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102

CV Raphael Leblois

Raphaël Leblois                                       E-mail : raphael.leblois@inrae.fr

 

Centre de Biologie pour la Gestion des Populations (CBGP)

UMR 1062 INRA-IRD-CIRAD-SupAgro

755 avenue du campus Agropolis,

Campus International de Baillarguet CS 30016

34980 Montferrier-sur-Lez cedex, France

tél : +33 (0)4 99 62 33 31   fax : +33 (0)4 99 62 33 45

 

ORCHID : 0000-0002-3051-4497                                                                 idHAL : raphael-leblois

Present Position

 

Sept 2010 – TodayResearcher (CRCN) at the Center for Biology and Management of Populations, National Institute for Agronomical Research (CBGP - INRA), Montpellier, France

 

Education & Research Trainings & Past Positions

 

2012 – 2017

Member of the "Institut de Biologie Computationnelle" IBC a multidisciplinary project center supported by the "Investissements d'Avenir" call from the French National Research Agency (ANR), Montpellier, France

 

2006-2010

Assistant Professor (« Maitre de conférence »)at the National Museum of Natural History of Paris (MNHN).

 

2005-2006

PostDoc (6 months):« Multilocus genetic analyses and demographic inferences with applications to human populations from Central Asia» with Pr. Evelyne Heyer et Dr. Renaud Vitalis, Musée de l’Homme - MNHN, Paris, France.

 

2004-2005

PostDoc, Lavoisier grant (1 year):« Bottleneck detection and inference of the number of founding individuals from SNPs markers », with Pr. Montgomery Slatkin, University of California, Berkeley, United-States.

 

2000-2004

PhD in Integrative Biology (3 ½ years): « Inference of dispersal parameters from genetic data in subdivided populations » under the supervision of Dr. François Rousset and Dr. Arnaud Estoup. Montpellier Supagro – University of Montpellier II, France.

 

1999-2000

MSc in Evolutionary Biology and Ecology, 6 months project: « Simulation study of the influence of mutational and demographic factors on the inference of demographic parameters from individual microsatellite genotypes » under the supervision of Dr. François Rousset et Dr. Arnaud Estoup. Montpellier Supagro – University of Montpellier II.

 

Languages     

FRENCH: Mother language

English: Read, written and spoken.

 

Editorial activities and scientific expertise

 

Regular referee for: Cladistic, Conservation Biology, Ecography, Ecology Letters, eLife, Evolutionnary Applications, Evolutionary Ecology Research, Forest Ecology and Management, Genetics, Heredity, Human Biology, Mitochondrial DNA, Molecular Ecology, and Molecular Ecology Resources, New Phytologist, Plant Ecology, PLosOne, Proceedings of the Royal Society London. Member of the Peer Community in Evolutionary Biology.

My strategy is to review with application between 3 and 5 publications per year, which roughly corresponds to my scientific production. In the current scientific context, with a strong increase of publication number, I prefer to do it that way and put quality ahead of quantity!

 

Expertise in theoretical and applied population genetics, conservation genetics, inference of dispersal, modelling in population genetics, coalescent theory.

 

 

Funding

 

·       2020-2024: ANR, with P.-A. Crochet et al., “INTROSPEC: Genomic consequences and evolutionary causes of introgression in the late stages of speciation”. 517 k€

 

·       2020-2022: LabEx CeMEB, with M.-P. Chapuis, “proLag: Proof of concept in Landscape genomics: from NGS data production to demographic inferences”. 20 k€

 

·       2018-2021: LabEx CeMEB, with C. Brouat & C. Smadja, “SPEED: DoeS PErsonality Explain spatial spreaD of invasive wild mice in Senegal? Behavioral ecology and population genomics approaches”. 26 k€

 

·       2017-2020: LabEx CeMEB, with g. Ganem & C. Brouat, “D‐RANGE: Environmental and evolutionary Drivers of species distributions and RANGE limits”. 26 k€

 

·       2017-2021: ANR, with S. Guindon, “GenoSpace: Improved statistical approaches for the analysis of biodiversity using genetic and spatial data”. 140 k€

 

·       2014: Young researcher project, funding from the IBC (Institute of Computational Biology, see below), with P. Pudlo, “Using haplotype lengths and linkage disequilibrium to infer the demographic history of populations from genomic data.”. 10 k€

 

·       2013: First Funding for exploratory projects (PROJET EXPLORATOIRE PREMIER SOUTIEN: PEPS), University of Montpellier, with P. Pudlo, “Understanding emerging diseases and epidemics: models, evolution, history and society”, 10 k€

 

·       2012-2017: participant to the PIA “IBC” with O. Gascuel (Projet Investissement d’Avenir “Institut de Biologie Computationelle”). Around 2-5 k€ per year for Master students, publication fees and Missions.

