M. M. Abang, M. Baum, S. Ceccarelli, S. Grando, C. C. Linde et al., During Parasitic and Saprophytic Phases in the Barley Scald Disease Cycle, Phytopathology, vol.96, issue.11, pp.1214-1222, 2006.
DOI : 10.1094/PHYTO-96-1214

S. Abel, P. Abel-zur-wiesch, B. M. Davis, and M. K. Waldor, Analysis of Bottlenecks in Experimental Models of Infection, PLOS Pathogens, vol.10, issue.6, 2015.
DOI : 10.1371/journal.ppat.1004823.g002

S. Ali, S. Soubeyrand, P. Gladieux, T. Giraud, M. Leconte et al., : Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms, Molecular Ecology Resources, vol.103, issue.4, pp.845-861, 2016.
DOI : 10.1094/PHYTO-09-12-0249-R

J. E. Barrick and R. E. Lenski, Genome dynamics during experimental evolution, Nature Reviews Genetics, vol.147, issue.12, p.827, 2013.
DOI : 10.1038/306368a0
URL : http://europepmc.org/articles/pmc4239992?pdf=render

C. T. Bergstrom, P. Mcelhany, and L. A. Real, Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens, Proc. Natl. Acad. Sci. USA. 96, pp.5095-5100, 1999.
DOI : 10.1103/PhysRevLett.76.4400

M. Bergua, M. P. Zwart, C. El-mohtar, T. Shilts, S. F. Elena et al., A Viral Protein Mediates Superinfection Exclusion at the Whole-Organism Level but Is Not Required for Exclusion at the Cellular Level, Journal of Virology, vol.88, issue.19, pp.11327-11338, 2014.
DOI : 10.1128/JVI.01612-14

P. Berthier, M. A. Beaumont, J. Cornuet, and G. Luikart, Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach, Genetics, vol.160, pp.741-751, 2002.
URL : https://hal.archives-ouvertes.fr/halsde-00295046

M. Betancourt, A. Fereres, A. Fraile, and F. Garcia-arenal, Estimation of the Effective Number of Founders That Initiate an Infection after Aphid Transmission of a Multipartite Plant Virus, Journal of Virology, vol.82, issue.24, pp.12416-12421, 2008.
DOI : 10.1128/JVI.01542-08

N. Boissot, A. Schoeny, and F. Vanlerberghe-masutti, Vat, an Amazing Gene Conferring Resistance to Aphids and Viruses They Carry: From Molecular Structure to Field Effects, Frontiers in Plant Science, vol.82, issue.e60832, pp.1-18, 2016.
DOI : 10.1128/AEM.04131-15
URL : https://hal.archives-ouvertes.fr/hal-01512038

J. P. Bollback, T. L. York, and R. Nielsen, Estimation of 2Nes From Temporal Allele Frequency Data, Genetics, vol.179, issue.1, pp.497-502, 2008.
DOI : 10.1534/genetics.107.085019

J. K. Brown, Durable Resistance of Crops to Disease: A Darwinian Perspective, Annual Review of Phytopathology, vol.53, issue.1, pp.513-539, 2015.
DOI : 10.1146/annurev-phyto-102313-045914

A. Caballero, Developments in the prediction of effective population size, Heredity, vol.73, issue.6, pp.657-679, 1994.
DOI : 10.1038/hdy.1994.174

W. J. Ewens, The sampling theory of selectively neutral alleles, Theoretical Population Biology, vol.3, issue.1, pp.87-112, 1972.
DOI : 10.1016/0040-5809(72)90035-4

W. Ewens, On the concept of the effective population size, Theoretical Population Biology, vol.21, issue.3, pp.373-378, 1982.
DOI : 10.1016/0040-5809(82)90024-7

W. J. Ewens, Mathematical population genetics. I. Theoretical introduction. Interdisciplinary applied mathematics, p.27, 2004.

F. Fabre, J. Chadoeuf, C. Costa, H. Lecoq, and C. Desbiez, Asymmetrical over-infection as a process of plant virus emergence, Journal of Theoretical Biology, vol.265, issue.3, pp.377-388, 2010.
DOI : 10.1016/j.jtbi.2010.04.027
URL : https://hal.archives-ouvertes.fr/hal-00608417

F. Fabre, J. Montarry, J. Coville, R. Senoussi, V. Simon et al., Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing, PLoS Pathogens, vol.23, issue.4, 2012.
DOI : 10.1371/journal.ppat.1002654.s005
URL : https://hal.archives-ouvertes.fr/hal-01208592

F. Fabre, B. Moury, E. I. Johansen, V. Simon, M. Jacquemond et al., Narrow Bottlenecks Affect Pea Seedborne Mosaic Virus Populations during Vertical Seed Transmission but not during Leaf Colonization, PLoS Pathogens, vol.163, issue.11, 2014.
DOI : 10.1371/journal.ppat.1003833.s003

A. F. Feder, S. Rhee, S. P. Holmes, R. W. Shafer, D. A. Petrov et al., More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1, Elife, vol.5, 2016.

