Tatiana GIRAUD

• Speciation in fungal pathogens : theory, comparative analyses, population genetics, population genomics, experiments, mainly on Microbotryum spp., the fungi responsible for the anther smut disease on Caryophyllaceae
• Evolutionary processes acting in the domestication of cheese and salami fungi (Penicillium)
• Evolution of mating-type chromosomes
• Evolution of modes of reproduction and mating systems in fungi
• Evolution of virulence and multiple infections in fungal plant pathogens, in particular in Microbotryum violaceum, and role of kin selection
• Speciation, domestication and gene flow in apple trees (Malus domestica, Malus sylvestris, Malus sieversii)
• Evolutionary causes responsible for plant disease emergence: host shifts and biological invasions
• Cospeciation versus host jumps in parasites

Topics description

to know more about our past achievements

to know more about our ongoing work

• Ecology and Evolution, Ecole Polytechnique (80h/year) 2009-2021
• Biodiversity and Ecosystèmes College de France 2021-2022
• Speciation, University Paris Saclay and Sorbonne University

Outreach video ont he evolution of plant pathogens (3 min) :

Outreach movie on sex chromosome evolution (5 minutes) :

Video on our research on the loss of diversity in cheese fungi :

Cours College de France online (in French):

https://www.college-de-france.fr/site/tatiana-giraud/index.htm

Speech at the French Academy of Science :

• 2021 – Elected Collège de France chaire annuelle Biodiversité et Ecosystèmes
  
• 2019 – Elected member of the French Academy of Sciences
  
• 2017 – Research Prize from the French Society of Ecology and Evolution
• 2017 – Grand Prix scientifique from the Louis D. Fondation Institut de France (French Academy of Sciences)
• 2015 – CNRS silver medal
• 2009 – Senior CNRS scientist
• 2006 – CNRS Bronze medal
• 15/06/04 – HDR diploma
• Since 2001 – CNRS scientist at the University Paris Sud
• 2000 – 2001 post-doc, University Paris Sud
• 1999 – 2000 post-doc, University Lausanne, Laurent Keller lab
• 1998-1999 assistant professor, University Paris 13, Pierre Jaisson lab
• 1995-1998 PhD, INRA Versailles, Yves Brygoo lab
• 1995 Master 2 Biodiversity and Evolution, University Paris 6, Pierre Capy lab
• 1992-1995 INA-PG

• 2010-present : senior editor Molecular Ecology
• 2017-present : managing board PCI Evol Biol
• 2023-present : editor Genome Biology and Evolution
• 2020-2023: editor Elife
• 2019-2021: associate editor Evolution
• 2010-2016: associate editor Molecular Ecology
• 2005-2012: associate editor Genetica
• 2009-2012: associate editor Infections, Genetics and Evolution

• ERC Advanced Grant 2019-2025 EvolSexChrom (PI)

https://www.college-de-france.fr/agenda/colloque/evolution-of-sex-chromosomes-and-supergenes/stepwise-recombination-suppression-on-fungal-mating-type-chromosomes-without-sexual-antagonism

https://www.college-de-france.fr/agenda/colloque/evolution-of-sex-chromosomes-and-supergenes/sheltering-of-deleterious-mutations-can-explain-the-stepwise-extension-of-recombination-suppression

• ANR Fungadapt 2020-2024 : Adaptation of cheese fungi
• Fondation Louis D. Institut de France 2017-2023 (PI)
• ERC Proof of Concept Grant 2017-2019 BLUE (PI)
• ERC Consolidating grant 2013-2018 GenomFun Adaptive divergence in fungi (PI)
• ANR GANDALF 2012-2016 : Genomic AND Adaptation for fungal LiFe history traits involved in host plant interactions.
• Interdisciplinary project (PIR CNRS) 2012 : médiation de la Biodiversité
• Paris region project on apple tree domestication (PI) 2012-2015
• ANR project « Fungi sex – Evolution of fungal mating types and fungal sex chromosomes” (PI) 2009 -2012
• ANR project Emerfundis «Emerging fungal diseases» Co-PI of with J. Carlier (CIRAD – UMR BGPI) 2008-2010
• ANR project « SpeciaFonge – Specificities of speciation in fungal pathogens” (PI) 2006 -2010
• ACI JC project « Speciation in parasites » (PI) 2003-2006

Current team

Alodie Snirc (IE CNRS), Jeanne Ropars (CR CNRS), Ricardo Rodriguez de la Vega (IR CNRS), Fanny Hartmann (MdC), Guislaine Refrégier (MdC), Amandine Labat (Tech AgroParisTech), Agathe Ballu (MdC AgroParisTech), Ewen Crequer (Thèse), Pierre Veron (Thèse), Elizabeth Chahine (CDD IE), Loreleï Boyer (Post-doc), Quentin Rougemont (Post-doc), Alice Namias (Post-doc), Pauline Michel (Thèse), Elise Lucotte (post-doc), Elsa de Filippo (Thèse), Ariel Offenstadt (Thèse), Lou Guyot (M2).

Alumni

– Master students: Anne Thomas, Aurélien Tellier, Ytournel Florence, Noel Véronique, Violaine Llaurens, Delphine Thévenet, Sylvain Marthey, Amélie Coantic, Damien de Vienne, Florian Jabbour, Benjamin Devier, Amanda Danae Thivaiou, Flavie Courjol, Ludovic Le Renard, Amira Aschi, Frédéric Labbé, Lorenza Buono, Alice Feurtey, Mathilde Delaunay, Jade Bruxaux, William Fontanaud, Charly Chauveau, Jérôme Chapuis, Thiviya Thiruvalluvar, Pilar Rodriguez, Elise Fruitet, Marine Duhamel, Estelle Didiot, Nina Vittorelli

– PhD students : Manuela Lopez-Villavicencio, Benjamin Genton, Mickaël Le Gac, Damien de Vienne, Benjamin Devier, Amandine Cornille, Hélène Badouin, Diane Leforestier, Emanuela Kerschbamer, Alice Feurtey, Ying-Chu Lo, Fantin Carpentier, Thibault Caron, Marine Duhamel, Bastien Bennetot, Emilie Tezenas

– PhD students (visiting, 4 months): Lily Peck, William Beckerson

– Post-docs : Lorys Villaréal, Roxana Yockteng, Guislaine Refrégier, Sylvain Billard, Manuela Lopez-Villavicencio, Carole Smadja, Gabriela Aguileta, Elodie Vercken, Pierre Gladieux, Michael Fontaine, Elsa Petit, Eric Fontanillas, Ricardo Rodriguez de la Vega, Jeanne Ropars, Amandine Cornille, Emilie Dumas, Taiadjana Fortuna, Noppol Kobmoo, Sara Branco, Fanny Hartmann, Yunyoung Kwak, Jade Bruxaux, Ozgur Taskent, Maud Thierry, Paul Jay, Thibault Caron, Marine Duhamel

– Technical staff: Stéphanie Le Prieur, Laetitia Giraud, Gilles Deparis, Sylvain Marthey, Myriam Berramdane, Emilie Levert

