Tatiana GIRAUD

Tatiana GIRAUD

 dernières mises à jour 01/01/0001
 Tatiana.Giraud@universite-paris-saclay.fr
 Génétique et Écologie Évolutives
 CNRS, DR CNRS
 Université Paris-Saclay, CNRS, Ecologie Systématique et Evolution
 publications - orcid  - HAL

  • Head of team GEE Evolutionary Genetics and Ecology
  • Senior scientist at the CNRS, Paris Saclay University
  • Member of the French Academy of Sciences
  • Former Professor at the College de France
  • Former Professor at the Ecole Polytechnique

Research Interests

  • Evolution of sex and mating-type chromosomes
  • Evolution of modes of reproduction and mating systems in fungi
  • Adaptation and horizontal gene transfers in the domesticated cheese and salami fungi (Penicillium)
  • 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
  • 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

Teaching assignments

  • Ecology and Evolution, College de France (2020-2021)
  • Ecology and Evolution, Ecole Polytechnique (2009-2020)
  • Host-symbiont association, speciation, Paris-Saclay University

Recognition and awards

  • 2019 Elected at 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
  • 2006 CNRS Bronze medal

Grants

  • ERC Advanced EvolSexChrom 2019-2025 (PI)
  • ANR Fungadapt 2019-2025
  • Fondation Louis D. Institut de France 2017-2022 (PI)
  • ERC Proof of Concept Grant 2017-2019 BLUE (PI)
  • ERC Cog 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
  • 2012-2015: Paris region project on apple tree domestication (PI)
  • 2009 -2012 : ANR project « Fungi sex – Evolution of fungal mating types and fungal sex chromosomes” (PI)
  • 2008-2010 : ANR project Emerfundis «Emerging fungal diseases» Co-PI of with J. Carlier (CIRAD – UMR BGPI)
  • 2006 -2010 : ANR project « SpeciaFonge – Specificities of speciation in fungal pathogens: impact of life cycles, genetic systems, coevolution and genomic fluidity” (PI)
  • 2003-2006: project ACI JC « Speciation in parasites » (PI)

Managing Boards

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

After the publication of our paper 1 in PLOS Biology, part of our methodology was questioned in a bioRxiv preprint and in a subsequent review paper using the material presented in the bioRxiv preprint. In order to clarify the different points of misunderstanding that have led to these criticisms, in this document we provide a response that, we hope, will demonstrate the validity of our approach. This debate is grounded on the very interesting question of which control scenario is appropriate to assess the efficiency of the sheltering effect, and we hope to contribute to this discussion with sound logical arguments and relevant biological concepts.

Publications

2024

  • Ament-Velásquez SL, Vogan AA, Wallerman O, Hartmann FE, Gautier V, Silar P, Giraud T, Johannesson H, Ma LJ. (2024) High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex. Genome Biology and Evolution, 3 (16) evae034
  • Crequer E, Coton E, Cueff G, Cristiansen JV, Frisvad JC, De La Vega RR, Giraud T, Jany JL, Coton M. (2024) Different metabolite profiles across Penicillium roqueforti populations associated with ecological niche specialisation and domestication. Microbiology,
  • Fountain‐Jones NM, Giraud T, Zinger L, Bik H, Creer S, Videvall E. (2024) Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions. Molecular Ecology, 2 (33) e17223
  • Jay P, Veber A, Giraud T. (2024) Deleterious mutations can contribute to the evolution of recombination suppression between sex chromosomes. bioRxiv,
  • Jay P, Jeffries D, Hartmann FE, Véber A, Giraud T. (2024) Why do sex chromosomes progressively lose recombination?. Trends Genet, 7 (40) 564-579
  • Leslibraires.fr . (2024) L'attention au vivant - Tatiana Giraud, Marie Ameller - Éditions de l'Observatoire. www.leslibraires.fr,
  • Lucotte EA, Jay P, Rougemont Q, Boyer L, Cornille AA, Snirc A, Labat A, Chahine E, Duhamel M, Gendelman J, Ma WJ, Hayes RK, Perlin MH, Hood M, Rodriguez de la Vega RC, Giraud T. (2024) Repeated loss of function at HD mating-type genes and of recombination suppression without mating-type locus linkage in anther-smut fungi. bioRxiv, 2024.03.03.583181
  • Timmis K, Hallsworth JE, McGenity TJ, Armstrong R, Colom MF, Karahan ZC, Chavarría M, Bernal P, Boyd ES, Ramos JL, Kaltenpoth M, Pruzzo C, Clarke G, López‐Garcia P, Yakimov MM, Perlmutter J, Greening C, Eloe‐Fadrosh E, Verstraete W, Nunes OC, Kotsyurbenko O, Nikel PI, Scavone P, Häggblom MM, Lavigne R, Le Roux F, Timmis JK, Parro V, Michán C, García JL, Casadevall A, Payne SM, Frey J, Koren O, Prosser JI, Lahti L, Lal R, Anand S, Sood U, Offre P, Bryce CC, Mswaka AY, Jores J, Kaçar B, Blank LM, Maaßen N, Pope PB, Banciu HL, Armitage J, Lee SY, Wang F, Makhalanyane TP, Gilbert JA, Wood TK, Vasiljevic B, Soberón M, Udaondo Z, Rojo F, Tamang JP, Giraud T, Ropars J, Ezeji T, Müller V, Danbara H, Averhoff B, Sessitsch A, Partida‐Martínez LP, Huang W, Molin S, Junier P, Amils R, Wu XL, Ron E, Erten H, De Martinis ECP, Rapoport A, Öpik M, Pokatong WDR, Stairs C, Amoozegar MA, Serna JG. (2024) A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society. Microbial Biotechnology, 5 (17) e14456

