K. Acevedo-whitehouse and A. Cunningham, Is MHC enough for understanding wildlife immunogenetics? Trends in Ecology & Evolution, pp.433-438, 2006.

M. Achtman, G. Morelli, and P. Zhu, Microevolution and history of the plague bacillus, Yersinia pestis, Proceedings of the National Academy of Sciences, vol.101, issue.51, pp.17837-17842, 2004.
DOI : 10.1073/pnas.0408026101

P. Ajmone-marsan, A. Valentini, and M. Cassandro, AFLP??? markers for DNA fingerprinting in cattle, Animal Genetics, vol.28, issue.6, pp.418-426, 1997.
DOI : 10.1111/j.1365-2052.1997.00204.x

S. Altizer, D. Harvell, and E. Friedle, Rapid evolutionary dynamics and disease threats to biodiversity, Trends in Ecology & Evolution, vol.18, issue.11, pp.589-596, 2003.
DOI : 10.1016/j.tree.2003.08.013

P. Andolfatto, Adaptive hitchhiking effects on genome variability, Current Opinion in Genetics & Development, vol.11, issue.6, pp.635-641, 2001.
DOI : 10.1016/S0959-437X(00)00246-X

R. Barrett and D. Schluter, Adaptation from standing genetic variation. Trends in Ecology and Evolution, pp.38-44, 2008.

R. Battistini and P. Verin, Man and the Environment in Madagascar, Junk, pp.311-337, 1972.
DOI : 10.1007/978-94-015-7159-3_9

M. Beaumont, Adaptation and speciation: what F ST can tell us? Trends in Ecology and Evolution, pp.435-440, 2005.

M. Beaumont and D. Balding, Identifying adaptive genetic divergence among populations from genome scans, Molecular Ecology, vol.28, issue.4, pp.969-980, 2004.
DOI : 10.1046/j.1420-9101.2001.00335.x

M. Beaumont and R. Nichols, Evaluating Loci for Use in the Genetic Analysis of Population Structure, Proceedings of the Royal Society B: Biological Sciences, vol.263, issue.1377, pp.1619-1626, 1996.
DOI : 10.1098/rspb.1996.0237

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B, vol.57, pp.289-300, 1995.

W. Black, C. Baer, M. Antolin, and N. Duteau, : Genome-Wide Sampling of Insect Populations, Annual Review of Entomology, vol.46, issue.1, pp.441-469, 2001.
DOI : 10.1146/annurev.ento.46.1.441

A. Bonin, F. Pompanon, P. Taberlet, E. Zimmer, and E. Roalson, Use of Amplified Fragment Length Polymorphism (AFLP) Markers in Surveys of Vertebrate Diversity, Molecular Evolution: Producing the Biochemical Data, pp.145-161, 2005.
DOI : 10.1016/S0076-6879(05)95010-6
URL : https://hal.archives-ouvertes.fr/halsde-00278828

A. Bonin, P. Taberlet, C. Miaud, and F. Pompanon, Explorative Genome Scan to Detect Candidate Loci for Adaptation Along a Gradient of Altitude in the Common Frog (Rana temporaria), Molecular Biology and Evolution, vol.23, issue.4, 2006.
DOI : 10.1093/molbev/msj087
URL : https://hal.archives-ouvertes.fr/halsde-00278818

E. Brygoo, Epidémiologie de la peste a ` Madagascar. Archives de l, Institut Pasteur de Madagascar, vol.35, pp.9-147, 1966.