– Maître de Conférences : Antoine Branca

Preprints

• Kaczmarek T, Chen X, Fior S, Venon A, Roman A, Ursu T, Giraud T, Mezhenskyj V, Koupilova K, Hood ME, Widmer A, Cornille A (2023) Sequential colonization events with restricted gene flow in a widespread European carnation species. https://doi.org/10.1101/2023.07.23.550186
• Moraga Carol, Branco Catarina, Rougemont Quentin, Veltsos Paris, Jedlička Pavel, Muyle Aline, Hanique Melissa, Tannier Eric, Liu Xiaodong, Mendoza-Galindo Eddy, Lemaitre Claire, Fields Peter, Cruaud Corinne, Labadie Karine, Belser Caroline, Briolay Jerome, Santoni Sylvain, Cegan Radim, Linheiro Raquel, Ricardo C. Rodriguez de la Vega, Adam Gabriele,  El Filali Adil, Mossion Vinciane, Boualem Adnane, Tavares Raquel, Chebbi Amine, Cordaux Richard, Fruchard Cécile, Prentout Djivan, Velt Amandine, Spataro Bruno, Delmotte Stephane, Weingartner Laura, Toegelova Helena, Tulpová Zuzana, Capal Petr, Šimková Hana, Štorchová Helena, Krüger Manuela, Abeyawardana Oushadee, Taylor Douglas, Olson Matthew, Sloan Daniel, Karrenberg Sophie, Delph Lynda, Charlesworth Deborah, Giraud Tatiana, Bendahmane Abdelhafid, Genova Alex, Madoui Amin, Hobza Roman, Marais Gabriel (2023) The Silene latifolia genome and its giant Y chromosome.  https://www.biorxiv.org/content/10.1101/2023.09.21.558754v1.full.pdf
• Peck L. D., T. Llewellyn, B. Bennetot, S. O’Donnell, R. W. Nowell, M. J. Ryan, J. Flood, R. Rodriguez de la Vega, J. Ropars, T. Giraud, P. D. Spanu and T. G. Barraclough. (2024) Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease https://doi.org/10.1101/2023.12.22.572981
• Crequer Ewen, Coton Emmanuel, Cueff Gwennina, Cristiansen Johan, Frisvad Jens, Rodriguez de la Vega Ricardo, Giraud Tatiana, Jany Jean-Luc, Coton Monika (2024) Different metabolite profiles across Penicillium roqueforti populations associated with ecological niche specialisation and domestication https://doi.org/10.1101/2024.01.12.575369
• Caron Thibault $, Crequer Ewen $, Le Piver M, Le Prieur S, Chauvin C, Brunel S, Snirc A, Vernadet JP, Roueyre D, Place M, Coton M, Coton E, Rodriguez de la vega R, Foulongne-Oriol* M, Branca* A, Giraud* T, Generation of diversity in the blue cheese mold Penicillium roqueforti by crosses between clonal lineages and QTL mapping for key phenotypes * co-senior authors $ co-first authors https://www.biorxiv.org/content/10.1101/2024.02.22.581506v1
• Lucotte E, Jay P, Rougemont R, Boyer L, Cornille C, Snirc A, Labat A, Chahine E, Duhamel D, Gendelman J, Hayes RK, Perlin MH, Hood* ME, Rodriguez de la Vega* R Giraud* T.  Loss of function of HD mating-type genes in anther-smut fungi and recombination suppression without mating-type locus linkage *cosenior authors Repeated loss of function at HD mating-type genes and of recombination suppression without mating-type locus linkage in anther-smut fungi https://doi.org/10.1101/2024.03.03.583181
• Hartmann FE, Rodriguez de la Vega RC, Rougemont Q, Deméné A, Badet T, Croll D, Labat A, Prospero S, Snirc A, Stauber L, Dutech C, Giraud T. Million years old recombination suppression and balancing selection in a region linked to the mating-type locus in the invasive chestnut blight fungal pathogen Cryphonectria parasitica

2024

• Jay Paul, Jeffries Daniel, Hartmann Fanny, Véber Amandine, Giraud Tatiana (2024) Why do sex chromosomes progressively lose recombination? Trends in Genetics
• Giraud T avec Marie Ameller 2024 « L’attention au Vivant » Editions de l’observatoire
• Lorena Ament-Velásquez S., Vogan Aaron A., Wallerman Ola, Hartmann Fanny, Gautier Valérie, Silar Philippe, Giraud Tatiana, Hanna Johannesson. High-quality genome assemblies of four members of the Podospora anserina species. GBE. https://doi.org/10.1093/gbe/evae034
• Fountain-Jones Nicholas M., Tatiana Giraud, Lucie Zinger, Holly Bik, Simon Creer & Elin Videvall (2024) Molecular ecology and microbiomes in the wild: methodological advances, common pitfalls and future directions. Molecular Ecology https://doi.org/10.1111/mec.17

2023

• Duhamel Marine, Hood* Michael E., Rodríguez de la Vega* Ricardo C., Giraud* Tatiana. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi* co-senior authors Nature Communications 14:5692   https://doi.org/10.1038/s41467-023-41413-4
  
• Crequer Ewen, Ropars Jeanne , Jany Jean-Luc, Caron Thibault, Coton Monika, Snirc Alodie,  Vernadet Jean-Philippe, Branca Antoine, Giraud* Tatiana, Coton Emmanuel * (2023) A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche * co-senior authors.  Evolutionary Applications 16 : 1438-1457 DOI: 10.1111/eva.13578.
• Lo Ying-Chu, Bruxaux Jade, Rodríguez de la Vega Ricardo C, Snirc Alodie, Coton Monika, Le Piver Mélanie, Le Prieur Stéphanie, Roueyre Daniel, Dupont Joëlle, Houbraken Jos, Debuchy Robert, Ropars Jeanne, Giraud* Tatiana and Branca* Antoine (2023) Footprints of domestication in dry-cured meat Penicillium fungi: convergent specific phenotypes and horizontal gene transfers. * co-senior authors. Evolutionary Applications 16: 1637-1660. * Co-senior authors https://doi.org/10.1111/eva.13591
• Tezenas Emilie, Giraud* Tatiana, Véber* Amandine, and Billiard* Sylvain, * co-senior authors (2023) The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing. PCI Evol Biol https://doi.org/10.24072/pcjournal.238. Recommended by PCI Evol Biol : Aurelien Tellier (2023) Maintenance of deleterious mutations and recombination suppression near mating-type loci under selfing. Peer Community Journal 3 : e14. DOI: 10.24072/pcjournal.238. https://doi.org/10.24072/pcjournal.238.
• Vittorelli Nina, Snirc Alodie, Levert Emilie, Gauthier Valérie, Lalanne Christophe, de Filippo Elsa, Rodriguez de la Vega Ricardo C., Gladieux Pierre, Grigoriev Igor, Debuchy Robert,  Silar Philippe, Giraud Tatiana,  Hartmann Fanny E. (2023) Stepwise recombination suppression around the mating-type locus in the fungus Schizothecium tetrasporum. PLoS Genetics https://doi.org/10.1371/journal.pgen.1010347
• Bennetot Bastien, Vernadet Jean-Philippe, Perkins Vincent, Hautefeuille Sophie, Rodríguez de la Vega Ricardo C., Snirc Alodie, Lessard Marie-Hélène, Peron Anne-Claire, Labrie Steve, Landaud Sophie, Giraud Tatiana, Ropars Jeanne (2022) Domestication of different varieties in the cheese-making fungus Geotrichum candidum  Recommended by PCI Evol Biol. Peer Community Journal 10.24072/pcjournal.266 – Volume 3 (2023), article no. e45
• Giraud Tatiana, Ropars Jeanne, Stukenbrock Eva H., Amato Katherine Ryan, Rodriguez de la Vega Ricardo (2023) Evolutionary ecology of human-associated microbes. Special issue introduction. Molecular Ecology. 10.1111/mec.16966

2022

• Jay P, Tezenas E, Veber A, Giraud T. (2022) Modeling the stepwise extension of recombination suppression on sex chromosomes and other supergenes through deleterious mutation sheltering. PloS Biology PLoS Biol 20(7): e3001698. https://doi.org/10.1371/journal.pbio.3001698
• Duhamel Marine, Carpentier Fantin, Begerow Dominik, Hood* Michael E., Rodríguez de la Vega* Ricardo C., Giraud* Tatiana. (2022) Onset and stepwise extensions of recombination suppression are common in mating-type chromosomes of Microbotryum anther-smut fungi * co-senior authors J. Evol. Biol. https://doi.org/10.1111/jeb.13991
• Carpentier F, Rodríguez de la Vega RC, Jay P, Duhamel M, Shykoff JA, Perlin MH, Wallen RM, Hood* ME, Giraud* T (2022 ) Degeneration tempo in non-recombining regions of anther-smut fungi* co-senior authors Mol Biol Evol https://doi.org/10.1093/molbev/msac060
• Bina Hamid, Yousefzadeh Hamed, Venon Anthony, Remoué Carine, Rousselet Agnès, Falque Matthieu, Shadab Faramarzi, Giraud Tatiana, Hossainpour Bato, Abdollahi Hamid, Nersesyan Anush, Cornille Amandine (2022) Evidence of an additional wild contributor, Malus orientalis Uglitzk., to the genome of cultivated apple varieties in the Caucasus and Iran. Mol Ecol https://doi.org/10.1111/mec.16667
  
• Ropars and Giraud T. (2022) Convergence in domesticated filamentous fungi : beneficial traits, genomic mechanisms and degeneration. Current Opinion in Microbiology
• Giraud T « Dynamique et évolution de la biodiversité et des écosystèmes» Fayard 2022.

