P. M. Agapow and A. Burt, Indices of multilocus linkage disequilibrium, Molecular Ecology Notes, vol.1, pp.101-102, 2001.

C. Albertini, M. Gredt, and P. Leroux, Polymorphism of 14 alpha-demethylase gene (CYP51) in the cereal eyespot fungi Tapesia acuformis and Tapesia yallundae, European Journal of Plant Pathology, vol.109, pp.117-128, 2003.

S. Ali, P. Gladieux, M. Leconte, A. Gautier, A. F. Justesen et al., Origin, migration routes and worldwide population genetic structure of the wheat yellow rust pathogen Puccinia striiformis f.sp. tritici, PLoS Pathog, vol.10, p.1003903, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01303130

S. Ali, P. Gladieux, H. Rahman, M. S. Saqib, M. Fiaz et al., Inferring the . tritici, Molecular Ecology, issue.23, pp.603-617, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01004260

J. Amselem, C. A. Cuomo, J. A. Van-kan, M. Viaud, E. P. Benito et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Environmental Microbiology, vol.17, issue.4, pp.1261-1274, 2011.

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

R. Beever and P. Weeds, Taxonomic and genetic variation of Botrytis and Botryotinia, Botrytis: Biology, pathology and control, pp.29-52, 2004.

R. E. Beever and S. L. Parkes, Use of nitrate non-utilising (Nit) mutants to determine vegetative compatibility in Botryotinia fuckeliana (Botrytis cinerea), European Journal of Plant Pathology, vol.109, pp.607-613, 2003.

K. Belkhir, P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme, Genetix 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, 1996.

K. Boyd-wilson, F. Obanor, R. C. Butler, P. Harris-virgin, G. I. Langford et al., Sources of Botrytis cinerea inoculum for flower infection in blackcurrants in New Zealand, Australasian Plant Pathology, vol.42, pp.27-32, 2013.

P. C. Brunner, S. F. Torriani, D. Croll, E. H. Stukenbrock, and B. A. Mcdonald, Biology and Evolution, vol.30, pp.1337-1347, 2013.

M. Choquer, E. Fournier, C. Kunz, C. Levis, J. M. Pradier et al., Botrytis cinerea virulence factors:new insights into a necrotrophic and polyphageous pathogen, Fems Microbiology Letters, vol.277, pp.1-10, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02659110

V. Decognet, M. Bardin, Y. Trottin-caudal, and P. C. Nicot, , pp.185-193, 200999.

M. L. Desprez-loustau, Y. Vitasse, S. Delzon, X. Capdevielle, B. Marcais et al.,

, Evolutionary Biology, vol.23, pp.87-97

C. Dutech, O. Fabreguettes, X. Capdevielle, R. , and C. , Multiple introductions of divergent genetic lineages in an invasive fungal pathogen, Cryphonectria parasitica, Heredity, vol.105, pp.220-228, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02664934

C. Dutech, B. Barres, J. Bridier, C. Robin, M. G. Milgroom et al., The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen, Molecular Ecology, vol.21, pp.3931-3946, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02647231

Y. Elad, B. Williamson, P. Tudzynski, and N. Delen, Botrytis spp. and diseases they cause in agricultural systems -an introduction, 2004.

P. A. Elmer and T. J. Michailides, Epidemiology in Botrytis cinerea in orchard and vine crops, Botrytis: Biology, Pathology and Control, pp.243-262, 2004.

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Molecular Ecology, vol.14, pp.2611-2620, 2005.

L. Excoffier, H. E. Lischer, P. Gladieux, V. Decognet, M. Fermaud et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Molecular Ecology Resources, vol.10, issue.4, pp.1261-1274, 2010.

P. S. Gladieux, V. Decognet, M. Fermaud, J. Confais, J. Roudet et al., Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript : Walker, A, Environmental Microbiology, vol.17, issue.4, pp.1261-1274, 2015.

