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Génétique Quantitative et Évolution - Le Moulon

ECLECTIC - Ecological genomics of multi-species interactions

Ecological genomics of multi-species interactions

Welcome to Amandine Cornille Lab at the Génétique Quantitative and Evolution-Le Moulon, Univ. Paris Saclay!

We use combinations of various approaches (laboratory experiments, field work, modeling, molecular biology, population genetics and genomics) for contributing to our understanding of plant diversity and of how plants, and their associated symbionts (parasites, mutualists), evolve and adapt to their environment.

Amandine Cornille has been awarded of the CNRS Paoletti prize in 2020 for her outstanding research as a young scientist in the field of biology!!!

photo apple sylvestris

ECLECTIC is attached to the LabEx SPS (Sciences des Plantes de Saclay) and to SEVE doctoral school.

See how to join the lab at the end of this webpage!


Anthony Venon
Amandine Cornille (she/her/hers) is a young CNRS scientist and group leader of the ECLECTIC team @CornilleAmand

Anthony Venon
Anthony Venon (he/him/his) is an INRAE assistant engineer (background: Cellular and Molecular biology Master, Sorbonne University, Paris, France) who works on several projects, focusing on the development of new sequencing technology in the team.

Amandine Hansart
Amandine Hansart (she/her/hers) is a CNRS engineer in agroecology. She organizes field work and vulgarization programs of the group on the wild and cultivated apple orchards.

Sergio Vazquez
Sergio Vazquez (he/him/his) is a PhD candidate (Doctoral School “Plant Science” ED 567) on the ecological and genomic bases of local adaptation of a major apple pest, the rosy apple aphid, under the supervision of Amandine Cornille. He holds a Master in Science at the University of Tsukuba in Japan (2017-2019).

Anthony Venon
Xilong Chen (he/him/his) is a postdoc supervised by Amandine Cornille, and works on the adaptive genomics of apple domestication, and before, he got his Ph.D. at Northwest A&F University, China.

Célia Lougmani
Célia Lougmani (she/her/hers) is a PhD candidate (INRAE / CLAND, Doctoral School “Plant Science” ED 567) supervised by Amandine Cornille, Karine Alix and Véronique Decroocq (INRAE Bordeaux) on the adaptive genomics of apricot and almond domestications. She holds a Master in Ecology Biodiversity and Evolution at the Univ. Paris Saclay, France.

Yuqi Nie (he/him/his) is a PhD candidate (Chinese Science Council, Doctoral School “Plant Science” ED 567) supervised by Amandine Cornille, on the adaptive genomics of fruit tree domestication.

Ronan Dodole (he/him/his) is a bioinformatician Master 2 intern (University of Rennes, France), carrying out his master 2 internship on the adaptive role of transposable elements in response to biotic stress, using the apple tree-aphid interaction as a model. He is supervised by Amandine Cornille, Amandine Hansart and Xilong Chen.

Aurélie Mesnil
Aurélie Mesnil (she/her/hers) is a postdoc working of the genomics of adaptation of fruit trees using population genomics. She got her Ph.D. at IFREMER-ASIM / IHPE, France.

Maxime Criado (he, him, his) is a master 2 student in bioinformatics (université Paris Saclay, France) working for his master 2 internship in the demonstration of co-evolved genes between apple trees and aphids. Amandine Cornille and Xilong Chen supervise him.


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Fondation BNP Paribas 2023-2026: FRUITRESCUE

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Fondation de la Recherche pour la Biodiversité

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ANR JCJC 2021-2025: Population genomics of TEs in trees (PLEASURE).

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IDEEV 2021: Role of TEs in the responses of fruit trees to abiotic and biotic stresses

La Diagonale “Coup de pouce” 2020 “Ya comme un pépin pour la planète”

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ECOTRON project 2020-2021 : Impact of climate changes on apples [http://www.cereep.ens.fr/spip.php?article9&lang=fr]

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ATIP-Avenir 2019-2021: Genomic bases of local adaptation in plant-pest interactions: insights from the cultivated apple and its aphid pests.