2021

• Hartmann Fanny E., Duhamel Marine, Carpentier Fantin, Hood Michael E., Foulongne-Oriol Marie, Silar Philippe, Malagnac Fabienne, Grognet Pierre, Giraud Tatiana (2021) Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes– Tansley Review. New Phytologist 229: 2470-2491.
• Hartmann FE, Ament-Velásquez SL, Vogan AA, Gautier V, Le Prieur SL, Johannesson H, Grognet P, Malagnac F, Silar P, Giraud T (2021) Variable sizes and ages of recombination suppression in mating-type chromosomes in closely-related model fungi in the Podospora anserina species complex Molecular Biology and Evolution 38: 2475–2492.
• Marden Emily, et al  (2021) Editorial – Sharing and Reporting Benefits from Biodiversity Research. Molecular Ecology 30 : 1103-1107.
• Blin P, Robic K, Khayi S, Cigna J, Munier E, Dewaegeneire P, Laurent A, Jaszczyszyn Y, Hong KW, Chan KG, Beury A, Reverchon S, Giraud T, Hélias V, Faure D (2021) Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen dianthicola Molecular Ecology 30: 608-624.
• Liu S, Decroocq S, Harte E, Tricon D, Chague A, Balakishiyeva G, Kostritsyna T, Turdiev T, Fisher-Le Saux M, Dallot S, Giraud T, Decroocq V. (2021) Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina) confirm its affiliation to the Armeniaca section Tree Genetics & Genomes 17:12.
• Caron T, Le Piver M, Péron AC, Lieben P, Lavigne R, Brunnel S, Pollet B, Roueyre D, Place M, Bonnarme P, Giraud* T, Branca* A, Landaud* S, Chassard* C (2021) Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavour and texture in blue cheeses *co-senior authors. Int J Food Microbiol https://www.sciencedirect.com/science/article/pii/S0168160521001331
• Fontaine MC, Labbé F, Dussert Y, Delière L, Richard-Cervera S., Giraud T, Delmotte F (2021) Europe as a bridgehead in the worldwide invasion history of the grapevine downy mildew Plasmopara viticola  Current Biology doi: 10.1016/j.cub.2021.03.009
• Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M and Gladieux P. (2021) Population genomics reveals molecular determinants of specialization to tomato in the polyphagous fungal pathogen Botrytis cinerea.  Phytopathology DOI: 10.1094/PHYTO-07-20-0302-FI
• Butlin Roger K., Servedio Maria R., Smadja Carole M., Bank Claudia, Barton Nicholas H., Flaxman Samuel M., Giraud Tatiana, Hopkins Robin, Larson Erica L., Maan Martine E., Meier Joana, Merrill Richard, Noor Mohamed A. F., Ortiz-Barrientos Daniel and Qvarnström Anna (2021) Homage to Felsenstein 1981, or why are there so few/many species? Perspective Evolution http://doi.org/10.1111/evo.14235
  
• Gautier V, Levert E, Giraud T & Silar P (2021) Essential role of melanin for fertility in the fungus Podospora anserina G3 https://doi.org/10.1093/g3journal/jkab159
• Groppi Alexis, Liu Shuo, Cornille Amandine, Decroocq Stéphane, Bui Quynh Trang, Tricon David, Cruaud Corinne, Arribat Sandrine, Belser Caroline, Marande William, Salse Jérôme, Huneau Cécile, Rodde Nathalie, Rhalloussi William, Cauet Stéphane, Istace Benjamin, Denis Erwan, Carrère Sébastien, Audergon Jean-Marc, Roch Guillaume, Lambert Patrick, Zhebentyayeva Tetyana, Liu Wei-Sheng, Bouchez Olivier, Roques Céline Lopez-, Serre Rémy-Félix, Debuchy Robert, Tran Joseph, Wincker Patrick, Chen Xilong, Pétriacq Pierre, Barre Aurélien, Nikolski Macha, Aury Jean-Marc, Abbott Albert Glenn, Giraud* Tatiana, Decroocq* Véronique (2021) Following the adaptive path of fruit tree domestication using population genomics: the case of apricots Nature Communications * corresponding authors  https://doi.org/10.1038/s41467-021-24283-6
• Foulongne-Oriol Marie, Taskent Ozgur, Kües Ursula, Sonnenberg Anton S. M., van Peer Arend and Giraud Tatiana (2021) Mating-type locus organization and mating-type chromosome in the bipolar edible button mushroom Agaricus bisporus. Genes https://www.mdpi.com/2073-4425/12/7/1079/pdf
• Kobmoo Noppol, Arnamnart Nuntanat, Pootakham Wirulda, Sonthirod Chutima, Khonsanit Artit, Kuephadungphan Wilawan, Suntivich Rinrada, Giraud Tatiana, Jennifer Janet Luangsa-ard. (2021) The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia https://doi.org/10.3767/persoonia.2021.47.04
• Olvera-Vazquez, S.G., Remoué, C., Venon, A., Rousselet, A., Grandcolas, O., Azrine M. Momont, L., Galan, M., Benoit L., David G., Alhmedi A., Beliën, T., Alins, G., Franck, P., Haddioui, A., Jacobsen, S.K., Andreev, R., Simon, S., Sigsgaard, L. , Guibert, E., Tournant L., Gazel, F., Mody, K., Khachtib, Y., Roman, A, Ursu, T., Zakharov I., Belcram H., Harry, M., Roth, M., Simon J.C., Oram, S., Ricard J.M., Agnello, A., Beers E. H., 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 geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa. https://peercommunityjournal.org/articles/10.24072/pcjournal.26/Recommended in PCI Evol Biol DOI: 10.1101/2020.12.11.421644
• Olvera-Vazquez S.G., Alhmedi A., Miñarro M., Shykoff J. A., Marchadier E., Rousselet A., Remoué C., Gardet R., Degrave A, Robert P., Chen X., Porcher J., Giraud T., Vander-Mijnsbrugge K., Raffoux X., Falque M., Alins, G., Didelot F., Beliën T., Dapena E., Lemarquand A. and Cornille A. Experimental test for local adaptation of the rosy apple aphid (Dysaphis plantaginea) to its host (Malus domestica) and to its climate in Europe. Preregistration Experimental test for local adaptation of the rosy apple aphid (2021) PCI Ecology 1101/2020.12.11.421644; https://ecology.peercommunityin.org/articles/rec?id=139

