M. Woolhouse, D. T. Haydon, and R. Antia, Emerging pathogens: the epidemiology and evolution of species jumps, Trends Ecol Evol, vol.20, pp.238-244, 2005.

S. J. Scharg and P. Wiener, Emerging infectious disease: what are the relative roles of ecology and evolution, Trends Ecol Evol, vol.10, pp.319-324, 1995.

J. Pulliam, Viral host jumps: Moving toward a predictive framework, EcoHealth, vol.5, pp.80-91, 2008.

J. Dijskra, Importance of host ranges and other biological properties for the taxonomy of plant viruses, Arch Virol, vol.5, pp.279-289, 1992.

N. Suehiro, T. Natsuaki, T. Watanabe, and S. Okuda, An important determinant of the ability of Turnip mosaic virus to infect Brassica spp and/or Raphanus sativus is in its P3 protein, J Gen Virol, vol.85, pp.2087-2098, 2004.

K. C. Chen, C. H. Chiang, J. Raja, F. L. Liu, and C. H. Tai, A single amino acid of NiaPro of Papaya ringspot virus determines host specificity for infection of papaya, Mol Plant-Microbe Interact, vol.21, pp.1046-1057, 2008.

S. Tatineni, C. J. Robertson, S. M. Garnsey, and W. O. Dawson, A plant virus evolved by acquiring multiple nonconserved genes to extend its host range, Proc Natl Acad Sci, vol.108, pp.17366-17371, 2011.

N. Poulicard, A. Pinel-galzi, O. Traoré, F. Vignols, and A. Ghesquière, Historical contingencies modulate the adaptability of Rice yellow mottle virus, PLOS Pathog, vol.8, p.1002482, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01522310

N. Vassilakos, V. Simon, A. Tzima, E. Johansen, and B. Moury, Genetic determinism and evolutionary reconstruction of a host jump in a plant virus, Mol Biol Evol, vol.33, pp.541-553, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01605232

A. Gibbs, Evolution and origins of tobamoviruses, Phil Trans R Soc B, vol.354, pp.593-602, 1999.

B. Wu, U. Melcher, X. Guo, X. Wang, and L. Fan, Assessment of codivergence of mastreviruses with their plant hosts, BMC Evol Biol, vol.8, pp.335-348, 2008.

M. Woolhouse and S. Gowtage-sequeria, Host range and emerging and reemerging pathogens, Emerg Infect Dis, vol.11, pp.1842-1847, 2005.

P. K. Anderson, A. A. Cunningham, N. G. Patel, F. J. Morales, and P. R. Epstein, Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers, Trends Ecol Evol, vol.19, pp.535-544, 2004.

B. Moury, F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

R. Jones, Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control, Virus Res, vol.141, pp.113-130, 2009.

A. A. Brunt, K. Crabtree, M. J. Dallwitz, A. J. Gibbs, and L. Watson, Plant Viruses Online: Descriptions and Lists from the VIDE Database. Version, 1996.

M. Hill, Diversity and evenness: a unifying notation and its consequences, Ecology, vol.54, pp.427-432, 1973.

A. G. Power and A. S. Flecker, The importance of species: Perspectives on Expendability and Triage, pp.330-347, 2003.

J. S. Weitz, T. Poisot, J. R. Meyer, C. O. Flores, and S. Valverde, Phage-bacteria infection networks, Trends Microbiol, vol.21, pp.82-91, 2013.

A. King, M. J. Adams, E. B. Carstens, and E. J. Lefkowitz, Virus taxonomy. Classification and nomenclature of viruses. Ninth report of the International Committee on Taxonomy of Viruses
URL : https://hal.archives-ouvertes.fr/pasteur-01977366

C. Desbiez, B. Moury, and H. Lecoq, The hallmarks of "green" viruses: Do plant viruses evolve differently from the others?, Inf Genet Evol, vol.11, pp.812-824, 2011.

G. S. Gilbert, R. Magarey, K. Suiter, and W. Co, Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens, Evol Appl, vol.5, pp.869-878, 2012.

