REFERENCES
Adreit, H., Santoso,
Andriantsimialona, D., Utami, D. W., Nottéghem, J. L., Lebrun, M.-H., &
Tharreau, D. (2007). Microsatellite markers for population studies of
the rice blast fungus, Magnaporthe grisea. Molecular Ecology
Notes , 7 , 667–670.
Ali, S., Gladieux, P., Leconte, M., Gautier, A., Justesen, A. F.,
Hovmoller, M. S., … De Vallavieille-Pope, C. (2014). Origin,
migration routes and worldwide population genetic structure of the wheat
yellow rust pathogen Puccinia striiformis f.sp. Tritici. PLOS
Pathogens , 10 , e1003903–e1003903. doi:
10.1371/journal.ppat.1003903
Arbealz, J. D., Moreno, L. T., Singh, N., Tung, C. W., Maron, L.,
Ospina, Y., … McCouch, S. (2015). Development and GBS-‐
genotyping of introgression lines (ILs) using two wild species of rice,
O. meridionalis and O. rufipogon, in a common recurrent parent, O.
sativa cv. Curinga. Molecular Breeding , 35 , 81.
Blanquart, F., Klatz, O., Nuismer, S. L., & Gandon, S. (2013). A
practical guide to measuring local adaptation. Ecology Letters ,16 , 1195–1205.
Brown, J. . K. M. (1994). Chance and selection in the evolution of
barley mildew. Trends in Microbiology , 2 , 470–475.
Bryant, D., & Moulton, V. (2004). Neighbor-Net: An agglomerative method
for the construction of phylogenetic networks. Molecular Biology
and Evolution , 21 , 255–265.
Burdon, J. J., & Thrall, P. H. (2008). Pathogen evolution across the
agro‐ecological interface: Implications for disease management.Evolutionary Applications , 1 , 57–65.
Burdon, J. J., & Thrall, P. H. (2014). What have we learned from
studies of wild plant-pathogen associations?—The dynamic interplay of
time, space and life-history. European Journal of Plant
Pathology , 138 , 417–429.
Chentoufi, L., Sahri, A., Arbaoui, M., Belqadi, L., Birouk, A., Roumet,
P., & Muller, M.-. H. (2014). Anchoring durum wheat diversity in the
reality of traditional agricultural systems: Varieties, seed management,
and farmers’ perception in two Moroccan regions. J Ethnobiol
Ethnomed , 10 . doi: 10.1186/1746-4269-10-58
De Mita, S., & Siol, M. (2012). EggLib: Processing, analysis and
simulation tools for population genetics and genomics. BMC
Genetics , 13 (1), 27–27. doi: 10.1186/1471-2156-13-27
de Vallavieille-Pope, C., Ali, S., Leconte, M., Enjalbert, J., Delos,
M., & Rouzet, J. (2012). Virulence dynamics and regional structuring of
Puccinia striiformis f. Sp. Tritici in France between 1984 and 2009.Plant Disease , 96 , 131–140.
Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T.
K., Orbach, M. J., … Birren, B. W. (2005). The genome sequence of
the rice blast fungus Magnaporthe grisea. Nature ,434 (7036), 980–986.
Dean, R., Van Kan, J., Pretorius, Z. A., Hammond-Kosack, K. E., Pietro,
A., Spanu, P. D., … Foster, G. D. (2012). The top 10 fungal
pathogens in molecular plant pathology. Molecular Plant
Pathology , 13 , 414–430.
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K.,
Buckler, E. S., & Mitchel, S. E. (2011). A robust, simple
genotyping-by-sequencing (GBS) approach for high diversity species.PLoS One , 6 , e19379–e19379.
Feuillet, C., Langridge, P., & Waugh, R. (2008). Cereal breeding takes
a walk on the wild side. Trends in Genetics , 24 , 24–32.