2020

• Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A and Giraud T (2020) Independent domestication events in the fungus maturing blue cheeses, Penicillium roqueforti Molecular Ecology 14 : 2639-2660.
• Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Wen-Juan M, Hood ME, Giraud T. (2020) Higher gene flow in sex-related chromosomes than in autosomes during fungal divergence. Molecular Biology and Evolution 37: 668–682.
• Hartmann FE, Snirc A, Cornille A, Godé C, Touzet O, Van Rossum F, Fournier E, Le Prieur S, Shykoff JA, Giraud T. (2020) Congruent population genetic structures and demographic histories in anther-smut fungi and their host plants Silene nutans and S. italica. Molecular Ecology 29: 1154-1172.
• Ma Wen-Juan, Carpentier F, Giraud T, Hood ME (2020) Differential gene expression between mating types is associated with sequence degeneration. Genome Biology and Evolution 12: 243–258
• Arnaise S, Shykoff JA Moller AP, Mousseau T, Giraud T. 2020. Anther-smut fungi from more contaminated sites in Chernobyl show lower infection ability and lower viability following experimental irradiation. Evolution and Ecology 10: 6409-6420
• Ropars J, Didiot E, Rodriguez de la Vega R, Bennetot B, Coton M, Coton E, Snirc A, Le Prieur S and Giraud T. 2020. Domestication of the emblematic white cheese-making fungus Penicillium camemberti and its diversification into two varieties Current Biology 30: 4441-4453
•  Dussert Y, Legrand L, Mazet ID, Couture C, Gouzy J, Piron MC, Serre RF, Bouchez O, Mestre P, Toffolatti S, Giraud T, Delmotte F. (2020) Identification of the first oomycete mating-type locus in the grapevine downy mildew pathogen, Plasmopara viticola Current Biology 30: P3897-3907
• Feurtey A., Guitton E, de Gracia M., Duvaux L, Shiller J, Bellanger MN, Expert P, Sannier M, Caffier V, Giraud T., Le Cam B, Lemaire C. (2020) Threat to Asian wild apple trees posed by gene flow from domesticated apple trees and their pestified pathogens. Molecular Ecology 29: 4925-4941 
• Ropars J, Bennetot B, Caron T, Lo YC and Giraud T. 2020. The domestication of Penicillium cheese fungi. Comptes Rendus de l’Académie des Sciences 343 :  155-176.
• Ament-Velásquez Lorena S., Johannesson Hanna, Giraud Tatiana, Debuchy Robert, J. Saupe Sven, Debets Alfons J.M., Bastiaans Eric, Malagnac Fabienne, Grognet Pierre, Peraza-Reyes Leonardo, Gladieux Pierre, Silar Philippe, M. Huhndorf Sabine, Miller Andrew, Vogan Aaron (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75:51-69.

2019

• Liu S, Cornille A, Decroocq S, Tricon D, Chague A, Eyquard JP, Liu W, Giraud* T, Decroocq* V (2019) The complex evolutionary history of apricots: species divergence, gene flow and multiple domestication events.* co-last authors Molecular Ecology 28: 5299-5314
• Bazzicalupo A, Carpentier F, Otto S and Giraud T (2019) No evidence of antagonistic selection in the evolutionary strata of fungal mating-type chromosomes (Microbotryum lychnidis-dioicae) G3 9: 1987-1998.
• Carpentier F, Rodríguez de la Vega RC, Branco S, Snirc S, Coelho M, Hood ME, Giraud T (2019) Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi  Genome Research 29: 944-953.
• 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 by combining population and comparative genomics in castrating anther-smut fungi. Ann Review Phytopath 57:431-457
  
• Hood ME, Antonovics J, Wolf M, Stern Z, Giraud T, Abbate J (2019) Sympatry and interference of divergent Microbotryum pathogen species. Ecology and Evolution 9:5457–5467
• Kobmoo N, Mongkolsamrit S, Tasanathai K, Arnamnart N, Luangsa-Ard JJ and Giraud T (2019) Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis). Molecular Phylogenetics and Evolution 140: 1065
• Beckerson William C, Rodriguez de la Vega Ricardo, Hartmann Fanny, Duhamel M, Giraud* Tatiana, Perlin* Michael H. (2019) Cause and effectors: whole genome comparisons reveal shared but rapidly evolving effector sets among host-specific plant-castrating fungi mBio *co-last authors 10 :  e02391-19

2018

• Branco  S, Carpentier F, Rodriguez de la Vega R, Badouin H, Snirc A, Le Prieur S, Coelho M, de Vienne D.M., Hartmann F, Begerow D, Hood ME, Giraud T (2018) Multiple convergent supergene evolution events in mating-type chromosomes. Nature Communications 9:2000.
• Hartmann FE, Rodríguez de la Vega RC, Brandenburg JT, Carpentier F, Giraud T (2018) Gene presence–absence polymorphism in castrating anther-smut fungi: recent gene gains and phylogeographic structure Genome Biology and Evolution 10: 1298–1314.
• Abbate J, Gladieux P, Hood ME, de Vienne DM, Antonovics JA, Snirc A, and Giraud T (2018) Co-occurrence among three divergent plant-castrating fungi in the same Silene host species. Molecular Ecology 27: 3357-3370 IF=6
• Kobmoo Noppol, Wichadakul Duangdao, Nuntanat Arnarmnart, Rodríguez de la Vega RC,  Luangsa-Ard Janet-Jennifer and Giraud Tatiana (2018)  A genome scan of diversifying selection in the ant-zombi Ophiocordyceps unilateralis complex of entomopathogenic fungi supports a role of enterotoxins in coevolution and host-specificity Molecular Ecology 18: 3582-3598
• Fortuna T, Namias A, Snirc A, Branca A, Shykoff JA, Hood ME, Raquin C, Giraud T. (2018) Multiple infections, relatedness and virulence in the anther-smut fungus castrating Saponaria plants Molecular Ecology   27: 4947-4959.

2017

• Branco S, Badouin H, Rodriguez de la Vega R, Gouzy J, Carpentier F, Aguileta G, Siguenza S, Brandenburg JT, Coelho M, Hood ME, Giraud T (2017) Evolutionary strata on young mating-type chromosomes despite lack of sexual antagonism PNAS 114: 7067–7072. Recommended by F1000
• Feurtey A, Cornille A., Shykoff JA, Snirc A, Giraud T. (2017) Crop-to-wild gene flow and its fitness consequences on a wild fruit tree: towards a comprehensive conservation strategy of the wild apple in Europe. Evol. App. 10: 180–188
• Ropars J, Lopez-Villavicencio, M, Snirc A, Giraud T. (2017) Blue cheese-making has shaped the population genetic structure of the mould Penicillium roqueforti. PLoS One. 12: e0171387.
• Badouin H, Gladieux P, Gouzy J, Siguenza S, Aguileta G, Snirc A, Le Prieur S, Jeziorski C, Branca A and Giraud T. (2017) Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Molecular Ecology 26: 2041–2062.
• 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 26: 1877–1890.
• Giraud T, Koskella B, Laine AL (2017) Microbial local adaptation: insights from natural populations, genomics and experimental evolution Mol Ecol 26: 1703–1710
• Coelho MA, Bakkeren G, Sun S, Hood ME, Giraud T. 2017. Fungal sex: the basidiomycota. Microbiol Spectrum 5(3):FUNK-0046-2016. doi:10.1128/microbiolspec.FUNK-0046-2016
• Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse MA 2017. Fungi as a Source of Food. Microbiology Spectrum 5. doi: 10.1128/microbiolspec.FUNK-0030-2016

2016

• Bueker B, Eberlein C, Gladieux P, Schaefer A, Snirc A, Bennett DJ, Begerow D, Hood ME, Giraud T (2016) Distribution and population structure of the anther smut fungus Microbotryum silenes-acaulis parasitizing an arctic-alpine plant Mol Ecol 25: 811-824.
• Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, de Vallavieille-Pope C and Enjalbert J. (2016) CloNcaSe: Estimation of sex frequency and effective population size by clonemate re-sampling in partially clonal organisms. Mol Ecol Res. 16(4):845-61.
• Aguileta G., Badouin H., Hood M. E., Møller A.P., Le Prieur S., Snirc A, Siguenza S., Mousseau T.A., Shykoff J.A., Cuomo C.A., and Giraud T. (2016) Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl Mol Ecol. 25: 3370–3383.
• Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard J-P, Karychev R, Dolgikh S, Kostritsyna T, Liu S, Liu W, Wenjuan G, Kang L, Asma Bayram M, Akparov Z, Giraud* T, Decroocq* V. (2016) New insights into the history of domesticated and wild apricot and its contribution to Plum pox virus resistance. Mol Ecol. 25(19):4712-29.
• Feurtey A, Gladieux P, Snirc A, Hood ME, Cornille A, Rosenthal, L and Giraud T (2016) Strong phylogeographic costructure between the anther fungus and its white campion host. New Phytol 212(3):668-679
• Ropars J, Lo YC, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T*, Lopez-Villavicencio*, M. (2016) Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. *Joint supervision and both corresponding authors Evolution. 70(9):2099-109.
• Fortuna TM, Snirc A, Badouin H, Gouzy J, Siguenza S, Esquerre D, Le Prieur S, Shykoff JA, and Giraud T. (2016) Polymorphic microsatellite markers for the tetrapolar anther-smut fungus Microbotryum saponariae based on genome sequencing. PLoS One 11:e0165656.
• Rodríguez de la Vega, RC., and Giraud T. (2016) Intragenome diversity of gene families encoding toxin-like proteins in venomous animals. Integr. Comp. Biol. 56(5):938-949.