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Projet européen INTERREG France-Wallonie-Vlaanderen « PROVERBIO 2019-2022: “Protection des vergers par lutte biologique : une sélection adaptée des auxiliaires”", avec le soutien du Fonds européen de développement régional, Met steun van het Europees Fonds voor Regionale Ontwikkeling

La Diagonale “Coup de pouce” 2019 “Ya comme un pépin”

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IDEEV 2020: On the genomic bases of adaptation in the aphid-bacteria interaction.

European LEADER project: Building a wild apple orchad on the Saclay plateau.

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IDEEV 2017 and 2018: Assembling de novo genome of a major aphid fruit tree pest

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LabEX Biodiversity Agrosystem Climate and Society Emergence project 2016-2018 “Impact of domestication of pest adaptation to fruit trees”.


Karine Alix, AgroParisTech, France

Arnaud Lemarquand and Frédérique Didelot at Unité expérimentale horticale INRAE (UEH), France

Camille Meslin, iEES, France

Emmanuelle Jacquin-Joly, iEES, France

Fabrice Legeai, INRAE, Rennes, France

Véronique Decroocq, INRAE, Bordeaux, France

Yann Bourgeois, Porthmouth University, UK

David Chagné, The New Zealand Institute for Plant & Food Research, NZ

Stéphane Bazot, Univ. Paris Saclay, France

Dominique Lavenier, INRIA, Rennes, France

Tatiana Giraud, Univ. Paris Saclay, France

Maud Tenaillon, Univ. Paris Saclay

Ammar Alhmedi and Tim Bellien, PC-Fruit, Belgium

Enrique Dapena and Marcos Minarros, SERIDA, Asturias, Spain

Jia-Long Yao, The New Zealand Institute for Plant & Food Research Limited, Auckland

Clément Lafon-Placette, Univ. Charles, Pragues, Czech Republic

Hamed Yousefzadeh, Univ. Tarbiat Modares, Iran


We are always on the lookout for excellent students and postdocs to join the lab!

You are in the right place if you are passionate about questions in ecology, evolution, genomics, together with the applied consequences of the finding. Interested prospective bachelor, Master, PhD students or postdocs should first send Amandine Cornille their CV and a brief description of your research interests and background, career goals, and why you are interested in joining the Amandine Cornille Lab.


Génétique Quantitative et Évolution - Le Moulon
Ferme du Moulon
F-91190 Gif-sur-Yvette
e-mail : amandine.cornille[at]inrae.fr or amandine.cornille[at]universite-paris-saclay.fr
Phone: + 33 1 69 33 23 52
Google Scholar profile
Research Gate
Twitter : [@CornilleAmand] & [@PommierVerger]

ECLECTIC is attached to the LabEx SPS, Sciences des Plantes de Saclay.


  • Xilong Chen Postdoc (CNRS)
  • Amandine Cornille Group leader (CNRS)
  • Amandine Hansart (INRAE)
  • Sergio Vazquez PhD Student (INRAE)
  • Anthony Venon (INRAE)

Former members

Alexis Trang Master 2 (2022), Pierre Colençon Licence (2022), Jorge Sandoval Master 2 (2022), Augusta Teresa Bachelor 2 (2022), Ian Fiorino Bachelor 2 (2022), Remi Seraphin Master 2 (2021-2022), Alexander Gavrilov Research (2022), Manuel Derrien Bachelor (2021-2022), Yongshua Jiang Research (2020-2022), Anne Flore Didelot Master 2 (2021), Marie Bouchaud Master 2 (2021), Arsene Arvyn BTS (2021), Eglantine Berger BTS (2021), Quentin Marcou Bachelor (2021), Aurélien Boulez Master 2 (2021), Noémie Delprouve Master 2 (2021), Aurélien Forler Bachelor2 (2020), Thomas Kazmareck PhD (2019-2020), Ana Agapito Master 2 (2019), Albert Kwarterg Master 2 (2019), Hamid Bina PhD candidate (2019)


