a new generation of protein database search programs, Nucleic LITERATURE CITED ,
Indices of multilocus linkage disequilibrium, Molecular Ecology Notes, vol.90, issue.1-2, pp.101-102, 2001. ,
DOI : 10.1073/pnas.93.2.770
Assessment of wheat breeding lines for slow yellow rusting (Puccinia striiformis West. tritici), Pak J Biol Sci, vol.10, pp.3440-3444, 2007. ,
Geographic limits of a clonal population of wheat yellow rust in the Mediterranean region, Molecular Ecology, vol.58, issue.20, pp.4165-79, 2009. ,
DOI : 10.1016/B978-0-12-148402-6.50011-0
Genetic structure of the poplar rust fungus Melampsora larici-populina: Evidence for isolation by distance in Europe and recent founder effects overseas, Infection, Genetics and Evolution, vol.8, issue.5, pp.577-87, 2008. ,
DOI : 10.1016/j.meegid.2008.04.005
Understanding the recent colonization history of a plant pathogenic fungus using population genetic tools and Approximate Bayesian Computation, Heredity, vol.38, issue.5, pp.269-79, 2012. ,
DOI : 10.2307/2408641
Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini, Molecular Biology and Evolution, vol.22, issue.4, pp.2499-513, 2009. ,
DOI : 10.1093/molbev/msi097
Evaluating Loci for Use in the Genetic Analysis of Population Structure, Proceedings of the Royal Society B: Biological Sciences, vol.263, issue.1377, pp.1619-1645, 1996. ,
DOI : 10.1098/rspb.1996.0237
Approximate Bayesian computation in population genetics, Genetics, vol.162, issue.4, pp.2025-2060, 2002. ,
) GENETIX 4.05, Logiciel Sous Windows TM Pour La Généique Des Populations, 1996. ,
The control of the false discovery rate in multiple testing under dependency, Annals of Statistics, vol.29, pp.1165-88, 2001. ,
Time-shift experiments and patterns of adaptation across time and space, Ecology Letters, vol.109, issue.1, pp.31-39, 2013. ,
DOI : 10.1073/pnas.1118386109
Pathogen evolution across the agro-ecological interface: implications for disease management, Evolutionary Applications, vol.20, issue.1, pp.57-65, 2008. ,
DOI : 10.1016/j.tree.2005.02.009
Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study, Molecular Ecology Notes, vol.101, issue.41, pp.747-756, 2007. ,
DOI : 10.2307/2408641
URL : https://hal.archives-ouvertes.fr/hal-00370267
Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data, Genetics, vol.144, issue.4, pp.2001-2015, 1996. ,
in Crop Domestication With Subsequent Expansion of Pandemic Clones on Rice and Weeds of Rice, Genetics, vol.170, issue.2, pp.613-643, 2005. ,
DOI : 10.1534/genetics.105.041780
Host???parasite ???Red Queen??? dynamics archived in pond sediment, Nature, vol.49, issue.7171, pp.450870-450873, 2007. ,
DOI : 10.1111/j.0014-3820.2001.tb00634.x
EggLib: processing, analysis and simulation tools for population genetics and genomics, BMC Genetics, vol.13, issue.1, p.27, 2012. ,
DOI : 10.1186/1471-2105-12-134
URL : https://hal.archives-ouvertes.fr/hal-01268349
On guard, Nature, vol.97, issue.6883, pp.801-804, 2002. ,
DOI : 10.1073/pnas.97.16.8807
FLOCK Provides Reliable Solutions to the ???Number of Populations??? Problem, Journal of Heredity, vol.15, issue.5, pp.734-743, 2012. ,
DOI : 10.1111/j.1365-294X.2006.02890.x
Spatial Inference of Admixture Proportions and Secondary Contact Zones, Molecular Biology and Evolution, vol.38, issue.2, pp.1963-73, 2009. ,
DOI : 10.1038/ng1702
The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen, Molecular Ecology, vol.19, issue.16, pp.3931-3977, 2012. ,
DOI : 10.1111/j.1365-294X.2010.04609.x
Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, vol.16, issue.8, pp.2611-2631, 2005. ,
DOI : 10.1098/rspb.2001.1600
Detecting loci under selection in a hierarchically structured population, Heredity, vol.15, issue.4, pp.285-98, 2009. ,
DOI : 10.1534/genetics.106.061432
Current Status of the Gene-For-Gene Concept, Annual Review of Phytopathology, vol.9, issue.1, pp.275-96, 1971. ,
DOI : 10.1146/annurev.py.09.090171.001423
Bayesian Clustering Using Hidden Markov Random Fields in Spatial Population Genetics, Genetics, vol.174, issue.2, pp.805-821, 2006. ,
DOI : 10.1534/genetics.106.059923
IMMUNITY, ANTIGENIC HETEROGENEITY, AND AGGREGATION OF HELMINTH PARASITES, Journal of Parasitology, vol.58, issue.2, pp.232-273, 2003. ,
DOI : 10.1645/0022-3395(2003)089[0232:IAHAAO]2.0.CO;2
Host-parasite coevolution and patterns of adaptation across time and space, Journal of Evolutionary Biology, vol.32, issue.6, pp.1861-1867, 2008. ,
DOI : 10.7208/chicago/9780226797670.001.0001
Populations on Wild and Cultivated Poplar and Influence of the Alternate Host, Phytopathology, vol.96, issue.9, pp.1027-1063, 2006. ,
DOI : 10.1094/PHYTO-96-1027
On the Origin and Spread of the Scab Disease of Apple: Out of Central Asia, PLoS ONE, vol.300, issue.1, p.1455, 2008. ,
DOI : 10.1371/journal.pone.0001455.s007
The population biology of fungal invasions, Molecular Ecology, vol.18, issue.9, pp.1969-86, 2015. ,
DOI : 10.1111/j.1365-294X.2008.04013.x
Panglobal distribution of a single clonal lineage of the Irish potato famine fungus., Proceedings of the National Academy of Sciences, vol.91, issue.24, pp.11591-95, 1994. ,
DOI : 10.1073/pnas.91.24.11591
FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics, Journal of Heredity, vol.86, issue.6, pp.485-86, 1995. ,
DOI : 10.1093/oxfordjournals.jhered.a111627
Origin and colonization history of newly virulent strains of the phytopathogenic fungus Venturia inaequalis, Fungal Genetics and Biology, vol.44, issue.4, pp.284-292, 2007. ,
DOI : 10.1016/j.fgb.2006.10.005
Current trends in microsatellite genotyping, Molecular Ecology Resources, vol.11, issue.4, pp.591-611, 2011. ,
DOI : 10.1046/j.0962-1083.2001.01418.x
Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites, Heredity, vol.142, issue.1, pp.158-171, 2011. ,