S. Y. Folimonova, Developing an understanding of cross-protection by Citrus tristeza virus, Frontiers in Microbiology, vol.4, p.76, 2013.
DOI : 10.3389/fmicb.2013.00076

M. Foll, H. Shim, and J. D. Jensen, WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data, Molecular Ecology Resources, vol.2, issue.Pt 5, pp.87-98, 2015.
DOI : 10.2307/2405519

F. García-arenal and B. A. Mcdonald, An Analysis of the Durability of Resistance to Plant Viruses, Phytopathology, vol.93, issue.8, pp.941-952, 2003.
DOI : 10.1094/PHYTO.2003.93.8.941

F. García-arenal, A. Fraile, and J. M. Malpica, Variation and evolution of plant virus populations, International Microbiology, vol.6, issue.4, pp.225-232, 2003.
DOI : 10.1007/s10123-003-0142-z

A. Gibbs, M. Gibbs, K. Ohshima, and F. Garcia-arenal, More About Plant Virus Evolution: Past, Present, and Future, Origin and Evolution of Viruses, pp.229-50, 2008.
DOI : 10.1016/B978-0-12-374153-0.00011-4

P. González-jara, A. Fraile, T. Canto, and F. Garcia-arenal, The Multiplicity of Infection of a Plant Virus Varies during Colonization of Its Eukaryotic Host, Journal of Virology, vol.83, issue.15, pp.7487-7494, 2009.
DOI : 10.1128/JVI.00636-09

P. González-jara, A. Fraile, T. Canto, and F. García-arenal, The Multiplicity of Infection of a Plant Virus Varies during Colonization of Its Eukaryotic Host, Journal of Virology, vol.87, issue.4, pp.2374-2374, 2013.
DOI : 10.1128/JVI.03255-12

I. Gordo and B. Charlesworth, On the speed of Muller's ratchet, Genetics, vol.156, pp.2137-2140, 2000.

M. Rojas and R. Gilbertson, Emerging plant viruses: a diversity of mechanisms and opportunities. In: Plant Virus Evolution, pp.27-51, 2008.

S. Abel, P. Abel-zur-wiesch, B. M. Davis, M. K. Waldor, S. Abel et al., Analysis of Bottlenecks References Analysis of Bottlenecks in Experimental Models of Infection, PLoS Pathog, issue.11, 2015.

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

V. Ayme, S. Souche, C. Caranta, M. Jacquemond, J. Chadoeuf et al., Resistance in Pepper, Molecular Plant-Microbe Interactions, vol.19, issue.5, pp.557-563, 2006.
DOI : 10.1094/MPMI-19-0557

V. Ayme, J. Petit-pierre, S. Souche, A. Palloix, and B. Moury, Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper, Journal of General Virology, vol.88, issue.5, pp.1594-1601, 2007.
DOI : 10.1099/vir.0.82702-0

J. E. Barrick, M. R. Kauth, C. C. Strelioff, and R. E. Lenski, Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects, Molecular Biology and Evolution, vol.55, issue.12, pp.1338-1347, 2010.
DOI : 10.1554/0014-3820(2001)055[2606:TPTBMA]2.0.CO;2

S. Bedhomme, G. Lafforgue, and S. F. Elena, Multihost Experimental Evolution of a Plant RNA Virus Reveals Local Adaptation and Host-Specific Mutations, Molecular Biology and Evolution, vol.7, issue.7, pp.1481-1492, 2012.
DOI : 10.1371/journal.ppat.1002122

L. Chao, Fitness of RNA virus decreased by Muller's ratchet, Nature, vol.348, issue.6300, pp.454-455, 1990.
DOI : 10.1038/348454a0

F. De-la-iglesia and S. F. Elena, Fitness Declines in Tobacco Etch Virus upon Serial Bottleneck Transfers, Journal of Virology, vol.81, issue.10, pp.4941-4947, 2007.
DOI : 10.1128/JVI.02528-06

E. Duarte, D. Clarke, A. Moya, E. Domingo, and J. Holland, Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet., Proc. Natl. Acad. Sci. USA. 89, pp.6015-6019, 1992.
DOI : 10.1073/pnas.89.13.6015