2023

  • Bennetot B, Vernadet JP, Perkins V, Hautefeuille S, Rodríguez De La Vega RC, O’Donnell S, Snirc A, Grondin C, Lessard MH, Peron AC, Labrie S, Landaud S, Giraud T, Ropars J. (2023) Domestication of different varieties in the cheese-making fungus Geotrichum candidum. Peer Community Journal, (3) e45
  • Crequer E, Ropars J, Jany JL, Caron T, Coton M, Snirc A, Vernadet JP, Branca A, Giraud T, Coton E. (2023) A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche. Evolutionary Applications, 8 (16) 1438-1457
  • Duhamel M, Hood ME, Rodríguez De La Vega RC, Giraud T. (2023) Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun, 1 (14) 5692
  • Giraud T, Ropars J, Stukenbrock EH, Amato KR, Rodriguez de la Vega R. (2023) Evolutionary ecology of human‐associated microbes. Molecular Ecology, 10 (32) 2369-2373
  • Lo YC, Bruxaux J, Rodríguez de la Vega RC, O'Donnell S, Snirc A, Coton M, Le Piver M, Le Prieur S, Roueyre D, Dupont J, Houbraken J, Debuchy R, Ropars J, Giraud T, Branca A. (2023) Domestication in dry‐cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evolutionary Applications, 9 (16) 1637-1660
  • Peck LD, Llewellyn T, Bennetot B, O’Donnell S, Nowell RW, Ryan MJ, Flood J, Rodŕıguez De La Vega RC, Ropars J, Giraud T, Spanu PD, Barraclough TG. (2023) Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease. Evolutionary Biology,
  • Tezenas E, Giraud T, Véber A, Billiard S. (2023) The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing. Peer Community Journal, (3) e14
  • Vittorelli N, Rodríguez De La Vega RC, Snirc A, Levert E, Gautier V, Lalanne C, De Filippo E, Gladieux P, Guillou S, Zhang Y, Tejomurthula S, Grigoriev IV, Debuchy R, Silar P, Giraud T, Hartmann FE, Heitman J. (2023) Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLoS Genet, 2 (19) e1010347

2022

  • 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
  • Carpentier F, Rodríguez De La Vega RC, Jay P, Duhamel M, Shykoff JA, Perlin MH, Wallen RM, Hood ME, Giraud T, Parsch J. (2022) Tempo of Degeneration Across Independently Evolved Nonrecombining Regions. Molecular Biology and Evolution, 4 (39) msac060
  • Duhamel M, Carpentier F, Begerow D, Hood ME, Rodríguez De La Vega RC, Giraud T. (2022) Onset and stepwise extensions of recombination suppression are common in mating‐type chromosomes of Microbotryum anther‐smut fungi. J of Evolutionary Biology, 12 (35) 1619-1634
  • Jay P, Tezenas E, Véber A, Giraud T, Hurst LD. (2022) Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. PLoS Biol, 7 (20) e3001698
  • Ropars J, Giraud T. (2022) Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Current Opinion in Microbiology, (70) 102236

2021

  • 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 D. dianthicola. Molecular Ecology, 2 (30) 608-624
  • Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. (2021) Homage to Felsenstein 1981, or why are there so few/many species?. Evolution, 5 (75) 978-988
  • Caron T, Piver ML, Péron AC, Lieben P, Lavigne R, Brunel S, 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, flavor and texture in blue cheeses. International Journal of Food Microbiology, (354) 109174
  • Fontaine MC, Labbé F, Dussert Y, Delière L, Richart-Cervera S, Giraud T, Delmotte F. (2021) Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola. Current Biology, 10 (31) 2155-2166.e4
  • Foulongne-Oriol M, Taskent O, Kües U, Sonnenberg ASM, Van Peer AF, Giraud T. (2021) Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus. Genes, 7 (12) 1079
  • Gautier V, Levert E, Giraud T, Silar P, Berman J. (2021) Important role of melanin for fertility in the fungus Podospora anserina. G3, 8 (11) jkab159
  • 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
  • Hartmann FE, Duhamel M, Carpentier F, Hood ME, Foulongne‐Oriol M, Silar P, Malagnac F, Grognet P, Giraud T. (2021) Recombination suppression and evolutionary strata around mating‐type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes. New Phytologist, 5 (229) 2470-2491
  • Hartmann FE, Ament-Velásquez SL, Vogan AA, Gautier V, Le Prieur S, Berramdane M, Snirc A, Johannesson H, Grognet P, Malagnac F, Silar P, Giraud T, Parsch J. (2021) Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex. Molecular Biology and Evolution, 6 (38) 2475-2492
  • Kobmoo N, Arnamnart N, Pootakham W, Sonthirod C, Khonsanit A, Kuephadungphan W, Suntivich R, Mosunova OV, Giraud T, Luangsa-ard JJ. (2021) The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. persoonia, 1 (47) 136-150
  • Liu S, Decroocq S, Harte E, Tricon D, Chague A, Balakishiyeva G, Kostritsyna T, Turdiev T, Saux MFL, Dallot S, Giraud T, Decroocq V. (2021) Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section. Tree Genetics & Genomes, 1 (17) 2
  • Marden E, Abbott RJ, Austerlitz F, Ortiz‐Barrientos D, Baucom RS, Bongaerts P, Bonin A, Bonneaud C, Browne L, Alex Buerkle C, Caicedo AL, Coltman DW, Cruzan MB, Davison A, DeWoody JA, Dumbrell AJ, Emerson BC, Fountain‐Jones NM, Gillespie R, Giraud T, Hansen MM, Hodgins KA, Heuertz M, Hirase S, Hooper R, Hohenlohe P, Kane NC, Kelley JL, Kinziger AP, McKenzie VJ, Moreau CS, Nazareno AG, Pelletier TA, Pemberton JM, Qu Y, Renaut S, Riginos C, Rodríguez‐Ezpeleta N, Rogers SM, Russell JA, Schoville SD, Shi S, Smith M, Sork VL, Stone GN, Taberlet P, Videvall E, Waits L, Warschefsky E, Wayne RK, Whibley A, Willoughby J, Yoder JB, Zinger L, Sibbett B, Narum S, Rieseberg LH. (2021) Sharing and reporting benefits from biodiversity research. Molecular Ecology, 5 (30) 1103-1107
  • Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. (2021) Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. Phytopathology®, 12 (111) 2355-2366
  • 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) e34
  • Petit E. (2021) A planned experiment on local adaptation in a host-parasite system: is adaptation to the host linked to its recent domestication?. PCI Ecology, 100079