 

·       2010-2014: ANR, with S. Planes et al., “IM-MODEL@CORALFISH: An isolation-migration model of the history of coral reef fish communities: theory and data”. 500 k€

 

·       2010-2014: ANR, with C. Denys et al., “MOHMIE: Modern Human installation in Morocco Influence on the small terrestrial vertebrate biodiversity and its Evolution”. 809 k€

 

·       2009-2013: ANR, with J. -M. Cornuet et al., “EMILE: Inference methods and software’s for Evolution”. 372 k€

 

·       2008-2011: CNRS Amazonia, with H. Fréville and C. Scotti-Saintagne, “CLIPS: Past climate change and ecological specialization in tropical species: input from population genetic approaches”. 100 k€

 

·       2008-2010: ANR, with P. Grandcolas et al., “BioNeoCal: Endemism in New Caledonia: phylogenetic and population study of its emergence”.940 k€

 

·       2007: MNHN - Bonus Qualité Recherche, R. Leblois : « Computer station for the development of inference methods from genetic data ». 4k€

 

·       2007-2009: MNHN - Bonus Qualité Recherche, with E. Porcher et al. : « Using DNA Barcode data to measure phylogenetic biodiversity in plant communities ». 32k€

 

Teaching

 

2006-Today: between 30 and 50h per year of population genetic teaching in various modules for 1st and 2d year Master students: population genetic data analysis, inference of demographic parameters, coalescent theory and DNA Barcoding.

 

2013-Today: co-organisation, with F. Rousset, of one week course for Master students in Biostatistics: “Population genetic models” (Master Biostatistique, University Montpellier).

 

2010-2018: co-organisation, with R. Vitalis, of one week course for Masters (2d year) and PhD students: “Data analyses in population genetics” (Master B2E - Parcours Darwin, University Montpellier).

 

2010-Today: co-organisation, with R. Vitalis, of one week course for Masters (1st year): “Data analyses in population genetics” (European Master MEME, University Montpellier).

         Participation to the MEME cohort selection with Y. Michalakis, R. Vitalis & O. Katz.

 

2006-2010: co-organisation, with R. Vitalis and E. Heyer, of one week course for Master students (Ecole Doctorale ParisVI-ParisVII-MNHN): “Molecular population genetics and coalescent theory”

 

Collective and administrative activities

 

 

2013-Today: Member of the scientific and organizing comity of MCEB congresses (Mathematical and Computational Evolutionary Biology).

 

2014-2019: Member of the user scientific comity of Migale (INRAe national computing and bio-informatic platform).

 

2014-2015: Member of the GAS "Groupe d'Animation Scientifique" of the CBGP.

 

2014-2016 and 2018-2020: Member of the "conseil d'unité CU" of the CBGP.

 

2011-2015: Scientific manager of the CBGP computer cluster (132 nodes, CBGP technical platform).

 

2008-2010: Internal seminar organisations at the “Origine, Structure and Evolution of biodiversity” lab (OSEB, MNHN, UMR 7205).

 

2008-2010: Scientific manager of the Museum computer cluster (76 nodes, MNHN, UMS 2700).

 

 

2007-2010: Member of the "conseil d'unité CU" of the “Origine, Structure and Evolution of biodiversity” lab (OSEB, MNHN, UMR 7205).

