Research and publications

• Publications

  2022

  Sanín, Borchsenius, Paris, Carvalho-Madrigal, Gómez Hoyos, Cardona, Arcila Marín, Ospina, Hoyos-Gómez, Manrique, Bernal (2022). The Tracking of Moist Habitats Allowed Aiphanes (Arecaceae) to Cover the Elevation Gradient of the Northern Andes. Frontiers in Plant Science, 27;13:881879. http://doi.org/10.3389/fpls.2022.881879.

   

  Sanín, Cardona, Valencia-Montoya, Torres Jiménez, Carvalho-Madrigal, Gómez, Bacon, Roquemen Tangarife, Jaramillo, Zapata, Valencia, Arboleda Valencia, Vargas, Paris (2022). Volcanic events coincide with plant dispersal across the Northern Andes. Global and Planetary Change, 210:103757, https://doi.org/10.1016/j.gloplacha.2022.103757.

   

  Sanín, Mejía-Franco, Paris, Valencia-Montoya, Salamin, Kessler, Olivares, Jaramillo, Cardona (2022). Geogenomics of montane palms points to Miocene– Pliocene Andean segmentation related to strike-slip tectonics. Journal of Biogeography, 00, 1–15, https://doi. org/10.1111/jbi.14327.

   

  2021

  Yardeni, Viruel, Paris, Hess, Crego, de la Harpe, Rivera, Barfuss, Till, Guzmán‐Jacob, Krömer, Lexer, O. Paun, Leroy (2021). Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Molecular Ecology Resources, https://doi.org/10.1111/1755-0998.13523.

   

  Kapun, Nunez, Bogaerts-Márquez, Murga-Moreno, Paris*, Outten, Coronado-Zamora, …., Petrov, Schmidt, Gonzalez, Flatt, Bergland (2021) Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Molecular Biology and Evolution, 38(12):5782–5805. (*M Paris is co-first author).

   

  Loiseau, Mota Machado, Paris, Koubínová, Dexter, Versieux, Lexer and Salamin (2021). Genome Skimming Reveals Widespread Hybridization in a Neotropical Flowering Plant Radiation. Frontiers in Ecology and Evolution, 9:668281. doi: 10.3389/fevo.2021.668281.

   

  Nunez, Paris, Machado, Bogaerts, Gonzalez, Flatt, Coronado, Kapun, Schmidt, Petrov, Alan Bergland (2021). Note: Updating the metadata of four misidentified samples in the DrosRTEC dataset. bioRxiv, DOI: 10.1101/2021.01.26.428249.

   

  2020

  de La Harpe, Paris*, Hess, Barfuss, Serrano-Serrano, Ghatak, Chaturvedi, Weckwerth, Till, Salamin, Wai, Ming & Lexer (2020). Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads. Plant, Cell & Environment, 43:12. (*M Paris is co-first author).

   

  Machado, Loiseau, Paris, Weigand, Versieux, Stehmann, Lexer, Salamin (2020). Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences. Botanical Journal of the Linnean Society, boz102.

   

  2019

  Chen, VanBuren, Paris*, Zhou, [...], Bennetzen, Lexer, Ming (In Press). The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics, 51, 1549–1558. (*M Paris is co-first author).

   

  Loiseau, Olivares, Paris, de la Harpe, [...], Lexer, Kessler & Salamin (2019). Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse Neotropical palm tribe Geonomateae. Frontiers in Plant Science, doi: 10.3389/fpls.2019.00864.

   

  de La Harpe  Hess, Loiseau, Salamin  Lexer & Paris (2018). A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms. Molecular Ecology Resources, 19(1):221-234.

   

  2018

  Roth, Florez‐Rueda, Paris & Städler (2018). Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm. The plant journal, 95(6):1084-1101.

   

  2017

  de La Harpe, Paris, Karger, Rolland, Kessler, Salamin & Lexer (2017). Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Molecular Ecology, 26(10):2608-2622.

   

  Roth, Florez-Rueda, Griesser, Paris, Städler (2017). Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages. Annals of botany, 121(1):107-118.

   

  Christe, Stölting, Paris, Fraїsse, Bierne & Lexer (2017). Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow. Molecular ecology, 26(1):59-76.

   

  2016

  Florez-Rueda, Paris, Schmidt, Widmer, Grossniklaus & Städler (2016). Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds. Molecular Biology and Evolution, 33(11):2935-2946.

   

  Lexer, Marthaler, Humbert, Barbará, de la Harpe, Bossolini, Paris, Martinelli, Versieux (2016). Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads. Botanical Journal of the Linnean Society, 181: 505-520.

   

  2015

  Stölting, Paris, Meier, Heinze, Castiglione, Bartha & Lexer (2015). Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree. New Phytologist, 207:723-734.

