T. Belete and N. Boyraz, Critical review on apple scab (Venturia inaequalis) biology, epidemiology, economic importance, management and defense mechanisms to the causal agent, Journal of Plant Physiology and Pathology, vol.5, issue.2, 2017.

W. Bleeker, U. Schmitz, and M. Ristow, Interspecific hybridisation between alien and native plant species in Germany and its consequences for native biodiversity, Biological Conservation, vol.137, issue.2, pp.248-253, 2007.

V. Caffier, P. Lasserre-zuber, M. Giraud, M. Lascostes, R. Stievenard et al.,

L. Cam and B. , Erosion of quantitative host resistance in the apple × Venturia inaequalis pathosystem. Infection, Genetics and Evolution, vol.27, pp.481-489, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01210000

C. Christe, K. N. Stölting, M. Paris, C. Fra?sse, N. Bierne et al., Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow, Molecular Ecology, vol.26, issue.1, pp.59-76, 2017.

, Accepted Article This article is protected by copyright. All rights reserved

A. J. Coffman, P. H. Hsieh, S. Gravel, and R. N. Gutenkunst, Computationally efficient composite likelihood statistics for demographic inference, Molecular Biology and Evolution, vol.33, issue.2, pp.591-593, 2015.

A. Cornille, A. Feurtey, U. Gélin, J. Ropars, K. Misvanderbrugge et al., Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples, Evolutionary Applications, vol.8, issue.4, pp.373-384, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02328871

A. Cornille, T. Giraud, M. J. Smulders, I. Roldán-ruiz, and P. Gladieux, The domestication and evolutionary ecology of apples, Trends in Genetics, vol.30, issue.2, pp.57-65, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02328898

A. Cornille, P. Gladieux, and T. Giraud, Crop-to-wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple, Evolutionary Applications, vol.6, issue.5, pp.737-748, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02328919

A. Cornille, P. Gladieux, M. J. Smulders, I. Roldan-ruiz, F. Laurens et al.,

I. Gabrielyan, New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties, PLoS Genetics, vol.8, issue.5, p.1002703, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01209929

D. Croll and A. L. Laine, What the population genetic structures of host and pathogen tell us about disease evolution, New Phytologist, vol.212, issue.3, pp.537-539, 2016.

P. Danecek, A. Auton, G. Abecasis, C. A. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2158, 2011.

J. R. Depotter, M. F. Seidl, T. A. Wood, and B. P. Thomma, Interspecific hybridization impacts host range and pathogenicity of filamentous microbes, Current Opinion in Microbiology, vol.32, pp.7-13, 2016.

S. Dray and A. B. Dufour, The ade4 package: implementing the duality diagram for ecologists, Journal of Statistical Software, vol.22, issue.4, pp.1-20, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434575

, Accepted Article This article is protected by copyright. All rights reserved

D. A. Earl and B. M. Vonholdt, STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conservation Genetics Resources, vol.4, issue.2, pp.359-361, 2012.

A. Eastwood, G. Lazkov, and A. Newton, The red list of trees of Central Asia. Fauna and Flora International, 2009.

N. C. Ellstrand, P. Meirmans, J. Rong, D. Bartsch, A. Ghosh et al.,

J. L. Strasburg, Introgression of crop alleles into wild or weedy populations, Evolution, and Systematics, vol.44, pp.325-345, 2013.

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.

D. Falush, M. Stephens, and J. K. Pritchard, Inference of population structure: Extensions to linked loci and correlated allele frequencies, Genetics, vol.164, issue.8, pp.1567-1587, 2003.

A. Feurtey, A. Cornille, J. A. Shykoff, A. Snirc, and T. Giraud, Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe, Evolutionary Applications, vol.10, issue.2, pp.180-188, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02328839

P. L. Forsline, H. S. Aldwinckle, E. E. Dickson, J. J. Luby, and S. C. Hokanson, , 2003.

, Collection, maintenance, characterization, and utilization of wild apples of Central Asia, Horticultural Reviews, vol.29, pp.1-62

P. Gladieux, V. Caffier, M. Devaux, and B. Le-cam, Host-specific differentiation among populations of Venturia inaequalis causing scab on apple, pyracantha and loquat, Fungal Genetics and Biology, vol.47, issue.6, pp.511-521, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02668199

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, issue.1, p.1455, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02669128

P. Gladieux, X. G. Zhang, I. Róldan-ruiz, V. Caffier, T. Leroy et al.,

L. Cam and B. , Evolution of the population structure of Venturia inaequalis, the apple scab fungus, Accepted Article This article is protected by copyright. All rights reserved associated with the domestication of its host, Molecular Ecology, vol.19, issue.4, pp.658-674, 2010.

Z. Gompert and C. Buerkle, INTROGRESS: a software package for mapping components of isolation in hybrids, Molecular Ecology Resources, vol.10, issue.2, pp.378-384, 2010.

R. N. Gutenkunst, R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data, PLoS Genetics, vol.5, issue.10, p.1000695, 2009.

S. A. Harris, J. P. Robinson, and B. E. Juniper, Genetic clues to the origin of the apple, Trends in Genetics, vol.18, issue.8, pp.426-430, 2002.

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, issue.14, pp.1801-1806, 2007.

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

, Bioinformatics, vol.24, pp.1403-1405

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, p.94, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00539267

L. Cam, B. Parisi, L. Arene, and L. , Evidence of two formae speciales in Venturia inaequalis, responsible for apple and pyracantha scab, Phytopathology, vol.92, pp.314-320, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02675372

L. Cam, B. Sargent, D. Gouzy, J. Amselem, J. Bellanger et al.,

C. Lemaire, Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata, Genes, Genomes, Genetics, vol.3, issue.8, pp.2405-2414, 2019.

