B. Facon, B. Genton, J. Shykoff, P. Jarne, and A. Estoup, A general ecoevolutionary framework for understanding bioinvasions, Trends Ecol Evol, vol.21, pp.130-135, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02667769

P. Anderson, A. Cunningham, N. Patel, F. Morales, and P. Epstein, Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers, Trends Ecol Evol, vol.19, pp.535-544, 2004.

P. Kareiva, S. Watts, R. Mcdonald, and T. Boucher, Domesticated nature: shaping landscapes and ecosystems for human welfare, Science, vol.316, pp.1866-1869, 2007.

D. Pimentel, L. Lach, R. Zuniga, and D. Morrison, Environmental and Economic Costs of Nonindigenous Species in theUnited States, BioScience, vol.50, pp.53-64, 2000.

S. Anagnostakis, Chestnut blight: The classical problem of an introduced pathogen, Mycologia, vol.29, pp.23-37, 1987.

W. Fry and S. Goodwin, Resurgence of the Irish potato famine fungus, BioScience, vol.47, pp.363-371, 1997.

M. Palm, Systematics and the Impact of Invasive Fungi on Agriculture in theUnited States, BioScience, vol.51, pp.141-147, 2001.

M. Wingfield, B. Slippers, J. Roux, and B. Wingfield, Worldwide Movement of Exotic Forest Fungi, Especially in theTropics and the Southern Hemisphere, BioScience, vol.51, pp.134-140, 2001.

F. Campbell, The Science of Risk Assessment for Phytosanitary Regulation and the Impact of Changing Trade Regulations, BioScience, vol.51, pp.148-153, 2001.

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, p.1, 2002.

L. Cui, A. Escalante, M. Imwong, and G. Snounou, The genetic diversity of Plasmodium vivax populations, Trends Parasitol, vol.19, pp.220-226, 2003.

D. Rizzo, Exotic species and fungi: Interactions with fungal, plant and animal communities, pp.857-880, 2005.

R. Bandyopadhyay, D. E. Frederickson, N. W. Mclaren, G. N. Odvody, and M. J. Ryley, Ergot: A New Disease Threat to Sorghum in the Americas and Australia, Plant Disease, vol.82, pp.356-367, 1998.

V. Garrison, E. Shinn, W. Foreman, D. Griffin, and C. Holmes, African and Asian Dust: From Desert Soils to Coral Reefs, BioScience, vol.53, pp.469-480, 2003.

J. Brown and M. Hovmøller, Aerial Dispersal of Pathogens on the Global and Continental Scales and Its Impact on Plant Disease, Science, vol.297, pp.537-541, 2002.

I. M. Parker and G. S. Gilbert, The Evolutionary Ecology of Novel Plant-Pathogen Interactions, Annu Rev Ecol Evol Syst, vol.35, pp.675-700, 2004.

C. E. Yarwood, Man-Made Plant Diseases, Science, vol.168, pp.218-220, 1970.

A. K. Sakai, F. W. Allendorf, J. S. Holt, D. M. Lodge, and J. Molofsky, The population biology of invasive species, Annu Rev Ecol Syst, vol.32, pp.305-332, 2001.

M. Fisher, G. Koenig, T. White, G. San-blas, and R. Negroni, Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration, Proc Natl Acad Sci, vol.98, pp.4558-4562, 2001.

M. Fisher, B. Rannala, V. Chaturvedi, and J. Taylor, Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections, Proc Natl Acad Sci, vol.99, pp.9067-9071, 2002.

S. Banke and B. A. Mcdonald, Migration patterns among global populations of the pathogenic fungus Mycosphaerella graminicola, Mol Ecol, vol.14, pp.1881-1896, 2005.

E. Stukenbrock, S. Banke, and B. Mcdonald, Global migration patterns in the fungal wheat pathogen Phaeosphaeria nodorum, Mol Ecol, vol.15, pp.2895-2904, 2006.

M. Nei, T. Maruyama, and R. Chakraborty, The Bottleneck Effect and Genetic Variability in Populations, Evolution, vol.29, pp.1-10, 1975.