2015

• Badouin H, Hood ME, Gouzy J, Aguileta G, Siguenza S, Perlin MH, Cuomo C, Fairhead C, Branca A, Giraud T (2015) Chaos of rearrangements in in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae. Genetics 200:1275-1284. Highlighted twice by F1000
• Ropars J, Rodríguez de la Vega RC, Lopez-Villavicencio M, Gouzy J, Sallet E, Debuchy R, Dupont J, Branca A, Giraud T. (2015) Adaptive horizontal gene transfers between multiple cheese-associated fungi. Curr. Biol. 19:2562–2569
• Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen Z, Toh, SS, Cuomo C, Perlin MH, Gladieux P, Giraud T (2015) Degeneration of the non-recombining regions in the mating type chromosomes of the anther smut fungi. Mol Biol Evol 32: 928-943. IF=13 Recommended by F1000
• Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. (2015) The population biology of fungal invasions. Mol Ecol. 24:1969-86. IF=6
• Cornille A., Feurtey A, Gélin U, Misvanderbrugge K., Gladieux P, Ropars J, 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. Evol App. 8: 373–384. IF=5.6
• 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 S, Giraud T, MacDiarmid R_, Newcomb R and Gleave (2015) A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal. 84(2):417-27.
• Idnurm A, Hood ME, Johannesson H and Giraud T.  (2015) Contrasted patterns in mating-type chromosomes in fungi: hotspots versus coldspots of recombination. Fung. Biol. Rev. 29:220-229.
• Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel, CE, Branca A (2015) Investigating the genomic bases of the differences between cider and dessert apple varieties. Evol. App. 8(7):650-61. IF=5.6
• Perlin MH, Amselem J, Fontanillas E, Toh SS, Chen Z, Goldberg J, Duplessis S, Henrissat B, Young S, Zeng Q, Aguileta G, Petit E, Badouin H, Andrews J, Razeeq D, Gabaldón T, Quesneville H, Giraud T, Hood ME, Schultz D, Cuomo CA. (2015) Sex and Parasites: Genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics 16:461. IF=4,3
• Pintye A, Ropars J, Harvey N, Shin HD, Leyronas C, Nicot PC, Giraud T*, Kiss L. (2015) Host Phenology and geography as drivers of differentiation in generalist mycoparasites. PLoS One 10(3):e0120703
• Gillot G, Jany J-L, Coton M, Le Floch G, Debaets S, Ropars J, López-Villavicencio M, Dupont J, Branca A, Giraud T, Coton E. (2015) Insights into Penicillium roqueforti genetic diversity. PLoS One 10(6): e0129849. IF=3,5

2014

• Cornille A, Giraud T, Smulders MJM, Roldán-Ruiz I, and Gladieux P. 2014. The domestication and evolutionary ecology of apples. Trends in Genetics 30: 57-65
• Cheeseman K, Ropars J, Renault, P, Dupont J, Gouzy J,  Branca A, Ceppi M, Debuchy R, Malagnac F, Goarin A, Silar P, Lacoste S, Sallet E, Bensimon A, Giraud* T, Brygoo Y. (2014)  Recent horizontal transfer of a large genomic region between cheese fungi Nature Communications * corresponding author; 5:2876
• Yuan JH, Cornille A, Giraud T, Zhou SL, Cheng FY (2014) Independent domestication of the common and flare tree peonies from different wild species. Mol Ecol 23: 82–95.
• Gladieux P, Ropars R, Badouin H, Branca A, Aguileta G, de Vienne DM, Rodriguez de la Vega R, Branco S, Giraud T. (2014) Invited Review : Fungal evolutionary genomics provide insights into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol. 23: 753–773.
• Ropars J, Aguileta G, de Vienne DM and Giraud T.2014.  Massive gene swamping among cheese making Penicillium fungi Microbial Cell 1: 107-109.
• Ropars J , López-Villavicencio M, Dupont J, Snirc A , Gillot G, Coton M, Jany JL, Coton E, Giraud T (2014)  Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti. Evolutionary Applications7(4): 433–441.
• Aguileta G, de Vienne DM, Ross ON, Hood ME, Giraud T, Petit E, and Gabaldón T. 2014. High variability of mitochondrial gene order in basidiomycetes. Genome Biology and Evolution 6 : 451-465.
• Buono L, López-Villavicencio M, Shykoff JA, Snirc A, Giraud T. (2014) Influence of multiple infection and relatedness on virulence: disease dynamics in an experimental plant population and its castrating parasite. PLoS One 9(6): e98526. IF=4.351
• Gibson AK, Refrégier G, Hood, ME, and Giraud T. (2014) Performance of a hybrid fungal pathogen on pure species and hybrid host plants. Int. J. Plant Sci. 175(6):724–730.

2013

• Hood ME, Petit E and Giraud T (2013) Extensive divergence between mating type chromosomes of the anther-smut fungus. Genetics 193: 309–315
• Cornille A., Giraud T., Bellard C., Tellier A, Le Cam B., Smulders R., Kleinschmit J, Roldan-Ruiz I, Gladieux P. (2013) Post-glacial recolonization of the European crabapple (Malus sylvestris Mill.), a wild relative of the domesticated apple. Mol Ecol. 22(8):2249-63.
• Fontaine MC, Gladieux P, Hood ME, and Giraud T (2013) History of the invasion of the anther smut pathogen on Silene latifolia in North America. New Phytologist 198(3):946-56
• de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME and Giraud T. (2013) Tansley Review:  Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations, and relation to coevolution. New Phytologist 198(2):347-85.
• Fontaine MC, Austerlitz F, Giraud T, Labbé F, Daciana P, Richard-Cervera S and Delmotte F (2013)  Genetic signature of a range expansion after recent invasion in Europe of the grapevine downy mildew pathogen Plasmopara viticola. Mol Ecol 22: 2771-2786
• Andrew RL, Bernatchez L, Bonin A, Buerkle AC, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers NC, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, and Rieseberg LH (2013) A Roadmap for Molecular Ecology. Molecular Ecology 22, 2605–2626.
• Selosse MA, Taschen E and Giraud T (2013) Do black truffles avoid sexual harassment by linking mating type and vegetative incompatibility? New Phytol 199: 10-13.
• de Vienne DM, Giraud T and Gouyon PH. (2013) Lineage selection and the maintenance of sex  PLoS One 8(6): e66906.
• 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. Evolutionary Applications. 6: 737-748.
• Gladieux P, Devier B, Aguileta G, Cruaud A and Giraud T (2013) Purifying selection after episodes of diversifying selection in plant pathogens Inf Genet Evol 17: 123-31.
• Fournier E, Gladieux P, and Giraud T (2013) The “Dr Jekyll and Mr Hyde fungus”: noble rot versus gray mold symptoms of Botrytis cinerea on grapes. Evolutionary Applications 6: 960–969.
• Luque G, Giraud T, Courchamp F (2013) Allee effects through caste interaction feedback in ants. J Anim Ecology 82, 956–965.
• López-Villavicencio M, Schoustra S, Giraud T, Debets AJM. (2013) Evidence for deleterious effects of recombination and advantages of sex independent of recombination using fungal models J Evol Biol 26: 1968-78..
• Nieuwenhuis BPS, Billiard S, Vuilleumier S, Petit E, Hood ME and Giraud T. (2013) Evolutionary advantages and drawbacks of bi- versus tetrapolarity in mating type determinism Heredity 111, 445–455.

