D. Foundation, Institut de France) to TG, and a Marie Curie European grant (PRESTIGE-2016-4-717 0013) to FEH. PT and CG thank the Région Hauts-de-France

, Enseignement Supérieur et de la Recherche (CPER Climibio), and the European Fund for 719 Regional Economic Development for their financial support

F. E. Hartmann, A. Snirc, A. Cornille, C. Godé, P. Touzet et al., , vol.723

L. Prieur, S. Shykoff, J. Giraud, T. Hartmann, F. E. Snirc et al., Genotype data from : Congruent population genetic 724 structures and divergence histories in anther-smut fungi and their host plants Silene italica and 725 the S. nutans species complex, vol.726, 2020.

L. Prieur, S. Shykoff, J. Giraud, and T. , Whole genome sequencing raw data of Microbotryum 728 fungi infecting Silene nutans and S. italica. NCBI Sequence Read Archive (SRA), 2020.

J. L. Abbate, P. Gladieux, M. E. Hood, D. M. De-vienne, J. Antonovics et al., , p.733

T. , Co-occurrence among three divergent plant-castrating fungi in the same Silene 734 host species, Molecular Ecology, vol.27, issue.16, pp.3357-3370, 2018.

J. Antonovics, M. E. Hood, and J. Partain, The ecology and genetics of a host shift: 736 Microbotryum as a model system, The American Naturalist, vol.160, issue.S4, pp.40-53, 2002.

H. Badouin, P. Gladieux, J. Gouzy, S. Siguenza, G. Aguileta et al., , 2017.

, Widespread selective sweeps throughout the genome of model plant pathogenic fungi and 740 identification of effector candidates, Molecular Ecology, vol.26, issue.7, pp.2041-2062

B. Barrès, F. Halkett, C. Dutech, A. Andrieux, J. Pinon et al., Genetic structure 743 of the poplar rust fungus Melampsora larici-populina: Evidence for isolation by distance 744 in Europe and recent founder effects overseas, Infection, Genetics and Evolution, vol.8, issue.5, pp.745-577, 2008.

L. G. Barrett, P. H. Thrall, J. J. Burdon, and C. C. Linde, Life history determines genetic 747 structure and evolutionary potential of host-parasite interactions, Trends in Ecology & 748 Evolution, vol.23, issue.12, pp.678-685, 2008.

R. Becker, A. Wilks, R. Brownrigg, T. Minka, and D. Deckmyn, maps: draw 750 geographical maps, 2017.

G. Bernasconi, J. Antonovics, A. Biere, D. Charlesworth, L. F. Delph et al., , p.753

A. , Silene as a model system in ecology and evolution, Heredity, vol.103, issue.1, 2009.

S. Branco, H. Badouin, . Rodríguez-de-la, R. C. Vega, J. Gouzy et al., , p.756

T. Giraud, Evolutionary strata on young mating-type chromosomes despite the 757 lack of sexual antagonism, Proceedings of the National Academy of Sciences, vol.114, pp.758-7067, 2017.

S. Branco, F. Carpentier, . Rodríguez-de-la, R. C. Vega, H. Badouin et al., , p.760

T. Giraud, Multiple convergent supergene evolution events in mating-type 761 chromosomes, Nature Communications, vol.9, issue.1, 2000.

L. Breiman, Random forests, Machine Learning, vol.45, pp.5-32, 2001.

E. Bucheli, B. Gautschi, and J. A. Shykoff, Host-specific differentiation in the anther 765 smut fungus Microbotryum violaceum as revealed by microsatellites, J. EVOL. BIOL, p.11, 2000.

C. C. Chang, C. C. Chow, L. C. Tellier, S. Vattikuti, S. M. Purcell et al., , 2015.

, Second-generation PLINK: rising to the challenge of larger and richer datasets

. Gigascience, , p.4

A. Cornille, P. Gladieux, M. J. Smulders, I. Roldán-ruiz, F. Laurens et al., , p.770

T. Giraud, New insight into the history of domesticated apple: Secondary 771 contribution of the European wild apple to the genome of cultivated varieties, PLOS 772 Genetics, vol.8, issue.5, p.1002703, 2012.

C. D. Criscione, R. Poulin, and M. S. Blouin, Molecular ecology of parasites: elucidating 774 ecological and microevolutionary processes, Molecular Ecology, vol.14, issue.8, pp.2247-2257, 2005.