E. Fournier, G. , and T. , Sympatric genetic differentiation of a generalist pathogenic fungus, Botrytis cinerea, on two different host plants, grapevine and bramble, Journal of Evolutionary Biology, vol.21, pp.122-132, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02333203

E. Fournier, T. Giraud, C. Albertini, and Y. Brygoo, Partition of the Botrytis cinerea complex in France using multiple gene genealogies, Mycologia, vol.97, pp.1251-1267, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02679817

E. Fournier, C. Levis, D. Fortini, P. Leroux, T. Giraud et al., Characterization of Bc-hch, the Botrytis cinerea homolog of the Neurospora crassa het-c vegetative incompatibility locus, and its use as a population marker, Mycologia, vol.95, pp.251-261, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02675884

E. Fournier, T. Giraud, A. Loiseau, D. Vautrin, A. Estoup et al., , 2002.

, Molecular Ecology Notes, vol.2, pp.253-255

O. Frenkel, T. L. Peever, M. I. Chilvers, H. Özkilinc, C. Can et al., Ecological genetic divergence of the fungal pathogen Didymella rabiei on sympatric wild and domesticated Cicer spp, Applied and Environmental Microbiology, vol.76, pp.30-39, 2010.

T. Giraud, P. Gladieux, and S. Gavrilets, Linking the emergence of fungal plant diseases with ecological speciation, Trends in Ecology & Evolution, vol.25, pp.387-395, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02333057

T. Giraud, D. Fortini, C. Levis, P. Leroux, and Y. Brygoo, RFLP markers show genetic recombination in Botryotinia fuckeliana (Botrytis cinerea) and transposable elements reveal two sympatric species, Molecular Biology and Evolution, vol.14, pp.1177-1185, 1997.

T. Giraud, L. Villareal, F. Austerlitz, M. Le-gac, and C. Lavigne, Importance of the life cycle in sympatric host race formation and speciation of pathogens, Phytopathology, vol.96, pp.280-287, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00531079

P. Gladieux, X. G. Zhang, D. Afoufa-bastien, R. M. Sanhueza, M. Sbaghi et al., On the origin and spread of the scab disease of apple: out of central Asia, PLoS ONE, vol.3, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02669128

P. Gladieux, E. Vercken, M. C. Fontaine, M. E. Hood, O. Jonot et al., Maintenance of fungal pathogen species that are specialized to different hosts: allopatric divergence and introgression through secondary contact, Molecular Biology and Evolution, vol.28, pp.459-471, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02333046

P. Gladieux, F. Guerin, T. Giraud, V. Caffier, C. Lemaire et al., Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants, Molecular Ecology, vol.20, pp.4521-4532, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02329021

P. Gladieux, X. G. Zhang, I. Roldan-ruiz, V. Caffier, T. Leroy et al., Evolution of the population structure of Venturia inaequalis, the apple scab fungus, associated with the domestication of its host, Molecular Ecology, vol.19, pp.658-674, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02663059

T. R. Gordon and J. H. Leveau, Plant Pathology: A Story About Biology, In Annual Review of Phytopathology, vol.48, pp.293-309, 2010.

D. A. Isenegger, P. K. Ades, R. Ford, P. W. Taylor, P. Gladieux et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Environmental Microbiology, vol.29, issue.4, pp.1261-1274, 2008.

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

M. Jakobsson and N. A. Rosenberg, CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics, vol.23, pp.1801-1806, 2007.

M. V. Jaspers, A. M. Seyb, M. C. Trought, and R. Balasubramaniam, Overwintering grapevine debris as an important source of Botrytis cinerea inoculum, Plant Pathology, vol.62, pp.130-138, 2013.

P. R. Johnston, K. Hoksbergen, D. Park, and R. E. Beever, Genetic diversity of Botrytis in New Zealand vineyards and the significance of its seasonal and regional variation, Plant Pathology, 2013.