Gallet, R., Bonnot, F., Milazzo, J., Adreit, H., Ravigne, V., Tharreau,
D., & Fournier, E. (2014). The variety mixture strategy assessed in a G
× G experiment with rice and the blast fungus Magnaporthe oryzae.Frontiers in Genetics , 4 , 312–312.
Gallet, R., Fontaine, C., Bonnot, F., Milazzo, J., Tertois, C., Adreit,
H., … Tharreau, D. (2016). Ecology and epidemiology evolution of
compatibility range in the rice_Magnaporthe oryzae system: An uneven
distribution of R genes between rice subspecies. Phytopathology ,106 , 348–354.
Gao, D., Mao, R., & Zhu, Y. (2012). Comparative Studies on
Intra-varietal Heterogeneity between Rice Landraces and Improved
Varieties. Rice Genomics and Genetics , 3 , 25–32.
Giraud, T., Gladieux, P., & Gavrilets, S. (2010). Linking the emergence
of fungal plant diseases with ecological speciation. Trends in
Ecology & Evolution , 25 , 387–395.
Gladieux, P., Feurtey, A., Hood, M. E., Snirc, A., Clavel, J., Dutech,
C., … Giraud, T. (2015). The population biology of fungal
invasions. Molecular Ecology , 24 , 1969–1986.
Gladieux, P., Guérin, F., Giraud, T., Caffier, V., Lemaire, C., Parisi,
L., … Le Cam, B. (2011). Emergence of novel fungal pathogens by
ecological speciation: Importance of the reduced viability of
immigrants. Molecular Ecology , 20 , 4521–4532.
Gladieux, P., Ravel, S., Rieux, A., Cros-Arteil, S., Adreit, H.,
Milazzo, J., … Tharreau, D. (2018). Coexistence of Multiple
Endemic and Pandemic Lineages of the Rice Blast Pathogen. MBio ,9 (2). Retrieved from
http://mbio.asm.org/content/9/2/e01806-17.abstract
Goyeau, H., Halkett, F., Zapater, M. F., Carlier, J., & Lannou, C.
(2007). Clonality and host selection in the wheat pathogenic fungus
Puccinia triticina. Fungal Genetics and Biology , 44 ,
474–483.
Goyeau, H., Park, R., Schaeffer, B., & Lannou, C. (2006). Distribution
of Pathotypes with Regard to Host Cultivars in French Wheat Leaf Rust
Populations. Plant Pathology , 96 , 264–273.
Guérin, F., Gladieux, P., & Le Cam, B. (2007). Origin and colonization
history of newly virulent strains of the phytopathogenic fungus Venturia
inaequalis. Fungal Genetics and Biology , 44 , 284–292.
He, X., Yan, S., Dong, G., Fugang, W., Lei, P., Cunwu, G., …
Youyong, Z. (2011). Comparison of Agronomic Traits between Rice
Landraces and Modern Varieties at Different Altitudes in the Paddy
Fields of Yuanyang Terrace, Yunnan Province. Journal of Resources
and Ecology , 2 (1), 46–50. doi:
10.3969/j.issn.1674-764x.2011.01.007
Hill, W. G. (2001). Selection Intensity. In Encyclopedia of
Genetics (pp. 1793–1794).
Jackman, S. D., Vandervalk, B. P., Mohamadi, H., Chu, J., Yeo, S.,
Hammond, A., … Birol, I. (2017). ABySS 2.0:
Resource-efficient assembly of large genomes using a Bloom filter .27 , 768–777.
Jiao, Y., Li, X., Liang, L., Takeuchi, K., Okuro, T., Zhang, D., & Sun,
L. (2012). Indigenous ecological knowledge and natural resource
management in the cultural landscape of China’s Hani Terraces.Ecological Resources , 27 , 247–263.
Jombart, T., Devillard, S., & Balloux, F. (2010). Discriminant analysis
of principal components: A new method for the analysis of genetically
structured populations. BMC Genetics , 11 , 95
http://www.biomedcentral.com/1471-2156/11/94.