D. Croll and A. Laine, What the population genetic structures of host and pathogen tell 777 us about disease evolution, New Phytologist, vol.212, issue.3, pp.537-539, 2016.

D. M. De-vienne, M. E. Hood, and T. Giraud, Phylogenetic determinants of potential host 779 shifts in fungal pathogens, Journal of Evolutionary Biology, vol.22, issue.12, pp.2532-2541, 2009.

D. M. De-vienne, G. Refrégier, M. E. Hood, A. Guigue, B. Devier et al., Hybrid sterility and inviability in the parasitic fungal species complex, p.783, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01800066

D. M. Microbotryum-;-de-vienne, G. Refrégier, M. López-villavicencio, A. Tellier, M. E. Hood et al., Cospeciation vs host-shift speciation: methods for testing, evidence from natural 787 associations and relation to coevolution, Journal of Evolutionary Biology, vol.22, issue.4, pp.347-385, 2013.

F. Delmotte, E. Bucheli, and J. A. Shykoff, Host and parasite population structure in a 790 natural plant-pathogen system, Heredity, vol.82, issue.3, pp.300-308, 1999.

S. Dray and A. Dufour, The ade4 Package: Implementing the Duality Diagram for 793, 2007.

. Ecologists, Journal of Statistical Software, vol.22, issue.1, pp.1-20

M. F. Dybdahl and C. M. Lively, The geography of coevolution: comparative population 795 structures for a snail and its trematode parasite, Evolution, vol.50, issue.6, pp.2264-2275, 1996.

J. Enjalbert, X. Duan, M. Leconte, M. S. Hovmøller, and C. De-vallavieille-pope, , 2005.

, Genetic evidence of local adaptation of wheat yellow rust (Puccinia striiformis f. sp. 799 tritici) within France, Molecular Ecology, vol.14, issue.7, pp.2065-2073

A. Estoup, P. Jarne, and J. Cornuet, Homoplasy and mutation model at microsatellite 802 loci and their consequences for population genetics analysis, Molecular Ecology, vol.11, issue.9, pp.803-1591, 2002.

A. Estoup, L. Raynal, P. Verdu, and J. Marin, Model choice using Approximate 805, 2018.

, Bayesian Computation and Random Forests: analyses based on model grouping to make 806 inferences about the genetic history of Pygmy human populations, Journal de la Société, vol.807

S. Française-de, Special Issue on Models and Inference in Population Genetics, vol.808, p.159

L. Excoffier and M. Foll, fastsimcoal: a continuous-time coalescent simulator of genomic 810 diversity under arbitrarily complex evolutionary scenarios, Bioinformatics, vol.27, issue.9, pp.1332-811, 2011.

L. Excoffier and H. E. Lischer, Arlequin suite ver 3.5: a new series of programs to 813 perform population genetics analyses under Linux and Windows, Molecular Ecology, vol.814, issue.3, pp.564-567, 2010.

A. Feurtey, P. Gladieux, M. E. Hood, A. Snirc, A. Cornille et al., Strong phylogeographic co-structure between the anther-smut fungus and its 817 white campion host, New Phytologist, vol.212, issue.3, pp.668-679, 2016.

A. Feurtey and E. H. Stukenbrock, Interspecific gene exchange as a driver of adaptive 819 evolution in fungi, Annual Review of Microbiology, vol.72, issue.1, pp.377-398, 2018.

M. C. Fisher, N. A. Gow, and S. J. Gurr, Tackling emerging fungal threats to animal 822 health, food security and ecosystem resilience, Phil. Trans. R. Soc. B, vol.371, p.20160332, 1709.

T. M. Fortuna, A. Snirc, H. Badouin, J. Gouzy, S. Siguenza et al., Polymorphic microsatellite markers for the tetrapolar anther-smut fungus 826 Microbotryum saponariae based on genome sequencing, PLOS ONE, vol.11, issue.11, p.825, 2016.

E. Fournier and T. Giraud, Sympatric genetic differentiation of a generalist pathogenic 829 fungus, Botrytis cinerea, on two different host plants, grapevine and bramble, Journal of 830 Evolutionary Biology, vol.21, issue.1, pp.122-132, 2008.

S. Gandon and Y. Michalakis, Local adaptation, evolutionary potential and host-parasite 832 coevolution: interactions between migration, mutation, population size and generation 833 time, Journal of Evolutionary Biology, vol.15, issue.3, pp.451-462, 2002.