2012

• Gibson AK, Hood ME, and Giraud T (2012)  Sibling competition arena: selfing and a competition arena can combine to constitute a barrier to gene flow in sympatry. Evolution 66: 1917-1930.
• Lê Van A., Gladieux P., Lemaire C., Cornille A., Giraud T., Durel C.-E., Caffier V. and Le Cam B. (2012) Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host. Evolutionary Applications 5 : 694–704.
• Billiard S, Lopez-Villavicencio M, Hood ME, Giraud T. (2012). Sex, outcrossing and mating types – Unsolved questions in fungi and in general. J Evol Biol 25(6):1020-1038.
• Dilmaghani A, Gladieux P, Gout L, Giraud T, Brunner P, Grandaubert J, Stachowiak A, Balesdent M-H and Rouxel T (2012) Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans. Mol Ecol 21(10):2519-33.
• Aguileta G, Lengelle J, Chiapello H, Giraud T, Viaud M, Fournier E, Rodolphe F, Marthey S, Gendrault-Jacquemard A, Wincker P, Dossat C, and Gout L (2012) Genes under positive selection in Botrytis. Infection, Genetics and Evolution. 12(5):987-96.
• Cornille A. , Gladieux P., Smulders R., Roldan-Ruiz I. , Laurens F. , Le Cam B., Nersesyan A., Clavel J., Olonova M., Feugey L., Gabrielian I., Zang X., Tenaillon M., Giraud T (2012) New insights into the history of domesticated apple: secondary contribution by several wild species to the genome of cultivated varieties. PloS Genet. 8(5): e1002703.
• Giraud T and Gourbière S (2012) The tempo and modes of evolution of reproductive isolation in fungi. Heredity 109: 204–214.
• Ropars J, Dupont J, Fontanillas E, Rodríguez de la Vega RC, Coton M, Malagnac F, Giraud T, López-Villavicencio M. (2012) Sex in cheese: evidence for sexuality in the fungus Penicillium roqueforti. PLoS One 7:11
• Petit E, Giraud T, de Vienne D M., Coelho M, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P, Young S, Cuomo  C and Hood ME. (2012) Linkage to the mating-type locus across the genus Microbotryum: insights into non-recombining chromosomes. Evolution 66: 3519–3533.

2011

• Gladieux P, Vercken E, Fontaine MC, Hood ME, Jonot O, Couloux A and Giraud T (2011) Maintenance of fungal pathogen species that are specialized to different hosts: allopatric divergence and introgression through secondary contact. Mol Biol Evol 28:459–471.
• Billiard S, Lopez-Villavicencio M, Devier B, Hood ME, Fairhead C, Giraud T. (2011) Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types. Biological Reviews. 86, 421–442.
• Gladieux P, Giraud T, Shykoff JA, Genton B, Jonot O and Kiss L (2011) Distinct invasion sources of common ragweed (Ambrosia artemisiifolia) in Eastern and Western Europe. Biological invasions 13:933–944.
• Kiss L, Pintye A, Kovacs GM, Jankovics T, Fontaine MC, Harvey N, Xu X, Nicot P, Bardin M, Shykoff JA and Giraud T (2011). Temporal isolation explains host-related genetic differentiation in a group of widespread mycoparasitic fungi. Mol Ecol 20, 1492–1507.
• Gaudeul M, Giraud T, Kiss L, and Shykoff JA (2011) Nuclear and chloroplast microsatellites show multiple introductions in the worldwide invasion history of common ragweed, Ambrosia artemisiifolia (Asteraceae). PLoS One  6: e17658.
• López-Villavicencio M,  Courjol F, Gibson AK, Hood ME, Jonot O, Shykoff JA and Giraud T (2011) Competition, cooperation among kin and virulence in multiple infections. Evolution 65:1357-1366
• Giraud T and Shykoff JA (2011)  Bacterial Cooperation and Virulence: kin selection versus infectivity. Heredity 107, 277–278.
• Amselem et al. 64 authors (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PloS Genetics 7 : e1002230.
• Gladieux P, Guérin F, Giraud T , Caffier V, Parisi L, Didelot F, Lemaire C, Le Cam B. (2011) Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants. Mol Ecol 20: 4521–4532.
• Cai L, Giraud T, Zhang N, Begerow D, Cai G and Shivas RG (2011) The evolution of species concepts and species recognition criteria in plant pathogenic fungi ” Fungal Diversity 50:121-133.

2010

• Vogel V, Pedersen JS, Giraud T, Krieger MJB, and Keller L (2010) The worldwide expansion of the Argentine ant. Diversity and Distributions 16, 170–186.
• Devier B, Aguileta G, Hood ME, Giraud T.  (2010)  Phylogenies of pheromone receptor genes in the Microbotryum violaceum species complex : insights into possible ancient events of speciation by hybridization. Mycologia 102: 689-696.
• Giraud F, Giraud T, Aguileta G, Fournier E, Samsond R, Cruaud C, Lacoste S, Tellier A, Dupont J (2010)  Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing. International Journal of Food Microbiology 137 : 204–213.
• Aguileta G, Lengelle J, Marthey S, Chiapello H, Rodolphe F, Gendrault-Jacquemard A., Yockteng R, Vercken E, Devier B, Fontaine MC, Wincker P, Dossat C, Cruaud C, Couloux A, Giraud T. (2010) Finding candidate genes under positive selection in non-model species: examples of genes involved in host specialization in pathogens. Mol Ecol 19, 292–306.
• Johnson  JJ, Giraud T, Anderson R and Hood M. E. (2010) The impact of genome defense on mobile elements in Microbotryum. Genetica 138:313–319.
• Hood ME, Mena-Alí JI, Gibson AK, Oxelman B, Giraud T, Yockteng R, Arroyo M, Conti F, Pedersen A, Gladieux P, and Antonovics P (2010) Distribution of the anther-smut pathogen Microbotryum on species of the Caryophyllaceae assessed from natural history collections New Phytol 187: 217-229.
• Giraud T, Gladieux P, Gavrilets S. (2010) Linking emergence of fungal plant diseases and ecological speciation. Trends Ecol Evol 25: 387–395.
• López-Villavicencio M., Aguileta G, Giraud T., de Vienne DM, Lacoste S., Couloux A., & Dupont J. (2010) Sex in Penicillium: combining phylogenetic and experimental approaches. Fung. Genet. Biol. 47: 693-706.
• Refrégier G, Hood ME, Giraud T. No evidence of Reproductive Character Displacement between two sister fungal species causing anther smut disease in Silene (2010). Int J Plant Sciences 171:847-859.
• Vercken E, Fontaine MC, Gladieux P, Hood ME, Jonot O, and Giraud T. (2010) Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and S. dioica. PloS Pathogens 6: e1001229.

2009

• Aguileta G, Hood ME, Refrégier G, Giraud T (2009) Invited review: Genome evolution in pathogenic and symbiotic fungi. Advances in Botanical Research. 49: 151-193.
• de Vienne DM, Giraud T, Martin O (2009) In response to comment on ‘A congruence index for testing topological similarity between trees’ Bioinformatics 25:150–151.
• Devier B, Aguileta G, Hood ME, Giraud T. (2009) Ancient trans-specific polymorphism at pheromone receptor genes in basidiomycetes. Genetics 181:209-223.
• de Vienne DM, Refrégier G, Hood ME, Guigue A, Devier B, Vercken E, Smadja C, Deseille A, and Giraud T. (2009) Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum J Evol Biol 22:683–698.
• Aguileta G, Refrégier G, Yockteng R, Giraud T. (2009) Invited review: Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protozoa. Infection, Genetics and Evolution.9: 656–670.
• Bernasconi G., J. Antonovics, A. Biere, D. Charlesworth, L.F. Delph, D. Filatov, T. Giraud, ME Hood,,G. Marais, D. McCauley, J. Pannell, J.A. Shykoff, B. Vyskot, LM Wolfe, A. Widmer (2009) Re-emergence of Silene as a classic model system in ecology and evolution Heredity 103 : 5–14.
• Gold  AD, Giraud T, Hood ME (2009) Within-host competitive exclusion among species of the anther smut pathogen BMC Ecol 9:11.
• Denchev CM, Giraud T & Hood ME (2009) Three new species of anthericolous smut fungi on Caryophyllaceae Mycologia Balcanica. 6: 79–84
• de Vienne DM, Hood ME, Giraud T (2009) Phylogenetic determinants of potential host shifts in fungal pathogens J Evol Biol 22 : 2532–2541.

