R. A. Lamb and D. P. Griffith, Paramyxoviridae: the viruses and their replication, Fields Virology, vol.1, pp.1449-1496, 2007.

H. E. Field, J. S. Mackenzie, and P. Daszak, Henipaviruses: Emerging Paramyxoviruses Associated with Fruit Bats, Curr. Top. Microbiol. Immunol, vol.315, pp.133-159, 2007.
DOI : 10.1007/978-3-540-70962-6_7

R. W. Renshaw, A. L. Glaser, H. Van-campen, F. Weiland, and E. J. Dubovi, Identification and Phylogenetic Comparison of Salem Virus, a Novel Paramyxovirus of Horses, Virology, vol.270, issue.2, pp.417-42910, 2000.
DOI : 10.1006/viro.2000.0305

J. F. Drexler, Bats host major mammalian paramyxoviruses, Nature Communications, vol.16, issue.796, pp.10-1038, 2012.
DOI : 10.1126/science.1108871

URL : https://hal.archives-ouvertes.fr/pasteur-00700110

D. Wilkinson, Highly Diverse Morbillivirus-Related Paramyxoviruses in Wild Fauna of the Southwestern Indian Ocean Islands: Evidence of Exchange between Introduced and Endemic Small Mammals, Journal of Virology, vol.88, issue.15, pp.8268-827710, 2014.
DOI : 10.1128/JVI.01211-14

URL : https://hal.archives-ouvertes.fr/hal-01274563

M. H. Jun, N. Karabatsos, and R. H. Johnson, A NEW MOUSE PARAMYXOVIRUS (J VIRUS), Australian Journal of Experimental Biology and Medical Science, vol.55, issue.6, pp.645-64763, 1977.
DOI : 10.1038/icb.1977.63

G. D. Maganga, Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity, PLoS ONE, vol.12, issue.10, 2014.
DOI : 10.1371/journal.pone.0115588.t002

J. Melade, An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism, Scientific Reports, vol.49, issue.1, pp.10-1038, 2016.
DOI : 10.1186/1471-2105-11-S1-S60

URL : https://hal.archives-ouvertes.fr/hal-01452887

B. G. Meerburg, G. R. Singleton, and A. Kijlstra, Rodent-borne diseases and their risks for public health, Critical Reviews in Microbiology, vol.24, issue.4, pp.221-27010, 2009.
DOI : 10.1016/j.pt.2008.01.001

J. N. Mills and J. Childs, Ecologic Studies of Rodent Reservoirs: Their Relevance for Human Health, Emerging Infectious Diseases, vol.4, issue.4, pp.529-53710, 1998.
DOI : 10.3201/eid0404.980403

J. M. Ramsey, Ecological Connectivity of Trypanosoma cruzi Reservoirs and Triatoma pallidipennis Hosts in an Anthropogenic Landscape with Endemic Chagas Disease, PLoS ONE, vol.7, issue.9, 2012.
DOI : 10.1371/journal.pone.0046013.t007

A. J. Mccarthy and S. J. Goodman, Reassessing conflicting evolutionary histories of the Paramyxoviridae and the origins of respiroviruses with Bayesian multigene phylogenies, Infection, Genetics and Evolution, vol.10, issue.1, pp.97-107, 2010.
DOI : 10.1016/j.meegid.2009.11.002

P. J. Miller, D. B. Boyle, B. T. Eaton, and L. Wang, Full-length genome sequence of Mossman virus, a novel paramyxovirus isolated from rodents in Australia, Virology, vol.317, issue.2, pp.330-344, 2003.
DOI : 10.1016/j.virol.2003.08.013

C. A. Tidona, H. W. Kurz, H. R. Gelderblom, and G. Darai, Isolation and Molecular Characterization of a Novel Cytopathogenic Paramyxovirus from Tree Shrews, Virology, vol.258, issue.2, pp.425-434, 1999.
DOI : 10.1006/viro.1999.9693

P. C. Woo, Complete Genome Sequence of a Novel Paramyxovirus, Tailam Virus, Discovered in Sikkim Rats, Journal of Virology, vol.85, issue.24, pp.13473-1347410, 2011.
DOI : 10.1128/JVI.06356-11

C. E. Thomas, Vaccination of Mice with Gonococcal TbpB Expressed In Vivo from Venezuelan Equine Encephalitis Viral Replicon Particles, Infection and Immunity, vol.74, issue.3, pp.1612-1620, 2006.
DOI : 10.1128/IAI.74.3.1612-1620.2006

K. Pond, S. L. Frost, and S. D. , Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection, Molecular Biology and Evolution, vol.22, issue.5, pp.1208-1222, 2005.
DOI : 10.1093/molbev/msi105