S. Gandon, Y. Capowiez, Y. Dubois, Y. Michalakis, and I. Olivieri, Local adaptation 836 and gene-for-gene coevolution in a metapopulation model, Proceedings of the Royal 837 Society of London. Series B: Biological Sciences, vol.263, pp.1003-1009, 1373.

H. Gerritsen, , 2013.

. Mapplots,

A. K. Gibson, M. E. Hood, and T. Giraud, Sibling competition arena: selfing and a 842 competition arena can combine to constitute a barrier to gene flow in sympatry, Evolution, vol.843, issue.6, pp.1917-1930, 2012.

T. Giraud, Patterns of within population dispersal and mating of the fungus 845, 2004.

, Microbotryum violaceum parasitising the plant Silene latifolia, Heredity, vol.93, issue.6, pp.559-565

T. Giraud and S. Gourbière, The tempo and modes of evolution of reproductive isolation 848 in fungi, Heredity, vol.109, issue.4, pp.204-214, 2012.

T. Giraud, R. Yockteng, S. Marthey, H. Chiapello, O. Jonot et al., , p.850

C. Dossat, Isolation of 60 polymorphic microsatellite loci in EST libraries of four 851 sibling species of the phytopathogenic fungal complex Microbotryum, Molecular Ecology, vol.852, issue.2, pp.387-392, 2008.

P. Gladieux, B. Devier, G. Aguileta, C. Cruaud, and T. Giraud, Purifying selection after 854 episodes of recurrent adaptive diversification in fungal pathogens. Infection, Genetics and 855 Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious 856 Diseases, vol.17, pp.123-131, 2013.

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: 859 allopatric divergence and introgression through secondary contact, Molecular Biology, vol.860, issue.1, pp.459-471, 2011.

C. Godé, P. Touzet, H. Martin, E. Lahiani, L. F. Delph et al., 862 Characterization of 24 polymorphic microsatellite markers for Silene nutans, a 863 gynodioecious-gynomonoecious species, and cross-species amplification in other Silene 864 species, Conservation Genetics Resources, vol.6, issue.4, pp.915-918, 2014.

M. S. Hafner and R. D. Page, Molecular phylogenies and host-parasite cospeciation: 867 gophers and lice as a model system, Philosophical Transactions of the Royal Society, p.868, 1995.

, London. Series B: Biological Sciences, vol.349, pp.77-83, 1327.

F. E. Hartmann, R. C. Vega, J. Brandenburg, F. Carpentier, and T. Giraud, Gene presence-absence polymorphism in castrating anther-smut fungi: recent 871 gene gains and phylogeographic structure, Genome Biology and Evolution, vol.870, issue.5, pp.1298-872, 2018.

F. E. Hartmann, R. C. Vega, F. Carpentier, P. Gladieux, A. Cornille et al., , p.874

M. E. Giraud and T. , Understanding adaptation, coevolution, host specialization, 875 and mating system in castrating anther-smut fungi by combining population and 876 comparative genomics, Annual Review of Phytopathology, vol.57, issue.1, pp.431-457, 2019.

M. E. Hood, J. Antonovics, M. Wolf, Z. L. Stern, T. Giraud et al., Sympatry 879 and interference of divergent Microbotryum pathogen species, Ecology and Evolution, vol.880, issue.0, p.0, 2019.

D. H. Huson, SplitsTree: analyzing and visualizing evolutionary data, Bioinformatics, vol.882, issue.1, pp.68-73, 1998.

D. H. Huson and D. Bryant, Application of phylogenetic networks in evolutionary studies, Molecular Biology and Evolution, vol.884, issue.2, pp.254-267, 2006.

M. Jakobsson and N. A. Rosenberg, CLUMPP: a cluster matching and permutation 886 program for dealing with label switching and multimodality in analysis of population 887 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, issue.11, pp.1403-1405

T. Jombart and I. Ahmed, adegenet 1.3-1: new tools for the analysis of genome-wide SNP 891 data, Bioinformatics, vol.27, issue.21, pp.3070-3071, 2011.

A. Jürgens, T. Witt, and G. Gottsberger, Reproduction and pollination in central European 893 populations of Silene and Saponaria species, Botanica Acta, vol.109, issue.4, pp.316-324, 1996.