  • Chen X. , Avia K., Forler A., Remoué C., Venon A. , Rousselet A., Lucas G., Kwarteng AO., Rover R., Le Guilloux M., Belcram H., Combes V., Corti H., Olverà-Vazquez S., Falque M., Alins G., Kirisits T., Ursu TM., Roman A., Volk GM., Bazot S., Cornille A. . (2023) Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [ Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple. Annals of Botany, 6 (131) 1025-1037
  • Chen X. , Cornille A. , An N., Xing L., Ma J., Zhao C., Wang Y., Han M., Zhang D.. (2023) The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties. Molecular Ecology, 18 (32) 5125-5139
  • Tenaillon MI., Burban E., Huynh S., Wojcik A., Thuillet AC., Manicacci D., Gérard PR., Alix K., Belcram H., Cornille A. , Brault M., Stevens R., Lagnel J., Dogimont C., Vigouroux Y., Glémin S.. (2023) Crop domestication as a step toward reproductive isolation. American Journal of Botany, 7 (110) e16173
  • Amandine C., Ebert D., Stukenbrock E., Rodríguez De La Vega RC., Tiffin P., Croll D., Tellier A.. (2022) Unraveling coevolutionary dynamics using ecological genomics. Trends in Genetics, 10 (38) 1003-1012
  • Bina H., Yousefzadeh H., Venon A. , Remoué C., Rousselet A., Falque M., Faramarzi S., Chen X. , Samanchina J., Gill D., Kabaeva A., Giraud T., Hosseinpour B., Abdollahi H., Gabrielyan I., Nersesyan A., Cornille A. . (2022) Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool. Molecular Ecology, 21 (31) 5581-5601
  • Cornille A. . (2022) HDR Ecological genomics of multi-species interactions.. ,
  • Brisou G., Piquerez SJM., Minoia S., Marcel F., Cornille A. , Carriero F., Boualem A., Bendahmane A.. (2021) Induced mutations in SlE8 and SlACO1 control tomato fruit maturation and shelf-life. Journal of Experimental Botany, erab330
  • Chen X. , Cornille A. , An N., Xing L., Ma J., Zhao C., Wang Y., Han M., Zhang D.. (2021) The Siberian wild apple is an additional contributor to the genome of the cultivated European and Chinese apple. bioRxiv,
  • Denoirjean T., Doury G., Cornille A. , Chen X. , Hance T., Ameline A.. (2021) Genetic structure of Malus sylvestris and potential link with preference/performance by the rosy apple aphid pest Dysaphis plantaginea. Sci Rep, 1 (11) 5732
  • Groppi A., Liu S., Cornille A. , Decroocq S., Bui QT., Tricon D., Cruaud C., Arribat S., Belser C., Marande W., Salse J., Huneau C., Rodde N., Rhalloussi W., Cauet S., Istace B., Denis E., Carrère S., Audergon JM., Roch G., Lambert P., Zhebentyayeva T., Liu WS., Bouchez O., Lopez-Roques C., Serre RF., Debuchy R., Tran J., Wincker P., Chen X. , Pétriacq P., Barre A., Nikolski M., Aury JM., Abbott AG., Giraud T., Decroocq V.. (2021) Population genomics of apricots unravels domestication history and adaptive events. Nat Commun, 1 (12) 3956
  • Koupilová K., Koubek T., Cornille A. , Janovský Z.. (2021) Local maladaptation of the anther-smut fungus parasitizing Dianthus carthusianorum. European Journal of Plant Pathology, 2 (160) 365-374
  • Olvera-Vazquez SG., Alhmedi A., Miñarro M., Shykoff JA., Marchadier E., Rousselet A., Remoué C., Gardet R., Degrave A., Robert P., Chen X. , Porchier J., Giraud T., Vander-Mijnsbrugee K., Raffoux X., Falque M., Alins G., Didelot F., Beliën T., Dapena E., Lemarquand A., Cornille A. . (2021) Experimental test for local adaptation of the rosy apple aphid (Dysaphis plantaginea) to its host (Malus domestica) and to its climate in Europe. PCI Ecology, (Pre-registration version)