Kamvar, Z. N., Tabima, J. F., & Grünwald, N. J. (2014). Poppr: An R
package for genetic analysis of populations with clonal, partially
clonal, and/or sexual reproduction. PeerJ , 2 , e281
http://dx.doi.org/10.7717/peerj.281-e281
http://dx.doi.org/10.7717/peerj.281.
Kniskern, J. M., Barrett, L. G., & Bergelsong, J. (2011). Maladaptation
in wild populations of the generalist plant pathogen Pseudomonas
syringae. Evolution , 65 , 818–830.
Laine, A.-L. (2007). Detecting local adaptation in a natural
plant–pathogen metapopulation: A laboratory vs. Field transplant
approach. Journal of Evolutionary Biology , 20 , 1665–1673.
Langella, O. (2008). POPULATIONS 1.2.3, Logiciel de génétique des
populations . Laboratoire Populations, Génétique et évolution, CNRS,
91190 Gif-sur-Yvette, France.
Latorre, S. M., Reyes-Avila, C. S., Malmgren, A., Win, J., Kamoun, S.,
& Burbani, H. A. (2020). Differential loss of effector genes in three
recently expanded pandemic clonal lineages of the rice blast fungus.BMC Biology , 18 , 1–15.
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment
with Burrowsâ\euro“Wheeler transform. Bioinformatics ,25 (14), 1754–1760.
Liao, J., Huang, H., Meusnier, I., Ducasse, A., Bonnot, F., Pan, L.,
… Morel, J.-B. (2016). Pathogen effectors and plant immunity
determine specialization of the blast fungus to rice subspecies.ELife , 5 , e19377–e19377.
McDonald, B. A. (2014). Using dynamic diversity to achieve durable
disease resistance in agricultural ecosystems. Tropical Plant
Pathology , 39 , 191–196.
Monat, C., Tranchant-Dubreuil, C., Kougbeadjo, A., Farcy, C.,
Ortega-Abboud, E., Amanzougarene, S., … Sabot, F. (2015). TOGGLE:
toolbox for generic NGS analyses. BMC Bioinformatics , 16 ,
374–374.
Parker, I. M., & Gilbert, G. S. (2004). The evolutionary ecology of
novel plant-pathogen interactions. Annual Review of Ecology,
Evolution, and Systematics , 35 , 675–700.
Pau, G., Fuchs, F., Sklyar, O., Boutros, M., & Huber, W. (2010).
EBImage—An R package for image processing with applications to
cellular phenotypes. Bioinformatics , 26 , 979–981.
Pickrell, J. K., & Pritchard, J. K. (2012). Inference of Population
Splits and Mixtures from Genome-Wide Allele Frequency Data. PLOS
Genetics , 8 (11), e1002967–e1002967.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R.,
Bender, D., … Sham, P. C. (2017). PLINK: A Tool Set for
Whole-Genome Association and Population-Based Linkage Analyses.The American Journal of Human Genetics , 81 (3), 559–575.
doi: 10.1086/519795
Raj, A., Stephens, M., & Pritchard, J. K. (2014). FastSTRUCTURE:
Variational Inference of Population Structure in Large SNP Data Sets.Genetics , 197 (2), 573 LP – 589.
Sahri, A., Chentoufi, L., Arbaoui, M., Ardisson, M., Belqadi, L.,
Birouk, A., … Muller, M.-H. (2014). Towards a comprehensive
characterization of durum wheat landraces in Moroccan traditional
agrosystems: Analysing genetic diversity in the light of geography,
farmers’ taxonomy and tetraploid wheat domestication history. BMC
Evolutionary Biology , 14 (1), 264–264. doi:
10.1186/s12862-014-0264-2
Saleh, D., Milazzo, J., Adreit, H., Fournier, E., & Tharreay, D.
(2014). South-East Asia is the center of origin, diversity and
dispersion of the rice blast fungus, Magnaporthe oryzae. New
Phytologist , 201 , 1440–1456.
