M. E. Woolhouse and S. Gowtage-sequeria, Host Range and Emerging and Reemerging Pathogens, Emerging Infectious Diseases, vol.11, issue.12, pp.1842-1847, 2005.
DOI : 10.3201/eid1112.050997

K. E. Jones, Global trends in emerging infectious diseases, Nature, vol.309, issue.7181, pp.990-993, 2008.
DOI : 10.1038/nature06536

S. Cleaveland, M. K. Laurenson, and L. H. Taylor, Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.356, issue.1411, pp.991-999, 2001.
DOI : 10.1098/rstb.2001.0889

M. E. Woolhouse, L. H. Taylor, and D. Haydon, Population Biology of Multihost Pathogens, Science, vol.292, issue.5519, pp.1109-1112, 2001.
DOI : 10.1126/science.1059026

D. T. Haydon, S. Cleaveland, L. H. Taylor, and M. K. Laurenson, Identifying reservoirs of infection: a conceptual and practical challenge, Emerg. Infect. Dis, vol.8, pp.1468-1473, 2002.

M. Viana, Assembling evidence for identifying reservoirs of infection, Trends in Ecology & Evolution, vol.29, issue.5, pp.270-279, 2014.
DOI : 10.1016/j.tree.2014.03.002

E. A. Archie, G. Luikart, and V. O. Ezenwa, Infecting epidemiology with genetics: a new frontier in disease ecology, Trends in Ecology & Evolution, vol.24, issue.1, pp.21-30, 2009.
DOI : 10.1016/j.tree.2008.08.008

E. Vaumourin, To be or not to be associated: power study of four statistical modeling approaches to identify parasite associations in cross-sectional studies, Frontiers in Cellular and Infection Microbiology, vol.158, p.62, 2014.
DOI : 10.1016/j.vetpar.2008.09.025

URL : https://hal.archives-ouvertes.fr/hal-01138870

R. Biek and L. A. Real, The landscape genetics of infectious disease emergence and spread, Molecular Ecology, vol.164, issue.17, pp.3515-3531, 2010.
DOI : 10.1111/j.1365-294X.2010.04679.x

M. C. Maiden, Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms, Proc. Natl. Acad. Sci. USA 95, pp.3140-3145, 1998.
DOI : 10.1073/pnas.95.6.3140

J. S. Brownstein, D. K. Skelly, T. R. Holford, and D. Fish, Forest fragmentation predicts local scale heterogeneity of Lyme disease risk, Oecologia, vol.78, issue.3, pp.469-475, 2005.
DOI : 10.1007/s00442-005-0251-9

G. Margos, MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi, Proc. Natl. Acad. Sci. USA 105, pp.8730-8735, 2008.
DOI : 10.1073/pnas.0800323105

D. S. Guttman, Multiple infections of Ixodes scapularis ticks by Borrelia burgdorferi as revealed by single-strand conformation polymorphism analysis, J. Clin. Microbiol, vol.34, pp.652-656, 1996.

W. G. Qiu, D. E. Dykhuizen, M. S. Acosta, and B. J. Luft, Geographic uniformity of the lyme disease spirochete (Borrelia burgdorferi) and its shared history with tick vector (Ixodes scapularis) in the Northeastern United States, Genetics, vol.160, pp.833-849, 2002.

C. D. Crowder, Genotypic Variation and Mixtures of Lyme Borrelia in Ixodes Ticks from North America and Europe, PLoS ONE, vol.34, issue.5, pp.1-9, 2010.
DOI : 10.1371/journal.pone.0010650.s001

K. Tsao, S. J. Bent, and D. Fish, Identification of Borrelia burgdorferi ospC genotypes in host tissue and feeding ticks by terminal restriction fragment length polymorphisms, Scientific RepoRts | Appl. Environ. Microbiol, vol.6, issue.79, pp.31273-31283, 2013.