C. Vacher, D. Piou, and M. Desprez-loustau, :e1740. 23. Sanjuán R. From molecular genetics to phylodynamics: Evolutionary relevance of mutation rates across viruses, PLOS Pathog, vol.3, p.1002685, 2008.

L. A. Frederico, T. A. Kunkel, and B. R. Shaw, A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy, Biochemistry, vol.29, pp.2532-2537, 1990.

A. Sicard, Y. Michalakis, S. Gutiérrez, and S. Blanc, The strange lifestyle of multipartite viruses, PLoS Pathog, vol.12, p.1005819, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01942651

S. Nee, The evolution of multicompartmental genomes in viruses, J Mol Evol, vol.25, pp.277-281, 1987.

L. Chao, Levels of selection, evolution of sex in RNA viruses, and the origin of life, J Theor Biol, vol.153, pp.229-246, 1991.

, Version postprint Comment citer ce document

B. Moury, F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

S. Ojosnegros, J. García-arriaza, C. Escarmís, S. C. Manrubia, and C. Perales, Viral genome segmentation can result from a trade-off between genetic content and particle stability, PLOS Genet, vol.7, p.1001344, 2011.

A. Sicard, M. Yvon, T. Timchenko, B. Gronenborn, and Y. Michalakis, Gene copy number is differentially regulated in a multipartite virus, Nature Comm, vol.4, p.2248, 2013.

M. Smith and J. , The Evolution of Sex

S. Gutiérrez, Y. Michalakis, and S. Blanc, Virus population bottlenecks during within-host progression and host-to-host transmission, Curr Opin Virol, vol.2, pp.546-555, 2012.

N. Tromas, M. P. Zwart, G. Lafforgue, and S. F. Elena, Within-host spatiotemporal dynamics of plant virus infection at the cellular level, PLOS Genet, vol.10, p.1004186, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02629906

J. Iranzo and S. C. Manrubia, Evolutionary dynamics of genome segmentation in multipartite viruses, Proc R Soc B, vol.279, pp.3812-3919, 2012.

A. D. Stewart, J. M. Logsdon, and S. E. Kelley, An empirical study of the evolution of virulence under both horizontal and vertical transmission, Evolution, vol.59, pp.730-739, 2005.

C. E. Taylor, D. Brown, R. Neilson, and A. T. Jones, The persistence and spread of Xiphinema diversicaudatum in cultivated and uncultivated biotopes, Ann Appl Biol, vol.124, pp.469-477, 1994.

C. A. De-la, L. Lopez, F. Tenllado, D. Ruiz, J. R. Sanz et al., The coat protein is required for the elicitation of the Capsicum L 2 gene-mediated resistance against the tobamoviruses, Mol Plant-Microbe Interact, vol.10, pp.107-113, 1997.

R. Tomita, S. Ken-taro, M. Hiroyuki, M. Sakamoto, and J. Murai, Genetic basis for the hierarchical interaction between Tobamovirus spp and L resistance gene alleles from different pepper species, Mol Plant-Microbe Interact, vol.24, pp.108-117, 2011.

K. Andersen and I. E. Johansen, A single conserved amino acid in the coat protein gene of pea seed-borne mosaic potyvirus modulates the ability of the virus to move systemically in Chenopodium quinoa, Virology, vol.241, pp.304-311, 1998.

K. T. Sekine, T. Ishihara, S. Hase, T. Kusano, and J. Shah, Single amino acid alterations in Arabidopsis thaliana RCY1 compromise resistance to Cucumber mosaic virus, but differentially suppress hypersensitive response-like cell death, Plant Mol Biol, vol.62, pp.669-682, 2006.

C. Desbiez, C. Chandeysson, and H. Lecoq, A short motif in the N-terminal part of the coat protein is a host-specific determinant of systemic infectivity for two potyviruses, Mol Plant Pathol, vol.15, pp.217-221, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02630706

, Version postprint Comment citer ce document

B. Moury, F. Fabre, E. Hébrard, R. Froissart, S. García-castillo et al., Influence of the plant growing conditions on the translocation routes and systemic infection of carnation mottle virus in Chenopodium quinoa plants, Journal of General Virology, vol.98, issue.4, pp.229-238, 2001.