   

  Bonin, Paris, Frerot, Bianco, Tetreau & Despres (2015). 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. Infection genetics and Evolution, 35:204-213.

   

  2014

  Després, Stalinski, Faucon, Navratil, Viari, Paris, Tetreau, Poupardin, Riaz, Bonin, Reynaud, David (2014). Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito. Biology Letters, 10:20140716.

   

  Després, Stalinski, Tetreau, Paris, Bonin, Navratil, Reynaud, David (2014). Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins. BMC Genomics, 15:926.

   

  Duchet, Tetreau, Albane, Rey, Besnard, Perrin, Paris, David, Lagneau & Després (2014). Persistence and recycling of bioinsecticidal Bti spores in contrasted environments: evidence from laboratory and field trials. Microbial Ecology, 67:57-586.

   

  2013

  Marcombe, Paris *, Paupy, Bringuier, Yebakima, Chamdre, David, Corbel & Després (2013). Insecticide-driven patterns of genetic variation in the dengue vector Aedes aegypti in Martinique Island. PLoS ONE, 8:e77857. (*M Paris is co-first author).

   

  Paris, Marcombe, Coissac, Corbel, David & Després (2013). Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti. Evolutionary Applications, 6(7):1012-1027.

   

  2012

  Stadler, Florez-Rueda & Paris (2012). Testing for “Snowballing” Hybrid Incompatibilities in Solanum: Impact of Ancestral Polymorphism and Divergence Estimates. Molecular Biology and Evolution, 29:31-4.

   

  Paris & Després (2012). Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing. Molecular Ecology, 21:1672-86.

   

  Boyer, Paris*, Jego, Lemperière & Ravanel (2012). Influence of insecticide Bacillus thuringiensis var. israelensis treatments on resistance and enzyme activities in Aedes rusticus larvae (Diptera: Culicidae).  Biological Control, 62:75-8. (*M Paris is co-first author).

   

  Paris, Melodelima, Coissac, Tetreau, Reynaud, David & Després (2012). Transcription profiling of resistance to Bti toxins in the mosquito Aedes aegypti using next-generation sequencing. Journal of Invertebrate Pathology, 109:201-208.

   

  Paris & Després (2012). ISIF (In SIlico Fingerprinting): a user-friendly in silico AFLP program. In "Data Production and Analysis in Population Genomics" (Bonin A, Pompanon F eds). Methods in Molecular Biology Series, Humana Press, 888:55-64.

   

  Paris, Meyer, Blassiau, Coissac, Taberlet & Després (2012). Two methods to easily obtain nucleotide sequences from AFLP loci of interest. In "Data Production and Analysis in Population Genomics" (Bonin A, Pompanon F eds). Methods in Molecular Biology Series, Humana Press, 888:91-108.

   

  Tetreau, Bayyareddy, Jones, Stalinski, Riaz, Paris, David, Adang & Després (2012). Larval midgut modifications associated with Bti resistance in the yellow fever mosquito using proteomic and transcriptomic approaches. BMC Genomics, 13:248.

   

   

  2011

  Paris, David & Després (2011). Fitness costs of resistance to Bti toxins in the dengue vector Aedes aegypti. Ecotoxicology, 20:1184-1194.

   

  Paris, Tetreau, Laurent, Lelu, Després & David (2011). Bti persistence in environment induces resistance to multiple Bti toxins. Pest Management Science, 67:122-128.

   

  2010

  Paris, Bonnes, Ficetola, Poncet & Després (2010). Amplified fragment length homoplasy: in silico analysis for model and non-model species. BMC Genomics, 11:287.

   

  Paris, Boyer, Bonin, Collado, David & Després (2010). Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatment. Molecular Ecology, 19:325-337.

   

  2009

  Bonin, Paris*, Tetreau, David & Després (2009). Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variation. BMC Genomics, 10:551. (*M Paris is co-first author).

   

  2008

  Paris, Roux, Berard & Reboud (2008). The effect of genetic background on herbicide resistance fitness cost and its associated dominance in Arabidopsis thaliana. Heredity, 101:499-506.

   

  Tilquin, Paris, Reynaud, Després, Ravanel, Geremia & Gury (2008). Long-lasting persistence of Bacillus thuringiensis sp. israelensis (Bti) in mosquito natural habitats. PLoS ONE, 3(10): e3432.

   

  Bonin, Paris, Tetreau, Després, David & Kilian (2008). A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal organism after a few generations of artificial selection. BMC Genomics, 9:459.

   

  Roux, Paris & Reboud (2008). Delaying weed adaptation to herbicide by environmental heterogeneity: a simulation approach. Pest Management science, 64:16-29.