N. Barton, Genetic hitchhiking, Philos Trans R Soc Lond B Biol Sci, vol.355, pp.1553-1562, 2000.

M. Jobling, M. Hurles, and C. Tyler-smith, Human Evolutionary Genetics: Origins, Peoples & Disease, vol.523, 2004.

C. Engelbrecht, T. C. Harrington, J. Steimel, and P. Capretti, Genetic variation in eastern North American and putatively introduced populations of Ceratocystis fimbriata f. platani, Mol Ecol, vol.13, pp.2995-3005, 2004.

K. Ivors, M. Garbelotto, I. Vries, C. Ruyter-spira, and B. T. Hekkert, Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations, Mol Ecol, vol.15, pp.1493-1505, 2006.

J. Cornuet and G. Luikart, Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks From Allele Frequency Data, Genetics, vol.144, pp.2001-2014, 1996.

G. Rivas, M. Zapater, C. Abadie, and J. Carlier, Founder effects and stochastic dispersal at the continental scale of the fungal pathogen of bananas Mycosphaerella fijiensis, Mol Ecol, vol.13, pp.471-482, 2004.

J. W. Taylor, D. Jacobson, and M. Fisher, The Evolution of Asexual Fungi: Reproduction, Speciation and Classification, Annu Rev Phytopathol, vol.37, pp.197-246, 1999.

M. G. Milgroom, Recombination and the multilocus structure of fungal populations, Annu Rev Phytopathol, vol.34, pp.457-477, 1996.

K. Ardlie, L. Kruglyak, and M. Seielstad, Patterns of linkage disequilibrium in the human genome, Nat Rev Genet, vol.3, pp.299-309, 2002.

R. S. Zeigler, Recombination in Magnaporthe grisea, Annu Rev Phytopathol, vol.36, pp.249-275, 1998.

C. Smart and W. Fry, Invasions by the late blight pathogen: renewed sex and enhanced fitness, Biological Invasions, vol.3, pp.235-243, 2001.

M. Donnelly, M. Licht, and T. Lehmann, Evidence for recent population expansion in the evolutionary history of the malaria vectors Anopheles arabiensis and Anopheles gambiae, Mol Biol Evol, vol.18, pp.1353-1364, 2001.

W. Mchardy and M. Paul, Apple Scab: Biology, Epidemiology, 1996.

T. Wirth, A. Meyer, and M. Achtman, Deciphering host migrations and origins by means of their microbes, Mol Ecol, vol.14, pp.3289-3306, 2005.

B. Juniper and D. Mabberley, The Story Of The Apple, vol.236, 2006.

S. Harris, J. Robinson, and B. Juniper, Genetic clues to the origin of the apple, Trends Genet, vol.18, pp.426-430, 2002.

F. Wood, The Silk Road. London: The Folio Society, vol.270, 2003.

J. F. Hancock, Plant Evolution and the Origin of Crop Species, vol.313, 2004.

J. Morgan and A. Richards, The Book of Apples, vol.304, 1993.

I. Tenzer and C. Gessler, Subdivision and genetic structure of four populations of Venturia inaequalis in Switzerland, Eur J Plant Pathol, vol.103, pp.565-571, 1997.

I. Tenzer and C. Gessler, Genetic Diversity of Venturia inaequalis Across Europe, Eur J Plant Pathol, vol.105, pp.545-552, 1999.

I. Tenzer, S. Degli-ivanissevich, M. Morgante, and C. Gessler, Identification of Microsatellite Markers and Their Application to Population Genetics of Venturia inaequalis, Phytopathology, vol.89, pp.748-753, 1999.

J. W. Taylor and M. Fisher, Fungal multilocus sequence typing-it's not just for bacteria, Curr Opin Microbiol, vol.6, pp.351-356, 2003.

J. Brown, Chance and selection in the evolution of barley mildew, Trends Microbiol, vol.2, pp.470-475, 1994.

F. Guérin, L. Cam, and B. , Breakdown of the scab resistance gene Vf in apple leads to a founder effect in population of the fungal pathogen Venturia inaequalis, Phytopathology, vol.94, pp.364-369, 2004.

F. Guérin, P. Gladieux, L. Cam, and B. , Origin and colonization history of newly virulent strains of the phytopathogenic fungus Venturia inaequalis, Fungal Genet Biol, vol.44, pp.284-292, 2007.

L. Excoffier, P. E. Smouse, and J. M. Quattro, Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data, Genetics, vol.131, pp.479-491, 1992.