DOI : 10.1046/j.1365-294X.2003.01773.x
Microsatellites as Targets of Natural Selection, Molecular Biology and Evolution, vol.24, issue.4, pp.285-298, 2013. ,
DOI : 10.1038/74238
Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae, BMC Genetics, vol.15, issue.1, 2014. ,
DOI : 10.1093/bioinformatics/btg359
The plant immune system, Nature, vol.308, issue.7117, pp.323-352, 2006. ,
DOI : 10.1126/science.1111404
Common misconceptions in molecular ecology: echoes of the modern synthesis, Molecular Ecology, vol.19, issue.17, pp.4171-4189, 2012. ,
DOI : 10.2307/2406450
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, 2013. ,
DOI : 10.1094/PDIS.1998.82.8.838
URL : https://hal.archives-ouvertes.fr/hal-01209912
Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms, Genetics, vol.74, issue.1, pp.175-95, 1973. ,
Estimating the effective number of breeders from heterozygote excess in progeny, Genetics, vol.151, issue.3, pp.1211-1217, 1999. ,
URL : https://hal.archives-ouvertes.fr/halsde-00295525
Fitness costs associated with unnecessary virulence factors and life history traits: evolutionary insights from the potato late blight pathogen Phytophthora infestans, BMC Evolutionary Biology, vol.10, issue.1, 2010. ,
DOI : 10.1186/1471-2148-10-283
URL : https://hal.archives-ouvertes.fr/hal-00729514
Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics, vol.89, issue.3, pp.583-90, 1978. ,
Chloroplast DNA footprints of postglacial recolonization by oaks, Proceedings of the National Academy of Sciences, vol.5, issue.6, pp.9996-10001, 1997. ,
DOI : 10.1038/hdy.1997.67
Structure of Melampsora larici-populina populations on wild and cultivated poplar, European Journal of Plant Pathology, vol.103, issue.2, pp.159-173, 1997. ,
DOI : 10.1023/A:1008650128568
Interactions between poplar clones and Melampsora populations and their implications for breeding for durable resistance., pp.139-154, 2005. ,
DOI : 10.1079/9780851999999.0139
Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data, Journal of Heredity, vol.90, issue.4, pp.502-505, 1999. ,
DOI : 10.1093/jhered/90.4.502
Challenges in analysis and interpretation of microsatellite data for population genetic studies, Ecology and Evolution, vol.47, issue.Suppl. 1, pp.4399-4428, 2014. ,
DOI : 10.1111/j.1439-0469.2008.00501.x
genepop???007: a complete re-implementation of the genepop software for Windows and Linux, Molecular Ecology Resources, vol.145, issue.1, pp.103-109, 2008. ,
DOI : 10.2307/2408641
URL : https://hal.archives-ouvertes.fr/halsde-00366752
reproduces sexually, Molecular Ecology, vol.37, issue.6, pp.1330-1374, 2012. ,
DOI : 10.1016/j.ijpara.2007.03.003
URL : https://hal.archives-ouvertes.fr/hal-01506273
Mutation analysis for the dissection of resistance, The Gene-for-Gene Relationship in Plant? Parasite Interactions. CAB International, pp.45-63, 1997. ,
Comparison of information content for microsatellites and SNPs in poultry and cattle, Animal Genetics, vol.80, issue.4, pp.451-453, 2008. ,
DOI : 10.1093/ps/80.1.6
Bayesian measures of model complexity and fit, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.93, issue.4, pp.583-639, 2002. ,
DOI : 10.1002/1097-0258(20000915/30)19:17/18<2265::AID-SIM568>3.0.CO;2-6
Poplar diseases, consequences on growth and wood quality, Biomass and Bioenergy, vol.10, issue.5-6, pp.267-74, 1996. ,
DOI : 10.1016/0961-9534(95)00121-2
Population Genetics of Fungal and Oomycete Effectors Involved in Gene-for-Gene Interactions, Molecular Plant-Microbe Interactions, vol.22, issue.4, pp.371-80, 2008. ,
DOI : 10.1094/MPMI-22-4-0371
A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems, PLoS Pathogens, vol.8, issue.9, p.1002893, 2012. ,
DOI : 10.1371/journal.ppat.1002893.g001
Microsatellites Are Molecular Clocks That Support Accurate Inferences about History, Molecular Biology and Evolution, vol.72, issue.5, pp.1017-1027, 2009. ,
DOI : 10.1086/375120
The influence of perenniality and seed banks on polymorphism in plantparasite interactions, Am Nat, vol.174, issue.6, pp.769-79, 2011. ,
What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity, Molecular Ecology, vol.12, issue.6, pp.1419-1439, 2006. ,
DOI : 10.1515/9781400860180
Estimating F-statistics for the analysis of population structure, Evolution, vol.38, pp.1358-70, 1984. ,
Darwinian interventions: taming pathogens through evolutionary ecology, Trends in Parasitology, vol.26, issue.2, pp.83-92, 2010. ,
DOI : 10.1016/j.pt.2009.11.009
Characterization of 41 microsatellite loci developed from the genome sequence of the poplar rust fungus, Melampsora larici-populina, Conservation Genetics Resources, vol.4, issue.1, pp.21-25, 2009. ,
DOI : 10.1007/s12686-009-9005-z
The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication, Molecular Ecology, vol.62, issue.13, pp.2739-55, 2011. ,
DOI : 10.1111/j.1558-5646.2008.00390.x
URL : https://hal.archives-ouvertes.fr/hal-01136973
Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach, Molecular Ecology, vol.15, issue.10, pp.2383-98, 2012. ,
DOI : 10.1046/j.1365-294X.2004.02098.x
URL : https://hal.archives-ouvertes.fr/hal-01191214
RAPID SPECIATION FOLLOWING RECENT HOST SHIFTS IN THE PLANT PATHOGENIC FUNGUS RHYNCHOSPORIUM, Evolution, vol.80, issue.6, pp.1418-1454, 2008. ,
DOI : 10.1094/PHYTO-96-0941
Germ banks affect the inference of past demographic events, Molecular Ecology, vol.180, issue.22, pp.5434-5480, 2012. ,
DOI : 10.1534/genetics.108.091231
Genetic diversity and disease control in rice, Nature, vol.277, issue.6797, pp.406718-406740, 2009. ,
DOI : 10.1126/science.277.5329.1038
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples, Genetics, vol.156, pp.2109-2118, 2000. ,
Thinking too positive? Revisiting current methods of population genetic selection inference, Trends in Genetics, vol.30, issue.12, pp.540-546, 2014. ,
