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

I. M. Parker and G. S. Gilbert, The evolutionary ecology of novel plant-pathogen interactions, Evolution, and Systematics, vol.35, pp.675-700, 2004.

M. Palm, Systematics and the impact of invasive fungi on agriculture in the United States, BioScience, vol.51, pp.141-147, 2001.

R. P. Singh, D. P. Hodson, Y. Jin, J. Huerta-espino, and M. G. Kinyua, Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen, CAB Reviews, vol.1, p.54, 2006.

R. P. Singh, H. M. William, J. Huerta-espino, and G. Rosewarne, Wheat rust in Asia: meeting the challenges with old and new technologies, 2004.

M. S. Hovmøller, A. H. Yahyaoui, E. A. Milus, and A. F. Justesen, Rapid global spread of two aggressive strains of a wheat rust fungus, Molecular Ecology, vol.17, pp.3818-3826, 2008.

C. Perrings, M. Williamson, E. Barbier, D. Delfino, and S. Dalmazzone, Biological invasion risks and the public good: an economic perspective, Conservation Ecology, vol.6, 2002.

F. Campbell, The science of risk assessment for phytosanitary regulation and the impact of changing trade regulations, BioScience, vol.51, pp.148-153, 2001.

J. Brown and M. S. Hovmøller, Aerial dispersal of fungi on the global and continental scales and its consequences for plant disease, Science, vol.297, pp.537-541, 2002.

C. De-vallavieille-pope, A. S. Leconte, M. Enjalbert, J. Delos, and M. , Virulence dynamics and regional structuring of Puccinia striiformis f. sp. tritici in France between, Plant Disease, vol.96, pp.131-140, 1984.
URL : https://hal.archives-ouvertes.fr/hal-01000302

M. S. Hovmøller, C. K. Sørensen, S. Walter, and A. F. Justesen, Diversity of Puccinia striiformis on cereals and grasses, Annual Review of Phytopathology, vol.49, pp.197-217, 2011.

M. S. Hovmøller, S. Walter, and A. F. Justesen, Escalating threat of wheat rusts, Science, vol.329, p.369, 2010.

S. Ali, S. Shah, H. Rahman, M. S. Saqib, and M. Ibrahim, Variability in wheat yield under yellow rust pressure in Pakistan, Turkish Journal of Agriculture and Forestry, vol.33, pp.537-546, 2009.

S. Ali, S. Shah, I. H. Khalil, H. Rahman, and K. Maqbool, Partial resistance to yellow rust in introduced winter wheat germplasm at the north of Pakistan, Australian Journal of Crop Science, vol.3, pp.37-43, 2009.

C. R. Wellings, Puccinia striiformis in Australia: A review of the incursion, evolution and adaptation of stripe rust in the period 1979-2006, Australian Journal of Agricultural Research, vol.58, pp.567-575, 2007.

R. W. Stubbs, Stripe rust, The Cereal Rusts, Diseases, Distribution, Epidemiology and Control, pp.61-101, 1985.

R. F. Stubbs and . Mexico, Pathogenicity analysis of yellow (stripe) rust of wheat and its significance in a global context, 1988.

J. A. Kolmer, Tracking wheat rust on a continental scale, Current Opinion in Plant Biology, vol.8, pp.441-449, 2005.

A. F. Justesen, C. J. Ridoutb, and M. S. Hovmøller, The recent history of Puccinia striiformis f.sp. tritici in Denmark as revealed by disease incidence and AFLP markers, Plant Pathology, vol.51, pp.13-23, 2002.

W. Boshoff, Z. A. Pretorius, and B. D. Van-niekerk, Establishment, distribution, and pathogenicity of Puccinia striiformis f.sp. tritici in South Africa, Plant Disease, vol.86, pp.485-492, 2002.

W. Rudorf and M. Job, Untersuchungen bezüglich des Spezialisierung von Puccinia graminis tritici. Puccinia trilicina und Puccinia glumarum tritici, sowie über Resistenz und ihre Vererbung in verschiedenen Kreuzungen, Pflanzenzüchtung, vol.19, pp.333-365, 1934.