R. Peakall and P. E. Smouse, genalex 6: genetic analysis in Excel. Population genetic software for teaching and research, Mol Ecol Notes, vol.6, pp.288-295, 2006.

F. Guérin, P. Franck, A. Loiseau, M. Devaux, L. Cam et al., Isolation of 21 new polymorphic microsatellite loci in the phytopathogenic fungus Venturia inaequalis, Mol Ecol Notes, vol.4, pp.268-270, 2004.

L. Excoffier, G. Laval, and S. Schneider, Arlequin (version 3.0): An integrated software package for, Evolutionary Bioinformatics Online, vol.1, pp.47-50, 2005.

J. Zhan, R. Pettway, and B. Mcdonald, The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow, Fungal Genet Biol, vol.38, pp.286-297, 2003.

R. S. Chen and B. A. Mcdonald, Sexual Reproduction Plays a Major Role in the Genetic Structure of Populations of the Fungus Mycosphaerella graminicola, Genetics, vol.142, pp.1119-1127, 1996.

M. Nei, Analysis of Gene Diversity in Subdivided Populations, Proc Natl Acad Sci, vol.70, pp.3321-3323, 1973.

A. El-mousadik and R. J. Petit, High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco, Theor Appl Genet, vol.92, pp.832-839, 1996.
URL : https://hal.archives-ouvertes.fr/hal-02696931

P. L. Leberg, Estimating allelic richness: Effects of sample size and bottlenecks, Mol Ecol, vol.11, pp.2445-2449, 2002.

A. Brown, M. W. Feldman, and E. Nevo, Multilocus structure of natural populations of Hordeum spontaneum, Genetics, vol.96, pp.523-536, 1980.

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

P. Zaffarano, B. Mcdonald, M. Zala, and C. Linde, Global Hierarchical Gene Diversity Analysis Suggests the Fertile Crescent Is Not the Center of Origin of the Barley Scald Pathogen Rhynchosporium secalis, Phytopathology, vol.96, pp.941-950, 2006.

S. Piry, G. Luikart, and J. Cornuet, BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data, J Hered, vol.90, pp.502-503, 1999.

M. Kimmel, R. Chakraborty, J. King, M. Bamshad, and W. Watkins, Signatures of population expansion in microsatellite repeat data, Genetics, vol.148, pp.1921-1930, 1998.

J. P. King, M. Kimmel, and R. Chakraborty, A Power Analysis of Microsatellite-Based Statistics for Inferring Past Population Growth, Mol Biol Evol, vol.17, pp.1859-1868, 2000.

D. E. Reich and D. B. Goldstein, Genetic evidence for a Paleolithic human population expansion in Africa, Proc Natl Acad Sci, vol.95, pp.8119-8123, 1998.

D. E. Reich, M. W. Feldman, and D. B. Goldstein, Statistical Properties of Two Tests that Use Multilocus Data Sets to Detect Population Expansions, Mol Biol Evol, vol.16, pp.453-466, 1999.

L. Cavalli-sforza and A. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, pp.550-570, 1967.

D. Dieringer and C. Schlotterer, microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets, Mol Ecol Notes, vol.3, pp.167-169, 2003.

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of Population Structure Using Multilocus Genotype Data, Genetics, vol.155, pp.945-959, 2000.

D. Falush, M. Stephens, and J. K. Pritchard, Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies, Genetics, vol.164, pp.1567-1587, 2003.

J. Corander, P. Waldmann, and M. J. Sillanpaa, Bayesian Analysis of Genetic Differentiation Between Populations, Genetics, vol.163, pp.367-374, 2003.

S. Piry, A. Alapetite, J. Cornuet, D. Paetkau, and L. Baudouin, GENECLASS2: A Software for Genetic Assignment and First-Generation Migrant Detection, J Hered, vol.95, pp.536-539, 2004.

B. Rannala and J. L. Mountain, Detecting immigration by using multilocus genotypes, Proc Natl Acad Sci, vol.94, pp.9197-920, 1997.

D. Paetkau, R. Slade, M. Burden, and A. Estoup, Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power, Mol Ecol, vol.13, pp.55-65, 2004.

P. Beerli and J. Felsenstein, Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach, Proc Natl Acad Sci, vol.98, pp.4563-4568, 2001.