DOI : 10.1016/j.tig.2014.09.010
Identifying adaptive genetic divergence among populations from genome scans, Molecular Ecology, vol.28, issue.4, pp.969-980, 2004. ,
DOI : 10.1046/j.1420-9101.2001.00335.x
Evaluating Loci for Use in the Genetic Analysis of Population Structure, Proceedings of the Royal Society B: Biological Sciences, vol.263, issue.1377, pp.1619-1626, 1996. ,
DOI : 10.1098/rspb.1996.0237
Interspecific reproductive barriers in the tomato clade: opportunities to decipher mechanisms of reproductive isolation, Sexual Plant Reproduction, vol.392, issue.3, pp.171-187, 2011. ,
DOI : 10.1038/33929
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans, PLoS Biology, vol.302, issue.11, p.310, 2007. ,
DOI : 10.1371/journal.pbio.0050310.sd021
How does adaptation sweep through the genome? Insights from long-term selection experiments, Proceedings of the Royal Society B: Biological Sciences, vol.7, issue.7291, 2012. ,
DOI : 10.1038/nature08923
Background Selection 20 Years on, Journal of Heredity, vol.337, issue.2, pp.161-171, 2013. ,
DOI : 10.1126/science.1225385
Recent Progress in Polymorphism-Based Population Genetic Inference, Journal of Heredity, vol.161, issue.4, pp.287-296, 2012. ,
DOI : 10.1371/journal.pgen.0030090
abc: an R package for approximate Bayesian computation (ABC), Methods in Ecology and Evolution, vol.11, issue.3, pp.475-479, 2012. ,
DOI : 10.1186/1471-2105-11-116
EggLib: processing, analysis and simulation tools for population genetics and genomics, BMC Genetics, vol.13, issue.1, p.27, 2012. ,
DOI : 10.1186/1471-2105-12-134
URL : https://hal.archives-ouvertes.fr/hal-01268349
BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, 2007. ,
DOI : 10.1186/1471-2148-7-214
Chapter Six -Advancing Knowledge on Biology of Rust Fungi Through Genomics, Advances in, pp.173-209, 2014. ,
Robust Demographic Inference from Genomic and SNP Data, PLoS Genetics, vol.92, issue.10, 2013. ,
DOI : 10.1371/journal.pgen.1003905.s020
Hitchhiking under positive Darwinian selection, Genetics, vol.155, pp.1405-1413, 2000. ,
On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure, Molecular Biology and Evolution, vol.329, issue.5, pp.1275-1291, 2014. ,
DOI : 10.1126/science.1190371
Current Status of the Gene-For-Gene Concept, Annual Review of Phytopathology, vol.9, issue.1, pp.275-296, 1971. ,
DOI : 10.1146/annurev.py.09.090171.001423
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective, Genetics, vol.180, issue.2, pp.977-993, 2008. ,
DOI : 10.1534/genetics.108.092221
URL : https://hal.archives-ouvertes.fr/halsde-00377961
Populations on Wild and Cultivated Poplar and Influence of the Alternate Host, Phytopathology, vol.96, issue.9, pp.1027-1036, 2006. ,
DOI : 10.1094/PHYTO-96-1027
URL : https://hal.archives-ouvertes.fr/hal-01136985
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data, PLoS Genetics, vol.81, issue.10, 2009. ,
DOI : 10.1371/journal.pgen.1000695.s001
Grinding up Wheat: A Massive Loss of Nucleotide Diversity Since Domestication, Molecular Biology and Evolution, vol.46, issue.7, pp.1506-1517, 2007. ,
DOI : 10.1023/A:1008692912820
URL : https://hal.archives-ouvertes.fr/hal-00697942
Estimation of levels of gene flow from DNA sequence data, Genetics, vol.132, pp.583-589, 1992. ,
The plant immune system, Nature, vol.308, issue.7117, pp.323-329, 2006. ,
DOI : 10.1126/science.1111404
Detecting a local signature of genetic hitchhiking along a recombining chromosome, Genetics, vol.160, pp.765-777, 2002. ,
Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms, Genetics, vol.74, pp.175-195, 1973. ,
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.9, issue.11, pp.1754-1760, 2009. ,
DOI : 10.1186/1471-2105-9-128
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.9, issue.11, pp.2078-2079, 2009. ,
DOI : 10.1146/annurev.genom.9.081307.164359
Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication, Scientific Reports, vol.38, issue.1, 2014. ,
DOI : 10.1093/nar/gkq603
Population genomics of domestic and wild yeasts, Nature, vol.26, issue.7236, pp.337-341, 2009. ,
DOI : 10.1099/00207713-50-5-1931
Indifferent, Affectionate, or Deceitful: Lifestyles and Secretomes of Fungi, PLoS Pathogens, vol.464, issue.3, 2012. ,
DOI : 10.1371/journal.ppat.1002515.g001
Estimating Allele Age and Selection Coefficient from Time-Serial Data, Genetics, vol.192, issue.2, 2012. ,
DOI : 10.1534/genetics.112.140939
Next-Generation DNA Sequencing Methods, Annual Review of Genomics and Human Genetics, vol.9, issue.1, pp.387-402, 2008. ,
DOI : 10.1146/annurev.genom.9.081307.164359
Genomes of obligate plant pathogens reveal adaptations for obligate parasitism, Proceedings of the National Academy of Sciences, vol.22, issue.9, pp.8921-8922, 2011. ,
DOI : 10.1105/tpc.110.077040
Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce, Molecular Ecology, vol.163, issue.16, pp.3599-3613, 2008. ,
DOI : 10.1016/j.mrfmmm.2004.07.022
Genomic scans for selective sweeps using SNP data, Genome Research, vol.15, issue.11, pp.1566-1575, 2005. ,
DOI : 10.1101/gr.4252305
Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors, Frontiers in Plant Science, vol.4, issue.98, 2014. ,
DOI : 10.1038/ncomms3673
URL : https://hal.archives-ouvertes.fr/hal-01269012
Population replacment following a major selection event in the plant pathogen Melampsora larici-populina ,
Effector proteins of rust fungi, Frontiers in Plant Science, vol.4, issue.2673, p.416, 2014. ,
DOI : 10.1038/ncomms3673
URL : https://hal.archives-ouvertes.fr/hal-01579674
Signals of recent positive selection in a worldwide sample of human populations, Genome Research, vol.19, issue.5, pp.826-837, 2009. ,
DOI : 10.1101/gr.087577.108