L. Van, A. Gladieux, P. Lemaire, C. Cornille, A. Giraud et al.,

L. Cam and B. , Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host, Evolutionary Applications, vol.5, issue.7, pp.694-704, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01209918

C. Lemaire, M. De-gracia, T. Leroy, M. Michalecka, H. Lindhard-pedersen et al., Emergence of new virulent populations of apple scab from nonagricultural disease reservoirs, New Phytologist, vol.209, issue.3, pp.1220-1229, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01392705

T. Leroy, V. Caffier, J. M. Celton, N. Anger, C. E. Durel et al., , 2016.

, When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis, New Phytologist, vol.210, issue.4, pp.1443-1452

T. Leroy, C. Lemaire, F. Dunemann, and B. Le-cam, The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species, BMC Evolutionary Biology, vol.13, issue.1, p.64, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01209912

W. E. Machardy, Apple scab: biology, epidemiology, and management, 1996.

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Research, vol.27, pp.209-229, 1967.

S. V. Nikiforova, D. Cavalieri, R. Velasco, and V. Goremykin, Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line, Molecular Biology and Evolution, vol.30, issue.8, pp.1751-1760, 2013.

M. Y. Omasheva, H. Flachowsky, N. A. Ryabushkina, A. S. Pozharskiy, and N. N. Galiakparov,

M. V. Hanke, To what extent do wild apples in Kazakhstan retain their genetic integrity?, Tree Genetics & Genomes, vol.13, issue.3, p.52, 2017.

E. Paradis and K. Schliep, ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R, Bioinformatics, vol.35, issue.3, pp.526-528, 2019.
URL : https://hal.archives-ouvertes.fr/ird-01920132

,

S. Raffaele and S. Kamoun, Genome evolution in filamentous plant pathogens: why bigger can be better, Nature Reviews Microbiology, vol.10, pp.417-430, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01608755

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2018.

S. Reim, A. Proft, S. Heinz, F. Lochschmidt, M. Höfer et al., Pollen movement in a Malus sylvestris population and conclusions for conservation measures, Plant Genetic Resources, vol.15, issue.1, pp.12-20, 2017.

J. M. Rhymer and D. Simberloff, Extinction by hybridization and introgression, Annual Review of Ecology and Systematics, vol.27, issue.1, pp.83-109, 1996.

F. Rousset, Genepop'007: a complete re-implementation of the genepop software for Windows and Linux, Molecular Ecology Resources, vol.8, pp.103-106, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00366752

D. Saleh, J. Milazzo, H. Adreit, E. Fournier, and D. Tharreau, South-East Asia is the center of origin, diversity and dispersion of the rice blast fungus, Magnaporthe oryzae, New Phytologist, vol.201, issue.4, pp.1440-1456, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02635448

R. A. Spotts and D. C. Ferree, Photosynthesis, transpiration, and water potential of apple leaves infected by Venturia inaequalis, Phytopathology, vol.69, issue.7, pp.717-719, 1979.

E. H. Stukenbrock, F. B. Christiansen, T. T. Hansen, J. Y. Dutheil, and M. H. Schierup, , 2012.

, Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species, Proceedings of the National Academy of Sciences, vol.109, pp.10954-10959

E. H. Stukenbrock, Hybridization speeds up the emergence and evolution of a new pathogen species, Nature Genetics, vol.48, issue.2, p.113, 2016.

M. Tine, H. Kuhl, P. A. Gagnaire, B. Louro, E. Desmarais et al., European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation, Nature Communications, vol.5, p.5770, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01922671

M. Todesco, M. A. Pascual, G. L. Owens, K. L. Ostevik, B. T. Moyers et al.,

L. H. Rieseberg, Hybridization and extinction, Evolutionary Applications, vol.9, issue.7, pp.892-908, 2016.

, Accepted Article This article is protected by copyright. All rights reserved

A. V. Vanden-broeck, M. Villar, E. Van-bockstaele, and J. Van-slycken, Natural hybridization between cultivated poplars and their wild relatives: evidence and consequences for native poplar populations, Annals of Forest Science, vol.62, issue.7, pp.601-613, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00883933

N. I. Vavilov, The role of Central Asia in the origin of cultivated plants, Bulletin of Applied Botany Genetics and Plant Breeding, vol.26, issue.3, pp.3-44, 1931.

R. Velasco, A. Zharkikh, J. Affourtit, A. Dhingra, A. Cestaro et al., The genome of the domesticated apple (Malus×domestica Borkh.), Nature Genetics, vol.42, issue.10, p.833, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02666876

H. Wang, F. G. Vieira, J. E. Crawford, C. Chu, and R. Nielsen, Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice, Genome Research, vol.27, issue.6, pp.1029-1038, 2017.

Y. Wang, C. D. Arenas, D. M. Stoebel, K. Flynn, E. Knapp et al.,

T. F. Cooper, Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness, Proceedings of the National Academy of Sciences, vol.113, issue.18, pp.5047-5052, 2016.

B. S. Weir and C. C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, vol.38, pp.1358-70, 1984.

D. E. Wolf, N. Takebayashi, and L. H. Rieseberg, Predicting the risk of extinction through hybridization, Conservation Biology, vol.15, issue.4, pp.1039-1053, 2001.

M. A. Zeder, E. Emshwiller, B. D. Smith, and D. G. Bradley, Documenting domestication: the intersection of genetics and archaeology, Trends in Genetics, vol.22, issue.3, pp.139-155, 2006.