Biography

I am an evolutionary biologist interested in different aspects of adaptation and speciation: pesticide resistance evolution, genomics of local adaptation, adaptation to climate, genomics of speciation, evolution of key innovation, phylogenomics, plant domestication, reproductive isolation, genome evolution,...

I am currently working/having fun in Prof. Thomas Flatt's team, focussing on climate adaptation and life-history clines, chromosomal inversion, and evolution of aging.

Research and publications

• Articles
  48 publications

  2026 2025 2024 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008

  Geology, climate, and competition as drivers of diversification in the neotropical palm genus Geonoma
  Yaël Assassa, Oriane Loiseau, Anna Weigand, Ingrid Olivares, María José Sanín, Natalia Arcila Marin, Margot Paris, Marylaure de La Harpe, Christophe Thébaud, Michael Kessler, Nicolas Salamin, Jonathan Rolland, New Phytologist (2026) | Journal article

  Multiple forms of balancing selection maintain inversion polymorphism
  Margot Paris, Esra Durmaz Mitchell, Envel Kerdaffrec, Doriane Rubin, Cécile Spichtig, Felicitas Zurbriggen, Joël Becker, Hannah Augustijnen, Harshavardhan Thyagarajan, Eliane Zinn, Fanny Gagliardi, Elliot Gobet, Tristan Rey, Yvan Rime, Sofia Ribeiro Machado, Jeremias Bachmann, Noemi Sgammeglia, Paul Schmidt, Thomas Flatt, Heredity (2026) | Journal article

  Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource
  Joaquin C B Nunez, Marta Coronado-Zamora, Mathieu Gautier, Martin Kapun, Sonja Steindl, Lino Ometto, Katja Hoedjes, Julia Beets, R Axel W Wiberg, Giovanni R Mazzeo, David J Bass, Denys Radionov, Iryna Kozeretska, Mariia Zinchenko, Oleksandra Protsenko, Svitlana V Serga, Cristina Amor-Jimenez, Sònia Casillas, Alejandro Sánchez-Gracia, Aleksandra Patenkovic, Amanda Glaser-Schmitt, Antonio Barbadilla, Antonio J Buendia-Ruíz, Astra Clelia Bertelli, Balázs Kiss, Banu Sebnem Önder, Bélen Roldán Matrín, Bregje Wertheim, Candice Deschamps, Carlos E Arboleda-Bustos, Carlos Tinedo, Christian Feller, Christian Schlötterer, Clancy Lawler, Claudia Fricke, Cristina P Vieira, Cristina Vieira, Darren J Obbard, Dorcas Juana Orengo, Doris Vela, Eduardo Amat, Elgion Loreto, Envel Kerdaffrec, Esra Durmaz Mitchell, Eva Puerma, Fabian Staubach, M Florencia Camus, Hervé Colinet, Jan Hrcek, Jesper Givskov Sørensen, Jessica Abbott, Molecular Biology and Evolution (2025) | Journal article

  Divergence and Selection in a Cryptic Species Complex (Geonoma undata: Arecaceae) in the Northern Andes of Colombia
  Carmen P Webster, Margot Paris, Ingrid Olivares, Martin F Wojciechowski, Michael Kessler, María José Sanín, Luciana Santoferrara, Genome Biology and Evolution (2025) | Journal article

  Germline proliferation trades off with lipid metabolism in Drosophila
  Marisa A Rodrigues, Chantal Dauphin-Villemant, Margot Paris, Martin Kapun, Esra Durmaz Mitchell, Envel Kerdaffrec, Thomas Flatt, Evolution Letters (2024) | Journal article

  Hyper-Cryptic radiation of a tropical montane plant lineage
  Ingrid Olivares, Sergio Tusso, María José Sanín, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris, Molecular Phylogenetics and Evolution (2024) | Journal article

  Geogenomics of montane palms points to Miocene–Pliocene Andean segmentation related to strike‐slip tectonics
  Sanín MJ and Mejía-Franco FG and Paris M and Valencia-Montoya WA and Salamin N and Kessler M and Olivares I and Jaramillo JS and Cardona A, Journal of biogeography (2022) | Journal article

  The Tracking of Moist Habitats Allowed Aiphanes (Arecaceae) to Cover the Elevation Gradient of the Northern Andes.
  Sanín MJ and Borchsenius F and Paris M and Carvalho-Madrigal S and Gómez Hoyos AC and Cardona A and Arcila Marín N and Ospina Y and Hoyos-Gómez SE and Manrique HF and Bernal R, Frontiers in plant science (2022) | Journal article