M. Sasaki, Molecular epidemiology of paramyxoviruses in Zambian wild rodents and shrews, Journal of General Virology, vol.95, issue.Pt_2, pp.325-330, 2014.
DOI : 10.1099/vir.0.058404-0

F. Brooks, Preliminary characterisation of Pentlands paramyxovirus-1, -2 and -3, three new paramyxoviruses of rodents, Veterinary Microbiology, vol.170, issue.3-4, pp.391-397010, 2014.
DOI : 10.1016/j.vetmic.2014.02.010

W. Ghawar, : Reservoirs of Zoonotic Cutaneous Leishmaniasis in Sidi Bouzid (Central Tunisia), Vector-Borne and Zoonotic Diseases, vol.11, issue.12, pp.1561-15680712, 2011.
DOI : 10.1089/vbz.2011.0712

E. P. Jones, H. M. Eager, S. I. Gabriel, F. Johannesdottir, and J. B. Searle, Genetic tracking of mice and other bioproxies to infer human history, Trends in Genetics, vol.29, issue.5, pp.298-308, 2013.
DOI : 10.1016/j.tig.2012.11.011

D. T. Hayman, K. D. Mcdonald, and M. Y. Kosoy, Evolutionary history of rat-borne Bartonella: the importance of commensal rats in the dissemination of bacterial infections globally, Ecol. Evol, vol.3, pp.3195-320310, 2013.

K. L. Gage and M. Y. 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

M. H. Green, Pandemic Disease in the Medieval World: Rethinking the Black Death, The Medieval Globe, vol.1, issue.1, 2014.

E. Lecompte, Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily, BMC Evolutionary Biology, vol.8, issue.1, pp.10-1186, 2008.
DOI : 10.1186/1471-2148-8-199

URL : https://hal.archives-ouvertes.fr/hal-00336780

K. P. Aplin, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats, PLoS ONE, vol.55, issue.11, 2011.
DOI : 10.1371/journal.pone.0026357.s007

URL : https://hal.archives-ouvertes.fr/ird-00714383

A. Cheke, The timing of arrival of humans and their commensal animals on western Indian Ocean oceanic islands, Phelsuma, vol.18, pp.38-69, 2010.

C. Tollenaere, 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 : 10.1093/oxfordjournals.molbev.a040192

URL : https://hal.archives-ouvertes.fr/halsde-00459761

C. Brouat, in Madagascar, Molecular Ecology, vol.38, issue.16, pp.4153-416710, 2014.
DOI : 10.2307/2408641

URL : https://hal.archives-ouvertes.fr/ird-00261411

E. R. Chare, E. A. Gould, and E. Holmes, Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses, Journal of General Virology, vol.84, issue.10, pp.2691-2703, 2003.
DOI : 10.1099/vir.0.19277-0

J. O. Wertheim and S. L. Kosakovsky-pond, Purifying Selection Can Obscure the Ancient Age of Viral Lineages, Molecular Biology and Evolution, vol.28, issue.12, pp.3355-3365, 2011.
DOI : 10.1093/molbev/msr170

P. Lopez, D. Casane, and H. Philippe, Heterotachy, an Important Process of Protein Evolution, Molecular Biology and Evolution, vol.19, issue.1, pp.1-7, 2002.
DOI : 10.1093/oxfordjournals.molbev.a003973

M. Kimura, The neutral theory of molecular evolution: A review of recent evidence., The Japanese Journal of Genetics, vol.66, issue.4, pp.367-386367, 1991.
DOI : 10.1266/jjg.66.367

M. Nei, T. Maruyama, and R. Chakraborty, THE BOTTLENECK EFFECT AND GENETIC VARIABILITY IN POPULATIONS, Evolution, vol.87, issue.1, pp.1-1010, 1975.
DOI : 10.1017/S0016672300012994

K. M. Pepin, S. Lass, J. R. Pulliam, A. F. Read, and J. Lloyd-smith, Identifying genetic markers of adaptation for surveillance of viral host jumps, Nature Reviews Microbiology, vol.82, issue.11, pp.802-81310, 1038.
DOI : 10.3201/eid1211.060652

J. M. Powell, The Crusades from the Perspective of Byzantium and the Muslim World (review), The Catholic Historical Review, vol.88, issue.1, 2002.
DOI : 10.1353/cat.2002.0042

K. Davis, The Origin and Growth of Urbanization in the World, American Journal of Sociology, vol.60, issue.5, pp.429-43710, 1955.
DOI : 10.1086/221602

L. White and . Jr, The Historical Roots of Our Ecologic Crisis, Science, vol.155, issue.3767, pp.1203-12071203, 1967.
DOI : 10.1126/science.155.3767.1203

H. Kruse, A. Kirkemo, and K. Handeland, Wildlife as Source of Zoonotic Infections, Emerging Infectious Diseases, vol.10, issue.12, pp.2067-207210, 2004.
DOI : 10.3201/eid1012.040707