D. Campbell and L. Bernatchez, Generic Scan Using AFLP Markers as a Means to Assess the Role of Directional Selection in the Divergence of Sympatric Whitefish Ecotypes, Molecular Biology and Evolution, vol.21, issue.5, pp.945-956, 2004.
DOI : 10.1093/molbev/msh101

P. Cavagna, G. Stone, and R. Stanyon, Black rat (Rattus rattus) genomic variability characterized by chromosome painting, Mammalian Genome, vol.61, issue.3, pp.157-163, 2002.
DOI : 10.1007/BF02684021

L. Cavalli-sforza, Population Structure and Human Evolution, Proceedings of the Royal Society B: Biological Sciences, vol.164, issue.995, pp.362-379, 1966.
DOI : 10.1098/rspb.1966.0038

B. Charlesworth, M. Nordborg, and D. Charlesworth, The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations, Genetical Research, vol.70, issue.2, pp.155-174, 1997.
DOI : 10.1017/S0016672397002954

P. Daszak, A. Cunningham, and A. Hyatt, Emerging Infectious Diseases of Wildlife-- Threats to Biodiversity and Human Health, Science, vol.287, issue.5452, pp.443-449, 2000.
DOI : 10.1126/science.287.5452.443

D. Dennis, K. Gage, N. Gratz, J. Poland, and E. Tikhomirov, Plague Manual: Epidemiology, Distribution, Surveillance and Control. World Health Organisation, 1999.

J. Duplantier, J. Catalan, A. Orth, B. Grolleau, and J. Britton-davidian, Systematics of the black rat in Madagascar: consequences for the transmission and distribution of plague, Biological Journal of the Linnean Society, vol.78, issue.3, pp.335-341, 2003.
DOI : 10.1046/j.1095-8312.2003.00142.x

H. Ellegren and B. Sheldon, Genetic basis of fitness differences in natural populations, Nature, vol.442, issue.7184, pp.169-175, 2008.
DOI : 10.1038/nature06737

L. Excoffier and N. Ray, Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology and Evolution, pp.347-351, 2008.

L. Excoffier, G. Laval, and S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evolutionary Bioinformatics Online, vol.1, pp.47-50, 2005.

M. Faure, P. David, F. Bonhomme, and N. Bierne, Genetic hitchhiking in a subdivided population of Mytilus edulis, BMC Evolutionary Biology, vol.8, issue.1, p.164, 2008.
DOI : 10.1186/1471-2148-8-164
URL : https://hal.archives-ouvertes.fr/halsde-00475073

R. Fisher, Combining independent tests of significance, American Statistician, issue.2, p.30, 1948.

M. Foll and O. Gaggiotti, A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective, Genetics, vol.180, issue.2, pp.977-993, 2008.
DOI : 10.1534/genetics.108.092221
URL : https://hal.archives-ouvertes.fr/halsde-00377961

K. Gage and M. Kosoy, NATURAL HISTORY OF PLAGUE: Perspectives from More than a Century of Research, Annual Review of Entomology, vol.50, issue.1, pp.505-528, 2005.
DOI : 10.1146/annurev.ento.50.071803.130337

R. Gibbs, G. Weinstock, and M. Metzker, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol.428, pp.493-521, 2004.

A. Guiyoule, B. Rasoamanana, and C. Buchrieser, Recent emergence of new variants of Yersinia pestis in Madagascar, Journal of Clinical Microbiology, vol.35, pp.2826-2833, 1997.

J. Haldane, THE ESTIMATION AND SIGNIFICANCE OF THE LOGARITHM OF A RATIO OF FREQUENCIES, Annals of Human Genetics, vol.75, issue.4, pp.309-311, 1956.
DOI : 10.1111/j.1469-1809.1955.tb01285.x

D. Hanson, H. Britten, M. Restani, and L. Washburn, High prevalence of Yersinia pestis in black-tailed prairie dog colonies during an apparent enzootic phase of sylvatic plague, Conservation Genetics, vol.2, issue.4, pp.789-795, 2007.
DOI : 10.1007/s10592-006-9226-6

C. Herrera and P. Bazaga, Population-genomic approach reveals adaptive floral divergence in discrete populations of a hawk moth-pollinated violet, Molecular Ecology, vol.8, issue.24, pp.5378-5390, 2008.
DOI : 10.1111/j.1365-294X.2008.04004.x

J. Hirschhorn and M. Daly, Genome-wide association studies for common diseases and complex traits, Nature Reviews Genetics, vol.158, issue.2, pp.95-108, 2005.
DOI : 10.1086/339258

H. Hoekstra and M. Nachman, Different genes underlie adaptive melanism in different populations of rock pocket mice, Molecular Ecology, vol.103, issue.5, pp.1185-1194, 2003.
DOI : 10.1038/18435

R. Ihaka and R. Gentleman, R: a language for data analysis and graphics, Journal of Computational and Graphical Statistics, vol.5, pp.299-314, 1996.