S. F. Elena and R. Sanjuán, Virus Evolution: Insights from an Experimental Approach, Annual Review of Ecology, Evolution, and Systematics, vol.38, issue.1, pp.27-52, 2007.
DOI : 10.1146/annurev.ecolsys.38.091206.095637

C. Escarmí-s, M. Dávila, N. Charpentier, A. Bracho, A. Moya et al., Genetic Lesions Associated with Muller's Ratchet in an RNA Virus, Journal of Molecular Biology, vol.264, issue.2, pp.255-267, 1996.
DOI : 10.1006/jmbi.1996.0639

A. E. Lipka, F. Tian, Q. Wang, J. Peiffer, M. Li et al., GAPIT: genome association and prediction integrated tool, Bioinformatics, vol.3, issue.18, pp.2397-2399, 2012.
DOI : 10.1371/journal.pgen.0030004

A. Luna and K. K. Nicodemus, snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package, Bioinformatics, vol.70, issue.2, pp.774-776, 2007.
DOI : 10.1086/338688

M. Lynch, R. Bürger, D. Butcher, and W. Gabriel, The Mutational Meltdown in Asexual Populations, Journal of Heredity, vol.84, issue.5, pp.339-344, 1993.
DOI : 10.1093/oxfordjournals.jhered.a111354

A. Malaspinas, O. Malaspinas, S. N. Evans, and M. Slatkin, Estimating Allele Age and Selection Coefficient from Time-Serial Data, Genetics, vol.192, issue.2, pp.599-607, 2012.
DOI : 10.1534/genetics.112.140939

J. M. Malpica, A. Fraile, I. Moreno, C. I. Obies, J. W. Drake et al., The rate and character of spontaneous mutation in an RNA virus, Genetics, vol.162, pp.1505-1511, 2002.

W. Marczewski, B. Flis, J. Syller, R. Schäfer-pregl, and C. Gebhardt, -Gene-Like Markers, Molecular Plant-Microbe Interactions, vol.14, issue.12, pp.1420-1425, 2001.
DOI : 10.1094/MPMI.2001.14.12.1420

F. Martínez, J. Sardanyés, S. F. Elena, and J. Daròs, Geometric Replication, Genetics, vol.188, issue.3, pp.637-646, 2011.
DOI : 10.1534/genetics.111.129114

I. Mathieson and G. Mcvean, Estimating Selection Coefficients in Spatially Structured Populations from Time Series Data of Allele Frequencies, Genetics, vol.193, issue.3, pp.973-984, 2013.
DOI : 10.1534/genetics.112.147611

M. Melotto, W. Underwood, J. Koczan, K. Nomura, and S. Y. He, Plant Stomata Function in Innate Immunity against Bacterial Invasion, Cell, vol.126, issue.5, pp.969-980, 2006.
DOI : 10.1016/j.cell.2006.06.054

C. R. Miller, P. Joyce, and H. A. Wichman, Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models, Genetics, vol.187, issue.1, pp.185-202, 2011.
DOI : 10.1534/genetics.110.121400

R. Miralles, P. J. Gerrish, A. Moya, and S. F. Elena, Clonal Interference and the Evolution of RNA Viruses, Science, vol.285, issue.5434, pp.1745-1747, 1999.
DOI : 10.1126/science.285.5434.1745

S. Miyashita and H. Kishino, Estimation of the Size of Genetic Bottlenecks in Cell-to-Cell Movement of Soil-Borne Wheat Mosaic Virus and the Possible Role of the Bottlenecks in Speeding Up Selection of Variations in trans-Acting Genes or Elements, Journal of Virology, vol.84, issue.4, pp.1828-1837, 2010.
DOI : 10.1128/JVI.01890-09

B. Monsion, R. Froissart, Y. Michalakis, and S. Blanc, Large Bottleneck Size in Cauliflower Mosaic Virus Populations during Host Plant Colonization, PLoS Pathogens, vol.4, issue.10, 2008.
DOI : 10.1371/journal.ppat.1000174.s002

M. R. Rojas and R. L. Gilbertson, Emerging Plant Viruses: a Diversity of Mechanisms and Opportunities, Plant virus evolution, pp.27-51, 2008.
DOI : 10.1007/978-3-540-75763-4_3

M. Rolland, C. Lacroix, A. Blanchard, T. Baldwin, C. Kerlan et al., Potato virus Y (PVY): From its discovery to the latest outbreaks, Virologie, vol.12, pp.261-273, 2008.