L. W. Pomeroy, O. N. Bjornstad, and E. C. Holmes, The Evolutionary and Epidemiological Dynamics of the Paramyxoviridae, Journal of Molecular Evolution, vol.83, issue.5, pp.98-10610, 2008.
DOI : 10.1099/0022-1317-83-6-1419

A. Padhi and L. Ma, Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa, Scientific Reports, vol.21, issue.1, pp.10-07040, 1038.
DOI : 10.1093/bioinformatics/bti320

K. E. Robbins, U.S. Human Immunodeficiency Virus Type 1 Epidemic: Date of Origin, Population History, and Characterization of Early Strains, Journal of Virology, vol.77, issue.11, pp.6359-6366, 2003.
DOI : 10.1128/JVI.77.11.6359-6366.2003

O. G. Pybus, The Epidemic Behavior of the Hepatitis C Virus, Science, vol.292, issue.5525, pp.2323-232510, 2001.
DOI : 10.1126/science.1058321

J. Cook and J. C. Beaglehole, The Voyage of the Endeavour, pp.1768-1771, 1968.

G. J. Harper, M. K. Steininger, C. J. Tucker, D. Juhn, and F. Hawkins, Fifty years of deforestation and forest fragmentation in Madagascar, Environmental Conservation, vol.5, issue.04, pp.325-33310, 2007.
DOI : 10.1016/S0006-3207(00)00041-0

S. M. Goodman, Rattus on Madagascar and the Dilemma of Protecting the Endemic Rodent Fauna, Conservation Biology, vol.9, issue.2, pp.450-453, 1995.
DOI : 10.1046/j.1523-1739.1995.9020450.x

J. Bouma, G. Varallyay, and N. Batjes, Principal land use changes anticipated in Europe, Agriculture, Ecosystems & Environment, vol.67, issue.2-3, pp.103-119, 1998.
DOI : 10.1016/S0167-8809(97)00109-6

N. Koning and E. Smaling, Environmental crisis or ???lie of the land???? The debate on soil degradation in Africa, Land Use Policy, vol.22, issue.1, pp.3-11, 2005.
DOI : 10.1016/j.landusepol.2003.08.003

S. Tong, S. W. Chern, Y. Li, M. A. Pallansch, and L. J. Anderson, Sensitive and Broadly Reactive Reverse Transcription-PCR Assays To Detect Novel Paramyxoviruses, Journal of Clinical Microbiology, vol.46, issue.8, pp.2652-265810, 2008.
DOI : 10.1128/JCM.00192-08

P. D. Schloss, Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities, Applied and Environmental Microbiology, vol.75, issue.23, pp.7537-754110, 2009.
DOI : 10.1128/AEM.01541-09

M. Kearse, Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, issue.12, pp.1647-1649, 2012.
DOI : 10.1093/bioinformatics/bts199

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-306610, 2002.
DOI : 10.1093/nar/gkf436

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-272910, 2013.
DOI : 10.1093/molbev/mst197

D. Posada and K. A. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818817, 1998.
DOI : 10.1093/bioinformatics/14.9.817

F. Ronquist, MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-542, 2012.
DOI : 10.1093/sysbio/sys029

A. J. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, pp.10-1186, 2007.
DOI : 10.1186/1471-2148-7-214

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

S. Y. Ho and S. Duchene, Molecular-clock methods for estimating evolutionary rates and timescales, Molecular Ecology, vol.7, issue.24, pp.5947-596510, 2014.
DOI : 10.1016/B978-1-4832-2734-4.50017-6

M. S. Gill, Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci, Molecular Biology and Evolution, vol.30, issue.3, pp.713-724, 2013.
DOI : 10.1093/molbev/mss265

P. Lemey, A. Rambaut, A. J. Drummond, and M. A. Suchard, Bayesian Phylogeography Finds Its Roots, PLoS Computational Biology, vol.90, issue.9, 2009.
DOI : 10.1371/journal.pcbi.1000520.s002

G. Baele, W. L. Li, A. J. Drummond, M. A. Suchard, and P. Lemey, Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics, Molecular Biology and Evolution, vol.30, issue.2, pp.239-24310, 2013.
DOI : 10.1093/molbev/mss243

F. Bielejec, A. Rambaut, M. A. Suchard, and P. Lemey, SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics, Bioinformatics, vol.27, issue.20, pp.2910-2912, 2011.
DOI : 10.1093/bioinformatics/btr481

W. L. Li and A. J. Drummond, Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics, Molecular Biology and Evolution, vol.29, issue.2, pp.751-761, 2012.
DOI : 10.1093/molbev/msr232

D. P. Martin, RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, pp.2462-2463, 2010.
DOI : 10.1093/bioinformatics/btq467