E. Holmes, Evolutionary history and phylogeography of human viruses Annual review of microbiology, pp.307-335, 2008.

T. Kuiken, R. Fouchier, G. Rimmelzwaan, and A. Osterhaus, Emerging viral infections in a rapidly changing world. Current opinion in biotechnology, pp.641-647, 2003.

S. Cleaveland, D. Haydon, and L. Taylor, Overviews of pathogen emergence: which pathogens emerge, when and why? Current topics in microbiology and immunology, pp.85-111, 2007.

S. Cleaveland, M. Laurenson, and L. 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.991-1000, 1411.
DOI : 10.1098/rstb.2001.0889

J. Childs, J. Richt, and J. Mackenzie, Introduction: conceptualizing and partitioning the emergence process of zoonotic viruses from wildlife to humans. Current topics in microbiology and immunology, pp.1-31, 2007.

. Ictv and . Icotov, Virus Taxonomy: 2015 Release 2016

D. Steinhauer and J. Holland, Rapid evolution of RNA viruses Annual review of microbiology, pp.409-442, 1987.

H. Badrane and N. Tordo, Host Switching in Lyssavirus History from the Chiroptera to the Carnivora Orders, Journal of Virology, vol.75, issue.17, pp.8096-104, 2001.
DOI : 10.1128/JVI.75.17.8096-8104.2001

N. Faria, M. Suchard, A. Rambaut, D. Streicker, and P. Lemey, Simultaneously reconstructing viral crossspecies transmission history and identifying the underlying constraints, Philosophical transactions of the Royal Society of London Series B, Biological sciences, vol.368, p.23382420, 1614.

E. Holmes, C. Woelk, R. Kassis, and H. Bourhy, Genetic Constraints and the Adaptive Evolution of Rabies Virus in Nature, Virology, vol.292, issue.2, pp.247-57, 2002.
DOI : 10.1006/viro.2001.1271

C. Rupprecht, A. Turmelle, and I. Kuzmin, A perspective on lyssavirus emergence and perpetuation, Current Opinion in Virology, vol.1, issue.6, pp.662-70, 2011.
DOI : 10.1016/j.coviro.2011.10.014

S. Meng, Y. Sun, X. Wu, J. Tang, G. Xu et al., Evolutionary dynamics of rabies viruses highlights the importance of China rabies transmission in Asia, Virology, vol.410, issue.2, pp.403-412, 2011.
DOI : 10.1016/j.virol.2010.12.011

P. Ming, J. Du, Q. Tang, J. Yan, S. Nadin-davis et al., Molecular characterization of the complete genome of a street rabies virus isolated in China, Virus Research, vol.143, issue.1, pp.6-14, 2009.
DOI : 10.1016/j.virusres.2009.02.014

H. Wu, L. Wang, X. Tao, H. Li, S. Rayner et al., Genetic diversity and molecular evolution of the rabies virus matrix protein gene in China. Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases, pp.248-53, 2013.

J. Wertheim, K. Pond, and S. , Purifying Selection Can Obscure the Ancient Age of Viral Lineages, Molecular Biology and Evolution, vol.28, issue.12, pp.3355-65, 2011.
DOI : 10.1093/molbev/msr170

R. Assenberg, O. Delmas, J. Ren, P. Vidalain, A. Verma et al., Structure of the Nucleoprotein Binding Domain of Mokola Virus Phosphoprotein, Journal of Virology, vol.84, issue.2, pp.1089-96, 2010.
DOI : 10.1128/JVI.01520-09

URL : https://hal.archives-ouvertes.fr/pasteur-00455306

M. Mavrakis, A. Mccarthy, S. Roche, D. Blondel, and R. Ruigrok, Structure and Function of the C-terminal Domain of the Polymerase Cofactor of Rabies Virus, Journal of Molecular Biology, vol.343, issue.4, pp.819-850, 2004.
DOI : 10.1016/j.jmb.2004.08.071

J. Steele and P. Fernandez, History of rabies and global aspects, The Natural History of Rabies. 2. Boca Raton, pp.1-26, 1991.

A. History, Key Concept 4.1 Globalizing Networks of Communication and Exchange

D. Streicker, A. Turmelle, M. Vonhof, I. Kuzmin, G. Mccracken et al., Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats, Science, vol.329, issue.5992, pp.676-685, 2010.
DOI : 10.1126/science.1188836

L. Villarreal, V. Defilippis, and K. Gottlieb, Acute and Persistent Viral Life Strategies and Their Relationship to Emerging Diseases, Virology, vol.272, issue.1, p.10873743, 2000.
DOI : 10.1006/viro.2000.0381

URL : http://doi.org/10.1006/viro.2000.0381

R. Engeman, K. Christensen, M. Pipas, and D. Bergman, Population Monitoring in Support of a Rabies Vaccination Program for Skunks in Arizona, Journal of Wildlife Diseases, vol.39, issue.3, pp.746-50, 2003.
DOI : 10.7589/0090-3558-39.3.746