  Volcanic events coincide with plant dispersal across the Northern Andes
  María José Sanín and Agustín Cardona and Wendy A. Valencia-Montoya and María Fernanda Torres Jiménez and Sara Carvalho-Madrigal and Andrés Camilo Gómez and Christine D. Bacon and Tomas Roquemen Tangarife and Juan Sebastián Jaramillo and Sebastián Zapata and Víctor Valencia and Jorge William Arboleda Valencia and Valentina Vargas and Margot Paris, Global and Planetary Change (2022) | Journal article

  Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource.
  Kapun M and Nunez JCB and Bogaerts-Márquez M and Murga-Moreno J and Paris M and Outten J and Coronado-Zamora M and Tern C and Rota-Stabelli O and Guerreiro MPG and Casillas S and Bergland AO, Molecular biology and evolution (2021) | Journal article

  Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations.
  Yardeni G and Viruel J and Paris M and Hess J and Groot Crego C and de La Harpe M and Rivera N and Barfuss MHJ and Till W and Guzmán-Jacob V and Krömer T and Lexer C and Paun O and Leroy T, Molecular ecology resources (2021) | Journal article

  Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations
  Yardeni G and Viruel J and Paris M and Hess J and Crego CG and de La Harpe M and Rivera N and Barfuss MHJ and Till W and Guzmán-Jacob V and Krömer T and Lexer C and Paun O and Leroy T, (2021) | Preprint

  Genome Skimming Reveals Widespread Hybridization in a Neotropical Flowering Plant Radiation
  Oriane Loiseau and Talita Mota Machado and Margot Paris and Darina Koubínová and Kyle G. Dexter and Leonardo M. Versieux and Christian Lexer and Nicolas Salamin, Frontiers in Ecology and Evolution (2021) | Journal article

  Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource
  Kapun M and Nunez JCB and Bogaerts-Márquez M and Murga-Moreno J and Paris M and Outten J and Coronado-Zamora M and Tern C and Rota-Stabelli O and Guerreiro MPG and Casillas S and Bergland AO, (2021) | Preprint

  Note: Updating the metadata of four misidentified samples in the DrosRTEC dataset
  Nunez JCB and Paris M and Machado H and Bogaerts M and Gonzalez J and Flatt T and Coronado M and Kapun M and Schmidt P and Petrov D and Bergland A, (2021) | Preprint

  Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation.
  De La Harpe M and Paris M and Hess J and Barfuss MHJ and Serrano-Serrano ML and Ghatak A and Chaturvedi P and Weckwerth W and Till W and Salamin N and Wai CM and Ming R and Lexer C, Plant, cell & environment (2020) | Journal article

  The bracteatus pineapple genome and domestication of clonally propagated crops.
  Chen LY and VanBuren R and Paris M and Zhou H and Zhang X and Wai CM and Yan H and Chen S and Alonge M and Ramakrishnan S and Liao Z and Liu J and Lin J and Yue J and Fatima M and Lin Z and Ming R, Nature genetics (2019) | Journal article

  Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae.
  Loiseau O and Olivares I and Paris M and de La Harpe M and Weigand A and Koubínová D and Rolland J and Bacon CD and Balslev H and Borchsenius F and Cano A and Couvreur TLP and Salamin N, Frontiers in plant science (2019) | Journal article

  A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms.
  de La Harpe M and Hess J and Loiseau O and Salamin N and Lexer C and Paris M, Molecular ecology resources (2019) | Journal article

  Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences
  Talita Mota Machado, Oriane Loiseau, Margot Paris, Anna Weigand, Leonardo M Versieux, João Renato Stehmann, Christian Lexer, Nicolas Salamin, Botanical Journal of the Linnean Society (2019) | Journal article

  Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads
  De La Harpe M and Paris M and Hess J and Barfuss MHJ and Serrano-Serrano ML and Ghatak A and Chaturvedi P and Weckwerth W and Till W and Salamin N and Wai CM and Ming R and Lexer C, (2018) | Preprint

  Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm.
  Roth M and Florez-Rueda AM and Paris M and Städler T, The Plant journal : for cell and molecular biology (2018) | Journal article

  Molecular ecology studies of species radiations: current research gaps, opportunities and challenges.
  de la Harpe M and Paris M and Karger DN and Rolland J and Kessler M and Salamin N and Lexer C, Molecular ecology (2017) | Journal article

  Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds.
  Florez-Rueda AM and Paris M and Schmidt A and Widmer A and Grossniklaus U and Städler T, Molecular biology and evolution (2016) | Journal article

  Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow.
  Christe C and Stölting KN and Paris M and Fraїsse C and Bierne N and Lexer C, Molecular ecology (2016) | Journal article

  Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads
  Lexer C and Eligio Bossolini and Fabienne Marthaler and Gustavo Martinelli and Leonardo M. Versieux and Margot Paris and Marylaure de la Harpe and Sarah Humbert and Thelma Barbará, Botanical journal of the Linnean Society. Linnean Society of London (2016) | Journal article