Structure of Melampsora larici-populina populations on wild and cultivated poplar, European Journal of Plant Pathology, vol.103, issue.2, pp.159-173, 1997. ,
DOI : 10.1023/A:1008650128568
Detecting recent positive selection in the human genome from haplotype structure, Nature, vol.411, issue.6909, pp.832-837, 2002. ,
DOI : 10.1038/35075590
Poplar diseases, consequences on growth and wood quality, Biomass and Bioenergy, vol.10, issue.5-6, pp.267-274, 1996. ,
DOI : 10.1016/0961-9534(95)00121-2
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989. ,
Progress and prospects in mapping recent selection in the genome, Heredity, vol.170, issue.6, pp.340-348, 2007. ,
DOI : 10.1093/oxfordjournals.molbev.a003805
Detection of selective sweeps in structured populations: a comparison of recent methods, Molecular Ecology, vol.4, issue.1, 2015. ,
DOI : 10.4310/SII.2011.v4.n1.a6
An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data, Molecular Biology and Evolution, vol.72, issue.2, 2012. ,
DOI : 10.1086/375120
Detecting and Measuring Selection from Gene Frequency Data, Genetics, vol.196, issue.3, 2014. ,
DOI : 10.1534/genetics.113.152991
A map of recent positive selection in the human genome, PLoS Biol, vol.4, 2006. ,
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication, Nature Genetics, vol.28, issue.9, pp.982-988, 2014. ,
DOI : 10.1093/bioinformatics/bts115
On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, issue.2, pp.256-276, 1975. ,
DOI : 10.1016/0040-5809(75)90020-9
Characterization of 41 microsatellite loci developed from the genome sequence of the poplar rust fungus, pp.Melampsora larici-populina, 2009. ,
The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication, Molecular Ecology, vol.62, issue.13, pp.2739-2755, 2011. ,
DOI : 10.1111/j.1558-5646.2008.00390.x
URL : https://hal.archives-ouvertes.fr/hal-01136973
Compound Tests for the Detection of Hitchhiking Under Positive Selection, Molecular Biology and Evolution, vol.24, issue.8, pp.1898-1908, 2007. ,
DOI : 10.1093/molbev/msm078
The Genome Sequence of Drosophila melanogaster, Science, vol.287, issue.5461, pp.2185-2195, 2000. ,
DOI : 10.1126/science.287.5461.2185
An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences, Mycologia, vol.98, issue.6, pp.896-905, 2006. ,
DOI : 10.1071/AP04020
Constructing genomic maps of positive selection in humans: Where do we go from here?, Genome Research, vol.19, issue.5, pp.711-722, 2009. ,
DOI : 10.1101/gr.086652.108
ON THE MECHANISM OF THE DEVELOPMENT OF MULTIPLE-DRUG-RESISTANT CLONES OF SHIGELLA, Japanese Journal of Microbiology, vol.74, issue.2, pp.219-227, 1960. ,
DOI : 10.1002/path.1700740226
Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples, Genetics, vol.156, pp.2109-2118, 2000. ,
to Partial Resistance in Potato: Evidence from French and Moroccan Populations, Phytopathology, vol.97, issue.3, pp.338-343, 2007. ,
DOI : 10.1094/PHYTO-97-3-0338
The population genetics of clonal and partially clonal diploids, Genetics, vol.164, pp.1635-1644, 2003. ,
PLANT SCIENCE: Seeking Agriculture's Ancient Roots, Science, vol.316, issue.5833, pp.1830-1835, 2007. ,
DOI : 10.1126/science.316.5833.1830
Thinking too positive? Revisiting current methods of population genetic selection inference, Trends in Genetics, vol.30, issue.12, pp.540-546, 2014. ,
DOI : 10.1016/j.tig.2014.09.010
Genetic structure of the poplar rust fungus Melampsora larici-populina: Evidence for isolation by distance in Europe and recent founder effects overseas, Infection, Genetics and Evolution, vol.8, issue.5, 2008. ,
DOI : 10.1016/j.meegid.2008.04.005
Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome, Science, vol.452, issue.7183, pp.1549-1551, 2010. ,
DOI : 10.1038/nature06556
Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model, Genetics, vol.185, issue.2, pp.587-602, 2010. ,
DOI : 10.1534/genetics.109.112391
Identifying adaptive genetic divergence among populations from genome scans, Molecular Ecology, vol.28, issue.4, pp.969-980, 2004. ,
DOI : 10.1046/j.1420-9101.2001.00335.x
The Bayesian revolution in genetics, Nature Reviews Genetics, vol.49, issue.4, pp.251-261, 2004. ,
DOI : 10.1093/molbev/msg043
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans, PLoS Biology, vol.302, issue.11, p.310, 2007. ,
DOI : 10.1371/journal.pbio.0050310.sd021
Accurate whole human genome sequencing using reversible terminator chemistry, Nature, vol.34, issue.7218, pp.53-59, 2008. ,
DOI : 10.1101/gr.8.3.175
URL : http://doi.org/10.1038/nature07517
Population genomics: a new generation of genome scans to bridge the gap with functional genomics, Molecular Ecology, vol.105, issue.16, pp.3583-3584, 2008. ,
DOI : 10.1111/j.1365-294X.2008.03854.x
) in the Zones of Host Sympatry and Allopatry, Phytopathology, vol.97, issue.5, pp.603-610, 2007. ,
DOI : 10.1094/PHYTO-97-5-0603
RXLR Effector Proteins, Journal of Biological Chemistry, vol.22, issue.41, pp.35834-35842, 2011. ,
DOI : 10.1093/molbev/msi049
How does adaptation sweep through the genome? Insights from long-term selection experiments, Proceedings of the Royal Society B: Biological Sciences, vol.7, issue.7291, pp.5029-5038, 2012. ,
DOI : 10.1038/nature08923
A bioinformatics workflow for detecting signatures of selection in genomic data, Frontiers in Genetics, vol.28, p.293, 2014. ,
DOI : 10.1016/j.tig.2012.03.002
Erosion of quantitative host resistance in the applex Venturia inaequalis pathosystem, Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis, vol.27, pp.481-489, 2014. ,
Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust, PLoS ONE, vol.22, issue.7889, 2011. ,
DOI : 10.1371/journal.pone.0024230.s010
Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors, BMC Genomics, vol.14, issue.1, 2013. ,
DOI : 10.1006/meth.2001.1262
Avirulence proteins from haustoria-forming pathogens, FEMS Microbiology Letters, vol.47, issue.2, pp.181-188, 2007. ,