O. Kaltz, S. Gandon, Y. Michalakis, and J. A. Shykoff, Local maladaptation in the 896 anther-smut fungus Microbotryum violaceum to its host plant Silene latifolia: evidence 897 from a cross-inoculation experiment. Evolution, International Journal of Organic, vol.898, issue.2, pp.395-407, 1999.

K. Keenan, P. Mcginnity, T. F. Cross, W. W. Crozier, and P. A. Prodöhl, diveRsity: An 900 R package for the estimation and exploration of population genetics parameters and their 901 associated errors, Methods in Ecology and Evolution, pp.782-788, 2016.

M. Kemler, M. Göker, F. Oberwinkler, and D. Begerow, Implications of molecular 904 characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes), 2006.

, BMC Evolutionary Biology, vol.6, p.35

S. Kephart, R. J. Reynolds, M. T. Rutter, C. B. Fenster, and M. R. Dudash, Pollination 907 and seed predation by moths on Silene and allied Caryophyllaceae: evaluating a model 908 system to study the evolution of mutualisms, New Phytologist, vol.169, issue.4, pp.667-680, 2006.

L. Lafuma and S. Maurice, Silene 911 italica (Caryophyllaceae), with attention to the gynomonoecious phenotype, Biological 912 Journal of the Linnean Society, vol.87, issue.4, pp.583-591, 2006.

E. Lahiani, M. Dufaÿ, V. Castric, S. Le-cadre, D. Charlesworth et al., , p.914

P. , Disentangling the effects of mating systems and mutation rates on cytoplamic 915 diversity in gynodioecious Silene nutans and dioecious Silene otites, Heredity, vol.111, issue.2, pp.916-157, 2013.

A. Laine, Spatial scale of local adaptation in a plant-pathogen metapopulation, Journal 918 of Evolutionary Biology, vol.18, issue.4, pp.930-938, 2005.

A. Laine, Temperature-mediated patterns of local adaptation in a natural plant-920 pathogen metapopulation, Ecology Letters, vol.11, issue.4, pp.327-337, 2008.

A. Laine, B. Barrès, E. Numminen, and J. P. Siren, Variable opportunities for 923 outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation, 2019.

. Elife, , vol.8

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memory-efficient 926 alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, 2009.

L. Gac, M. Hood, M. E. Fournier, E. Giraud, and T. , Phylogenetic evidence of host-929 specific cryptic species in the anther smut fungus. Evolution; International Journal of 930 Organic Evolution, vol.61, pp.15-26, 2007.

L. Gac, M. Hood, M. E. Giraud, and T. , Evolution of reproductive isolation within a 932 parasitic fungal species complex, Evolution, issue.7, pp.1781-1787, 2007.

C. C. Linde, J. Zhan, and B. A. Mcdonald, Population structure of Mycosphaerella 935 graminicola: from lesions to continents, Phytopathology, vol.92, issue.9, pp.946-955, 2002.

S. Liu, A. Cornille, S. Decroocq, D. Tricon, A. Chague et al., From hybrid speciation of wild Armeniaca species to multiple domestication 939 events in Eastern Asia: the complex evolutionary history of apricots, p.938, 2019.

M. López-villavicencio, O. Jonot, A. Coantic, M. E. Hood, J. Enjalbert et al., , 2007.

, Multiple infections by the anther smut pathogen are frequent and involve related strains, 942 PLOS Pathogens, vol.3, issue.11

M. Lutz, M. Göker, M. Piatek, M. Kemler, D. Begerow et al., Anther 944 smuts of Caryophyllaceae: Molecular characters indicate host-dependent species 945 delimitation, Mycological Progress, vol.4, issue.3, pp.225-238, 2005.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, 2011.

, EMBnet.Journal, vol.17, issue.1, pp.10-12

H. Martin, P. Touzet, M. Dufay, C. Godé, E. Schmitt et al., , 2017.

, Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive 950 isolation in allopatry, Evolution, vol.71, issue.6, pp.1519-1531

H. Martin, P. Touzet, F. Van-rossum, D. Delalande, and J. Arnaud, Phylogeographic 952 pattern of range expansion provides evidence for cryptic species lineages in Silene nutans 953 in Western Europe, Heredity, vol.116, issue.3, pp.286-294, 2016.

K. D. Mccoy, T. Boulinier, and C. Tirard, Comparative host-parasite population 955 structures: disentangling prospecting and dispersal in the black-legged kittiwake Rissa 956 tridactyla, Molecular Ecology, vol.14, issue.9, pp.2825-2838, 2005.