2020

  • Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Åsa, Silar P, Huhndorf SM, Miller AN, Vogan AA. (2020) The taxonomy of the model filamentous fungus Podospora anserina. MC, (75) 51-69
  • Arnaise S, Shykoff JA, Møller AP, Mousseau TA, Giraud T. (2020) Anther‐smut fungi from more contaminated sites in Chernobyl show lower infection ability and lower viability following experimental irradiation. Ecology and Evolution, 13 (10) 6409-6420
  • 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, Giraud T. (2020) Independent domestication events in the blue‐cheese fungus Penicillium roqueforti. Molecular Ecology, 14 (29) 2639-2660
  • Dussert Y, Legrand L, Mazet ID, Couture C, Piron MC, Serre RF, Bouchez O, Mestre P, Toffolatti SL, Giraud T, Delmotte F. (2020) Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola. Current Biology, 20 (30) 3897-3907.e4
  • Feurtey A, Guitton E, De Gracia Coquerel 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, 24 (29) 4925-4941
  • Hartmann FE, Snirc A, Cornille A, Godé C, Touzet P, Van Rossum F, Fournier E, Le Prieur S, Shykoff J, Giraud T. (2020) Congruent population genetic structures and divergence histories in anther‐smut fungi and their host plants Silene italica and the Silene nutans species complex. Molecular Ecology, 6 (29) 1154-1172
  • Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Ma WJ, Hood ME, Giraud T. (2020) Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence. Molecular Biology and Evolution, 3 (37) 668-682
  • Ma WJ, Carpentier F, Giraud T, Hood ME, Mank J. (2020) Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration. Genome Biology and Evolution, 4 (12) 243-258
  • Ropars J, Didiot E, Rodríguez De La Vega RC, Bennetot B, Coton M, Poirier E, Coton E, Snirc A, Le Prieur S, Giraud T. (2020) Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Current Biology, 22 (30) 4441-4453.e4
  • Ropars J, Caron T, Lo YC, Bennetot B, Giraud T. (2020) La domestication des champignons Penicillium du fromage. Comptes Rendus. Biologies, 2 (343) 155-176

2019

  • Bazzicalupo AL, Carpentier F, Otto SP, Giraud T. (2019) Little Evidence of Antagonistic Selection in the Evolutionary Strata of Fungal Mating-Type Chromosomes ( Microbotryum lychnidis-dioicae). G3 Genes|Genomes|Genetics, 6 (9) 1987-1998
  • Beckerson WC, Rodríguez De La Vega RC, Hartmann FE, Duhamel M, Giraud T, Perlin MH, Taylor JW. (2019) Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi. mBio, 6 (10) e02391-19
  • Carpentier F, Rodríguez De La Vega RC, Branco S, Snirc A, Coelho MA, Hood ME, Giraud T. (2019) Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi. Genome Res., 6 (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 in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annu. Rev. Phytopathol., 1 (57) 431-457
  • Hood ME, Antonovics J, Wolf M, Stern ZL, Giraud T, Abbate JL. (2019) Sympatry and interference of divergent Microbotryum pathogen species. Ecology and Evolution, 9 (9) 5457-5467
  • Kobmoo N, Mongkolsamrit S, Arnamnart N, Luangsa-ard JJ, Giraud T. (2019) Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis). Molecular Phylogenetics and Evolution, (140) 106580
  • 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. Molecular Ecology, 24 (28) 5299-5314

2018

  • Abbate JL, Gladieux P, Hood ME, De Vienne DM, Antonovics J, Snirc A, Giraud T. (2018) Co‐occurrence among three divergent plant‐castrating fungi in the same Silene host species. Molecular Ecology, 16 (27) 3357-3370
  • Branco S, Carpentier F, Rodríguez De La Vega RC, Badouin H, Snirc A, Le Prieur S, Coelho MA, De Vienne DM, Hartmann FE, Begerow D, Hood ME, Giraud T. (2018) Multiple convergent supergene evolution events in mating-type chromosomes. Nat Commun, 1 (9) 2000
  • Fortuna TM, Namias A, Snirc A, Branca A, Hood ME, Raquin C, Shykoff JA, Giraud T. (2018) Multiple infections, relatedness and virulence in the anther‐smut fungus castrating Saponaria plants. Molecular Ecology, 23 (27) 4947-4959
  • Giraud T, Mank J. (2018) Dosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomes. PCI Evol Biol, 2 100044
  • Hartmann FE, Rodríguez De La Vega RC, Brandenburg JT, Carpentier F, Giraud T, Van De Peer Y. (2018) Gene Presence–Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure. Genome Biology and Evolution, 5 (10) 1298-1314
  • Kobmoo N, Wichadakul D, Arnamnart N, Rodríguez De La Vega RC, Luangsa‐ard JJ, Giraud T. (2018) A genome scan of diversifying selection in Ophiocordyceps zombie‐ant fungi suggests a role for enterotoxins in co‐evolution and host specificity. Molecular Ecology, 18 (27) 3582-3598