X. M. Chen, Epidemiology and control of stripe rust, Canadian Journal of Plant Pathology, vol.27, pp.314-337, 2005.

S. G. Markell and E. A. Milus, Emergence of a Novel Population of Puccinia striiformis f. sp. tritici in Eastern United States, Phytopathology, vol.98, pp.632-639, 2008.

E. A. Milus, K. Kristensen, and M. S. Hovmøller, Evidence for increased aggressiveness in a recent widespread strain of Puccinia striiformis f.sp. tritici causing stripe rust of wheat, Phytopathology, vol.99, pp.89-94, 2009.

J. Enjalbert, X. Duan, M. Leconte, M. S. Hovmøller, and C. De-vallavieille-pope, Genetic evidence of local adaptation of wheat yellow rust (Puccinia striiformis f. sp. tritici) within France, Molecular Ecology, vol.14, pp.2065-2073, 2005.

M. S. Hovmøller, A. F. Justesen, and J. Brown, Clonality and long-distance migration of Puccinia striiformis f.sp. tritici in north-west, Europe. Plant Pathology, vol.51, pp.24-32, 2002.

X. Chen, R. F. Line, and H. Leung, Relationship between virulence variation and DNA polymorphism in Puccinia striiformis, Phytopathology, vol.83, pp.1489-1497, 1993.

M. Mboup, M. Leconte, A. Gautier, A. M. Wan, and W. Chen, Evidence of genetic recombination in wheat yellow rust populations of a Chinese oversummering area, Fungal Genetics and Biology, vol.46, pp.299-307, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02659286

B. Bahri, S. Shah, S. Hussain, M. Leconte, and J. Enjalbert, Genetic diversity of wheat yellow rust population in Pakistan and its relationship with host resistance, Plant Pathology, vol.60, pp.649-660, 2011.

M. S. Hovmøller and A. F. Justesen, Appearance of atypical Puccinia striiformis f. sp. tritici phenotypes in north-western, Europe. Australian Journal of Agricultural Research, vol.58, pp.518-524, 2007.

B. Bahri, M. Leconte, A. Ouffroukh, C. De-vallavieille-pope, and J. Enjalbert, Geographic limits of a clonal population of wheat yellow rust in the Mediterranean region, Molecular Ecology, vol.18, pp.4165-4179, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02658810

S. Ali, M. Leconte, A. Walker, J. Enjalbert, and C. De-vallavieille-pope, Reduction in the sex ability of worldwide clonal populations of Puccinia striiformis f.sp. tritici, Fungal Genetics and Biology, vol.47, pp.828-838, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02661769

J. Enjalbert, X. Duan, G. T. Vautrin, C. De-vallavieille-pope, and C. , Isolation of twelve microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Puccinia striiformis f. sp. tritici, Molecular Ecology Notes, vol.2, pp.563-565, 2002.

S. Ali, A. Gautier, M. Leconte, J. Enjalbert, D. Vallavieille-pope et al., A rapid genotyping method for an obligate fungal pathogen, Puccinia striiformis f.sp. tritici, based on DNA extraction from infected leaf and Multiplex PCR genotyping, BMC Research Notes, vol.4, p.240, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01019765

C. Dutech, O. Fabreguettes, X. Capdevielle, and C. Robin, 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

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

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

H. Gao, S. Williamson, and C. D. Bustamante, A markov chain monte carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data, Genetics, vol.176, pp.1635-1651, 2007.

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. Nei, F. Tajima, and Y. Tateno, Accuracy of estimated phylogenetic trees from molecular data, Journal of Molecular Evolution, vol.19, pp.153-170, 1983.

O. Langella, POPULATIONS 1.2.3, Logiciel de génétique des populations, 2008.

K. Belkhir, L. Chikhi, N. Raufaste, and F. Bonhomme, GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations, vol.5000, 2004.

S. Arnaud-haond and K. Belkhir, GenClone 1.0: A new program to analyse genetics data on clonal organisms, Molecular Ecology Notes, vol.7, pp.15-17, 2007.