2008

• Fournier E and Giraud T (2008) Sympatric genetic differentiation of populations of a generalist pathogenic fungus, Botrytis cinerea, on two different host plants, grapevine and bramble J Evol Biol 21:122-132.
• Giraud T, Yockteng R, Marthey S, Chiapello H, Jonot O, Lopez-Villavicencio M, de Vienne DM, Hood ME, Refrégier G, Gendrault-Jacquemard A, Wincker P and Dossat C. (2008) Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum. Molecular Ecology Resources 8: 387–392.
• Le Gac M and Giraud T (2008) Existence of a pattern of reproductive character displacement in Basidiomycota but not in Ascomycota. J Evol Biol 21:761–772.
• Refrégier G, Le Gac M, Jabbour F, Widmer A, Shykoff JA, Yockteng R, Hood ME, and Giraud T (2008) Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation; BMC Evol Biol 8:100.
• Salvaudon L, Giraud T, Shykoff, JA (2008) Genetic diversity in natural populations: A fundamental component of plant-microbe interactions. Curr. Op. Plant Biology 11: 135-143.
• Giraud T, Yockteng R, Lopez-Villavicencio M, Refrégier G, and Hood, M. E. (2008) Invited Mini-Review: the mating system of Microbotryum violaceum: selfing under heterothallism Eukaryotic cell 7: 765–775.
• Giraud T, Refrégier G, de Vienne D. M., Le Gac M. and Hood, M. E. (2008) Invited Review: Speciation in fungi Fung. Genet. Biol. 45: 791–802.
• Aguileta, G, Marthey, S. Chiapello, H., Lebrun, M.-H. Rodolphe F., Fournier, E, Gendrault-Jacquemard, A., Giraud T (2008) Assessing the performance of single-copy genes for recovering robust phylogenies. Syst Biol 57: 613-627.
• Giraud T, Enjalbert J, Fournier E, Delmotte F and Dutech C. (2008) Population genetics of fungal diseases of plants. Parasite. 15:449-454
• Sloan DB, Giraud T and Hood ME^. (2008) Maximized virulence in a sterilizing pathogen: the anther-smut fungus and its co-evolved hosts J Evol Biol 21:1544–1554.
• Marthey S, Aguileta G, Rodolphe F, Gendrault-Jacquemard A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, and Chiapello H (2008) FUNYBASE: the FUNGAL phYlogenomic database. BMC Bioinformatics 9: 456.

2007

• Tellier A, Villaréal L and Giraud T (2007) Antagonistic pleiotropy may help population-level selection in maintaining genetic polymorphism for transmission rate in a model phytopathogenic fungus. Heredity 98:45-52.
• Le Gac M, Hood ME, Fournier E, and Giraud T (2007) Phylogenetic evidence of host-specific cryptic species in the anther smut fungus. Evolution 61: 15–26.
• de Vienne DM, Giraud T and Shykoff JA (2007) When can host shifts produce congruent host and parasite phylogenies? A simulation approach. J Evol Biol 20:1428-1438.
• Dutech C, Enjalbert E, Fournier E, Delmotte F, Barrès B, Carlier J, Tharreau D, and Giraud T (2007) Challenges of microsatellite isolation in fungi. Fung Genet Biol. 44: 933-949.
• Le Gac M, Hood ME and Giraud T (2007) Evolution of reproductive isolation within a parasitic fungal complex. Evolution 61: 1781–1787.
• Yockteng R. Marthey, S. Chiapello, H., Hood, ME, Rodolphe F., Gendrault-Jacquemard A, Devier, B., Wincker, P., Dossat, C. and Giraud, T. (2007) Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes. BMC Genomics. 8:272.
• Lopez-Villavicencio M, Jonot O, Coantic A, Hood, ME, Enjalbert J and Giraud T (2007) Multiple infections by the anther smut pathogen are frequent and involve related strains. PLoS Pathogens 3(11):e176.
• de Vienne DM, Giraud T and Martin O. (2007) A Congruence Index for Testing Topological Similarity between Trees. Bioinformatics. 23: 3119-3124.

2006

• Porcher E, Giraud T and Lavigne C (2006) Genetic Differentiation in neutral markers and quantitative traits in selfing metapopulations: confronting theory and experiments with Arabidopsis thaliana. Genet. Res. 87:1-12.
• Giraud T, Jonot O and Shykoff JA (2006) Common sex-linked deleterious alleles in a parasitic fungus alter infection success but show no pleiotropic advantage. J. Evol. Biol. 19: 970-980.
• Giraud T, Villaréal L, Austerlitz F, Le Gac M and Lavigne C (2006) Importance of the life cycle in sympatric host race formation and speciation of pathogens. Phytopathology. 96: 280-287.
• Giraud T (2006) Speciation in parasites:  host switching does not automatically lead to allopatry. Trends in Parasitology 22: 151-152.
• Pedersen JS, Krieger MJB, Vogel V, Giraud T, and Keller L (2006) Native supercolonies of unrelated individuals in the invasive Argentine ant. Evolution 60: 782-791.
• Giraud T (2006) Selection against migrant pathogens: The immigrant inviability barrier in pathogens. Heredity 97: 316-318.
• Koskella B, Giraud T and M. E. Hood (2006) Pathogen relatedness affects the prevalence of within-host competition. Am. Nat. 168:121-126.

2005

• Till-Bottraud I, Giraud T, Fournier E, Torres C, Vautrin D, Solignac M, Genton B and Arroyo MTK (2004) Isolation of seven microsatellite loci, using an enrichment protocol, in the high Andean Asteraceae Chaetanthera pusilla. Mol. Ecol. Notes 4:462-464. 5:381-383.
• Tellier A, Villaréal L and Giraud T (2005) Maintenance of sex-linked deleterious alleles by selfing and group selection in metapopulations of the phytopathogenic fungus Microbotryum violaceum. Am. Nat. 165:577-589.
• Lopez-Villavicencio M, Branca A, Giraud T, Shykoff JA (2005) Sex-specific effect of Microbotryum violaceum (Uredinales) spores on healthy plants of the gynodioecious Gypsophila repens (Caryophyllaceae). Am. J. Bot. 92(5):896-900.
• Hood ME, Katawczik M and Giraud T (2005) Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum. Genetics. 170: 1081-1089.
• Lopez-Villavicencio M, Enjalbert E, Hood ME, Shykoff JA, Raquin C, Giraud T (2005) The anther smut disease on Gypsophila repens: a case of parasite sub-optimal performance following a recent host shift? J. Evol. Biol. 18:1293-1303.
• Genton B, Jonot O, Thévenet D, Fournier E, Blatrix R, Vautrin D, Solignac M and Giraud T (2005) Isolation of five microsatellite loci, using an enrichment protocol, in the invasive weed Ambrosia artemisiifolia. Mol. Ecol. Notes. 5:381-383.
• Giraud T, Jonot O and Shykoff JA (2005) Selfing propensity under choice conditions in a parasitic fungus, Microbotryum violaceum, and parameters influencing infection success in artificial inoculations ^.Int. J. Plant Sci. 166: 649-657.
• Genton B, Shykoff JA and Giraud T (2005) High genetic diversity in French invasive populations of common ragweed Ambrosia artemisiifolia as a consequence of multiple sources of introduction. Mol. Ecol. 14 :4275-4285.
• Fournier E, Giraud T, Albertini C and Brygoo Y (2005) Partition of the Botrytis cinerea complex in France using multiple gene genealogies. Mycologia. 97: 1251-1267

2004

• Le Gac M and Giraud T (2004) What is sympatric speciation in parasites? Trends Parasitol. 20:207-208.
• Giraud T (2004) Patterns of within population dispersion and mating of the fungus Microbotryum violaceum parasitising the plant Silene latifolia. Heredity. 93:559-565.
• Porcher E, Giraud T, Goldringer I and Lavigne C (2004) Experimental demonstration of a causal relationship between heterogeneity of selection and genetic differentiation at quantitative traits. Evolution. 58:1434–1445.

2003

• Fournier E, Levis C., Fortini D, Leroux P, Giraud T and Brygoo Y (2003) Characterization of Bc-hch, the Botrytis cinerea homolog of the Neurospora crassa het-c vegetative incompatibility locus, and its use as population marker. Mycologia. 95: 251-261.
• Duan X, Enjalbert J, Vautrin D, Solignac M and Giraud T (2003) Isolation of 12 microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Puccinia triticina. Mol. Ecol. Notes. 3:65-67.
• Thomas A, Shykoff J, Jonot O and Giraud T (2003) Sex ratio bias in populations of the phytopathogenic fungus Microbotryum violaceum from several host species. Int. J. Plant Sci. 164: 641-647.