S. Goodman and J. Benstead, The climate of Madagascar In:The Natural History of Madagasca, Jury MR, pp.75-87, 2003.

B. Lazzaro, Natural selection on the Drosophila antimicrobial immune system, Current Opinion in Microbiology, vol.11, issue.3, pp.284-289, 2008.
DOI : 10.1016/j.mib.2008.05.001

I. Lowry, . Pp, G. Schatz, P. Phillipson, S. Goodman et al., The classification of natural and anthropogenic vegetation in Madagascar, In:Natural Change and Human Impact in Madagasca, pp.93-123, 1997.

G. Luikart, P. England, D. Tallmon, S. Jordan, and P. Taberlet, The power and promise of population genomics: from genotyping to genome typing, Nature Reviews Genetics, vol.4, issue.12, pp.981-994, 2003.
DOI : 10.1038/nrg1226
URL : https://hal.archives-ouvertes.fr/halsde-00279787

H. Meudt and A. Clarke, Almost Forgotten or Latest Practice? AFLP applications, analyses and advances, Trends in Plant Science, vol.12, issue.3, pp.106-117, 2007.
DOI : 10.1016/j.tplants.2007.02.001

C. Meyer, R. Vitalis, P. Saumitou-laprade, and V. Castric, , a model species for tolerance to heavy metal, Molecular Ecology, vol.8, issue.8, pp.2050-2062, 2009.
DOI : 10.1111/j.1365-294X.2009.04159.x

A. Midamegbe, R. Vitalis, T. Malausa, and R. Streiff, Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species, Molecular Ecology, vol.8, issue.7
DOI : 10.1111/j.1365-294X.2011.05035.x

R. Migliani, S. Chanteau, and L. Rahalison, Epidemiological trends for human plague in Madagascar during the second half of the 20th century: a survey of 20 900 notified cases, Tropical Medicine and International Health, vol.78, issue.8, pp.1228-1237, 2006.
DOI : 10.1016/S0140-6736(99)05163-6

N. Miller, M. Ciosi, and T. Sappington, Genome scan of Diabrotica virgifera virgifera for genetic variation associated with crop rotation tolerance, Journal of Applied Entomology, vol.158, issue.6, pp.378-385, 2007.
DOI : 10.1046/j.1365-294x.1999.00620.x

R. Nielsen, C. Bustamante, and A. Clark, A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees, PLoS Biology, vol.17, issue.6, pp.976-985, 2005.
DOI : 10.1371/journal.pbio.0030170.sd002

P. Nosil, S. Egan, and D. Funk, HETEROGENEOUS GENOMIC DIFFERENTIATION BETWEEN WALKING-STICK ECOTYPES: "ISOLATION BY ADAPTATION" AND MULTIPLE ROLES FOR DIVERGENT SELECTION, Evolution, vol.28, issue.2, pp.316-336, 2008.
DOI : 10.1046/j.1365-294x.1999.00620.x

P. Nosil, D. Funk, and D. Ortiz-barrientos, Divergent selection and heterogeneous genomic divergence, Molecular Ecology, vol.105, issue.3, pp.375-402, 2009.
DOI : 10.1111/j.1365-294X.2008.03946.x

S. Piertney and M. Oliver, The evolutionary ecology of the major histocompatibility complex, Heredity, vol.11, pp.7-21, 2006.
DOI : 10.1038/sj.hdy.6800724

F. Pompanon, A. Bonin, E. Bellemain, and P. Taberlet, Genotyping errors: causes, consequences and solutions, Nature Reviews Genetics, vol.5, issue.11, pp.847-859, 2005.
DOI : 10.1093/bioinformatics/btg112
URL : https://hal.archives-ouvertes.fr/halsde-00278823