O. Berry, M. D. Tocher, and S. D. Sarre, Can assignment tests measure dispersal?, Mol Ecol, vol.13, pp.551-561, 2004.

S. Manel, O. Gaggiotti, and R. Waples, Assignment methods: matching biological questions with appropriate techniques, Trends Ecol Evol, vol.20, pp.136-142, 2005.
URL : https://hal.archives-ouvertes.fr/halsde-00276308

L. Jorde, M. Bamshad, and A. Rogers, Using mitochondrial and nuclear DNA markers to reconstruct human evolution, Bioessays, vol.20, pp.126-136, 1998.

P. C. Brunner, S. Schurch, and B. A. Mcdonald, The origin and colonization history of the barley scald pathogen Rhynchosporium secalis, J Evol Biol, vol.20, pp.1-12, 2007.

B. C. Couch, I. Fudal, M. Lebrun, D. Tharreau, and B. Valent, Origins of Host-Specific Populations of the Blast Pathogen Magnaporthe oryzae in Crop Domestication With Subsequent Expansion of Pandemic Clones on Rice and Weeds of Rice, Genetics, vol.170, pp.613-630, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02681928

L. Gomez-alpizar, I. Carbone, and J. B. Ristaino, An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies, Proc Natl Acad Sci, vol.104, pp.3306-3311, 2007.

L. Raboin, A. Selvi, K. M. Oliveira, F. Paulet, and C. Calatayud, Evidence for the dispersal of a unique lineage from Asia to America and Africa in the sugarcane fungal pathogen Ustilago scitaminea, Fungal Genet Biol, vol.44, pp.64-76, 2007.

E. Stukenbrock, S. Banke, M. Javan-nikkhah, and B. Mcdonald, Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation, Mol Biol Evol, vol.24, pp.398-411, 2007.

S. B. Goodwin, B. A. Cohen, and W. E. Fry, Panglobal Distribution of a Single Clonal Lineage of the Irish Potato Famine Fungus, Proc Natl Acad Sci, vol.91, pp.11591-11595, 1994.

T. Burgess, B. Wingfield, and M. Wingfield, Comparison of genotypic diversity in native and introduced populations of Sphaeropsis sapinea isolated from Pinus radiata, Mycological Research, vol.105, pp.1331-1339, 2001.

K. Wikler and T. R. Gordon, An initial assessment of genetic relationships among populations of Fusarium circinatum in different parts of the world, Can J Bot, vol.78, pp.709-717, 2000.

. Fao, FAOSTAT Archives, 2004.

L. Jin and R. Chakraborty, Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics, Heredity, vol.74, pp.274-285, 1995.

M. Donnelly, F. Simard, and T. Lehmann, Evolutionary studies of malaria vectors, Trends Parasitol, vol.18, pp.75-80, 2002.

G. Malvarez, I. Carbone, N. J. Grunwald, K. V. Subbarao, and M. Schafer, New Populations of Sclerotinia sclerotiorum from Lettuce in California and Peas and Lentils in Washington, Phytopathology, vol.97, pp.470-483, 2007.

M. Kauer, D. Dieringer, and C. Schlotterer, Nonneutral Admixture of Immigrant Genotypes in African Drosophila melanogaster Populations from Zimbabwe, Mol Biol Evol, vol.20, pp.1329-1337, 2003.

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

C. Pfaff, E. Parra, C. Bonilla, K. Hiester, and P. Mckeigue, Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium, Am J Hum Genet, vol.68, pp.198-207, 2001.

E. Wilson, Studies of the ascigerous stage of Venturia inaequalis, Phytopathology, vol.18, pp.375-418, 1928.

E. Boehm, S. Freeman, E. Shabi, and T. Michailides, Microsatellite Primers Indicate the Presence of Asexual Populations of Venturia inaequalis in Coastal Israeli Apple Orchards, Phytoparasitica, vol.31, pp.236-251, 2003.

J. Hume, E. Lyons, and K. Day, Human migration, mosquitoes and the evolution of Plasmodium falciparum, Trends Parasitol, vol.19, pp.144-149, 2003.

D. Joy, X. Feng, J. Mu, T. Furuya, and K. Chotivanich, Early origin and recent expansion of Plasmodium falciparum, Science, vol.300, pp.318-321, 2003.