2017

  • Badouin H, Gladieux P, Gouzy J, Siguenza S, Aguileta G, Snirc A, Le Prieur S, Jeziorski C, Branca A, Giraud T. (2017) Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Molecular Ecology, 7 (26) 2041-2062
  • Branco S, Badouin H, Rodríguez De La Vega RC, Gouzy J, Carpentier F, Aguileta G, Siguenza S, Brandenburg JT, Coelho MA, Hood ME, Giraud T. (2017) Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism. Proc. Natl. Acad. Sci. U.S.A., 27 (114) 7067-7072
  • Coelho MA, Bakkeren G, Sun S, Hood ME, Giraud T, Heitman J, Gow NAR. (2017) Fungal Sex: The Basidiomycota. Microbiol Spectr, 3 (5) 5.3.12
  • Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse MA, Heitman J, Howlett BJ, Stukenbrock EH. (2017) Fungi as a Source of Food. Microbiol Spectr, 3 (5) 5.3.09
  • 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
  • Giraud T, Gabaldón T. (2017) Dating nodes in a phylogeny using inferred horizontal gene transfers. PCI Evol Biol, 2 100037
  • Giraud T, Koskella B, Laine AL. (2017) Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Molecular Ecology, 7 (26) 1703-1710
  • 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
  • Ropars J, López-Villavicencio M, Snirc A, Lacoste S, Giraud T, Cocolin L. (2017) Blue cheese-making has shaped the population genetic structure of the mould Penicillium roqueforti. PLoS ONE, 3 (12) e0171387

2016

  • Aguileta G, Badouin H, Hood ME, Møller AP, Le Prieur S, Snirc A, Siguenza S, Mousseau TA, Shykoff JA, Cuomo CA, Giraud T. (2016) Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl. Molecular Ecology, 14 (25) 3370-3383
  • Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, Chen W, De Vallavieille‐Pope C, Enjalbert J. (2016) cloncase : Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms. Molecular Ecology Resources, 4 (16) 845-861
  • 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 M icrobotryum silenes‐acaulis parasitizing an arctic–alpine plant. Molecular Ecology, 3 (25) 811-824
  • 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
  • Fortuna TM, Snirc A, Badouin H, Gouzy J, Siguenza S, Esquerre D, Le Prieur S, Shykoff JA, Giraud T, Wilson RA. (2016) Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing. PLoS ONE, 11 (11) e0165656
  • Rodríguez De La Vega RC, Giraud T. (2016) Intragenome Diversity of Gene Families Encoding Toxin-like Proteins in Venomous Animals. Integr. Comp. Biol., 5 (56) 938-949
  • Ropars J, Lo YC, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T, López‐Villavicencio M. (2016) Fertility depression among cheese‐making Penicillium roqueforti strains suggests degeneration during domestication. Evolution, 9 (70) 2099-2109

2015

  • Badouin H, Hood ME, Gouzy J, Aguileta G, Siguenza S, Perlin MH, Cuomo CA, Fairhead C, Branca A, Giraud T. (2015) Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae. Genetics, 4 (200) 1275-1284
  • 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, 4 (8) 373-384
  • 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 CA, Perlin MH, Gladieux P, Giraud T. (2015) Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi. Molecular Biology and Evolution, 4 (32) 928-943
  • Gillot G, Jany JL, Coton M, Le Floch G, Debaets S, Ropars J, López-Villavicencio M, Dupont J, Branca A, Giraud T, Coton E, Lumbsch HT. (2015) Insights into Penicillium roqueforti Morphological and Genetic Diversity. PLoS ONE, 6 (10) e0129849
  • Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. (2015) The population biology of fungal invasions. Molecular Ecology, 9 (24) 1969-1986
  • Idnurm A, Hood ME, Johannesson H, Giraud T. (2015) Contrasted patterns in mating-type chromosomes in fungi: Hotspots versus coldspots of recombination. Fungal Biology Reviews, 3-4 (29) 220-229
  • 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
  • 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 DJ, Cuomo CA. (2015) Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics, 1 (16) 461
  • Pintye A, Ropars J, Harvey N, Shin HD, Leyronas C, Nicot PC, Giraud T, Kiss L, Zhang Z. (2015) Host Phenology and Geography as Drivers of Differentiation in Generalist Fungal Mycoparasites. PLoS ONE, 3 (10) e0120703
  • Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas Émilie, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T. (2015) Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Current Biology, 19 (25) 2562-2569
  • 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, Warren B, Deng C, Kumar S, Chagné D, Bus VGM, Volz RK, Rikkerink EHA, Gardiner SE, Giraud T, MacDiarmid R, Gleave AP. (2015) A micro RNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal, 2 (84) 417-427

2014

  • Aguileta G, De Vienne DM, Ross ON, Hood ME, Giraud T, Petit E, Gabaldón T. (2014) High Variability of Mitochondrial Gene Order among Fungi. Genome Biology and Evolution, 2 (6) 451-465
  • Buono L, López-Villavicencio M, Shykoff JA, Snirc A, Giraud T, Vinatzer BA. (2014) Influence of Multiple Infection and Relatedness on Virulence: Disease Dynamics in an Experimental Plant Population and Its Castrating Parasite. PLoS ONE, 6 (9) e98526
  • Cheeseman K, Ropars J, Renault P, Dupont J, Gouzy J, Branca A, Abraham AL, Ceppi M, Conseiller E, Debuchy R, Malagnac F, Goarin A, Silar P, Lacoste S, Sallet E, Bensimon A, Giraud T, Brygoo Y. (2014) Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat Commun, 1 (5) 2876
  • 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
  • Gibson AK, Refrégier G, Hood ME, Giraud T. (2014) Performance of a Hybrid Fungal Pathogen on Pure-Species and Hybrid Host Plants. International Journal of Plant Sciences, 6 (175) 724-730
  • Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, De Vienne DM, Rodríguez De La Vega RC, Branco S, Giraud T. (2014) Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Molecular Ecology, 4 (23) 753-773
  • 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 P enicillium roqueforti . Evolutionary Applications, 4 (7) 433-441
  • Ropars J, Aguileta G, De Vienne D, Giraud T. (2014) Massive gene swamping among cheese-making Penicillium fungi. MIC, 3 (1) 107-109
  • 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

