Quentin Rougemont

Position: Post-doctoral Research
Detailed position: Post-doctoral researcher at CNRS on the evolution of mating-types chromosomes on Microbotryum spp.

Team: Evolutionary genetics and ecology

Contact details:
Laboratoire Écologie, Systématique et Évolution – IDEEV
Université Paris Saclay
Bât. 680 – 12, route 128
91190 Gif Sur Yvette



Email: quentin.rougemont (at) universite-paris-saclay.fr

Laboratoire Ecologie, Systématique et Evolution

Research interests

  • Evolution of recombination and of mating type chromosomes on various Microbotryum species, a clade a fungi causing anther smut disease in Caryophyllaceae. To this aim I aim at developping (among other) a pangenomic approach.
  • Evolution of sexuals chromosomes and other kinds of supergene in Microbotyrum spp and Heliconius numata tropical butterflies.
  • Local adaptation, gene flow, recombination on various fishes species.
  • Speciation, Inference of evolutionary history on various species (Salmonideae, Heliconius among other)
  • Consequences of demographic event and of recombination variation on the efficacy of selection and on the genetic load.
  • Conservation genetics.
Laboratoire Ecologie, Systématique et Evolution

Career path

* 2022 — 2023 : 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»

Laboratoire Ecologie, Systématique et Evolution


A ) Preprints

  • Q Rougemont, T Leroy, EB Rondeau, BF Koop, L Bernatchez, Allele surfing causes maladaptation in a Pacific salmon of conservation concern. In revision doi: https://doi.org/10.1101/2022.11.10.515805
  • 30. Q Rougemont, B Huber, S Martin, A Whibley, C Estrada, D Solano, R Orpet, W.O McMillan, B Frérot, M Joron. Subtle introgression footprints at the end of the speciation continuum in a clade of Heliconius butterflies https://doi.org/10.1101/2022.12.19.520581
  • 29. Q Rougemont MÁ Rodríguez de Cara, P Jay, M Chouteau, A Whibley, B, F Piron-Prunier, R Rogner Ramos, AVL Freitas, C Salazar, K Lucas Silva-Brandão, T Texeira Torres, M Joron Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow in a butterfly bioRxiv PCI-Evol-Bio 09.29.462348; doi: https://doi.org/10.1101/2021.09.29.462348
  • 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 Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome bioRxiv 2022.06.14.496192; accepted doi: https://doi.org/10.1101/2022.06.14.496192

B ) Book Chapter

  • T Leroy & Q Rougemont (2021) Population genetics analysis methods: from population structure inferences to genome scans for selection. In: Molecular Plant Taxonomy (Springer)
  • H Cayuela, J Prunier, Q Rougemont Genomic approaches to study dispersal in free-ranging animal populations: insights for wildlife management (in review, available on demand).

C ) Published Articles

  • A Xuereb, Q Rougemont, X. Dallaire, JS. More, E Normandeau, B Bougas, A. Perreault-Payette, B Koop,  R Whitler, TD Beacham, L Bernatchez. Re-evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data. Evolutionay applications. https://doi.org/10.1111/eva.13489
  • 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, Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex Heredity https://org/10.1038/s41437-022-00547-9
  • Y Dorant, M Laporte, Q Rougemont, H Cayuela, R Rochette, L Bernatchez Fishery genomics: Are adaptive markers the decisive swivel for delineating population units in marine species? Molecular Ecology. https://doi.org/10.1111/mec.16653
  • 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 Complex genome-wide variation underlie migratory behavior in a pacific salmon. Molecular Ecology https://doi.org/10.1111/mec.16339
  • 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 288: 20212006. https://doi.org/10.1098/rspb.2021.2006
  • 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
  • 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
  • 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
  • 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).
  • C Perrier, Q Rougemont, Charmentier A (2020) Genomic footprints of adaptive divergence in Mediterranean blue tits in heterogeneous environment. Evolutionary Applications. https://doi.org/10.1111/eva.13035
  • 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
  • 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).
  • 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
  • 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.
  • 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)
  • 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.
  • 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 * : see also: doi:10.1111/evo.13504
  • 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
  • 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
  • Q Rougemont, C Perrier, PA Gagnaire, 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
  • 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/
  • 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
  • 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.
  • 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
  • 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