Saleh, D., Xu, P., Shen, Y., Li, C., Adreit, H., Milazzo, J., …
Tharreau, D. (2012). Sex at the origin: An Asian population of the rice
blast fungus Magnaporthe oryzae reproduces sexually. Molecular
Ecology , 21 , 1330–1344.
Schulze-Lefert, P., & Panstruga, R. (2011). A molecular evolutionary
concept connecting nonhost resistance, pathogen host range, and pathogen
speciation. Trends Plant Sci 16(3):1 17-25. Trends in Plant
Sciences , 16 , 17–25.
Sheng, G. (1990). Yuanyang county chronicles(in Chinese).Gui-Yang: Gui Zhou National Press , pp. 94–127.
Silué, D., & Nottéghem, J. L. (1990). Production of perithecia of
Magnaporthe grisea on rice plants. Mycological Research ,94 , 1151 1152-1151 1152.
Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis
and post-analysis of large phylogenies. Bioinformatics ,30 (9), 1312–1313.
Stukenbrock, E. H., & McDonald, B. A. (2008). The origins of plant
pathogens in agro-ecosystems. Annual Review of Phytopathology ,46 , 75–100.
Thach, T., Ali, St., T. ,. Ali, S. ,. de Vallavieille-Pope, C. ,.
Justesen, A. F. ,. &. Hovmøller, M. S. (2016). Worldwide population
structure of the wheat rust fungus Puccinia striiformis in the past.
Fungal Genetics and Biology, 87, 1–8., de Vallavieille-Pope, C.,
Justesen, A. F., & Hovmøller, M. S. (2016). Worldwide population
structure of the wheat rust fungus Puccinia striiformis in the past.Fungal Genetics and Biology , 87 , 1–8.
Tharreau, D., Fudal, I., Andriantsimialona, D., Santoso, Utami, D.,
Fournier, E., … Nottéghem, J.-L. (2009). World population
structure and migration of the rice blast fungus, Magnaporthe oryzae. InAdvances in genetics genomics and control of rice blast disease
(2009) (pp. 209–215). Springer Netherlands.
Thierry, M., Milazzo, J., Adreit, H., Ravel, S., Borron, S., Sella, V.,
… Gladieux, P. (2021). Ecological differentiation and incipient
speciation in the fungal pathogen causing rice blast. BioRxiv ,2020.06.02.129296 .
Tilman, D. (2011). Global food demand and the sustainable
intensification of agriculture. Proceeding of National Academy of
Science , 108 , 20260–20264.
Valent, B., Crawford, M. S., Weaver, C. G., & Chumley, F. G. (1986).
Genetic studies of fertility and pathogenicity in Magnaporthe grisea
(Pyricularia oryzae). Iowa State Journal of Research , 60 ,
569–594.
Yang, L., Liu, M., Lun, F., Yuan, Z., Zhang, Y., & Min, Q. (2017). An
analysis on crops choice and its driving Factors in Agricultural
Heritage Systems – A Case of Honghe Hani Rice Terraces System.Sustainability , 9 , 1162.
Zhan, J., & McDonald, B. A. (2013). Field-based experimental evolution
of three cereal pathogens using a mark–release–recapture strategy.Plant Pathology , 62 , 106–114.
Zhan, J., Thrall, P. H., Papaïx, J., Xie, L., & Burdon, J. J. (2015).
Playing on a pathogen’s weakness: Using evolution to guide sustainable
plant disease control strategies. Annual Review of
Phytopathology , 53 , 19–43.
Zhang, C., Dong, S.-S., Xu, J.-Y., He, W.-M., & Yang, T.-L. (2019).
PopLDdecay: A fast and effective tool for linkage disequilibrium decay
analysis based on variant call format files. Bioinformatics ,35 , 1786–1788.
Zhong, Z., Chen, M., Lin, L., Han, Y., Bao, J., & Tang, W. (2018).
Population genomic analysis of the rice blast fungus reveals specific
events associated with expansion of three main clades. The ISME
Journal , 12 , 1867–1878.