E. Rousseau, F. Fabre, R. Senoussi, L. Mailleret, A. Palloix et al., Estimating virus effective population size and selection without neutral markers, PLOS Pathogens, vol.28, issue.24
DOI : 10.1371/journal.ppat.1006702.s011
URL : https://hal.archives-ouvertes.fr/hal-01658535

I. M. Rouzine, A. Rodrigo, and J. M. Coffin, Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology, Microbiology and Molecular Biology Reviews, vol.65, issue.1, pp.151-185, 2001.
DOI : 10.1128/MMBR.65.1.151-185.2001

M. Rubio, M. Nicolai, C. Caranta, and A. Palloix, Allele mining in the pepper gene pool provided new complementation effects between pvr2-eIF4E and pvr6-eIF(iso)4E alleles for resistance to pepper veinal mottle virus, Journal of General Virology, vol.78, issue.12, pp.2808-2814, 2009.
DOI : 10.1128/JVI.78.12.6102-6111.2004

S. Ruffel, M. Dussault, A. Palloix, B. Moury, A. Bendahmane et al., A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukaryotic initiation factor 4E (eIF4E), The Plant Journal, vol.78, issue.6, pp.1067-1075, 2002.
DOI : 10.1128/jvi.76.5.2491-2497.2002

S. Ruffel, M. Dussault, M. Lesage, A. Moretti, A. Palloix et al., Involvement of the eukaryotic translation initiation factor eIF4E in Solanaceae-Potyvirus interactions, European Association for Research on Plant Breeding (EUCARPIA), pp.167-170, 2004.

S. Ruffel, J. Gallois, B. Moury, C. Robaglia, A. Palloix et al., Simultaneous mutations in translation initiation factors eIF4E and eIF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper, Journal of General Virology, vol.87, issue.7, pp.2089-2098, 2006.
DOI : 10.1099/vir.0.81817-0

S. Sacristán, J. M. Malpica, A. Fraile, and F. Garcia-arenal, Estimation of Population Bottlenecks during Systemic Movement of Tobacco Mosaic Virus in Tobacco Plants, Journal of Virology, vol.77, issue.18, pp.9906-9911, 2003.
DOI : 10.1128/JVI.77.18.9906-9911.2003

S. Sacristán, M. Diaz, A. Fraile, and F. Garcia-arenal, Contact Transmission of Tobacco Mosaic Virus: a Quantitative Analysis of Parameters Relevant for Virus Evolution, Journal of Virology, vol.85, issue.10, pp.4974-4981, 2011.
DOI : 10.1128/JVI.00057-11

A. Sage-palloix, F. Jourdan, T. Phaly, G. Nemouchi, V. Lefebvre et al., Analysis of diversity in pepper genetic resources: distribution of horticultural and resistance traits in the INRA pepper germplasm, Progress in research on Capsicum & Eggplant, pp.32-42, 2007.

R. Sanjuan, M. R. Nebot, N. Chirico, L. M. Mansky, and R. Belshaw, Viral Mutation Rates, Journal of Virology, vol.84, issue.19, pp.9733-9748, 2010.
DOI : 10.1128/JVI.00694-10

N. Sierro, J. N. Battey, S. Ouadi, L. Bovet, S. Goepfert et al., Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis, Genome Biology, vol.17, issue.6, p.60, 2013.
DOI : 10.1093/bioinformatics/17.9.847

J. Wang, Estimation of effective population sizes from data on genetic markers, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.92, issue.4, pp.1395-1409, 2005.
DOI : 10.1073/pnas.92.25.11549

R. S. Waples, A generalized approach for estimating effective population size from temporal changes in allele frequency, Genetics, vol.121, pp.379-391, 1989.

B. Webster, M. Ott, and W. C. Greene, Evasion of Superinfection Exclusion and Elimination of Primary Viral RNA by an Adapted Strain of Hepatitis C Virus, Journal of Virology, vol.87, issue.24, pp.13354-13369, 2013.
DOI : 10.1128/JVI.02465-13

E. G. Williamson and M. Slatkin, Using maximum likelihood to estimate population size from temporal changes in allele frequencies, Genetics, vol.152, pp.755-761, 1999.

S. Wright, Evolution in Mendelian populations, Genetics, vol.16, pp.97-159, 1931.

S. Yeh and D. Gonsalves, Evaluation of Induced Mutants of Papaya Ringspot Virus for Control by Cross Protection, Phytopathology, vol.74, issue.9, pp.1086-1091, 1984.
DOI : 10.1094/Phyto-74-1086

E. Yuste, S. Sánchez-palomino, C. Casado, E. Domingo, and C. López-galíndez, Drastic fitness loss in human immunodeficiency virus type 1 upon serial bottleneck events, J. Virol, vol.73, pp.2745-2751, 1999.

