.1016/j.virusres.2012.08.022

URL : https://hal.archives-ouvertes.fr/pasteur-00836609

S. Goodman, L. Chan, M. Nowak, and A. Yoder, (Chiroptera: Pteropodidae), Journal of Mammalogy, vol.91, issue.3, pp.593-606, 2010.
DOI : 10.1111/j.1365-294X.2008.03994.x

N. Weyeneth, S. Goodman, W. Stanley, and M. Ruedi, bats (Chiroptera: Miniopteridae) from the Comoro Archipelago inferred from mitochondrial DNA, Molecular Ecology, vol.129, issue.24, pp.5205-5219, 2008.
DOI : 10.3161/001.006.0201

B. Ramasindrazana, S. Goodman, M. Schoeman, and B. Appleton, bats (Chiroptera: Miniopteridae) from Madagascar and the Comoros using bioacoustics overlaid on molecular genetic and morphological characters, Biological Journal of the Linnean Society, vol.24, issue.2, pp.284-302, 2011.
DOI : 10.1111/j.1420-9101.2011.02262.x

S. Goodman, C. Maminirina, N. Weyeneth, H. Bradman, and L. Christidis, (Chiroptera, Miniopteridae), Zoologica Scripta, vol.102, issue.Supplement, pp.339-363, 2009.
DOI : 10.3161/001.006.0201

R. Sikes and W. Gannon, Guidelines of the American Society of Mammalogists for the use of wild mammals in research, Journal of Mammalogy, vol.32, issue.1, pp.235-253, 2011.
DOI : 10.2307/1382178

O. Theodor, An illustrated catalogue of the Rothschild Collection of Nycteribiidae (Diptera) in the British Museum (Natural History): With keys and short descriptions for the identification of subfamilies, genera, species and subspecies, Trustees of the British Museum (Natural History, 1967.

O. Folmer, M. Black, W. Hoeh, R. Lutz, and R. Vrijenhoek, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Molecular Marine Biology and Biotechnology, vol.3, pp.294-299, 1994.

M. Whiting, Mecoptera is paraphyletic: multiple genes and phylogeny of Mecoptera and Siphonaptera, Zoologica Scripta, vol.544, issue.3, pp.93-104, 2002.
DOI : 10.1111/j.1365-3113.1987.tb00222.x

A. Drummond, B. Ashton, M. Cheung, J. Heled, and M. Kearse, Geneious v5.3. Available from http, 2009.

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1080/106351598261067

URL : https://academic.oup.com/mbe/article-pdf/17/4/540/3914687/mbev_17_04_0540.pdf

D. Swofford, Phylogenetic Analysis Using Parsimony (*and Other Methods) version 4.0b10, 2002.

D. Posada, jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.39, issue.3, pp.1253-1256, 2008.
DOI : 10.1007/BF00160155

URL : https://academic.oup.com/mbe/article-pdf/25/7/1253/3543852/msn083.pdf

J. Nylander, F. Ronquist, J. Huelsenbeck, and J. Nieves-aldrey, Bayesian Phylogenetic Analysis of Combined Data, Systematic Biology, vol.42, issue.1, pp.47-67, 2004.
DOI : 10.1007/BF02352289

URL : https://academic.oup.com/sysbio/article-pdf/53/1/47/19504018/53-1-47.pdf

P. Legendre, Y. Desdevises, and E. Bazin, A Statistical Test for Host???Parasite Coevolution, Systematic Biology, vol.51, issue.2, pp.217-234, 2002.
DOI : 10.1080/10635150252899734

URL : https://academic.oup.com/sysbio/article-pdf/51/2/217/19502770/51-2-217.pdf

M. Fourment and M. Gibbs, PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change, BMC Evolutionary Biology, vol.6, issue.1, 2006.

