CNRS researcher in evolution and ecology at CNRS and Université Paris-Saclay from November 2022.
micro-macro- evolutionary links during the speciation process
Affiliation
UMR 8079 CNRS-UPS-AgroParisTech,
12 route 128 91190 Gif-sur-Yvette, France
2022 - 2025 Postdocal researcher in evolution and ecology at CNRS and Université Paris-Saclay from November 2022.
Working with Tatiana Giraud.
sex chromosome evolution in Microbtryum species
2020 - 2022 PostDoc at CNRS CEFE Montpellier with Mathieu Joron. Demography and population genomics of heliconius numata.
2016 - 2020 Postdoc at Université Laval with Louis Bernatchez. Modeling demographic and selective process within natural population.
2012 - 2015 Phd Thesis at INRAE (French research institute for agronomy), Rennes, France.
population genomics and experimental approaches to study speciation in European lampreys. Rennes, France Supervision : Guillaume Evanno, Sophie Launey.
4 articles published (see publication list). Phd Thesisavailable here
2012 Master thesis at INRAE (French research institute for agronomy), Rennes, France.
Combining population gentics and otholotith microchemistry to study dispersal and genetic differentiation in Alosa sp. Supervision : Sophie Launey, Elodie Reveillac .
Article published in 2022 in Heredity, master thesisavailable here
2017 Python MOOC online
2015 Approximate Bayesian Computation and Random Forest with Pr. Jérôme Goudet and Camille Roux at [Lausanne University] (https://www.unil.ch/unil/fr/home.html)
2009 - 2012 Master in Environmental sciences and engineering at l’institut agro, Rennes, France.
Studied applied ecology and biodiversity, sciences Studied population genetics (6 month internship in population genetics of Atlantic salmon at Exeter University with Jamie Stevens
Genome Assembly
Genome Annotation
Pangenome Graph
Population genomics and molecular evolution
Phylogenetics
Approximate Bayesian Computation - Random Forest
A) Submitted
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). https://link.springer.com/protocol/10.1007/978-1-0716-0997-2_16.available here
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.here
C) Accepted Articles
note: the “*” indicates co-first authorship
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
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
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
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.
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.available here.
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
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
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
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
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
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/jkad033available here
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
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/s41437-022-00547-9available here
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.16653available here
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
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
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.1008348available here
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
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
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.13035available here
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
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.12765available here
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
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
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
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.13486available here
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.13209available here
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
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.13664available here
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
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.12750available here
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
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/ncomms7686available here