DOI : 10.1007/978-3-642-75818-8_3
URL : https://academic.oup.com/femsle/article-pdf/269/2/181/19603441/269-2-181.pdf
Background Selection 20 Years on, Journal of Heredity, vol.337, issue.2, pp.161-171, 2013. ,
DOI : 10.1126/science.1225385
Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data, Genetics, vol.144, 1996. ,
Diversification and evolution of the avirulence gene AVR-Pita1 in field isolates of Magnaporthe oryzae, Fungal Genetics and Biology, vol.47, issue.12, pp.973-980, 2010. ,
DOI : 10.1016/j.fgb.2010.08.003
Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes, Proceedings of the National Academy of Sciences, vol.50, issue.41, pp.17651-17656, 2010. ,
DOI : 10.1016/S0168-9525(00)02024-2
Pivoting the Plant Immune System from Dissection to Deployment, Science, vol.11, issue.9, pp.746-751, 2013. ,
DOI : 10.1038/nbt0993-1048
Base calling for high-throughput short-read sequencing: dynamic programming solutions, BMC Bioinformatics, vol.14, issue.1, 2013. ,
DOI : 10.1093/bioinformatics/bts256
Rapid and multiregional adaptation to host partial resistance in a plant pathogenic oomycete: Evidence from European populations of Plasmopara viticola, the causal agent of grapevine downy mildew, Infection, Genetics and Evolution, vol.27, pp.500-508, 2014. ,
DOI : 10.1016/j.meegid.2013.10.017
EggLib: processing, analysis and simulation tools for population genetics and genomics, BMC Genetics, vol.13, issue.1, p.27, 2012. ,
DOI : 10.1186/1471-2105-12-134
URL : https://hal.archives-ouvertes.fr/hal-01268349
Incompatibilities Involving Yeast Mismatch Repair Genes: A Role for Genetic Modifiers and Implications for Disease Penetrance and Variation in Genomic Mutation Rates, PLoS Genetics, vol.19, issue.6, 2008. ,
DOI : 10.1371/journal.pgen.1000103.s003
Power of Neutrality Tests to Detect Bottlenecks and Hitchhiking, Journal of Molecular Evolution, vol.57, issue.0, pp.190-200, 2003. ,
DOI : 10.1007/s00239-003-0027-y
URL : https://hal.archives-ouvertes.fr/hal-00427408
Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array, Scientific Reports, vol.413, issue.1, p.4245, 2014. ,
DOI : 10.1038/35097083
Plant immunity: towards an integrated view of plant???pathogen interactions, Nature Reviews Genetics, vol.28, issue.8, pp.539-548, 2010. ,
DOI : 10.1038/nrg2812
Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes, Proc. Natl. Acad. Sci. U. S. A. 103, pp.8888-8893, 2006. ,
DOI : 10.1002/pro.5560060626
Potential of Eurasian poplar rust to overcome a major quantitative resistance factor, Plant Pathology, vol.10, issue.3, pp.523-534, 2010. ,
DOI : 10.1007/s00122-002-1115-x
BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007. ,
DOI : 10.1186/1471-2148-7-214
Obligate biotrophy features unraveled by the genomic analysis of rust fungi, Proceedings of the National Academy of Sciences, vol.2, issue.10, pp.9166-9171, 2011. ,
DOI : 10.1371/journal.pone.0001097
URL : https://hal.archives-ouvertes.fr/hal-01000169
Biotrophic Fungi (Powdery Mildews, Rusts, and Smuts) In The Ecological Genomics of Fungi, pp.149-168, 2013. ,
Chapter Six -Advancing Knowledge on Biology of Rust Fungi Through Genomics, Advances in, pp.173-209, 2014. ,
Spatial Inference of Admixture Proportions and Secondary Contact Zones, Molecular Biology and Evolution, vol.38, issue.2, pp.1963-1973, 2009. ,
DOI : 10.1038/ng1702
Flax Rust Resistance Gene Specificity is Based on Direct Resistance-Avirulence Protein Interactions, Annual Review of Phytopathology, vol.45, issue.1, pp.289-306, 2007. ,
DOI : 10.1146/annurev.phyto.45.062806.094331
Somatic gene mutation and human disease other than cancer, Mutation Research/Reviews in Mutation Research, vol.543, issue.2, pp.125-136, 2003. ,
DOI : 10.1016/S1383-5742(03)00010-3
Hitchhiking under positive Darwinian selection, Genetics, vol.155, pp.1405-1413, 2000. ,
Current Status of the Gene-For-Gene Concept, Annual Review of Phytopathology, vol.9, issue.1, pp.275-296, 1971. ,
DOI : 10.1146/annurev.py.09.090171.001423
An Overview of Plant Defenses against Pathogens and Herbivores, The Plant Health Instructor, 2008. ,
DOI : 10.1094/PHI-I-2008-0226-01
Statistical tests of neutrality of mutations, Genetics, vol.133, pp.693-709, 1993. ,
Populations on Wild and Cultivated Poplar and Influence of the Alternate Host, Phytopathology, vol.96, issue.9, pp.1027-1036, 2006. ,
DOI : 10.1094/PHYTO-96-1027
URL : https://hal.archives-ouvertes.fr/hal-01136985
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing, BMC Genomics, vol.23, issue.21, p.245, 2011. ,
DOI : 10.1093/bioinformatics/btm404
, the apple scab fungus, associated with the domestication of its host, Molecular Ecology, vol.18, issue.4, pp.658-674, 2010. ,
DOI : 10.1016/S1087-1845(02)00538-8
Field guide to next-generation DNA sequencers, Molecular Ecology Resources, vol.463, issue.Suppl. 1, pp.759-769, 2011. ,
DOI : 10.1038/463303a
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica), Science, vol.296, issue.5565, pp.92-100, 2002. ,
DOI : 10.1126/science.1068275
Life with 6000 Genes, Science, vol.274, issue.5287, pp.563-567, 1996. ,
DOI : 10.1126/science.274.5287.546
Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans, Molecular Microbiology, vol.17, issue.1, pp.67-80, 2006. ,
DOI : 10.1073/pnas.95.10.5661
Genome structure impacts molecular evolution at the AvrLm1 avirulence locus of the plant pathogen Leptosphaeria maculans, Environmental Microbiology, vol.4, issue.12, pp.2978-2992, 2007. ,
DOI : 10.1111/j.1365-2958.2004.04288.x
Clonality and host selection in the wheat pathogenic fungus Puccinia triticina, Fungal Genetics and Biology, vol.44, issue.6, pp.474-483, 2007. ,
DOI : 10.1016/j.fgb.2007.02.006
Statistical Inference for Hardy-Weinberg Proportions in the Presence of Missing Genotype Information, PLoS ONE, vol.10, issue.12, p.83316, 2013. ,