T. Jombart, adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, vol.24, pp.1403-1405, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00428105

T. Jombart, S. Devillard, and F. Balloux, Discriminant analysis of principal components: a new method for the analysis of genetically structured populations, Bmc Genetics, vol.11, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00539267

S. Karchani-balma, A. Gautier, A. Raies, and E. Fournier, Geography, plants and growing systems shape the genetic structure of Tunisian Botrytis cinerea populations, Phytopathology, vol.98, pp.1271-1279, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02666903

P. Leroux, M. Gredt, M. Leroch, and A. Walker, Exploring mechanisms of resistance to respiratory inhibitors in field strains of Botrytis cinerea, the causal agent of gray mold, Applied and Environmental Microbiology, vol.76, pp.6615-6630, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02668785

Z. H. Ma and T. J. Michailides, Genetic structure of Botrytis cinerea populations from different host plants in California, Plant Disease, vol.89, pp.1083-1089, 2005.

F. Martinez, B. Dubos, and M. Fermaud, The role of saprotrophy and virulence in the population dynamics of Botrytis cinerea in vineyards, Phytopathology, vol.95, pp.692-700, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682988

F. Martinez, M. F. Corio-costet, C. Levis, M. Coarer, and M. Fermaud, New PCR primers applied to characterize distribution of Botrytis cinerea populations in French vineyards, Vitis, vol.47, pp.217-226, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02666271

M. Mboup, B. Bahri, M. Leconte, C. De-vallavieille-pope, O. Kaltz et al., Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation, Evolutionary Applications, vol.5, pp.341-352, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01000343

B. A. Mcdonald and C. Linde, The population genetics of plant pathogens and breeding strategies for durable resistance, Euphytica, vol.124, pp.163-180, 2002.

M. G. Milgroom and T. L. Peever, Population biology of plant pathogens -The synthesis of plant disease epidemiology and population genetics, Plant Disease, vol.87, pp.608-617, 2003.

J. A. Morgan, V. T. Vredenburg, L. J. Rachowicz, R. A. Knapp, M. J. Stice et al.,

, Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis, Proceedings of the National Academy of Sciences, vol.104, pp.13845-13850

A. B. Munkacsi, S. Stoxen, M. , and G. , Ustilago maydis populations tracked maize through domestication and cultivation in the Americas, Proceedings of the Royal Society B: Biological Sciences, vol.275, pp.1037-1046, 2008.

G. Munoz, P. Hinrichsen, Y. Brygoo, G. , T. Gladieux et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Environmental Microbiology, vol.106, issue.4, pp.1261-1274, 2002.

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

T. L. Peever, L. Olsen, A. Ibanez, and L. W. Timmer, Genetic differentiation and host specificity among populations of Alternaria spp. causing brown spot of grapefruit and tangerine x grapefruit hybrids in Florida, Phytopathology, vol.90, pp.407-414, 2000.

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

B. A. Rajaguru and M. W. Shaw, Genetic differentiation between hosts and locations in populations of latent Botrytis cinerea in southern England, Plant Pathology, vol.59, pp.1081-1090, 2010.

M. Raymond and F. Rousset, GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism, Journal of Heredity, vol.86, pp.248-249, 1995.
URL : https://hal.archives-ouvertes.fr/halsde-00186383

S. Robert, V. Ravigne, M. F. Zapater, C. Abadie, and J. Carlier, Contrasting fijiensis, Molecular Ecology, vol.21, pp.1098-1114, 2012.

M. G. Roca, M. Weichert, U. Siegmund, P. Tudzynski, and A. Fleissner, Germling fusion via conidial anastomosis tubes in the grey mould Botrytis cinerea requires NADPH oxidase activity, Fungal Biology, vol.116, pp.379-387, 2012.

S. Samuel, T. Veloukas, A. Papavasileiou, and G. S. Karaoglanidis, Differences in frequency of transposable elements presence in Botrytis cinerea populations from several hosts in Greece, Plant Disease, vol.96, pp.1286-1290, 2012.