C. Zeyl and J. A. Devisser, Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae, Genetics, vol.157, pp.53-61, 2001.

J. Zhan, C. Mundt, M. Hoffer, and B. Mcdonald, Local adaptation and effect of host genotype on the rate of pathogen evolution: an experimental test in a plant pathosystem, Journal of Evolutionary Biology, vol.91, issue.Suppl. 1, pp.634-647, 2002.
DOI : 10.1094/PHYTO.2001.91.10.1011

J. Zhan, P. H. Thrall, and J. J. Burdon, Achieving sustainable plant disease management through evolutionary principles, Trends in Plant Science, vol.19, issue.9, pp.570-575, 2014.
DOI : 10.1016/j.tplants.2014.04.010

J. Zhan, P. H. Thrall, J. Papaïx, L. Xie, and J. J. Burdon, Playing on a Pathogen's Weakness: Using Evolution to Guide Sustainable Plant Disease Control Strategies, Annual Review of Phytopathology, vol.53, issue.1, pp.19-43, 2015.
DOI : 10.1146/annurev-phyto-080614-120040
URL : https://hal.archives-ouvertes.fr/hal-01536434

Z. Zhang, E. Ersoz, C. Lai, R. J. Todhunter, H. K. Tiwari et al., Mixed linear model approach adapted for genome-wide association studies, Nature Genetics, vol.82, issue.4, pp.355-360, 2010.
DOI : 10.1093/biomet/54.1-2.326

Y. Zhu, H. Chen, J. Fan, and Y. Wang, Genetic diversity and disease control in rice, Nature, vol.277, issue.6797, p.718, 2000.
DOI : 10.1126/science.277.5329.1038

M. P. Zwart and S. F. Elena, Matters of Size: Genetic Bottlenecks in Virus Infection and Their Potential Impact on Evolution, Annual Review of Virology, vol.2, issue.1, pp.161-179, 2015.
DOI : 10.1146/annurev-virology-100114-055135

M. P. Zwart, J. Daròs, and S. F. Elena, One Is Enough: In Vivo Effective Population Size Is Dose-Dependent for a Plant RNA Virus, PLoS Pathogens, vol.55, issue.7, p.1002122, 2011.
DOI : 10.1371/journal.ppat.1002122.s002

M. P. Zwart, J. Daros, and S. F. Elena, Effects of Potyvirus Effective Population Size in Inoculated Leaves on Viral Accumulation and the Onset of Symptoms, Journal of Virology, vol.86, issue.18, pp.9737-9747, 2012.
DOI : 10.1128/JVI.00909-12

S. Wright, Evolution in Mendelian populations, Genetics, vol.16, issue.2, pp.97-159, 1931.

J. Vucetich, T. Waite, and L. Nunney, FLUCTUATING POPULATION SIZE AND THE RATIO OF EFFECTIVE TO CENSUS POPULATION SIZE, Evolution, vol.87, issue.6, pp.2017-2021, 1997.
DOI : 10.1111/j.1365-2311.1984.tb00719.x

S. Gutiérrez, Y. Michalakis, and S. Blanc, Virus population bottlenecks during within-host progression and host-to-host transmission. Current Opinion in Virology, pp.546-555, 2012.

R. Waples, T. Antao, and G. Luikart, Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size, Genetics, vol.197, issue.2, pp.769-780, 2014.
DOI : 10.1534/genetics.114.164822

S. Wright, Statistical genetics in relation to evolution

M. Kimura and J. Crow, THE MEASUREMENT OF EFFECTIVE POPULATION NUMBER, Evolution, vol.87, issue.3, pp.279-288, 1963.
DOI : 10.1086/279872

A. Caballero, Developments in the prediction of effective population size, Heredity, vol.73, issue.6, pp.657-679, 1994.
DOI : 10.1038/hdy.1994.174

U. Motro and G. Thomson, ON HETEROZYGOSITY AND THE EFFECTIVE SIZE OF POPULATIONS SUBJECT TO SIZE CHANGES, Evolution, vol.13, issue.5, pp.1059-1066, 1982.
DOI : 10.1111/j.1558-5646.1975.tb00807.x

I. Rouzine, R. A. Coffin, and J. , Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology, Microbiology and Molecular Biology Reviews, vol.65, issue.1, pp.151-185, 2001.
DOI : 10.1128/MMBR.65.1.151-185.2001