E. Paradis, C. J. Strimmer, and K. , APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

URL : https://academic.oup.com/bioinformatics/article-pdf/20/2/289/533578/btg412.pdf

R. Team, R: A Language and Environment for Statistical Computing, 2013.

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

URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-7-214?site=bmcevolbiol.biomedcentral.com

A. Brower, Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution., Proceedings of the National Academy of Sciences, vol.91, issue.14, pp.6491-6495, 1994.
DOI : 10.1073/pnas.91.14.6491

C. Dick, High host specificity of obligate ectoparasites, Ecological Entomology, vol.81, issue.5, pp.446-450, 2007.
DOI : 10.5962/bhl.part.5666

R. Wenzel, V. Tipton, and A. Kiewlicz, The streblid batflies of Panama (Diptera Calypterae: Streblidae), Ectoparasites of Panama, pp.405-675, 1966.
DOI : 10.5962/bhl.part.5666

C. Dick and B. Patterson, Against all odds: Explaining high host specificity in dispersal-prone parasites, International Journal for Parasitology, vol.37, issue.8-9, pp.871-876, 2007.
DOI : 10.1016/j.ijpara.2007.02.004

C. Dick and B. Patterson, Bat flies: Obligate ectoparasites of bats, Micromammals and Macroparasites, pp.179-194, 2006.
DOI : 10.1007/978-4-431-36025-4_11

M. Hastriter, A review of Ascodipterinae (Diptera: Streblidae) of the Oriental and Australasian regions with a description of three new species of Ascodipteron adensamer and a key to the subfamily, Zootaxa, vol.1636, pp.1-32, 2007.

L. Ching and A. Marshall, The breeding biology of the bat-fly Eucampsipoda sundaicum Theodor, 1955 (Diptera: Nycteribiidae), Malayan Nature Journal, vol.21, pp.171-180, 1968.

A. Marshall, The life cycle of Basilia hispida Theodor 1967 (Diptera: Nycteribiidae) in Malaysia*, Parasitology, vol.67, issue.01, pp.1-18, 1970.
DOI : 10.5962/bhl.part.7277

B. Patterson, C. Dick, and K. Dittmar, Roosting habits of bats affect their parasitism by bat flies (Diptera: Streblidae), Journal of Tropical Ecology, vol.23, issue.02, pp.177-189, 2007.
DOI : 10.1017/S0266467406003816

A. Marshall, The comparative ecology of insects ectoparasitic upon bats in west Malaysia, Proceedings of the Fifth International Bat Research Conference, pp.135-142, 1980.

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.1525-1534, 2005.
DOI : 10.1098/rspb.1995.0117

R. Johnstone and G. Hurst, Maternally inherited male-killing microorganisms may confound interpretation of mitochondrial DNA variability, Biological Journal of the Linnean Society, vol.124, issue.4, pp.453-470, 1996.
DOI : 10.1016/B978-0-12-078403-5.50012-8

URL : https://academic.oup.com/biolinnean/article-pdf/58/4/453/14064464/j.1095-8312.1996.tb01446.x.pdf

S. Goodman, C. Maminirina, H. Bradman, L. Christidis, and B. Appleton, Journal of Zoological Systematics and Evolutionary Research, vol.312, issue.supplement, pp.75-86, 2010.
DOI : 10.3161/001.005.s101

N. Weyeneth, S. Goodman, B. Appleton, R. Wood, and M. Ruedi, Wings or winds: inferring bat migration in a stepping-stone archipelago, Journal of Evolutionary Biology, vol.12, issue.6, pp.1298-1306, 2011.
DOI : 10.1046/j.1365-294X.2003.01773.x

C. Emerick and R. Duncan, Age progressive volcanism in the Comores Archipelago, western Indian Ocean and implications for Somali plate tectonics, Earth and Planetary Science Letters, vol.60, issue.3, pp.415-428, 1982.
DOI : 10.1016/0012-821X(82)90077-2

J. Nougier, J. Cantagrel, and J. Karche, The Comores archipelago in the western Indian Ocean: volcanology, geochronology and geodynamic setting, Journal of African Earth Sciences (1983), vol.5, issue.2, pp.135-145, 1986.
DOI : 10.1016/0899-5362(86)90003-5

A. Monadjem, S. Goodman, W. Stanley, and B. Appleton, In press) A cryptic new species of Miniopterus from south-eastern Africa based on molecular and morphological characters, Zootaxa