L. Rahalison, M. Ranjalahy, and J. Duplantier, Susceptibility to Plague of the Rodents in Antananarivo, Madagascar, pp.439-442, 2003.
DOI : 10.1007/0-306-48416-1_87

J. Robins, P. Mclenachan, and M. Phillips, Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes, Molecular Phylogenetics and Evolution, vol.49, issue.2, pp.460-466, 2008.
DOI : 10.1016/j.ympev.2008.08.001

C. Schlotterer, Hitchhiking mapping ??? functional genomics from the population genetics perspective, Trends in Genetics, vol.19, issue.1, pp.32-38, 2003.
DOI : 10.1016/S0168-9525(02)00012-4

G. Sorci, A. Moller, and T. Boulinier, Genetics of host-parasite interactions. Trends in Ecology and Evolution, pp.196-200, 1997.

N. Stenseth, B. Atshabar, and M. Begon, Plague: Past, Present, and Future, PLoS Medicine, vol.56, issue.1, pp.9-13, 2008.
DOI : 10.1371/journal.pmed.0050003.sd002

J. Stinchcombe and H. Hoekstra, Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits, Heredity, vol.143, issue.2, pp.158-170, 2008.
DOI : 10.1093/jhered/esh012

J. Storz, INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence, Molecular Ecology, vol.15, issue.113, pp.671-688, 2005.
DOI : 10.1111/j.1365-294X.2005.02437.x

J. Storz and H. Hoekstra, The Study of Adaptation and Speciation in the Genomic Era, Journal of Mammalogy, vol.88, issue.1, pp.1-4, 2007.
DOI : 10.1644/06-MAMM-S-232R1.1

R. Thomas, A. Barnes, and T. Quan, SUSCEPTIBILITY TO YERSINIA PESTIS IN THE NORTHERN GRASSHOPPER MOUSE (ONYCHOMYS LEUCOGASTER), Journal of Wildlife Diseases, vol.24, issue.2, pp.327-333, 1988.
DOI : 10.7589/0090-3558-24.2.327

C. Tollenaere, L. Rahalison, and M. Ranjalahy, CCR5 polymorphism and plague resistance in natural populations of the black rat in Madagascar, Infection, Genetics and Evolution, vol.8, issue.6, pp.891-897, 2008.
DOI : 10.1016/j.meegid.2008.07.005

C. Tollenaere, C. Brouat, and J. Duplantier, in the western Indian Ocean, with special emphasis on the colonization history of Madagascar, Journal of Biogeography, vol.17, issue.3, pp.398-410, 2010.
DOI : 10.1111/j.1365-2699.2009.02228.x
URL : https://hal.archives-ouvertes.fr/halsde-00459761

S. Tsakas and C. Krimbas, Testing the heterogeneity of F values: a suggestion and a correction, Genetics, vol.84, pp.399-401, 1976.

J. Turner, M. Mcallister, J. Xu, and R. Tapping, The Resistance of BALB/cJ Mice to Yersinia pestis Maps to the Major Histocompatibility Complex of Chromosome 17, Infection and Immunity, vol.76, issue.9, pp.4092-4099, 2008.
DOI : 10.1128/IAI.00488-08

X. Vekemans, AFLP-surv version 1.0. Distributed by the author, 2002.

S. Via and J. West, The genetic mosaic suggests a new role for hitchhiking in ecological speciation, Molecular Ecology, vol.175, issue.19, pp.4334-4345, 2008.
DOI : 10.1111/j.1365-294X.2008.03921.x

R. Vitalis, K. Dawson, and P. Boursot, Interpretation of variation across marker loci as evidence of selection, Genetics, vol.158, pp.1811-1823, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00273259

R. Vitalis, K. Dawson, P. Boursot, and K. Belkhir, DetSel 1.0: A Computer Program to Detect Markers Responding to Selection, Journal of Heredity, vol.94, issue.5, pp.429-431, 2003.
DOI : 10.1093/jhered/esg083
URL : https://hal.archives-ouvertes.fr/hal-00273253