M. Jacquot, High-Throughput Sequence Typing Reveals Genetic Differentiation and Host Specialization among Populations of the Borrelia burgdorferi Species Complex that Infect Rodents, PLoS ONE, vol.79, issue.2, p.88581, 2014.
DOI : 10.1371/journal.pone.0088581.s001

D. Brisson and D. E. Dykhuizen, ospC Diversity in Borrelia burgdorferi: Different Hosts Are Different Niches, Genetics, vol.168, issue.2, pp.713-722, 2004.
DOI : 10.1534/genetics.104.028738

C. Herrmann, L. Gern, and M. J. Voordouw, Species Co-Occurrence Patterns among Lyme Borreliosis Pathogens in the Tick Vector Ixodes ricinus, Applied and Environmental Microbiology, vol.79, issue.23, pp.7273-7280, 2013.
DOI : 10.1128/AEM.02158-13

D. Brisson and D. E. Dykhuizen, A modest model explains the distribution and abundance of Borrelia burgdorferi strains, Am. J. Trop. Med. Hyg, vol.74, pp.615-622, 2006.

D. Brisson, D. E. Dykhuizen, and R. S. Ostfeld, Conspicuous impacts of inconspicuous hosts on the Lyme disease epidemic, Proceedings of the Royal Society B: Biological Sciences, vol.11, issue.12, pp.227-235, 2008.
DOI : 10.2307/3282982

N. Rudenko, Detection of Borrelia burgdorferi Sensu Stricto ospC Alleles Associated with Human Lyme Borreliosis Worldwide in Non-Human-Biting Tick Ixodes affinis and Rodent Hosts in Southeastern United States, Applied and Environmental Microbiology, vol.79, issue.5, pp.1444-1453, 2013.
DOI : 10.1128/AEM.02749-12

G. Stanek and M. Reiter, The expanding Lyme Borrelia complex???clinical significance of genomic species?, Clinical Microbiology and Infection, vol.17, issue.4, pp.487-493, 2011.
DOI : 10.1111/j.1469-0691.2011.03492.x

D. E. Dykhuizen, Short report: The propensity of different Borrelia burgdorferi sensu stricto genotypes to cause disseminated infections in humans, Am. J. Trop. Med. Hyg, vol.78, pp.806-810, 2008.

I. N. Wang, Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto, Genetics, vol.151, pp.15-30, 1999.

G. Seinost, Four clones of Borrelia burgdorferi sensu stricto cause invasive infection in humans, Infect. Immun, vol.67, pp.3518-3524, 1999.

A. Estrada-peña, J. De-la-fuente, R. S. Ostfeld, and A. Cabezas-cruz, Interactions between tick and transmitted pathogens evolved to minimise competition through nested and coherent networks, Scientific Reports, vol.55, issue.1, p.10361, 2015.
DOI : 10.1080/10635150600755453

G. Devevey, T. Dang, C. J. Graves, S. Murray, and D. Brisson, First arrived takes all: inhibitory priority effects dominate competition between co-infecting Borrelia burgdorferi strains, BMC Microbiology, vol.15, issue.1, pp.1-9, 2015.
DOI : 10.1111/eva.12165

A. Swei, V. C. Bowie, and R. C. Bowie, Comparative genetic diversity of Lyme disease bacteria in Northern Californian ticks and their vertebrate hosts, Ticks and Tick-borne Diseases, vol.6, issue.3, pp.414-423, 2015.
DOI : 10.1016/j.ttbdis.2015.03.011

N. Tonetti, M. J. Voordouw, J. Durand, S. Monnier, and L. Gern, Genetic variation in transmission success of the Lyme borreliosis pathogen Borrelia afzelii, Ticks and Tick-borne Diseases, vol.6, issue.3, pp.334-343, 2015.
DOI : 10.1016/j.ttbdis.2015.02.007

G. Margos, S. Vollmer, N. H. Ogden, and D. Fish, Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato, Infection, Genetics and Evolution, vol.11, issue.7, pp.1545-1563, 2011.
DOI : 10.1016/j.meegid.2011.07.022

M. Marsot, Which forest bird species are the main hosts of the tick, Ixodes ricinus, the vector of Borrelia burgdorferi sensu lato, during the breeding season?, International Journal for Parasitology, vol.42, issue.8, pp.781-788, 2012.
DOI : 10.1016/j.ijpara.2012.05.010