  • Olvera-Vazquez SG., Remoué C., Venon A. , Rousselet A., Grandcolas O., Azrine M., Momont L., Galan M., Benoit L., David GM., Alhmedi A., Beliën T., Alins G., Franck P., Haddioui A., Jacobsen SK., Andreev R., Simon S., Sigsgaard L., Guibert E., Tournant L., Gazel F., Mody K., Khachtib Y., Roman A., Ursu TM., Zakharov IA., Belcram H., Harry M., Roth M., Simon JC., Oram S., Ricard JM., Agnello A., Beers EH., Engelman J., Balti I., Salhi-Hannachi A., Zhang H., Tu H., Mottet C., Barrès B., Degrave A., Razmjou J., Giraud T., Falque M., Dapena E., Miñarro M., Jardillier L., Deschamps P., Jousselin E., Cornille A. . (2021) Large-scale geography survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa. Peer Community Journal, (1)
  • İltaş Ömer., Svitok M., Cornille A. , Schmickl R., Lafon Placette C.. (2021) Early evolution of reproductive isolation: A case of weak inbreeder/strong outbreeder leads to an intraspecific hybridization barrier in Arabidopsis lyrata. Evolution, 6 (75) 1466-1476
  • Cornille A. , Antolín F., Garcia E., Vernesi C., Fietta A., Brinkkemper O., Kirleis W., Schlumbaum A., Roldán-Ruiz I.. (2019) A Multifaceted Overview of Apple Tree Domestication. Trends in Plant Science, 8 (24) 770 - 782
  • Hartmann FE., Rodríguez de la Vega RC., Carpentier F., Gladieux P., Cornille A. , Hood ME., Giraud T.. (2019) Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annu. Rev. Phytopathol., 1 (57) annurev-phyto-082718-095947
  • Liu S., Cornille A. , Decroocq S., Tricon D., Chague A., Eyquard JP., Liu WS., Giraud T., Decroocq V.. (2019) The complex evolutionary history of apricots: species divergence, gene flow and multiple domestication events. Mol Ecol, mec.15296
  • Peace CP., Bianco L., Troggio M., van de Weg E., Howard NP., Cornille A. , Durel CE., Myles S., Migicovsky Z., Schaffer RJ., Costes E., Fazio G., Yamane H., van Nocker S., Gottschalk C., Costa F., Chagné D., Zhang X., Patocchi A., Gardiner SE., Hardner C., Kumar S., Laurens F., Bucher E., Main D., Jung S., Vanderzande S.. (2019) Apple whole genome sequences: recent advances and new prospects. Hortic Res, 1 (6) 59
  • Ruhsam M., Jessop W., Cornille A. , Renny J., Worrell R.. (2019) Crop-to-wild introgression in the European wild apple Malus sylvestris in Northern Britain. Forestry (Lond), 1 (92) 85-96
  • Volk GM., Cornille A. , Korban SS.. (2019) Genetic Diversity and Domestication History in Pyrus. Springer Link, 51-62
  • Feurtey A., Cornille A. , Shykoff JA., Snirc A., Giraud T.. (2017) Crop‐to‐wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe. Evolutionary Applications, 2 (10) 180-188
  • Petit E., Silver C., Cornille A. , Gladieux P., Rosenthal L., Bruns E., Yee S., Antonovics J., Giraud T., Hood ME.. (2017) Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Molecular Ecology, 7 (26) 1877-1890
  • Cornille A. , Salcedo A., Kryvokhyzha D., Glémin S., Holm K., Wright SI., Lascoux M.. (2016) Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Molecular Ecology, 2 (25) 616–629