S. P. Simwami, K. Khayhan, D. A. Henk, D. M. Aanensen, T. Boekhout et al., , 2011.

E. H. Stukenbrock and B. A. Mcdonald, The origins of plant pathogens in agroecosystems, Annual Review of Phytopathology, vol.46, pp.75-100, 2008.

J. W. Taylor and M. C. Fisher, Fungal multilocus sequence typing -it's not just for bacteria, Current Opinion in Microbiology, vol.6, pp.351-356, 2003.

J. W. Taylor, E. Turner, J. P. Townsend, J. R. Dettman, and D. Jacobson, Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi, Philosophical Transactions of the Royal Society B-Biological Sciences, vol.361, pp.1947-1963, 2006.

G. The-angiosperm-phylogeny, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III, Botanical Journal of the Linnean Society, vol.161, pp.105-121, 2009.

A. Walker, A. Gautier, J. Confais, D. Martinho, M. Viaud et al., Botrytis pseudocinerea, a new cryptic species causing gray mold in French vineyards in sympatry with Botrytis cinerea, Phytopathology, vol.101, pp.1433-1445, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01019801

P. D. Williams, Darwinian interventions: taming pathogens through evolutionary ecology, Trends in Parasitology, vol.26, pp.83-92, 2010.

B. Williamson, B. Tudzynsk, P. Tudzynski, and J. A. Van-kan, Botrytis cinerea: the cause of grey mould disease, Molecular Plant Pathology, vol.8, pp.561-580, 2007.

J. S. Zhan, B. A. Mcdonald, P. Gladieux, V. Decognet, M. Fermaud et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Environmental Microbiology, vol.20, issue.4, pp.1261-1274, 2011.

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

, Table 1: Populations of Botrytis cinerea collected in three French regions, on various host plants and in different cropping systems, 2005.

P. Gladieux, V. Decognet, M. Fermaud, J. Confais, J. Roudet et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Environmental Microbiology, vol.17, issue.4, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

P. Gladieux, V. Decognet, M. Fermaud, J. Confais, J. Roudet et al., Locations from the Northeast,Southwest and Southeast of France are shown in blue, purple, and green, respectively. Version postprint Comment citer ce document, Map of Botrytis cinerea populations collected from three French regions on various host plants and in various cropping conditions, on four dates between, vol.17, pp.1261-1274, 2005.

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

P. Gladieux, V. Decognet, M. Fermaud, J. Confais, J. Roudet et al., Individuals were organized into 20 groups (5 genetic clusters of origin x 4 sampling dates). The colours represent cluster membership of the individuals: red: SOLANUM clusters, purple: RUBUS clusters, green: VITIS clusters (VITIS1: dark green, VITIS2: medium green, VITIS3: light green). ce document, Principal components analysis (PCA) of the 3546 B. cinerea isolates collected between 2005 and 2007 on several hosts, vol.3, pp.1261-1274, 2015.

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

P. Gladieux, V. Decognet, M. Fermaud, J. Confais, J. Roudet et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Diversity measured in the five B. cinerea clusters and for the four sampling dates. Colors and marks indicate clusters: INDOOR (red), vol.4, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

A. S. Walker, P. Gladieux, V. Decognet, M. Fermaud, J. Confais et al., Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management, Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Manuscrit d'auteur / Author manuscript Version définitive du manuscrit publié dans / Final version of the manuscript, vol.17, pp.1261-1274, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02638009

, Clonal fraction, multilocus linkage disequilibrium, and numbers of significantly linked pairs of loci in the five clusters identified by clustering analyses. Clusters: INDOOR (red square), RUBUS (purple square), VITIS1 (green triangles), VITIS2 (green circles) and VITIS3 (green diamonds). The clonal fraction represents the proportion of different multilocus genotypes, Figure, vol.5