M. Leslie, S. Messenger, R. Rohde, J. Smith, R. Cheshier et al., Bat-associated Rabies Virus in Skunks, Emerging Infectious Diseases, vol.12, issue.8, pp.1274-1281, 2006.
DOI : 10.3201/eid1208.051526

URL : http://doi.org/10.3201/eid1208.051526

N. Mollentze, R. Biek, and D. Streicker, The role of viral evolution in rabies host shifts and emergence, Current Opinion in Virology, vol.8, pp.68-72, 2014.
DOI : 10.1016/j.coviro.2014.07.004

M. Borucki, H. Chen-harris, V. Lao, G. Vanier, D. Wadford et al., Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission, PLoS Neglected Tropical Diseases, vol.28, issue.11, p.24278493, 2013.
DOI : 10.1371/journal.pntd.0002555.s012

C. Parrish, E. Holmes, D. Morens, E. Park, D. Burke et al., Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases, Microbiology and Molecular Biology Reviews, vol.72, issue.3, pp.457-70, 2008.
DOI : 10.1128/MMBR.00004-08

M. Woolhouse, D. Haydon, and R. Antia, Emerging pathogens: the epidemiology and evolution of species jumps, Trends in Ecology & Evolution, vol.20, issue.5, pp.238-282, 2005.
DOI : 10.1016/j.tree.2005.02.009

R. Sanjuan, J. Cuevas, A. Moya, and S. Elena, Epistasis and the Adaptability of an RNA Virus, Genetics, vol.170, issue.3, p.15879507, 2005.
DOI : 10.1534/genetics.105.040741

L. Wiltzer, K. Okada, S. Yamaoka, F. Larrous, H. Kuusisto et al., Interaction of Rabies Virus P-Protein With STAT Proteins is Critical to Lethal Rabies Disease, Journal of Infectious Diseases, vol.209, issue.11, pp.1744-53, 2014.
DOI : 10.1093/infdis/jit829

URL : https://hal.archives-ouvertes.fr/pasteur-01479389

L. Dacheux, N. Berthet, G. Dissard, E. Holmes, O. Delmas et al., Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses, Journal of Virology, vol.84, issue.18, pp.9557-74, 2010.
DOI : 10.1128/JVI.00771-10

URL : https://hal.archives-ouvertes.fr/pasteur-00507428

A. Criscuolo and S. Brisse, AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics, vol.102, issue.5-6, pp.5-6500, 2013.
DOI : 10.1016/j.ygeno.2013.07.011

J. Goecks, A. Nekrutenko, J. Taylor, and T. Galaxy, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biology, vol.11, issue.8, p.20738864, 2010.
DOI : 10.1186/gb-2010-11-8-r86

D. Blankenberg, V. Kuster, G. Coraor, N. Ananda, G. Lazarus et al., Galaxy: a web-based genome analysis tool for experimentalists. Current protocols in molecular biology, pp.1-21, 2010.
DOI : 10.1002/0471142727.mb1910s89

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264107

B. Giardine, C. Riemer, R. Hardison, R. Burhans, L. Elnitski et al., Galaxy: A platform for interactive large-scale genome analysis, Genome Research, vol.15, issue.10, pp.1451-1456, 2005.
DOI : 10.1101/gr.4086505

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089

M. Larkin, G. Blackshields, N. Brown, R. Chenna, P. Mcgettigan et al., Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2955, 2007.
DOI : 10.1093/bioinformatics/btm404

URL : https://hal.archives-ouvertes.fr/hal-00206210

D. Darriba, G. Taboada, R. Doallo, and D. Posada, jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, p.772, 2012.
DOI : 10.1109/TAC.1974.1100705

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594756

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

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

M. Anisimova and O. Gascuel, Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative Systematic biology, pp.539-52, 2006.
DOI : 10.1080/10635150600755453

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.335.5101

A. Rambaut, T. Lam, L. M. Pybus, and O. , Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evolution, 2016.

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

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

V. Minin, E. Bloomquist, and M. Suchard, Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics, Molecular Biology and Evolution, vol.25, issue.7, pp.1459-71, 2008.
DOI : 10.1093/molbev/msn090

M. Gill, P. Lemey, N. Faria, A. Rambaut, B. Shapiro et al., Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci, Molecular Biology and Evolution, vol.30, issue.3, pp.713-737, 2013.
DOI : 10.1093/molbev/mss265

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563973

W. Delport, A. Poon, S. Frost, K. Pond, and S. , Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology, Bioinformatics, vol.26, issue.19, pp.2455-2462, 2010.
DOI : 10.1093/bioinformatics/btq429

S. Pond and S. Frost, Datamonkey: rapid detection of selective pressure on individual sites of codon alignments, Bioinformatics, vol.21, issue.10, pp.2531-2534, 2005.
DOI : 10.1093/bioinformatics/bti320