DOI : 10.1371/journal.pone.0083316.s001
The DNA sequence and biological annotation of human chromosome???1, Nature, vol.65, issue.7091, pp.315-321, 2006. ,
DOI : 10.1159/000133633
Origin and colonization history of newly virulent strains of the phytopathogenic fungus Venturia inaequalis, Fungal Genetics and Biology, vol.44, issue.4, pp.284-292, 2007. ,
DOI : 10.1016/j.fgb.2006.10.005
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans, Nature, vol.10, issue.7262, pp.393-398, 2009. ,
DOI : 10.1038/nature08358
Contribution à l'étude des déterminants génétiques impliqués dans le processus infectieux de Melampsora larici-populina, 2010. ,
The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics, Journal of Pathogens, vol.1, issue.3, p.716041, 2011. ,
DOI : 10.1146/annurev.arplant.59.032607.092811
(Poplar Leaf Rust), Molecular Plant-Microbe Interactions, vol.25, issue.3, pp.279-293, 2012. ,
DOI : 10.1094/MPMI-09-11-0238
URL : https://hal.archives-ouvertes.fr/hal-01267890
Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts, Proceedings of the National Academy of Sciences, vol.29, issue.9, pp.2219-2228, 2013. ,
DOI : 10.1093/nar/29.9.e45
Tackling the population genetics of clonal and partially clonal organisms, Trends in Ecology & Evolution, vol.20, issue.4, pp.194-201, 2005. ,
DOI : 10.1016/j.tree.2005.01.001
Grinding up Wheat: A Massive Loss of Nucleotide Diversity Since Domestication, Molecular Biology and Evolution, vol.46, issue.7, pp.1506-1517, 2007. ,
DOI : 10.1023/A:1008692912820
URL : https://hal.archives-ouvertes.fr/hal-00697942
Soft Sweeps: Molecular Population Genetics of Adaptation From Standing Genetic Variation, Genetics, vol.169, issue.4, pp.2335-2352, 2005. ,
DOI : 10.1534/genetics.104.036947
A test of neutral molecular evolution based on nucleotide data, Genetics, vol.116, pp.153-159, 1987. ,
Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biology, vol.8, issue.7, p.143, 2007. ,
DOI : 10.1186/gb-2007-8-7-r143
as an Alternate Host, Phytopathology, vol.100, issue.5, pp.432-435, 2010. ,
DOI : 10.1094/PHYTO-100-5-0432
The plant immune system, Nature, vol.308, issue.7117, pp.323-329, 2006. ,
DOI : 10.1126/science.1111404
Host resistance to a fungal tomato pathogen lost by a single base-pair
change in an avirulence gene, Nature, vol.367, issue.6461, pp.384-386, 1994. ,
DOI : 10.1038/367384a0
The " hitchhiking effect " revisited, Genetics, vol.123, pp.887-899, 1989. ,
Visualization of molecular interactions by fluorescence complementation, Nature Reviews Molecular Cell Biology, vol.58, issue.6, pp.449-456, 2006. ,
DOI : 10.1111/j.1365-2958.2005.04852.x
Species Complex, Molecular Plant-Microbe Interactions, vol.21, issue.5, pp.658-670, 2008. ,
DOI : 10.1094/MPMI-21-5-0658
Detecting a local signature of genetic hitchhiking along a recombining chromosome, Genetics, vol.160, pp.765-777, 2002. ,
A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation, PLoS ONE, vol.15, issue.3, p.286, 2007. ,
DOI : 10.1371/journal.pone.0000286.s005
Origins of the coalescent. 1974-1982, Genetics, vol.156, pp.1461-1463, 2000. ,
Improved base calling for the Illumina Genome Analyzer using machine learning strategies, Genome Biology, vol.10, issue.8, p.83, 2009. ,
DOI : 10.1186/gb-2009-10-8-r83
Analysis of plant microbe interactions in the era of next generation sequencing technologies, Frontiers in Plant Science, vol.13, p.216, 2014. ,
DOI : 10.1186/1471-2164-13-668
Hybrid error correction and de novo assembly of single-molecule sequencing reads, Nature Biotechnology, vol.13, issue.7, pp.693-700, 2012. ,
DOI : 10.1186/gb-2004-5-2-r12
Neutrality tests using DNA polymorphism from multiple samples, Genetics, vol.163, pp.1147-1151, 2003. ,
Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication, Scientific Reports, vol.38, issue.1, p.4678, 2014. ,
DOI : 10.1093/nar/gkq603
Population genomics of domestic and wild yeasts, Nature, vol.26, issue.7236, pp.337-341, 2009. ,
DOI : 10.1099/00207713-50-5-1931
Lysin Motif-Containing Proteins LYP4 and LYP6 Play Dual Roles in Peptidoglycan and Chitin Perception in Rice Innate Immunity, The Plant Cell, vol.24, issue.8, pp.3406-3419, 2012. ,
DOI : 10.1105/tpc.112.102475
On the current status of Phakopsora pachyrhizi genome sequencing, Frontiers in Plant Science, vol.5, 2014. ,
DOI : 10.3389/fpls.2014.00377
URL : https://hal.archives-ouvertes.fr/hal-01268956
Fungal Effectors and Plant Susceptibility, Annual Review of Plant Biology, vol.66, issue.1, pp.513-545, 2015. ,
DOI : 10.1146/annurev-arplant-043014-114623
The power and promise of population genomics: from genotyping to genome typing, Nature Reviews Genetics, vol.6, issue.12, pp.981-994, 2003. ,
DOI : 10.1086/302574
URL : https://hal.archives-ouvertes.fr/halsde-00279787
Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample, PLoS ONE, vol.2, issue.2, p.30087, 2012. ,
DOI : 10.1371/journal.pone.0030087.t001
Plant PRRs and the Activation of Innate Immune Signaling, Molecular Cell, vol.54, issue.2, pp.263-272, 2014. ,
DOI : 10.1016/j.molcel.2014.03.028
Next-Generation DNA Sequencing Methods, Annual Review of Genomics and Human Genetics, vol.9, issue.1, pp.387-402, 2008. ,
DOI : 10.1146/annurev.genom.9.081307.164359
Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, issue.7057, pp.376-380, 2005. ,
DOI : 10.1089/cmb.1995.2.275
Population Genetics of Plant Pathogens, The Plant Health Instructor, 2004. ,
DOI : 10.1094/PHI-A-2004-0524-01
Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.351, issue.6328, pp.652-654, 1991. ,
DOI : 10.1038/351652a0
Genomes of obligate plant pathogens reveal adaptations for obligate parasitism, Proceedings of the National Academy of Sciences, vol.22, issue.9, pp.8921-8922, 2011. ,