2013

  • Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. (2013) A road map for molecular ecology. Molecular Ecology, 10 (22) 2605-2626
  • 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 E uropean crabapple ( Malus sylvestris M ill.), a wild contributor to the domesticated apple. Molecular Ecology, 8 (22) 2249-2263
  • De Vienne DM, Refrégier G, López‐Villavicencio M, Tellier A, Hood ME, Giraud T. (2013) Cospeciation vs host‐shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytologist, 2 (198) 347-385
  • De Vienne DM, Giraud T, Gouyon PH, Kolokotronis SO. (2013) Lineage Selection and the Maintenance of Sex. PLoS ONE, 6 (8) e66906
  • Fontaine MC, Austerlitz F, Giraud T, Labbé F, Papura D, Richard‐Cervera S, Delmotte F. (2013) Genetic signature of a range expansion and leap‐frog event after the recent invasion of Europe by the grapevine downy mildew pathogen Plasmopara viticola. Molecular Ecology, 10 (22) 2771-2786
  • Fontaine MC, Gladieux P, Hood ME, Giraud T. (2013) History of the invasion of the anther smut pathogen on S ilene latifolia in N orth A merica. New Phytologist, 3 (198) 946-956
  • Fournier E, Gladieux P, Giraud T. (2013) The ‘ D r J ekyll and M r H yde fungus’: noble rot versus gray mold symptoms of B otrytis cinerea on grapes. Evolutionary Applications, 6 (6) 960-969
  • Gladieux P, Devier B, Aguileta G, Cruaud C, Giraud T. (2013) Purifying selection after episodes of recurrent adaptive diversification in fungal pathogens. Infection, Genetics and Evolution, (17) 123-131
  • Hood ME, Petit E, Giraud T. (2013) Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus. Genetics, 1 (193) 309-315
  • Luque GM, Giraud T, Courchamp F, Gilburn A. (2013) Allee effects in ants. Journal of Animal Ecology, 5 (82) 956-965
  • López‐Villavicencio M, Debets AJM, Slakhorst M, Giraud T, Schoustra SE. (2013) Deleterious effects of recombination and possible nonrecombinatorial advantages of sex in a fungal model. J of Evolutionary Biology, 9 (26) 1968-1978
  • Nieuwenhuis BPS, Billiard S, Vuilleumier S, Petit E, Hood ME, Giraud T. (2013) Evolution of uni- and bifactorial sexual compatibility systems in fungi. Heredity, 6 (111) 445-455
  • Selosse MA, Taschen E, Giraud T. (2013) Do black truffles avoid sexual harassment by linking mating type and vegetative incompatibility?. New Phytologist, 1 (199) 10-13

2012

  • Aguileta G, Lengelle J, Chiapello H, Giraud T, Viaud M, Fournier E, Rodolphe F, Marthey S, Ducasse A, Gendrault A, Poulain J, Wincker P, Gout L. (2012) Genes under positive selection in a model plant pathogenic fungus, Botrytis. Infection, Genetics and Evolution, 5 (12) 987-996
  • Billiard S, López‐Villavicencio M, Hood ME, Giraud T. (2012) Sex, outcrossing and mating types: unsolved questions in fungi and beyond. J of Evolutionary Biology, 6 (25) 1020-1038
  • Cornille A, Gladieux P, Smulders MJM, Roldán-Ruiz I, Laurens F, Le Cam B, Nersesyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud T, Mauricio R. (2012) New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties. PLoS Genet, 5 (8) e1002703
  • Dilmaghani A, Gladieux P, Gout L, Giraud T, Brunner PC, Stachowiak A, Balesdent MH, Rouxel T. (2012) Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans. Molecular Ecology, 10 (21) 2519-2533
  • Gibson AK, Hood ME, Giraud T. (2012) Sibling competition arena: selfing and a competition arena can combine to constitute a barrier to gene flow in sympatry. Evolution, 6 (66) 1917-1930
  • Giraud T, Gourbière S. (2012) The tempo and modes of evolution of reproductive isolation in fungi. Heredity, 4 (109) 204-214
  • 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
  • Petit E, Giraud T, De Vienne DM, Coelho MA, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P, Young SK, Cuomo C, Perlin MH, Hood ME. (2012) Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes. Evolution, 11 (66) 3519-3533
  • Ropars J, Dupont J, Fontanillas E, Rodríguez De La Vega RC, Malagnac F, Coton M, Giraud T, López-Villavicencio M, Corradi N. (2012) Sex in Cheese: Evidence for Sexuality in the Fungus Penicillium roqueforti. PLoS ONE, 11 (7) e49665

2011

  • Amselem J, Cuomo CA, Van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, De Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, Ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M, Richardson PM. (2011) Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet, 8 (7) e1002230
  • Billiard S, López-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, 2 (86) 421-442
  • Cai L, Giraud T, Zhang N, Begerow D, Cai G, Shivas RG. (2011) The evolution of species concepts and species recognition criteria in plant pathogenic fungi. Fungal Diversity, 1 (50) 121-133
  • Gaudeul M, Giraud T, Kiss L, Shykoff JA, Bruun HH. (2011) Nuclear and Chloroplast Microsatellites Show Multiple Introductions in the Worldwide Invasion History of Common Ragweed, Ambrosia artemisiifolia. PLoS ONE, 3 (6) e17658
  • Giraud T, Shykoff JA. (2011) Bacterial cooperation controlled by mobile elements: kin selection versus infectivity. Heredity, 3 (107) 277-278
  • Gladieux P, Giraud T, Kiss L, Genton BJ, Jonot O, Shykoff JA. (2011) Distinct invasion sources of common ragweed (Ambrosia artemisiifolia) in Eastern and Western Europe. Biol Invasions, 4 (13) 933-944
  • Gladieux P, Guérin F, Giraud T, Caffier V, Lemaire C, Parisi L, Didelot F, Le Cam B. (2011) Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants: IMMIGRANT INVIABILITY IN VENTURIA INAEQUALIS. Molecular Ecology, 21 (20) 4521-4532
  • Gladieux P, Vercken E, Fontaine MC, Hood ME, Jonot O, Couloux A, Giraud T. (2011) Maintenance of Fungal Pathogen Species That Are Specialized to Different Hosts: Allopatric Divergence and Introgression through Secondary Contact. Molecular Biology and Evolution, 1 (28) 459-471
  • Kiss L, Pintye A, Kovács GM, Jankovics T, Fontaine MC, Harvey N, Xu X, Nicot PC, Bardin M, Shykoff JA, Giraud T. (2011) Temporal isolation explains host‐related genetic differentiation in a group of widespread mycoparasitic fungi. Molecular Ecology, 7 (20) 1492-1507
  • López‐Villavicencio M, Courjol F, Gibson AK, Hood ME, Jonot O, Shykoff JA, Giraud T. (2011) Competition, cooperation among kin, and virulence in multiple infections. Evolution, 5 (65) 1357-1366