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2013.

A. Chao, N. J. Gotelli, T. C. Hsieh, S. E. Ma, and K. H. , Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies, Ecological Monographs, vol.84, pp.45-67, 2014.

L. Watson and M. J. Dallwitz, The families of angiosperms: automated descriptions, with interactive identification and information retrieval, Austral Syst Bot, vol.4, pp.601-695, 1991.

L. Watson and M. J. Dallwitz, The families of flowering plants: Descriptions, illustrations, identification and information retrieval, 1992.

P. F. Stevens, Angiosperm Phylogeny Website Version 12, 2012.

C. O. Flores, S. Valverde, and J. S. Weitz, Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages, ISME J, vol.7, pp.520-532, 2013.

B. Moury, B. Janzac, Y. Ruellan, V. Simon, B. Khalifa et al., Interaction patterns between Potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae, J Virol, vol.88, pp.9799-9807, 2014.

J. Hillung, J. M. Cuevas, S. Valverde, and S. F. Elena, Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection, Evolution, vol.68, pp.2467-2480, 2014.

B. Moury, F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

, 3: Evidence of nestedness (a) and modularity (b)

, Glycine max, Pisum sativum, Vicia faba, Vigna unguiculata, Cucumis sativus and Phaseolus vulgaris, and the following virus species: BWYV (beet western yellows polerovirus), AMV (alfalfa mosaic alfamovirus), CMV (cucumber mosaic cucumovirus, TRSV (tobacco ringspot nepovirus), TSV (tobacco streak ilarvirus), SLRSV (strawberry latent ringspot sadwavirus), TRV (tobacco rattle tobravirus), BCTV (beet curly top curtovirus), PSV (peanut stunt cucumovirus), RCNMV (red clover necrotic mosaic dianthovirus), TBRV (tomato black ring nepovirus), SMV (soybean mosaic potyvirus) and ClYMV

, Module 2 contained the following plant species: Cucurbita pepo, Chenopodium album, Spinacia oleracea, Tetragonia tetragonioides, Beta vulgaris, Gomphrena globosa, Chenopodium amaranticolor and Chenopodium quinoa, and the following virus species: CarMV (carnation mottle carmovirus), OkMV (okra mosaic tymovirus), CVMoV (carnation vein mottle potyvirus), ArMV (arabis mosaic nepovirus

. Tumv, PFBV (pelargonium flower break carmovirus), TNV-A (tobacco necrosis A necrovirus), BYMV (bean yellow mosaic potyvirus), HVS (helenium carlavirus Version postprint Comment citer ce document, BtMV (beet mosaic potyvirus), CymRSV (cymbidium ringspot tombusvirus)

B. Moury, F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

, PSbMV (pea seedborne mosaic potyvirus), SqMV (squash mosaic comovirus), BNYVV (beet necrotic yellow vein benyvirus) and CPMMV (cowpea mild mottle carlavirus)

, Module 3 contained the following plant species: Nicotiana tabacum, Nicotiana glutinosa, Nicotiana clevelandii, Lycopersicon esculentum, Petunia x hybrida, Zinnia elegans, Nicotiana rustica, Physalis floridana and Datura stramonium, and the following virus species: TEV (tobacco etch potyvirus), CVB (chrysanthemum B carlavirus), SPMMV (sweet potato mild mottle ipomovirus), RMV (ribgrass mosaic tobamovirus), PopMV (poplar mosaic carlavirus), PTV (peru tomato mosaic potyvirus), PVMV (pepper veinal mottle potyvirus) and PhyMV

, Version postprint Comment citer ce document

B. Moury, F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298

F. Fabre, E. Hébrard, and R. Froissart, Determinants of host species range in plant viruses, Journal of General Virology, vol.98, issue.4, pp.862-873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522298