DOI : 10.1105/tpc.110.077040
A physical map of the human genome, Nature, vol.88, issue.6822, pp.934-941, 2001. ,
DOI : 10.1073/pnas.88.17.7474
Host jumps shaped the diversity of extant rust fungi (Pucciniales), New Phytologist, vol.33, issue.3, 2015. ,
DOI : 10.1071/AP04020
Molecular diagnostics for personal medicine using a nanopore, Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, vol.20, issue.6, pp.367-381, 2010. ,
DOI : 10.1088/0957-4484/20/18/185101
CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis, Proceedings of the National Academy of Sciences, vol.133, issue.2, 2007. ,
DOI : 10.1104/pp.103.027979
Sequence-specific error profile of Illumina sequencers, Nucleic Acids Research, vol.9, issue.13, p.90, 2011. ,
DOI : 10.1186/1471-2105-9-431
Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce, Molecular Ecology, vol.163, issue.16, pp.3599-3613, 2008. ,
DOI : 10.1016/j.mrfmmm.2004.07.022
The genome sequence and effector complement of the flax rust pathogen Melampsora lini, Frontiers in Plant Science, vol.5, p.98, 2014. ,
DOI : 10.3389/fpls.2014.00098
Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire, BMC Genomics, vol.19, issue.1, 2011. ,
DOI : 10.1093/hmg/ddq416
A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees, PLoS Biology, vol.17, issue.6, p.170, 2005. ,
DOI : 10.1371/journal.pbio.0030170.sd002
Algorithms for inferring haplotypes, Genetic Epidemiology, vol.164, issue.4, pp.334-347, 2004. ,
DOI : 10.1002/gepi.20024
Slightly Deleterious Mutant Substitutions in Evolution, Nature, vol.68, issue.5428, pp.96-98, 1973. ,
DOI : 10.1038/newbio237170a0
Development of Neutral and Nearly Neutral Theories, Theoretical Population Biology, vol.49, issue.2, pp.128-142, 1996. ,
DOI : 10.1006/tpbi.1996.0007
Genome-wide scans for footprints of natural selection, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.2, issue.2, pp.185-205, 2010. ,
DOI : 10.1186/1475-4924-2-11
A Telomeric Avirulence Gene Determines Efficacy for the Rice Blast Resistance Gene Pi-ta, THE PLANT CELL ONLINE, vol.12, issue.11, pp.2019-2032, 2000. ,
DOI : 10.1105/tpc.12.11.2019
Genetic analysis with nanoPCR, Integrative Biology, vol.29, issue.10, pp.1155-1163, 2012. ,
DOI : 10.1038/nbt.1739
Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean, BMC Genetics, vol.10, issue.1, 2009. ,
DOI : 10.1186/1471-2156-10-7
Étude des traits d'histoire de vie de Melampsora larici-populina " , agent de la rouille du peuplier : de leur déterminisme génétique à leurs conséquences évolutives, Thèse de doctorat en Biologie végétale et forestière, 2015. ,
Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors, Frontiers in Plant Science, vol.4, issue.98, p.540, 2014. ,
DOI : 10.1038/ncomms3673
URL : https://hal.archives-ouvertes.fr/hal-01269012
How Do Filamentous Pathogens Deliver Effector Proteins into Plant Cells?, PLoS Biology, vol.26, issue.2, p.1001801, 2014. ,
DOI : 10.1371/journal.pbio.1001801.t001
URL : https://hal.archives-ouvertes.fr/hal-01268569
Effector proteins of rust fungi, Frontiers in Plant Science, vol.4, issue.2673, p.416, 2014. ,
DOI : 10.1038/ncomms3673
URL : https://hal.archives-ouvertes.fr/hal-01579674
Structure of Melampsora larici-populina populations on wild and cultivated poplar, European Journal of Plant Pathology, vol.103, issue.2, pp.159-173, 1997. ,
DOI : 10.1023/A:1008650128568
Interactions between poplar clones and Melampsora populations and their implications for breeding for durable resistance., pp.139-154, 2005. ,
DOI : 10.1079/9780851999999.0139
Encodes an RXLR-dEER Effector, Molecular Plant-Microbe Interactions, vol.21, issue.11, pp.1460-1470, 2008. ,
DOI : 10.1094/MPMI-21-11-1460
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers, BMC Genomics, vol.13, issue.1, p.241, 2012. ,
DOI : 10.1186/1471-2164-13-341
Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00880072
Genome evolution in filamentous plant pathogens: why bigger can be better, Nature Reviews Microbiology, vol.13, issue.6, pp.417-430, 2012. ,
DOI : 10.1111/j.1364-3703.2011.00733.x
URL : https://hal.archives-ouvertes.fr/hal-01608755
Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans, BMC Genomics, vol.11, issue.1, 2010. ,
DOI : 10.1186/1471-2164-11-637
URL : https://hal.archives-ouvertes.fr/hal-01606572
Internalization of Flax Rust Avirulence Proteins into Flax and Tobacco Cells Can Occur in the Absence of the Pathogen, The Plant Cell, vol.22, issue.6, pp.2017-2032, 2010. ,
DOI : 10.1105/tpc.109.072983
Challenges and progress towards understanding the role of effectors in plant???fungal interactions, Current Opinion in Plant Biology, vol.15, issue.4, pp.477-482, 2012. ,
DOI : 10.1016/j.pbi.2012.05.003
Transcript Profiling of Poplar Leaves upon Infection with Compatible and Incompatible Strains of the Foliar Rust Melampsora larici-populina, PLANT PHYSIOLOGY, vol.144, issue.1, pp.347-366, 2007. ,
DOI : 10.1104/pp.106.094987
URL : https://hal.archives-ouvertes.fr/hal-01194961
Theoretical analysis of mutation hotspots and their DNA sequence context specificity, Mutation Research/Reviews in Mutation Research, vol.544, issue.1, pp.65-85, 2003. ,
DOI : 10.1016/S1383-5742(03)00032-2
, enters the genomic era, Molecular Plant Pathology, vol.25, issue.3, pp.225-241, 2005. ,
DOI : 10.1080/07060660309507054
Detecting recent positive selection in the human genome from haplotype structure, Nature, vol.411, issue.6909, pp.832-837, 2002. ,
DOI : 10.1038/35075590
Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi, PLoS ONE, vol.34, issue.1, 2012. ,
DOI : 10.1371/journal.pone.0029847.s006
URL : https://hal.archives-ouvertes.fr/hal-01608656
A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase, The American Journal of Human Genetics, vol.78, issue.4, 2006. ,
DOI : 10.1086/502802