2010

  • Aguileta G, Lengelle J, Marthey S, Chiapello H, Rodolphe F, Gendrault 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: LOOKING FOR GENES INVOLVED IN HOST SPECIALIZATION. Molecular Ecology, 2 (19) 292-306
  • Devier B, Aguileta G, Hood ME, Giraud T. (2010) Using phylogenies of pheromone receptor genes in the Microbotryum violaceum species complex to investigate possible speciation by hybridization. Mycologia, 3 (102) 689-696
  • Giraud T, Gladieux P, Gavrilets S. (2010) Linking the emergence of fungal plant diseases with ecological speciation. Trends in Ecology & Evolution, 7 (25) 387-395
  • Giraud F, Giraud T, Aguileta G, Fournier E, Samson R, Cruaud C, Lacoste S, Ropars J, 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, 2-3 (137) 204-213
  • Hood ME, Mena‐Alí JI, Gibson AK, Oxelman B, Giraud T, Yockteng R, Arroyo MTK, Conti F, Pedersen AB, Gladieux P, Antonovics J. (2010) Distribution of the anther‐smut pathogen Microbotryum on species of the Caryophyllaceae. New Phytologist, 1 (187) 217-229
  • Johnson LJ, Giraud T, Anderson R, Hood ME. (2010) The impact of genome defense on mobile elements in Microbotryum. Genetica, 3 (138) 313-319
  • López-Villavicencio M, Aguileta G, Giraud T, De Vienne DM, Lacoste S, Couloux A, Dupont J. (2010) Sex in Penicillium: Combined phylogenetic and experimental approaches. Fungal Genetics and Biology, 8 (47) 693-706
  • Refrégier G, Hood ME, Giraud T. (2010) No Evidence of Reproductive Character Displacement between Two Sister Fungal Species Causing Anther Smut Disease in Silene. International Journal of Plant Sciences, 8 (171) 847-859
  • Vercken E, Fontaine MC, Gladieux P, Hood ME, Jonot O, Giraud T, Howlett BJ. (2010) Glacial Refugia in Pathogens: European Genetic Structure of Anther Smut Pathogens on Silene latifolia and Silene dioica. PLoS Pathog, 12 (6) e1001229
  • Vogel V, Pedersen JS, Giraud T, Krieger MJB, Keller L. (2010) The worldwide expansion of the Argentine ant. Diversity and Distributions, 1 (16) 170-186

2009

  • Aguileta G, Hood ME, Refrégier G, Giraud T. (2009) Chapter 3 Genome Evolution in Plant Pathogenic and Symbiotic Fungi. ScienceDirect, (49) 151-193
  • Aguileta G, Refrégier G, Yockteng R, Fournier E, Giraud T. (2009) Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists. Infection, Genetics and Evolution, 4 (9) 656-670
  • Bernasconi G, Antonovics J, Biere A, Charlesworth D, Delph LF, Filatov D, Giraud T, Hood ME, Marais GAB, McCauley D, Pannell JR, Shykoff JA, Vyskot B, Wolfe LM, Widmer A. (2009) Silene as a model system in ecology and evolution. Heredity, 1 (103) 5-14
  • De Vienne DM, Refrégier G, Hood ME, Guigue A, Devier B, Vercken E, Smadja C, Deseille A, Giraud T. (2009) Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum. J of Evolutionary Biology, 4 (22) 683-698
  • De Vienne DM, Giraud T, Martin OC. (2009) In response to comment on ‘A congruence index for testing topological similarity between trees’. Bioinformatics, 1 (25) 150-151
  • De Vienne DM, Hood ME, Giraud T. (2009) Phylogenetic determinants of potential host shifts in fungal pathogens. J of Evolutionary Biology, 12 (22) 2532-2541
  • Denchev CM, Giraud T, Hood ME. (2009) Three new species of anthericolous smut fungi on Caryophyllaceae. DOI.org (Datacite),
  • Devier B, Aguileta G, Hood ME, Giraud T. (2009) Ancient Trans -specific Polymorphism at Pheromone Receptor Genes in Basidiomycetes. Genetics, 1 (181) 209-223
  • Gold A, Giraud T, Hood ME. (2009) Within-host competitive exclusion among species of the anther smut pathogen. BMC Ecol, 1 (9) 11