B. A. Mcdonald and E. H. Stukenbrock, Rapid emergence of pathogens in agro-959 ecosystems: global threats to agricultural sustainability and food security, Phil. Trans. R, 2016.

. Soc, , vol.371, 1709.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., , p.962

M. A. , The Genome Analysis Toolkit: a MapReduce framework for analyzing 963 next-generation DNA sequencing data, Genome Research, vol.20, issue.9, pp.1297-1303, 2010.

Y. Michalakis, A. W. Sheppard, V. Noel, and I. Olivieri, Population structure of a 966 herbivorous insect and its host plant on a microgeographic scale, Evolution, vol.47, issue.5, pp.1611-967, 1993.

Y. Naciri, P. D. Pasquier, M. Lundberg, D. Jeanmonod, and B. Oxelman, A 969 phylogenetic circumscription of Silene sect. Siphonomorpha (Caryophyllaceae) in the 970 Mediterranean Basin, Taxon, vol.66, issue.1, pp.91-108, 2017.

M. Nei, Genetic distance between populations, The American Naturalist, vol.106, issue.949, p.292, 1972.

C. M. Nieberding, M. Durette-desset, A. Vanderpoorten, J. C. Casanova, and A. Ribas, , p.974

V. Deffontaine and J. R. Michaux, Geography and host biogeography matter for 975 understanding the phylogeography of a parasite, Molecular Phylogenetics and Evolution, vol.976, issue.2, pp.538-554, 2008.

C. M. Nieberding and I. Olivieri, Parasites: proxies for host genealogy and ecology? 978, Trends in Ecology & Evolution, vol.22, issue.3, pp.156-165, 2007.

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of Phylogenetics and Evolution in 980 R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.

E. Petit, C. Silver, A. Cornille, P. Gladieux, L. Rosenthal et al., , 2017.

, Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts, 983 Molecular Ecology, vol.26, issue.7, pp.1877-1890

S. Piry, G. Luikart, and J. M. Cornuet, BOTTLENECK: A computer program for detecting 985 recent reductions in the effective population size using allele frequency data, vol.90, pp.502-986, 1999.

R. Poulin, Parasite biodiversity, 2005.

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using 989 multilocus genotype data, Genetics, vol.155, issue.2, pp.945-959, 2000.

P. Pudlo, J. Marin, A. Estoup, J. Cornuet, M. Gautier et al., Reliable 991 ABC model choice via random forests, Bioinformatics, vol.32, issue.6, pp.859-866, 2016.

S. Purcell, B. Neale, K. Todd-brown, L. Thomas, M. A. Ferreira et al.,

C. , PLINK: A tool set for whole-genome association and population-based linkage 995 analyses, The American Journal of Human Genetics, vol.81, issue.3, pp.559-575, 2007.

J. Rameau, D. Mansion, and G. Dumé, Flore forestière française: Plaines et collines. 998 Forêt privée française, 1989.

J. Rameau, D. Mansion, and G. Dumé, Flore forestière française: guide écologique 1000 illustré. Région méditerranéenne, 2008.

L. Raynal, J. Marin, P. Pudlo, M. Ribatet, C. P. Robert et al., ABC random 1002 forests for Bayesian parameter inference, Bioinformatics, vol.35, issue.10, pp.1720-1728, 2019.

G. Refrégier, M. Le-gac, F. Jabbour, A. Widmer, J. A. Shykoff et al., Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: 1006 prevalence of host shifts and importance of delimiting parasite species for inferring 1007 cospeciation, BMC Evolutionary Biology, vol.8, p.100, 2008.

D. Saleh, J. Milazzo, H. Adreit, E. Fournier, and D. Tharreau, South-East Asia is the 1009 center of origin, diversity and dispersion of the rice blast fungus, Magnaporthe oryzae, New Phytologist, vol.201, issue.4, pp.1440-1456, 1010.

E. H. Stukenbrock, S. Banke, and B. A. Mcdonald, Global migration patterns in the 1012 fungal wheat pathogen Phaeosphaeria nodorum, Molecular Ecology, vol.15, issue.10, pp.2895-2904, 1013.

E. H. Stukenbrock and B. A. Mcdonald, The origins of plant pathogens in agro-1015 ecosystems, Annual Review of Phytopathology, vol.46, issue.1, pp.75-100, 2008.

