Quentin ROUGEMONT

• Compréhension des mécanismes de spéciation : étudier le lien micro- macro- en évolution
• Evolution de la recombinaison chez les champignons du genre Microbotryum 
• Evolution des chromosomes de types sexuels et supergene chez Microbotyrum et les papillons du genre Heliconius numata
• Adaptation locale chez les poissons
• Spéciation et inférence de l’histoire évolutive chez diverses espèces (Salmonidés, papillons Heliconius par exemple)
• Conséquences des processus démographiques et de la recombinaison sur l’efficacité de la sélection et le fardeau génétique.
• Génétique de la conservation

* 2026 – present: CRCN,  CNRS, Université Paris-Saclay

* 2023 — 2025 : Post-Doc, CNRS, Université Paris-Saclay, Gif-Sur-Yvette – Equipe T. Giraud, génomique des champignons Microbotryum.

* 2020 – 2022 : Post-Doc, CNRS, CEFE, Montpellier, France – Equipe M. Joron. Génomique des papillons Silvaniformes

* 2016 – 2020 : Post-Doc, Université Laval, Québec, Canada – Equipe de L. Bernatchez, Génomique des salmonidés et autres espèces de poissons.

* 2012 – 2015 : Doctorat de Biologie évolutive, INRAE, Rennes, France – Directeurs : G. Evanno et S. Launey, «Évolution de la divergence entre la lamproie fluviatile (Lampetra fluviatilis) et la lamproie de planer (Lampetra planeri) inférée par approches expérimentales et de génomique des populations»

A ) soumis – en révision

• 39. A mosaic of genomic architectures underpins parasitism loss in a jawless vertebrate
  Arne Jacobs, Nolwenn Decanter, Ole K. Tørresen, Benedicte Garmann-Aarhus, Maria Capstick, Quentin Rougemont, Frédéric Guillaume, Romane Normand, Julien Tremblay, Jean-Pierre Destouches, Anne-Laure Besnard, Ahmed Souissi, Gilles Lassalle, Solenn Stoeckel, Eric J. Petit, Siv NK Hoff, Daniel J. Park, Bernard J. Pope, Sissel Jentoft, Leif Asbjørn Vøllestad, Kjetill S. Jakobsen, Guillaume Evanno
  bioRxiv 2026.05.11.724254; doi: https://doi.org/10.64898/2026.05.11.724254

B ) Chapitres d’Ouvrage

• 38. T Leroy & Q Rougemont (2021) Population genetics analysis methods: from population structure inferences to genome scans for selection. In: Molecular Plant Taxonomy (Springer), [available here]
• 37. H Cayuela, J Prunier, Q Rougemont Genomic approaches to study dispersal in free-ranging animal populations: insights for wildlife management. In applied environnemental genomics. CSIRO. (2023). DOI: 10.1071/9781486314935, [available here]