2008

  • Aguileta G, Marthey S, Chiapello H, Lebrun MH, Rodolphe F, Fournier E, Gendrault-Jacquemard A, Giraud T, Ané C. (2008) Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies. Systematic Biology, 4 (57) 613-627
  • Fournier E, Giraud T. (2008) Sympatric genetic differentiation of a generalist pathogenic fungus, Botrytis cinerea , on two different host plants, grapevine and bramble. J of Evolutionary Biology, 1 (21) 122-132
  • Gac ML, Giraud T. (2008) Existence of a pattern of reproductive character displacement in Homobasidiomycota but not in Ascomycota. J of Evolutionary Biology, 3 (21) 761-772
  • Giraud T, Yockteng R, Marthey S, Chiapello H, Jonot O, Lopez‐Villavicencio M, De Vienne DM, Hood ME, Refregier G, Gendrault‐Jacquemard A, Wincker P, 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, 2 (8) 387-392
  • Giraud T, Yockteng R, López-Villavicencio M, Refrégier G, Hood ME. (2008) Mating System of the Anther Smut Fungus Microbotryum violaceum : Selfing under Heterothallism. Eukaryot Cell, 5 (7) 765-775
  • Giraud T, Enjalbert J, Fournier E, Delmotte F, Dutech C. (2008) Population genetics of fungal diseases of plants. Parasite, 3 (15) 449-454
  • Giraud T, Refrégier G, Le Gac M, De Vienne DM, Hood ME. (2008) Speciation in fungi. Fungal Genetics and Biology, 6 (45) 791-802
  • Marthey S, Aguileta G, Rodolphe F, Gendrault A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, Chiapello H. (2008) FUNYBASE: a FUNgal phYlogenomic dataBASE. BMC Bioinformatics, 1 (9) 456
  • Refrégier G, Le Gac M, Jabbour F, Widmer A, Shykoff JA, Yockteng R, Hood ME, 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, 1 (8) 100
  • Salvaudon L, Giraud T, Shykoff JA. (2008) Genetic diversity in natural populations: a fundamental component of plant–microbe interactions. Current Opinion in Plant Biology, 2 (11) 135-143
  • Sloan DB, Giraud T, Hood ME. (2008) Maximized virulence in a sterilizing pathogen: the anther‐smut fungus and its co‐evolved hosts. J of Evolutionary Biology, 6 (21) 1544-1554

2007

  • De Vienne DM, Giraud T, Martin OC. (2007) A congruence index for testing topological similarity between trees. Bioinformatics, 23 (23) 3119-3124
  • De Vienne DM, Giraud T, Shykoff JA. (2007) When can host shifts produce congruent host and parasite phylogenies? A simulation approach. J of Evolutionary Biology, 4 (20) 1428-1438
  • Dutech C, Enjalbert J, Fournier E, Delmotte F, Barrès B, Carlier J, Tharreau D, Giraud T. (2007) Challenges of microsatellite isolation in fungi. Fungal Genetics and Biology, 10 (44) 933-949
  • Le Gac M, Hood ME, Giraud T. (2007) Evolution of reproductive isolation within a parasitic fungal species complex. Evolution, 7 (61) 1781-1787
  • Le Gac M, Hood ME, Fournier E, Giraud T. (2007) Phylogenetic evidence of host-specific cryptic species in the anther smut fungus. Evolution, 1 (61) 15-26
  • López-Villavicencio M, Jonot O, Coantic A, Hood ME, Enjalbert J, Giraud T, Achtman M. (2007) Multiple Infections by the Anther Smut Pathogen Are Frequent and Involve Related Strains. PLoS Pathog, 11 (3) e176
  • Tellier A, Villaréal LMMA, Giraud T. (2007) Antagonistic pleiotropy may help population-level selection in maintaining genetic polymorphism for transmission rate in a model phytopathogenic fungus. Heredity, 1 (98) 45-52
  • Yockteng R, Marthey S, Chiapello H, Gendrault A, Hood ME, Rodolphe F, Devier B, Wincker P, Dossat C, Giraud T. (2007) Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes. BMC Genomics, 1 (8) 272

2006

  • Giraud T, Jonot O, Shykoff JA. (2006) Common sex-linked deleterious alleles in a plant parasitic fungus alter infection success but show no pleiotropic advantage. Journal of Evolutionary Biology, 3 (19) 970-980
  • Giraud T, Villaréal LMMA, Austerlitz F, Le Gac M, Lavigne C. (2006) Importance of the Life Cycle in Sympatric Host Race Formation and Speciation of Pathogens. Phytopathology®, 3 (96) 280-287
  • Giraud T. (2006) Speciation in parasites: host switching does not automatically lead to allopatry. Trends in Parasitology, 4 (22) 151-152
  • Giraud T. (2006) Speciation: Selection against migrant pathogens: the immigrant inviability barrier in pathogens. Heredity, 5 (97) 316-318
  • Koskella B, Giraud T, Hood ME. (2006) Pathogen Relatedness Affects the Prevalence of Within‐Host Competition. The American Naturalist, 1 (168) 121-126
  • Pedersen JS, Krieger MJB, Vogel V, Giraud T, Keller L. (2006) Native supercolonies of unrelated individuals in the invasive Argentine ant. Evolution, 4 (60) 782-791
  • Porcher E, Giraud T, Lavigne C. (2006) Genetic differentiation of neutral markers and quantitative traits in predominantly selfing metapopulations: confronting theory and experiments with Arabidopsis thaliana. Genet. Res., 1 (87) 1-12

2005

  • Fournier E, Giraud T, Albertini C, Brygoo Y. (2005) Partition of the Botrytis cinerea complex in France using multiple gene genealogies. Mycologia, 6 (97) 1251-1267
  • Genton BJ, Shykoff JA, Giraud T. (2005) High genetic diversity in French invasive populations of common ragweed, Ambrosia artemisiifolia , as a result of multiple sources of introduction. Molecular Ecology, 14 (14) 4275-4285
  • Genton BJ, Jonot O, Thevenet D, Fournier E, Blatrix R, Vautrin D, Solignac M, Giraud T. (2005) Isolation of five polymorphic microsatellite loci, using an enrichment protocol, in the invasive weed Ambrosia artemisiifolia (Asteraceae).. Molecular Ecology Notes, 2 (5) 381-383
  • Giraud T, Jonot O, Shykoff JA. (2005) Selfing Propensity under Choice Conditions in a Parasitic Fungus, Microbotryum violaceum , and Parameters Influencing Infection Success in Artificial Inoculations. International Journal of Plant Sciences, 4 (166) 649-657
  • Hood ME, Katawczik M, Giraud T. (2005) Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum. Genetics, 3 (170) 1081-1089
  • Lopez-Villavicencio M, Enjalbert JJ, 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 ?. Journal of Evolutionary Biology, 5 (18) 1293-1303
  • López‐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). American J of Botany, 5 (92) 896-900
  • Tellier A, Villaréal LMMA, Giraud T. (2005) Maintenance of Sex‐Linked Deleterious Alleles by Selfing and Group Selection in Metapopulations of the Phytopathogenic Fungus Microbotryum violaceum. The American Naturalist, 5 (165) 577-589