URL : https://hal.archives-ouvertes.fr/hal-00965448

G. Stanek, G. P. Wormser, J. Gray, F. Strle, and . Lyme-borreliosis, Lyme borreliosis, The Lancet, vol.379, issue.9814, pp.461-473, 2012.
DOI : 10.1016/S0140-6736(11)60103-7

B. Pisanu, Introduced Siberian chipmunks are more heavily infested by ixodid ticks than are native bank voles in a suburban forest in France, International Journal for Parasitology, vol.40, issue.11, pp.1277-83, 2010.
DOI : 10.1016/j.ijpara.2010.03.012

K. A. Lee and K. C. Klasing, A role for immunology in invasion biology, Trends in Ecology & Evolution, vol.19, issue.10, pp.523-529, 2004.
DOI : 10.1016/j.tree.2004.07.012

M. Marsot, Modification du risque d'une maladie multi-hôtes suite à l'introduction d'une espèce réservoir: cas de la maladie de Lyme et du tamia de Sibérie en Ile-de-France, 2011.

C. Millins, An invasive mammal (grey squirrel, Sciurus carolinensis) commonly hosts diverse and atypical genotypes of the zoonotic pathogen Borrelia burgdorferi sensu lato, Appl. Environ. Microbiol, vol.81, pp.109-124, 2015.

J. N. Thompson, Specific Hypotheses on the Geographic Mosaic of Coevolution, The American Naturalist, vol.153, issue.S5, pp.1-14, 1999.
DOI : 10.1086/303208

G. Vourc-'h, Mapping human risk of infection with Borrelia burgdorferi sensu lato, the agent of Lyme borreliosis, in a periurban forest in France, Ticks and Tick-borne Diseases, p.8, 2015.

P. Humair, Molecular Identification of Bloodmeal Source in <I>Ixodes ricinus</I> Ticks Using 12S rDNA As a Genetic Marker, Journal of Medical Entomology, vol.44, issue.5, pp.869-880, 2007.
DOI : 10.1603/0022-2585(2007)44[869:MIOBSI]2.0.CO;2

M. Jacquot, Comparative Population Genomics of the Borrelia burgdorferi Species Complex Reveals High Degree of Genetic Isolation among Species and Underscores Benefits and Constraints to Studying Intra-Specific Epidemiological Processes, PLoS ONE, vol.24, issue.4, 2014.
DOI : 10.1371/journal.pone.0094384.s008

URL : https://hal.archives-ouvertes.fr/pasteur-01054563

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

D. A. Benson, GenBank, Nucleic Acids Research, vol.41, issue.D1, pp.36-42, 2013.
DOI : 10.1093/nar/gks1195

T. Lassmann and E. L. Sonnhammer, Kalign?an accurate and fast multiple sequence alignment algorithm, BMC Bioinformatics, vol.6, issue.1, p.298, 2005.
DOI : 10.1186/1471-2105-6-298

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

H. Akaike, A new look at the statistical model identification, IEEE Transactions on Automatic Control, vol.19, issue.6, pp.716-723, 1974.
DOI : 10.1109/TAC.1974.1100705

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

D. Swofford, PAUP* : phylogenetic analysis using parsimony, version 4, 2003.

D. Bryant and V. Moulton, Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks, Molecular Biology and Evolution, vol.21, issue.2, pp.255-265, 2004.
DOI : 10.1093/molbev/msh018

D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006.
DOI : 10.1093/molbev/msj030

A. Clauset, M. E. Newman, and C. Moore, Finding community structure in very large networks, Physical Review E, vol.70, issue.6, pp.1-6, 2004.
DOI : 10.1103/PhysRevE.70.066111

G. Csardi and T. Nepusz, The igraph software package for complex network research, InterJournal Complex Sy, p.1695, 2006.

S. Wright, The Interpretation of Population Structure by F-Statistics with Special Regard to Systems of Mating, Evolution, vol.19, issue.3, pp.395-420, 1965.
DOI : 10.2307/2406450