  The genetic architecture of a complex trait: Resistance to multiple toxins produced by Bacillus thuringiensis israelensis in the dengue and yellow fever vector, the mosquito Aedes aegypti.
  Bonin A and Paris M and Frérot H and Bianco E and Tetreau G and Després L, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases (2015) | Journal article

  Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.
  Stölting KN and Paris M and Meier C and Heinze B and Castiglione S and Bartha D and Lexer C, The New phytologist (2015) | Journal article

  Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito.
  Després L and Stalinski R and Faucon F and Navratil V and Viari A and Paris M and Tetreau G and Poupardin R and Riaz MA and Bonin A and Reynaud S and David JP, Biology letters (2014) | Journal article

  Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins.
  Després L and Stalinski R and Tetreau G and Paris M and Bonin A and Navratil V and Reynaud S and David JP, BMC genomics (2014) | Journal article

  Persistence and recycling of bioinsecticidal Bacillus thuringiensis subsp. israelensis spores in contrasting environments: evidence from field monitoring and laboratory experiments.
  Duchet C and Tetreau G and Marie A and Rey D and Besnard G and Perrin Y and Paris M and David JP and Lagneau C and Després L, Microbial ecology (2014) | Journal article

  Insecticide-driven patterns of genetic variation in the dengue vector Aedes aegypti in Martinique Island.
  Marcombe S and Paris M and Paupy C and Bringuier C and Yebakima A and Chandre F and David JP and Corbel V and Despres L, PloS one (2013) | Journal article

  Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti.
  Paris M and Marcombe S and Coissac E and Corbel V and David JP and Després L, Evolutionary applications (2013) | Journal article

  Larval midgut modifications associated with Bti resistance in the yellow fever mosquito using proteomic and transcriptomic approaches.
  Tetreau G and Bayyareddy K and Jones CM and Stalinski R and Riaz MA and Paris M and David JP and Adang MJ and Després L, BMC genomics (2012) | Journal article

  Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing.
  Paris M and Despres L, Molecular ecology (2012) | Journal article

  In silico fingerprinting (ISIF): a user-friendly in silico AFLP program.
  Paris M and Després L, Methods in molecular biology (Clifton, N.J.) (2012) | Journal article

  Two methods to easily obtain nucleotide sequences from AFLP loci of interest.
  Paris M and Meyer CL and Blassiau C and Coissac E and Taberlet P and Després L, Methods in molecular biology (Clifton, N.J.) (2012) | Journal article

  Transcription profiling of resistance to Bti toxins in the mosquito Aedes aegypti using next-generation sequencing.
  Paris M and Melodelima C and Coissac E and Tetreau G and Reynaud S and David JP and Despres L, Journal of invertebrate pathology (2011) | Journal article

  Testing for "snowballing" hybrid incompatibilities in Solanum: impact of ancestral polymorphism and divergence estimates.
  Städler T and Florez-Rueda AM and Paris M, Molecular biology and evolution (2011) | Journal article

  Fitness costs of resistance to Bti toxins in the dengue vector Aedes aegypti.
  Paris M and David JP and Despres L, Ecotoxicology (London, England) (2011) | Journal article

  Persistence of Bacillus thuringiensis israelensis (Bti) in the environment induces resistance to multiple Bti toxins in mosquitoes.
  Paris M and Tetreau G and Laurent F and Lelu M and Despres L and David JP, Pest management science (2010) | Journal article

  Amplified fragment length homoplasy: in silico analysis for model and non-model species.
  Paris M and Bonnes B and Ficetola GF and Poncet BN and Després L, BMC genomics (2010) | Journal article

  Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatment.
  Paris M and Boyer S and Bonin A and Collado A and David JP and Despres L, Molecular ecology (2009) | Journal article

  Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations.
  Bonin A and Paris M and Tetreau G and David JP and Després L, BMC genomics (2009) | Journal article

  Long lasting persistence of Bacillus thuringiensis Subsp. israelensis (Bti) in mosquito natural habitats.
  Tilquin M and Paris M and Reynaud S and Despres L and Ravanel P and Geremia RA and Gury J, PloS one (2008) | Journal article

  A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection.
  Bonin A and Paris M and Després L and Tetreau G and David JP and Kilian A, BMC genomics (2008) | Journal article

  The effects of the genetic background on herbicide resistance fitness cost and its associated dominance in Arabidopsis thaliana.
  Paris M and Roux F and Bérard A and Reboud X, Heredity (2008) | Journal article

  Delaying weed adaptation to herbicide by environmental heterogeneity: a simulation approach.
  Roux F and Paris M and Reboud X, Pest management science (2008) | Journal article