C ) Articles acceptés

• 36. B. Monod-Broca, H. Cayuela, J.G, Prunier, … Q. Rougemont* J.P. Lena. Species distribution models predict genome-wide polymorphism and gene flow in an endangered amphibian. Heredity (2026) [available here]
• 35. M. Toscani, A. Malik1, A. Riera-Begue1, C Dowling, Q Rougemont, RC Rodríguez de la Vega, T Giraud, S. Schilling and R. Melzer, An ancient X chromosomal region harbours three genes potentially controlling sex determination in Cannabis sativa, New Phytologist (2026), [available here]
• 34. Q. Rougemont, E Lucotte, L Boyer, A. Jalaber, A. Snirc, T Giraud, Ricardo C Rodríguez de la Vega, EASYstrata: a new workflow to infer evolutionary strata along sex chromosomes and other supergenes, doi: https://doi.org/10.1093/nargab/lqaf110, [available here]
• 33. L Guichard, R Lagadec, L Michel, H Mayeur, M FUENTES, J Pain, N Heier, Q Rougemont, MC Rodicio, A Barreiro-Iglesias, P Blader, M Schubert and S Mazan, 2024. The lamprey habenula provides an extreme example for the temporal regulation of asymmetric development. Frontiers in Cell and Developmental Biology, doi: DOI 10.3389/fcell.2025.1528797 , [available here]
• 32. C Moraga*, C Branco*, Q Rougemont*, P Veltsos, P Jedlička, [….], D Charlesworth, T Giraud, A. Bendahmane, A. Di Genova, A. Madoui, R Hobza, G.A.B. Marais The Silene latifolia genome and its giant Y chromosome. Science.
• 31. E Lucotte, P Jay, Q Rougemont, L Boyer, A Cornille, A Snirc, A Labat, E Chahine, M Duhamel, J Gendelman, RK Hayes, MH Perlin, A Widmer, J Antonovics, E Bruns, ME Hood, RC Rodríguez de la Vega, T Giraud Loss of function of HD mating-type genes in anther-smut fungi and recombination suppression without mating-type loci linkage, doi: https://doi.org/10.1101/2024.03.03.583181. In review.[available here]
• 30. FE Hartmann, RC Rodriguez de la Vega, Q Rougemont, A Deméné, T Badet, D Croll, A Labat, S Prospero, A Snirc, L Stauber, C Dutech, T Giraud, Million years old recombination suppression in a region linked to the mating-type locus in the chestnut blight fungus Cryphonectria parasitics. doi: https://doi.org/10.1101/2024.03.29.587348 In review. [available here]
• 29. Q Rougemont, T Leroy, EB Rondeau, BF Koop, L Bernatchez (2023) Allele surfing causes maladaptation in a Pacific salmon of conservation concern. Plos Genetics DOI: 10.1371/journal.pgen.1010918.[available here]
• 28. Q Rougemont, B Huber, S Martin, A Whibley, C Estrada, D Solano, R Orpet, W.O McMillan, B Frérot, M Joron (2023) Subtle introgression footprints at the end of the speciation continuum in a clade of Heliconius butterflies. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msad166 [here]
• 27. MÁ Rodríguez de Cara*, P Jay*, Q. Rougemont*, M Chouteau, A Whibley, B, F Piron-Prunier, R Rogner Ramos, AVL Freitas, C Salazar, K Lucas Silva-Brandão, T Texeira Torres, M Joron (2023) Supergene formation is associated with a major shift in genome-wide patterns of diversity in a butterfly. Peer-Community Journal (10.24072/pcjournal.298).[available here]
• 26. EB Rondeau, KA Christensen, DR Minkley, JS Leong, MTT Chan, CA Despins, A Mueller, D Sakhrani, CA Biagi, Q Rougemont, E Normandeau, SJM Jones, RH Devlin, RE Withler, TD Beacham, KA Naish, JM Yáñez, R Neira, L Bernatchez, WS Davidson, BF Koop (2023) Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome 2023.06.14.496192; G3, https://doi.org/10.1093/g3journal/jkad033[available here]
• 25. A Xuereb, Q Rougemont, JS. More, E Normandeau, TD Beacham, L Bernatchez (2023) Refining conservation units in Pacific Salmon. Evolutionary applications. https://doi.org/10.1111/eva.13489 [available here]
• 24. Q Rougemont, C Perrier, AL Besnard, I Lebel, Y Abdallah, E Feunteun, E Réveillac, E Lasne, A Acou, DJ Nachon, F Cobo, G Evanno, JL Baglinière, S Launey (2022) Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex Heredity 10.1038/s41437-022-00547-9[available here]
• 23. Y Dorant, M Laporte, Q Rougemont, H Cayuela, R Rochette, L Bernatchez (2022). Landscape genomics of the American lobster (Homarus americanus). Molecular Ecology. https://doi.org/10.1111/mec.16653[available here]
• 22. Q Rougemont, A Xuereb, X Dallaire, JS Moore, E Normandeau, EB Rondeau, RE Withler, DM Van Doornik, PA Crane, KA Naish, JC Garza, TD Beacham, BF Koop, L Bernatchez (2022) Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon Molecular Ecology https://doi.org/10.1111/mec.16339.
  * voir perspective: https://doi.org/10.1111/mec.16792[available here]
• 21. Xuereb A, Rougemont Q, Tiffin P, Xue H, Phifer-Rixey M (2021) Individual-based eco-evolutionary models for understanding adaptation in changing seas. Proc. R. Soc. B https://doi.org/10.1098/rspb.2021.2006[here]
• 20. L Benestan, Q Rougemont, E Parent, E Normandeau, L Bernatchez, Y Lambert, C Audet, G Parent (2021) Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus). Evolutionary Applications. https://doi.org/10.1111/eva.13143 [available here]
• 19. Q Rougemont, J-S Moore, T. Leroy, E. Normandeau, E.B. Rondeau, R.E. Withler, D.M.Van Doornik, P.A. Crane, K.A. Naish, J.C Garza, T.D. Beacham, B.F. Koop, L Bernatchez (2020) Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific salmon. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1008348 [available here]