M. Foll, Y. Poh, N. Renzette, A. Ferrer-admettla, C. Bank et al., Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective, PLoS Genetics, vol.5, issue.2
DOI : 10.1371/journal.pgen.1004185.s014

J. Quenouille, J. Montarry, A. Palloix, and B. Moury, Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown, Molecular Plant Pathology, vol.7, issue.2, pp.109-118, 2013.
DOI : 10.1371/journal.ppat.1002122
URL : https://hal.archives-ouvertes.fr/hal-01208677

M. Brockhurst, N. Colegrave, and D. Rozen, Next-generation sequencing as a tool to study microbial evolution, Molecular Ecology, vol.157, issue.3, pp.972-980, 2011.
DOI : 10.1073/pnas.0602917103

R. Sanjuán, A. Moya, and S. Elena, The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus, Proceedings of the National Academy of Sciences, vol.44, issue.6, pp.8396-8401, 2004.
DOI : 10.2307/2409502

S. Elena, A. Fraile, and F. García-arenal, Evolution and Emergence of Plant Viruses
DOI : 10.1016/B978-0-12-800098-4.00003-9

M. Nei and F. Tajima, Genetic drift and estimation of effective population size, Genetics, vol.98, pp.625-640, 1981.

R. Waples, A generalized approach for estimating effective population size from temporal changes in allele frequency, Genetics, vol.121, pp.379-391, 1989.

E. Williamson and M. Slatkin, Using maximum likelihood to estimate population size from temporal changes in allele frequencies, Genetics, vol.152, pp.755-761, 1999.

E. Anderson, E. Williamson, and E. Thompson, Monte Carlo evaluation of the likelihood for N e from temporal spaced samples, Genetics, vol.156, pp.2109-2118, 2000.

P. Berthier, M. Beaumont, J. Cornuet, and G. Luikart, Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach, Genetics, vol.160, pp.741-751, 2002.
URL : https://hal.archives-ouvertes.fr/halsde-00295046

R. Vitalis, M. Gautier, K. Dawson, and M. Beaumont, Detecting and Measuring Selection from Gene Frequency Data, Genetics, vol.196, issue.3, pp.799-817, 2014.
DOI : 10.1534/genetics.113.152991

C. Illingworth, L. Parts, S. Schiffels, G. Liti, and V. Mustonen, Quantifying Selection Acting on a Complex Trait Using Allele Frequency Time Series Data, Molecular Biology and Evolution, vol.331, issue.6023, pp.1187-1197, 2012.
DOI : 10.1126/science.1198914

A. Malaspinas, Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective, Molecular Ecology, vol.329, issue.5648, pp.24-41, 2016.
DOI : 10.1126/science.1190371

J. Bollback, T. York, and R. Nielsen, Estimation of 2Nes From Temporal Allele Frequency Data, Genetics, vol.179, issue.1, pp.497-502, 2008.
DOI : 10.1534/genetics.107.085019

A. Malaspinas, O. Malaspinas, S. Evans, and M. Slatkin, Estimating Allele Age and Selection Coefficient from Time-Serial Data, Genetics, vol.192, issue.2, pp.599-607, 2012.
DOI : 10.1534/genetics.112.140939
URL : http://www.genetics.org/content/genetics/192/2/599.full.pdf

M. Steinrücken, A. Bhaskar, and Y. Song, A novel spectral method for inferring general diploid selection from time series genetic data, The Annals of Applied Statistics, vol.8, issue.4, 2014.
DOI : 10.1214/14-AOAS764SUPP

R. French and D. Stenger, : Dynamics of Population Growth Within Plants May Explain Limited Variation, Annual Review of Phytopathology, vol.41, issue.1, pp.199-214, 2003.
DOI : 10.1146/annurev.phyto.41.052002.095559

F. García-arenal, A. Fraile, and J. Malpica, Variation and evolution of plant virus populations, International Microbiology, vol.6, issue.4, pp.225-232, 2003.
DOI : 10.1007/s10123-003-0142-z

S. Sacristán, J. Malpica, A. Fraile, and F. García-arenal, Estimation of Population Bottlenecks during Systemic Movement of Tobacco Mosaic Virus in Tobacco Plants, Journal of Virology, vol.77, issue.18
DOI : 10.1128/JVI.77.18.9906-9911.2003

S. Elena, S. Bedhomme, P. Carrasco, J. Cuevas, F. De-la-iglesia et al., The Evolutionary Genetics of Emerging Plant RNA Viruses, Molecular Plant-Microbe Interactions, vol.24, issue.3, pp.287-293, 2011.
DOI : 10.1094/MPMI-09-10-0214