Studying Plant-Pathogen Interactions in the Genomics Era: Beyond Molecular Koch's Postulates to Systems Biology, Annual Review of Phytopathology, vol.48, issue.1, pp.457-479, 2010. ,
DOI : 10.1146/annurev-phyto-073009-114411
Next-generation DNA sequencing, Nature Biotechnology, vol.105, issue.10, pp.1135-1145, 2008. ,
DOI : 10.1101/gr.8.3.175
The population genomics of plant adaptation, New Phytologist, vol.15, issue.Pt 2, pp.313-332, 2010. ,
DOI : 10.1016/S0169-5347(00)01994-7
Horizontal Gene Transfer in Eukaryotic Plant Pathogens, Annual Review of Phytopathology, vol.52, issue.1, pp.583-614, 2014. ,
DOI : 10.1146/annurev-phyto-102313-050127
Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism, Science, vol.91, issue.25, pp.1543-1546, 2010. ,
DOI : 10.1073/pnas.91.25.12283
Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis, Nature, vol.13, issue.6745, pp.667-671, 1999. ,
DOI : 10.1073/pnas.96.1.302
Fungal Effector Proteins, Annual Review of Phytopathology, vol.47, issue.1, pp.233-263, 2009. ,
DOI : 10.1146/annurev.phyto.112408.132637
A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems, PLoS Pathogens, vol.8, issue.9, p.1002893, 2012. ,
DOI : 10.1371/journal.ppat.1002893.g001
The Origins of Plant Pathogens in Agro-Ecosystems, Annual Review of Phytopathology, vol.46, issue.1, 2008. ,
DOI : 10.1146/annurev.phyto.010708.154114
The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species, Genome Research, vol.21, issue.12, pp.2157-2166, 2011. ,
DOI : 10.1101/gr.118851.110
Haplotyping by capillary electrophoresis, Journal of Chromatography A, vol.1079, issue.1-2, pp.41-49, 2005. ,
DOI : 10.1016/j.chroma.2005.03.078
Evolutionary relationship of DNA sequences in finite populations, Genetics, vol.105, pp.437-460, 1983. ,
A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome, PLoS Biology, vol.8, issue.2, p.171, 2007. ,
DOI : 10.1371/journal.pbio.0050171.st013
: Reproduction, Speciation and Classification, Annual Review of Phytopathology, vol.37, issue.1, pp.197-246, 1999. ,
DOI : 10.1146/annurev.phyto.37.1.197
Towards population genomics of effector-effector target interactions, New Phytologist, vol.87, issue.4, pp.929-939, 2010. ,
DOI : 10.1094/PHYTO.1997.87.3.284
Of PAMPs and Effectors: The Blurred PTI-ETI Dichotomy, The Plant Cell, vol.23, issue.1, pp.4-15, 2011. ,
DOI : 10.1105/tpc.110.082602
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray), Science, vol.313, issue.5793, pp.1596-1604, 2006. ,
DOI : 10.1126/science.1128691
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis, Science, vol.313, issue.5791, pp.1261-1266, 2006. ,
DOI : 10.1126/science.1128796
Reference-free detection of isolated SNPs, Nucleic Acids Research, vol.7, issue.2, p.11, 2015. ,
DOI : 10.1046/j.1469-0691.2001.00200.x
URL : https://hal.archives-ouvertes.fr/hal-01083715
Quantitative resistance can lead to evolutionary changes in traits not targeted by the resistance QTLs, Evolutionary Applications, vol.6, issue.3, pp.370-380, 2014. ,
DOI : 10.1111/eva.12000
Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants, PLoS Pathogens, vol.24, issue.11, 2010. ,
DOI : 10.1371/journal.ppat.1001180.s009
Structures of the flax-rust effector AvrM reveal insights into the molecular basis of plant-cell entry and effector-triggered immunity, Proc. Natl, 2013. ,
DOI : 10.1107/S0907444904026460
An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data, Molecular Biology and Evolution, vol.72, issue.2, 2012. ,
DOI : 10.1086/375120
The Sequence of the Human Genome, Science, vol.6, issue.5507, pp.1304-1351, 2001. ,
DOI : 10.1093/nar/28.1.33
URL : https://hal.archives-ouvertes.fr/hal-00465088
Poplar rust systematics and refinement of Melampsora species delineation. Fungal Divers, pp.227-248, 2011. ,
Recombination and the power of statistical tests of neutrality, Genetical Research, vol.74, issue.1, pp.65-79, 1999. ,
DOI : 10.1017/S0016672399003870
A LysM Receptor-Like Kinase Plays a Critical Role in Chitin Signaling and Fungal Resistance in Arabidopsis, THE PLANT CELL ONLINE, vol.20, issue.2, pp.471-481, 2008. ,
DOI : 10.1105/tpc.107.056754
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication, Nature Genetics, vol.28, issue.9, pp.982-988, 2014. ,
DOI : 10.1093/bioinformatics/bts115
On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, issue.2, pp.256-276, 1975. ,
DOI : 10.1016/0040-5809(75)90020-9
Indirect measures of gene flow and migration: FST not equal to 1/(4Nm + 1). Hered, pp.117-125, 1999. ,
The wheat powdery mildew genome shows the unique evolution of an obligate biotroph, Nature Genetics, vol.2, issue.9, pp.1092-1096, 2013. ,
DOI : 10.1073/pnas.0403715101
Evolution in Mendelian Populations, Genetics, vol.16, issue.2, pp.97-159, 1931. ,
Characterization of 41 microsatellite loci developed from the genome sequence of the poplar rust fungus, pp.Melampsora larici-populina, 2009. ,
The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication, Molecular Ecology, vol.62, issue.13, pp.2739-2755, 2011. ,
DOI : 10.1111/j.1558-5646.2008.00390.x
URL : https://hal.archives-ouvertes.fr/hal-01136973
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes, Nature Biotechnology, vol.36, issue.1, pp.105-111, 2012. ,
DOI : 10.1016/0040-5809(75)90020-9
Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity, Proceedings of the National Academy of Sciences, vol.22, issue.12, pp.14682-14687, 2011. ,
DOI : 10.1105/tpc.110.076760
Among-site rate variation and its impact on phylogenetic analyses, Trends in Ecology & Evolution, vol.11, issue.9, pp.367-372, 1996. ,
DOI : 10.1016/0169-5347(96)10041-0
URL : http://abacus.gene.ucl.ac.uk/ziheng/pdf/1996YangTREEv11p367.pdf
High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus, Nature Communications, vol.30, p.2673, 2013. ,
DOI : 10.1038/ng.2343