• 18. Q Rougemont, V Dolo, A Oger, AL Besnard, MA Coutellec, S Launey, C Perrier, G Evanno (2020) Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype. Heredity. https://doi.org/10.1038/s41437-020-00367-9. [available here]
• 17. Q Rougemont*, H Cayuela*, M Laporte, C Mérot, E Normandeau, S Jentoft, P Sirois, M. Castonguay, T Jansen, K Praebel, M Clément, L Bernatchez (2020). Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Molecular Ecology. https://doi.org/10.1111/mec.15499 (*: Co-first authorship).[available here]
• 16. C Perrier, Q Rougemont, Charmentier A (2020) Demographic history and genomics of local adaptation in blue tits. Evolutionary Applications. https://doi.org/10.1111/eva.13035 [available here]
• 15. Y Dorant, H Cayuela, K Wellband, M Laporte, Q Rougemont, C Mérot, E Normandeau, R Rochette, L Bernatchez (2020) Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species. Molecular Ecology. https://doi.org/10.1111/mec.15565 [available here] * see perspective: https://doi.org/10.1111/mec.15665
• 14. Q Rougemont*, M Letwein*, M Duranton*, PA Gagnaire, L Bernatchez (2020) Using haplotype information for conservation genomics. Trends in Ecology & Evolution, https://doi.org/10.1016/j.tree.2019.10.012 (*: Co-first authorship).[available here]
• 13. Q Rougemont, A Carrier, J leluyer, AL Ferchaud, JM Farrell, D Hatin, PBrodeur, L Bernatchez (2019) Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin. Evolutionary Applications, https://doi.org/10.1111/eva.12765 [available here]
• 12. T Leroy, Q Rougemont, JL Dupouey, C Bodenes, C Lalanne, C Belser, K Labadie, G Le Provost, JM Aury, A Kremer, C Plomion (2019) Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers. New Phytologist, https://doi.org/10.1101/246637 [available here]
• 11. Y Dorant, Q Rougemont*, L Benestan*, E Normandeau, B Boyle, R Rochette, L Bernatchez (2019) Comparing Pool-seq, Rapture and GBS genotyping for inferring population structure; the American lobster (Homarus americanus) as a case study. Ecology & Evolution, https://doi.org/10.1002/ece3.5240 (*: Co-authorship)[available here]
• 10. H Cayuela, Q Rougemont, JG Prunier, JS Moore, J Clobert, A Besnard, L Bernatchez (2018) Demographic and genetic approaches to study dispersal in wild animal populations: a methodological review. Molecular Ecology, https://doi.org/10.1111/mec.14848 [available here]
• 9. Q Rougemont* L Bernatchez (2018) The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations. Evolution, https://doi.org/10.1111/evo.13486 [available here] * see perspective : https://doi:10.1111/evo.13504
• 8. M Voillemot, Q Rougemont, C Roux JR Pannell (2018) The divergence history of the perennial plant Linaria cavanillesii confirms a recent loss of self-incompatibility. Journal of Evolutionary Biology, https://doi.org/10.1111/jeb.13209 [available here]
• 7. JS Moore, LN. Harris, J LeLuyer, BJ Sutherland, Q Rougemont, RF Tallman, AT Fisk L. Bernatchez (2017) Migratory difficulty drives habitat choice and local adaptation in anadromous Arctic Char (Salvelinus alpinus): evidence from integration of genomics and acoustic telemetry. Molecular Ecology, https://doi.org/10.1111/mec.14393 [available here]
• 6. Q Rougemont, PA Gagnaire, C Perrier, C Genthon, AL Besnard, S Launey G Evanno (2017) Parallel patterns of genomic divergence among multiple pairs of lamprey ecotypes explained by a common history of divergence and secondary gene flow. Molecular Ecology, https://doi.org/10.1111/mec.13664 [available here]
• 5. Q Rougemont, C Roux S Neuenschwander, J Goudet G Evanno (2016) Reconstructing the demograhic history of divergence between European river and brook lampreys using Approximate Bayesian Computations. Peer-j, https://peerj.com/articles/1910/ [available here]
• 4. Q Rougemont, A Gaigher, E Lasne, J Côte, M Coke, AL Besnard, S Launey G Evanno (2015) Low reproductive isolation and highly variable levels of gene flow reveal limited progress toward speciation between European river and brook lampreys, Journal of Evolutionary Biology, https://doi.org/10.1111/jeb.12750 [available here]
• 3. J Martin Q Rougemont, H Drouineau, S Launey, P Jattteau, G Bareille, S Berail, C Pécheyran, E Feunteun, S Roques, D Clavé, DJ Nachon, C Antunes, M Mota, E Réveillac F Daverat (2015) Dispersal capacities of anadromous Allis shad population inferred from a coupled genetic and otolith approach. Canadian Journal of Fisheries and Aquatic Science, https://doi.org/10.1139/cjfas-2014-0510. [available here]
• 2. R Lagadec, L Laguerre, A Menuet, A Amara, C Rocancourt, P Péricard, BG Godard, MC Rodicio, I. Rodriguez-Moldes, H Mayeur, Q Rougemont, S Mazan and A Boutet (2015) The ancestral role of Nodal signaling in breaking L/R symmetry in the vertebrate forebrain, Nature Communication. https://www.nature.com/articles/ncomms7686 [available here]
• 1. Q Rougemont, AL Besnard, JL Baglinière S Launey (2014) Characterization of thirteen new microsatellite markers for allis shad (Alosa alosa) and twaite shad (Alosa fallax). Conservation Genetic Ressources, https://doi.org/10.1007/s12686-014-0352-z [available here]