2004

  • Gac ML, Giraud T. (2004) What is sympatric speciation in parasites?. Trends in Parasitology, 5 (20) 207-208
  • Giraud T. (2004) Patterns of within population dispersal and mating of the fungus Microbotryum violaceum parasitising the plant Silene latifolia. Heredity, 6 (93) 559-565
  • Porcher E, Giraud T, Goldringer I, Lavigne C. (2004) Experimental demonstration of a causal relationship between heterogeneity of selection and genetic differentiation in quantitative traits. Evolution, 7 (58) 1434-1445
  • Till‐Bottraud I, Giraud T, Fournier E, Torres C, Vautrin D, Solignac M, Genton B, Arroyo MTK. (2004) Isolation of seven polymorphic microsatellite loci, using an enrichment protocol, in the high Andean Asteraceous Chaetanthera pusilla. Molecular Ecology Notes, 3 (4) 462-464

2003

  • Duan X, Enjalbert J, Vautrin D, Solignac M, Giraud T. (2003) Isolation of 12 microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Puccinia triticina. Molecular Ecology Notes, 1 (3) 65-67
  • Fournier E, Levis C, Fortini D, Leroux P, Giraud T, Brygoo Y. (2003) Characterization of Bc- hch, the Botrytis cinerea homolog of the Neurospora crassa het-c vegetative incompatibility locus, and its use as a population marker. Mycologia, 2 (95) 251-261
  • Thomas A, Shykoff J, Jonot O, Giraud T. (2003) Sex‐Ratio Bias in Populations of the Phytopathogenic Fungus Microbotryum violaceum from Several Host Species. International Journal of Plant Sciences, 4 (164) 641-647

2002

  • Brunet F, Giraud T, Godin F, Capy P. (2002) Do Deletions of Mos1-Like Elements Occur Randomly in the Drosophilidae Family?. J Mol Evol, 2 (54) 227-234
  • Enjalbert J, Duan X, Giraud T, Vautrin D, De Vallavieille‐Pope C, Solignac M. (2002) Isolation of twelve microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Puccinia striiformis f.sp. tritici. Molecular Ecology Notes, 4 (2) 563-565
  • Fournier E, Giraud T, Loiseau A, Vautrin D, Estoup A, Solignac M, Cornuet JM, Brygoo Y. (2002) Characterization of nine polymorphic microsatellite loci in the fungus Botrytis cinerea (Ascomycota). Molecular Ecology Notes, 3 (2) 253-255
  • Giraud T, Pedersen JS, Keller L. (2002) Evolution of supercolonies: The Argentine ants of southern Europe. Proc. Natl. Acad. Sci. U.S.A., 9 (99) 6075-6079
  • Giraud T, Fournier E, Vautrin D, Solignac M, Shykoff JA. (2002) Isolation of 44 polymorphic microsatellite loci in three host races of the phytopathogenic fungus Microbotryum violaceum. Molecular Ecology Notes, 2 (2) 142-146
  • Giraud T, Fournier E, Vautrin D, Solignac M, Vercken E, Bakan B, Brygoo Y. (2002) Isolation of eight polymorphic microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Fusarium culmorum. Molecular Ecology Notes, (2) 121
  • Muñoz G, Hinrichsen P, Brygoo Y, Giraud T. (2002) Genetic characterisation of Botrytis cinerea populations in Chile. Mycological Research, 5 (106) 594-601

2001

  • Giraud T, Blatrix R, Poteaux C, Solignac M, Jaisson P. (2001) High genetic relatedness among nestmate queens in the polygynous ponerine ant Gnamptogenys striatula in Brazil. Behavioral Ecology and Sociobiology, 2-3 (49) 128-134

2000

  • Giraud T, Blatrix R, Poteaux C, Solignac M, Jaisson P. (2000) Population structure and mating biology of the polygynous ponerine ant Gnamptogenys striatula in Brazil. Molecular Ecology, 11 (9) 1835-1841

1999

  • Giraud T, Fortini D, Levis C, Lamarque C, Leroux P, LoBuglio K, Brygoo Y. (1999) Two Sibling Species of the Botrytis cinerea Complex, transposa and vacuma , Are Found in Sympatry on Numerous Host Plants. Phytopathology®, 10 (89) 967-973

1998

  • Giraud T, Fortini D, Levis C, Brygoo Y. (1998) The Minisatellite MSB1, in the Fungus Botrytis cinerea, Probably Mutates by Slippage. Molecular Biology and Evolution, 11 (15) 1524-1531

1997

  • Giraud T, Fortini D, Levis C, Leroux P, Brygoo Y. (1997) RFLP markers show genetic recombination in Botryotinia fuckeliana (Botrytis cinerea) and transposable elements reveal two sympatric species. Molecular Biology and Evolution, 11 (14) 1177-1185

Recommendations for PCI Evol Biol:

Giraud T, Gabaldón T. (2017) Dating nodes in a phylogeny using inferred horizontal gene transfers. PCI Evol Biol, 2 100037
Giraud T, Mank J. (2018) Dosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomes. PCI Evol Biol, 2 100044

Book Chapter:

  • 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 Penicillium. 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 2nd edition. 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.

Bibliographie

  1. Jay P., Tezenas E., Véber A., Giraud T. , Hurst LD.. (2022) Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. PLoS Biol, 7 (20) e3001698