Z. A. Szpiech, M. Jakobsson, and N. A. Rosenberg, ADZE: a rarefaction approach for 1018 counting alleles private to combinations of populations, Bioinformatics, vol.24, issue.21, pp.2498-1019, 2008.

D. R. Taylor and S. R. Keller, Historical range expansion determines the phylogenetic 1021 diversity introduced during contemporary species invasion, Evolution, vol.61, issue.2, 2007.

A. Tellier, D. M. De-vienne, T. Giraud, M. E. Hood, and G. Refrégier, Theory and 1024 examples of reciprocal influence between hosts and pathogens, from short-term to long 1025 term interactions: coevolution, cospeciation and pathogen speciation following host shifts, 2010.

, In Immunology and Immune System Disorders. Host-Pathogen Interactions: Genetics, p.1027

, Immunology and Physiology, pp.37-77

M. Thines, An evolutionary framework for host shifts -jumping ships for survival, Phytologist, vol.224, issue.2, pp.605-617, 1029.

J. N. Thompson, The geographic mosaic of coevolution, 2005.

P. Thrall, A. Biere, and J. Antonovics, Plant life-history and disease susceptibility -the 1032 occurrence of Ustilago-Violacea on different species within the Caryophyllaceae, Journal 1033 of Ecology, vol.81, issue.3, pp.489-498, 1993.

J. Tison and B. De-foucault, Flora gallica: flore de France (Biotope), 2014.

S. S. Toh and M. H. Perlin, Resurgence of less-studied smut fungi as models of 1036 phytopathogenesis in the omics age, Phytopathology, vol.106, issue.11, pp.1244-1254, 2016.

Y. E. Tsai and P. S. Manos, Host density drives the postglacial migration of the tree 1039 parasite, Epifagus virginiana, Proceedings of the National Academy of Sciences, vol.107, issue.39, pp.1040-17035, 2010.

T. Tutin, V. Heywood, N. Burges, D. Valentine, S. Walters et al., Flora 1042 Europaea. Royaume-Uni, 2001.

F. Van-rossum, H. Martin, S. Le-cadre, B. Brachi, M. J. Christenhusz et al., Phylogeography of a widely distributed species reveals a cryptic assemblage of 1045 distinct genetic lineages needing separate conservation strategies. Perspectives in Plant 1046 Ecology, Evolution and Systematics, vol.35, pp.44-51, 2018.

E. Vercken, M. C. Fontaine, P. Gladieux, M. E. Hood, O. Jonot et al., Glacial 1048 refugia in pathogens: European genetic structure of anther smut pathogens on Silene 1049 latifolia and Silene dioica, PLOS Pathogens, vol.6, issue.12, p.1001229, 2010.

D. Wegmann, C. Leuenberger, S. Neuenschwander, and L. Excoffier, ABCtoolbox: a 1052 versatile toolkit for approximate Bayesian computations, BMC Bioinformatics, vol.11, issue.1, 2010.

H. Wickham, ggplot2: elegant graphics for data analysis, 2009.

D. J. Wilson, D. Falush, and G. Mcvean, Germs, genomes and genealogies, p.1057, 2005.

, Ecology & Evolution, vol.20, issue.1, pp.39-45

N. D. Wolfe, C. P. Dunavan, and J. Diamond, Origins of major human infectious diseases, Nature, vol.447, issue.7142, pp.279-283, 1059.

P. L. Zaffarano, B. A. Mcdonald, and C. C. Linde, Rapid speciation following recent host 1061 shifts in the plant pathogenic fungus Rhynchosporium, Evolution, vol.62, issue.6, pp.1418-1436, 2008.

, We deposited the genome 1069 1014_3 1322_HAM 1322_LEFF1 1322_LEFF2 1322_LEFF3 1322_NAJ1 1322_NAJ2 1322_NAJ3 1322_NAJ4 1322_OLL3 1322_OLL4 1322_TOMB2 1409_1 1409_6 1409_7 1437 1438 1470 1472_1_1 1472_1_2 1472_2 1472_3 1532 303_01 303_03 436_1 705_4 705 1135_1 1135_2 1135_4 1251_A1 1395_1 1395_2 1395_3 1396_1 1396_3 1396_4 1397_3 1397_6 1397_9 1398_3 1398_4 1399_1 1399_2 1435 1466_3 1466_6 1466_8 1467_1

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