  • Decroocq S., Cornille A. , Tricon D., Babayeva S., Chague A., Eyquard JP., Karychev R., Dolgikh S., Kostritsyna T., Liu S., Liu W., Geng W., Liao K., Asma BM., Akparov Z., Giraud T., Decroocq V.. (2016) New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Molecular Ecology, 19 (25) 4712–4729
  • Feurtey A., Gladieux P., Hood ME., Snirc A., Cornille A. , Rosenthal L., Giraud T.. (2016) Strong phylogeographic co-structure between the anther-smut fungus and its white campion host. New Phytologist, 3 (212) 668-679
  • Kryvokhyzha D., Holm K., Chen X. , Cornille A. , Glémin S., Wright S., Lagercrantz U., Lascoux M.. (2016) The influence of demographic history on gene expression variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). , 1106-21
  • Cornille A. , Feurtey A., Gélin U., Ropars J., Misvanderbrugge K., Gladieux P., Giraud T.. (2015) Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evolutionary Applications, n/a-n/a
  • Leforestier D., Ravon E., Muranty H., Cornille A. , Lemaire C., Giraud T., Durel CE., Branca A.. (2015) Genomic basis of the differences between cider and dessert apple varieties. Evolutionary Applications, 7 (8) 650-661
  • Yao JL., Xu J., Cornille A. , Tomes S., Karunairetnam S., Luo Z., Bassett H., Whitworth C., Rees-George J., Ranatunga C., Snirc A., Crowhurst R., de Silva N., Kumar S., Chagne D., Bus V., Volz R., Rikkerink E., Gardiner SE., Giraud T., Newcomb R., MacDiarmid R., Gleave AP.. (2015) A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal, 417-427
  • Cornille A. , Giraud T., Smulders MJM., Roldán-Ruiz I., Gladieux P.. (2014) The domestication and evolutionary ecology of apples. Trends in Genetics, 2 (30) 57-65
  • Schnitzler A., Arnold C., Cornille A. , Bachmann O., Schnitzler C.. (2014) Wild European Apple (Malus sylvestris (L.) Mill.) Population Dynamics: Insight from Genetics and Ecology in the Rhine Valley. Priorities for a Future Conservation Programme. PLoS ONE, 5 (9) e96596
  • Yuan JH., Cornille A. , Giraud T., Cheng FY., Hu YH.. (2014) Independent domestications of cultivated tree peonies from different wild peony species. Molecular Ecology, 1 (23) 82-95
  • Cornille A. , Gladieux P., Giraud T.. (2013) Crop‐to‐wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple. Evol Appl, 5 (6) 737-748
  • Cornille A. , Giraud T., Bellard C., Tellier A., Le Cam B., Smulders MJM., Kleinschmit J., Roldan-Ruiz I., Gladieux P.. (2013) Postglacial recolonization history of the European crabapple ( Malus sylvestris Mill.), a wild contributor to the domesticated apple. Mol Ecol, 8 (22) 2249-2263
  • Cornille A. , Underhill JG., Cruaud A., Hossaert-McKey M., Johnson SD., Tolley KA., Kjellberg F., van Noort S., Proffit M.. (2012) Floral volatiles, pollinator sharing and diversification in the fig–wasp mutualism: insights from Ficus natalensis, and its two wasp pollinators (South Africa). Proceedings of the Royal Society of London B: Biological Sciences, 1734 (279) 1731-1739
  • Cornille A. , Gladieux P., Smulders MJ., Roldan-Ruiz I., Laurens F., Le Cam B., Nersesyan A., Clavel J., Olonova M., Feugey L., Gabrielyan I., Zhang XG., Tenaillon MI., Giraud T.. (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS genetics, 5 (8) e1002703
  • Lê Van A., Gladieux P., Lemaire C., Cornille A. , Giraud T., Durel CE., Caffier V., Le Cam B.. (2012) Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host. Evolutionary Applications, 7 (5) 694-704