2002

• Brunet F, Giraud T, Fabienne G and Capy P (2002) Do deletions of the Mos1-like elements occur randomly in the Drosophilidae family ? J. Mol. Evol. 54:227-234.
• Giraud T, Fournier E, Vautrin D, Solignac M, Vercken E, Bakan B and Brygoo Y. (2002) Isolation of eight polymorphic microsatellite loci, using an enrichment protocol, in the phythopathogenic fungus Fusarium culmorum. Mol. Ecol. Notes. 2:121-123.
• Giraud T, Fournier E, Vautrin D, Solignac M and Shykoff JA (2002) Isolation of 44 polymorphic microsatellite loci in three host races of the phytopathogenic fungus Microbotryum violaceum. Mol. Ecol. Notes. 2:142-146.
• Muñoz G, Hinrichsen P, Brygoo Y and Giraud T (2002) Genetic characterisation of Botrytis cinerea populations in Chile. Mycological Research 106:595-602.
• Fournier E, Giraud T, Loiseau A, Vautrin D, Estoup A, Solignac M, Cornuet JM, and Brygoo Y (2002) Isolation of nine microsatellite loci in the phytopathogenic fungus Botrytis cinerea (Ascomycota). Mol. Ecol. Notes. 2:253-255.
• Giraud T, Pedersen JS and Keller L (2002) Evolution of supercolonies: the Argentine ants of Southern Europe. Proc. Natl. Acad. Sci. USA. 99:6075-6079.
• Enjalbert J, Duan X, Vautrin D, Giraud T, de Vallavieille Pope C, Solignac M (2002) Isolation of twelve microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Puccinia striifomis f.sp. tritici Mol. Ecol. Notes. 2:563-565.

2001

• Giraud T, Blatrix R, Poteaux C, Solignac M and Jaisson P (2001) High genetic relatedness among nestmate queens in the polygynous ponerine ant Gnamptogenys striatula in Brazil. Behav. Ecol. Sociobiol. 49:128-134.

2000

• Giraud T, Blatrix R, Poteaux C, Solignac M and Jaisson P (2000) Population structure, mode of colony foundation and mating biology of the polygynous ponerine ant Gnamptogenys striatula in Brazil. Mol. Ecol. 9:1835-1841

1999

• Giraud T, Fortini D, Levis C, Lamarque C, Leroux P, LoBuglio K and Brygoo Y (1999) Two sibling species of the Botrytis cinerea complex, transposa and vacuma, are found in sympatry on numerous host plants. Phytopathology 89:967-973..
• Giraud T, Blatrix R, Solignac M and Jaisson P (1999) Polymorphic DNA markers in the ant Gnamptogenys striatula. Mol. Ecol. 8:2141-2143.

1998

• Giraud T, Levis C, Fortini D and Brygoo Y (1998) The minisatellite MSB1 in the fungus Botrytis cinerea probably mutates by slippage. Mol. Biol. Evol. 15:1524-1531.

1997

• Giraud T, Levis C, Fortini D, Leroux P and Brygoo Y (1997) RFLP markers show genetic recombination in Botrytis cinerea and transposable elements reveal two sympatric species. Mol. Biol. Evol. 14:1177-1185.
• Levis C, Giraud T, Fortini D and Brygoo Y (1997) Telomeric DNA of Botrytis cinerea: a useful tool for strain identification. FEMS Microbiol. Letter 157:267-272.

1996

• Giraud T and Capy P (1996) Somatic activity of the mariner transposable element in natural populations of Drosophila simulans. Proc. R. Soc. B Lond. 263:1481-1486.

Recommendations for PCI Evol Biol

• Giraud T and Ropars J. 2022. The variety of bread-making practices promotes diversity conservation in food microbial communities. https://doi.org/10.1101/679472
• Giraud T and Rodriguez de la Vega R. 2021. Identification of distinct YX-like loci for sex determination and self-incompatibility in an androdioecious shrub 10.24072/pci.genomics.100011.
• Giraud T. and Mank J. 2018. Dosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomes Peer Community in Evolutionary Biology, Peer Community in Evolutionary Biology, 100044 doi: 10.24072/pci.evolbiol.100044.
• Giraud T. and Gabaldón T. 2017. Dating nodes in a phylogeny using inferred horizontal gene transfers. Peer Community in Evolutionary Biology, 100037. doi: 10.24072/pci.evolbiol.100037

Book and Book Chapters

• Giraud T « Dynamique et évolution de la biodiversité et des écosystèmes» Fayard 2022.
• Brygoo Y, Caffier V, Carlier J, Fabre J-V, Fernandez D, Giraud T, Mourichon X, Neema C, Notteghem J-L, Pope C, Tharreau D and Lebrun M-H (1998) Reproduction and population structure in phytopathogenic fungi. In Molecular variability of fungal pathogens. P Bridge, Y Couteaudier and JM Clarkson, ed. CAB, UK. Pp 297-303.
• Leroux P, Chapeland F, Giraud T, Brygoo Y and Gredt M (1998) Resistance to sterol biosynthesis inhibitors and various other fongicides in Borytis cinerea. In: Modern Fungicides and Antifungal Compounds. Cook A, ed. Hampshire, UK. Pp 133-148.
• Tellier A, de Vienne DM, Giraud T , Hood ME and Refrégier G. (2010) Theory and examples of reciprocal influence between hosts and pathogens, from short-term to long term interactions: coevolution, cospeciation and pathogen speciation following host shifts. In: “Host-Pathogen Interactions: Genetics, Immunology and Physiology.” Nova Science Publishers, NY. Editor(s): Barton AW. Book Series: Immunology and Immune System Disorders   Pages: 37-77
• Gladieux P, Byrnes E, Fisher M, Aguileta G, Heitman J, and Giraud T (2011) Epidemiology and evolution of fungal pathogens, in plants and animals. In Genetics and Evolution of Infectious Diseases. Ed Tibayrenc M. New York: Elsevier; 2011. pp. 59–131.
• Aguileta G., and Giraud T. (2012) Application of codon models to the study of fungal genome evolution. In: Codon Evolution. Mechanisms and Models. Gina M. Cannarozzi and Adrian Schneider (eds.) Oxford University Press.
• Gouyon PH, de Vienne DM and Giraud T (2014) Sex and Evolution. In: Handbook of Evolutionary Thinking, Springer; Eds Huneman P, Heams T, Lecointre G, Silberstein M
• Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Dupont J, Swennen D, Dumas E, Giraud T, and Branca A (2016) Diversity and mechanisms of genomic adaptation in In Aspergillus and Penicillium in the post-genomic era, De Vries R ed.
• Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. (2016) The population biology of fungal invasions. In: Invasion Genetics: The Baker and Stebbins Legacy, Rieseberg L and Barrette S, eds.
• Gladieux P, Byrnes E, Fisher M, Aguileta G, Billmyre B, Heitman J, and Giraud T (2016) Epidemiology and evolution of fungal pathogens, in plants and animals. In Genetics and Evolution of Infectious Diseases 2^nd Ed Tibayrenc M. New York: Elsevier. pp. 59–131.
• Dupont Joëlle, Dequin Sylvie, Giraud Tatiana, Le Tacon François, Marsit Souhir, Ropars Jeanne, Richard Franck, Selosse Marc-André. Fungi as food sources. (2017) In “The Fungal Kingdom”. Eds, Joseph Heitman, Barbara Howlett, Pedro Crous, Eva Stukenbrock, Timothy James, and Neil Gow. ASP Press.
• Coelho Marco A., Bakkeren Guus, Sun Sheng, Hood Michael E. and Giraud Tatiana (2017) Fungal sex : the Basidiomycota. In “The Fungal Kingdom”. Eds, Joseph Heitman, Barbara Howlett, Pedro Crous, Eva Stukenbrock, Timothy James, and Neil Gow. ASP Press.