M. Foll, H. Shim, and J. Jensen, WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data, Molecular Ecology Resources, vol.2, issue.Pt 5, pp.87-98, 2014.
DOI : 10.2307/2405519

T. Turner, A. Stewart, A. Fields, W. Rice, and A. Tarone, Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster, PLoS Genetics, vol.25, issue.3, p.1001336, 2011.
DOI : 10.1371/journal.pgen.1001336.s012

F. Fabre, J. Montarry, J. Coville, R. Senoussi, V. Simon et al., Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing, PLoS Pathogens, vol.23, issue.4, pp.1-9, 2012.
DOI : 10.1371/journal.ppat.1002654.s005
URL : https://hal.archives-ouvertes.fr/hal-01208592

S. Huse, J. Huber, H. Morrison, M. Sogin, and D. Welch, Accuracy and quality of massively parallel DNA pyrosequencing):R143 Available from: 10.1186/gb, Genome Biology, vol.8, issue.7, 2007.

T. Mago?cmago?c and S. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.5, issue.7, pp.2957-2963, 2011.
DOI : 10.1371/journal.pone.0011840

R. Team, R: a language and environment for statistical computing Available from: http://www, 2013.

A. Gallais, Théorie de la sélection en amélioration des plantes, 1990.

M. Khelifa, D. Massé, S. Blanc, and M. Drucker, Evaluation of the minimal replication time of Cauliflower mosaic virus in different hosts, Virology, vol.396, issue.2, pp.238-245, 2010.
DOI : 10.1016/j.virol.2009.09.032

W. Ewens, Mathematical population genetics 1 -Theoretical introduction

F. Musso, On the Relation Between the Eigen Model and the Asexual Wright???Fisher Model, Bulletin of Mathematical Biology, vol.5, issue.103, pp.103-115, 2012.
DOI : 10.1186/1471-2148-5-44

M. Lenormand, F. Jabot, and G. Deffuant, Adaptive approximate Bayesian computation for complex models, Computational Statistics, vol.11, issue.1, pp.2777-27962777, 2013.
DOI : 10.1186/1471-2105-11-116
URL : https://hal.archives-ouvertes.fr/hal-00638484

R. E. Consortium, Heterogeneity of selection and the evolution of resistance Available from: http://www.sciencedirect.com/science, Trends in Ecology & Evolution, vol.2, pp.110-118, 2013.

P. Carrasco, F. De-la-iglesia, and S. Elena, Distribution of Fitness and Virulence Effects Caused by Single-Nucleotide Substitutions in Tobacco Etch Virus, Journal of Virology, vol.81, issue.23, pp.12979-12984, 2007.
DOI : 10.1128/JVI.00524-07

R. Kassen and T. Bataillon, Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria, Nature Genetics, vol.20, issue.Suppl., pp.484-488, 2006.
DOI : 10.1006/meth.1999.0901

M. Lacerda and C. Seoighe, Population genetics inference for longitudinally-sampled mutants under strong selection Available from: http://genetics.org/content, Genetics, vol.1983, issue.3, pp.1237-1250, 1237.

D. Laehnemann, A. Borkhardt, and A. Mchardy, Denoising DNA deep sequencing data???high-throughput sequencing errors and their correction, Briefings in Bioinformatics, vol.20, issue.1, pp.154-179, 2016.
DOI : 10.1186/1471-2105-9-11

J. Clark, Why environmental scientists are becoming Bayesians, Ecology Letters, vol.96, issue.1, pp.2-14, 2005.
DOI : 10.1201/9781420057669

T. Rhodes, O. Nikolaitchik, J. Chen, D. Powell, and W. Hu, Genetic Recombination of Human Immunodeficiency Virus Type 1 in One Round of Viral Replication: Effects of Genetic Distance, Target Cells, Accessory Genes, and Lack of High Negative Interference in Crossover Events, Journal of Virology, vol.79, issue.3, pp.1666-1677, 2005.
DOI : 10.1128/JVI.79.3.1666-1677.2005

B. Moury, B. Janzac, Y. Ruellan, V. Simon, M. Khalifa et al., Interaction Patterns between Potato Virus Y and eIF4E-Mediated Recessive Resistance in the Solanaceae, Journal of Virology, vol.88, issue.17, pp.9799-980700930, 1128.
DOI : 10.1128/JVI.00930-14