J. Goudet, FSTAT, a program to estimate and test gene diversities and fixation indices.2.9, 2001.

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

Z. A. Szpiech, M. Jakobsson, and N. A. Rosenberg, ADZE: a rarefaction approach for counting alleles private to combinations of populations, Bioinformatics, vol.24, pp.2498-2504, 2008.

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

J. Maynard-smith, N. H. Smith, M. O'rourke, and B. G. Spratt, How clonal are bacteria?, pp.4384-4388, 1993.

A. Dilmaghani, P. Gladieux, L. Gout, G. T. Brunner, and P. C. , Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans, Molecular Ecology, vol.21, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01000602

A. Cornille, P. Gladieux, M. Smulders, I. Roldan-ruiz, and F. Laurens, 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, p.1002703, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01209929

J. M. Cornuet, V. Ravigne, and A. Estoup, Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0), BMC Bioinformatics, vol.11, p.401, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02658867

K. Csilléry, O. François, and M. Blum, abc: an R package for approximate Bayesian computation (ABC), Methods in Ecology and Evolution, vol.3, pp.475-479, 2012.

M. Nei, Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics, vol.89, pp.583-590, 1978.

B. S. Weir and C. C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution Psychiatrique, vol.38, pp.1358-1370, 1984.

D. B. Goldstein, L. A. Ruiz, L. L. Cavalli-sforza, and M. W. Feldman, An evaluation of genetic distances for use with microsatellite loci, Genetics, vol.139, pp.463-471, 1995.

N. Fagundes, N. Ray, M. A. Beaumont, S. Neuenschwander, and F. M. Salzano, Statistical evaluation of alternative models of human evolution, Proceedings of the National Academy of Science of the United States of America, vol.104, pp.17614-17619, 2007.

J. M. Cornuet, F. Santos, M. A. Beaumont, C. P. Robert, and J. M. Marin, Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation, Bioinformatics, vol.24, pp.2713-2719, 2008.

M. A. Beaumont, W. Zhang, and D. J. Balding, Approximate Bayesian computation in population genetics, Genetics, vol.162, pp.2025-2035, 2002.

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.

P. Gladieux, X. Zhang, D. Afoufa-bastien, R. Sanhueza, and M. Sbaghi, On the origin and spread of the scab disease of apple: out of Central Asia, PLoS ONE, vol.3, p.1455, 2008.

G. Schofl and C. Schlotterer, Microsatellite variation and differentiation in African and non-African populations of Drosophila simulans, Molecular Ecology, vol.15, pp.3895-3905, 2006.

G. B. Cummins, The rusts fungi of cereals, grasses, and bamboos, 1971.

Y. Jin, L. J. Szabo, and M. Carson, Century-old mystery of Puccinia striiformis life history solved with the identification of Berberis as an Alternate Host, Phytopathology, vol.100, pp.432-435, 2010.

R. Ray, K. V. Gururaja, and T. V. Ramchandra, Predictive distribution modeling for rare Himalayan medicinal plant Berberis aristata DC, Journal of Environmental Biology, vol.32, pp.725-730, 2011.

A. Perveen and M. Qaiser, Pollen flora of Pakistan-LXV. berberidaceae, Pakistan Journal of Botany, vol.42, pp.1-6, 2010.

S. Ali, P. Gladieux, H. Rahman, M. S. Saqib, and M. Fiaz, Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici, Molecular Ecology, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01303146

M. A. Carleton, A serious new wheat rust in this country, Science, vol.42, pp.58-59, 1915.

E. A. Milus, E. Seyran, and R. Mcnew, Aggressiveness of Puccinia striiformis f. sp. tritici isolates in the South-Central United States, Plant Disease, vol.90, pp.847-852, 2006.

C. R. Wellings, D. G. Wright, F. Keiper, and R. Loughman, First detection of wheat stripe rust in Western Australia: evidence for a foreign incursion, Australasian Plant Pathology, vol.32, pp.321-322, 2003.

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

R. Bultin, The costs and benefits of sex: new insights from old asexual lineages, Nature Reviews Genetics, vol.3, pp.313-317, 2002.