R. Djidjou-demasse, B. Moury, and F. Fabre, Mosaics often outperform pyramids: insights from a model comparing strategies for the deployment of plant resistance genes against viruses in agricultural landscapes, New Phytologist, vol.53, issue.1, pp.239-253, 2017.
DOI : 10.1146/annurev-phyto-080614-120040
URL : https://hal.archives-ouvertes.fr/hal-01604528

V. Ayme, S. Souche, C. Caranta, M. Jacquemond, J. Chadoeuf et al., Resistance in Pepper, Molecular Plant-Microbe Interactions, vol.19, issue.5, pp.557-563, 2006.
DOI : 10.1094/MPMI-19-0557

M. Zwart, J. Daròs, and S. Elena, One Is Enough: In Vivo Effective Population Size Is Dose-Dependent for a Plant RNA Virus, PLoS Pathogens, vol.55, issue.7, pp.1-12, 2011.
DOI : 10.1371/journal.ppat.1002122.s002

S. Gutiérrez, E. Pirolles, M. Yvon, V. Baecker, Y. Michalakis et al., The multiplicity of cellular infection changes depending on the route of cell infection PLOS 43, p.44

F. De-la-iglesia and S. Elena, Fitness Declines in Tobacco Etch Virus upon Serial Bottleneck Transfers, Journal of Virology, vol.81, issue.10, pp.4941-4947, 2007.
DOI : 10.1128/JVI.02528-06

Z. Patwa and L. Wahl, The fixation probability of beneficial mutations, Journal of The Royal Society Interface, vol.86, issue.1, pp.1279-1289, 2008.
DOI : 10.1073/pnas.31.12.382

F. Fabre, E. Rousseau, L. Mailleret, and B. Moury, Durable strategies to deploy plant resistance in agricultural landscapes, New Phytologist, vol.77, issue.4, pp.1064-1075, 2012.
DOI : 10.1094/PHYTO.2003.93.5.616
URL : https://hal.archives-ouvertes.fr/hal-01000305

F. Fabre, E. Rousseau, L. Mailleret, and B. Moury, Epidemiological and evolutionary management of plant resistance: optimizing the deployment of cultivar mixtures in time and space in agricultural landscapes, Evolutionary Applications, vol.406, issue.10, pp.919-932, 2015.
DOI : 10.1038/35021046
URL : https://hal.archives-ouvertes.fr/hal-01239676

F. Zanini and R. Neher, FFPopSim: an efficient forward simulation package for the evolution of large populations, Bioinformatics, vol.186, issue.24, pp.3332-3333, 2012.
DOI : 10.1534/genetics.110.123240

M. A. Bracho, A. Moya, and E. Barrio, Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity., Journal of General Virology, vol.79, issue.12, pp.2921-2928, 1998.
DOI : 10.1099/0022-1317-79-12-2921

D. Laehnemann, A. Borkhardt, and A. C. Mchardy, Denoising DNA deep sequencing data???high-throughput sequencing errors and their correction, Briefings in Bioinformatics, vol.20, issue.1, pp.154-179, 2016.
DOI : 10.1186/1471-2105-9-11

J. Montarry, J. Doumayrou, V. Simon, and B. Moury, Genetic background matters: a plant-virus gene-for-gene interaction is strongly influenced by genetic contexts, Molecular Plant Pathology, vol.15, issue.9
DOI : 10.1046/j.1420-9101.2002.00428.x
URL : https://hal.archives-ouvertes.fr/hal-01462654

M. Negroni and H. Buc, Mechanisms of Retroviral Recombination, Annual Review of Genetics, vol.35, issue.1, pp.275-302, 2001.
DOI : 10.1146/annurev.genet.35.102401.090551

V. Potapov and J. L. Ong, Examining Sources of Error in PCR by Single-Molecule Sequencing, PLOS ONE, vol.9, issue.12, p.169774, 2017.
DOI : 10.1371/journal.pone.0169774.s008

J. D. Roberts, B. D. Preston, L. A. Johnston, A. Soni, L. A. Loeb et al., Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro., Molecular and Cellular Biology, vol.9, issue.2, pp.469-476, 1989.
DOI : 10.1128/MCB.9.2.469

M. G. Ross, C. Russ, M. Costello, A. Hollinger, N. J. Lennon et al., Characterizing and measuring bias in sequence data, Genome Biology, vol.14, issue.5, p.51, 2013.
DOI : 10.1073/pnas.1017351108

R. 1. Boitard, S. Rodríguez, W. Jay, F. Mona, S. Austerlitz et al., Inferring Population Size History from Large Samples of Genome-Wide Molecular Data -An Approximate Bayesian Computation Approach, PLOS Genetics, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01605807