Journal articles59 documents

  • Emeline Charbonnel, Claire Daguin-Thiébaut, Lucille Caradec, Eléonore Moittié, Olivier Gilg, et al.. Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations. Heredity, Nature Publishing Group, 2022, 128 (5), pp.364-376. ⟨10.1038/s41437-022-00515-3⟩. ⟨hal-03658284⟩
  • Aurélien Miralles, Philippe Geniez, Menad Beddek, Daniel Mendez Aranda, José Carlos Brito, et al.. Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas. Zootaxa, Magnolia Press, 2020, 4747 (2), pp.302-326. ⟨10.11646/zootaxa.4747.2.4⟩. ⟨hal-02524382⟩
  • Christian Burban, Susana Rocha, Raphaël Leblois, Jean-Pierre Rossi, Laure Saune, et al.. From sympatry to parapatry: a rapid change in the spatial context of incipient allochronic speciation. Evolutionary Ecology, Springer Verlag, 2020, 34 (1), pp.101-121. ⟨10.1007/s10682-019-10021-4⟩. ⟨hal-02624010⟩
  • Ken S. Toyama, Pierre-André Crochet, Raphaël Leblois. Sampling schemes and drift can bias admixture proportions inferred by structure. Molecular Ecology Resources, Wiley/Blackwell, In press, ⟨10.1111/1755-0998.13234⟩. ⟨hal-02924101⟩
  • Amandine Juhel, Corentin Barbu, Muriel Valantin-Morison, Bertrand Gauffre, Raphaël Leblois, et al.. Limited genetic structure and demographic expansion of the Brassicogethes aeneus populations in France and in Europe. Pest Management Science, Wiley, 2019, 75 (3), pp.667-675. ⟨10.1002/ps.5162⟩. ⟨hal-02619087⟩
  • Emmanuelle Stoetzel, Aude Lalis, Violaine Nicolas, Stéphane Aulagnier, Touria Benazzou, et al.. Quaternary terrestrial microvertebrates from mediterranean northwestern Africa: State-of-the-art focused on recent multidisciplinary studies. Quaternary Science Reviews, Elsevier, 2019, 224, pp.105966. ⟨10.1016/j.quascirev.2019.105966⟩. ⟨hal-02380618⟩
  • Danielle Macedo, Isabel Caballero, Mariana Mateos, Raphaël Leblois, Shelby Mccay, et al.. Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites. PeerJ, PeerJ, 2019, 7, pp.1-35. ⟨10.7717/peerj.7780⟩. ⟨hal-02619696⟩
  • Orianne Tournayre, Jean-Baptiste Pons, Maxime Leuchtmann, Raphaël Leblois, Sylvain Piry, et al.. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range. Ecology and Evolution, Wiley Open Access, 2019, 9, pp.2272-12290. ⟨10.1002/ece3.5714⟩. ⟨hal-02621425⟩
  • Valentin Hivert, Raphael Leblois, Eric Petit, Mathieu Gautier, Renaud Vitalis. Measuring Genetic Differentiation from Pool-seq Data. Genetics, Genetics Society of America, 2018, 210 (1), pp.315-330. ⟨10.1534/genetics.118.300900⟩. ⟨hal-01936905⟩
  • Raphaël Leblois, Mathieu Gautier, Audrey Rohfritsch, Julien Foucaud, Christian Burban, et al.. Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. Molecular Ecology, Wiley, 2018, 27 (1), pp.264-278. ⟨10.1111/mec.14411⟩. ⟨hal-02626319⟩
  • Dimitrios Petsopoulos, Raphaël Leblois, Laure Saune, Kahraman Ipekdal, Filippos A. Aravanopoulos, et al.. Crossing the Mid-Aegean Trench: vicariant evolution of the Eastern pine processionary moth, Thaumetopoea wilkinsoni (Lepidoptera: Notodontidae), in Crete. Biological Journal of the Linnean Society, Linnean Society of London, 2018, 124 (2), pp.228-236. ⟨10.1093/biolinnean/bly041⟩. ⟨hal-02621677⟩
  • Francois Rousset, Champak Reddy Beeravolu, Raphaël Leblois. Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations. Journal de la Société Française de Statistique, Société Française de Statistique et Société Mathématique de France, 2018, 159 (3), pp.142-166. ⟨hal-01998088⟩
  • R. A. Coleman, B. Gauffre, Alexandra Pavlova, L. B. Beheregaray, J. Kearns, et al.. Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish. Heredity, Nature Publishing Group, 2018, 120 (6), pp.515-532. ⟨10.1038/s41437-017-0008-3⟩. ⟨hal-02621504⟩
  • Jean-Baptiste Ledoux, Maša Frleta-Valić, Silvija Kipson, Agostinho Antunes, Emma Cebrian, et al.. Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: Implications for conservation plans in the Eastern Adriatic Sea. Journal of Biogeography, Wiley, 2018, 45 (12), pp.2645-2657. ⟨10.1111/jbi.13461⟩. ⟨hal-02624223⟩
  • Anna Wereszczuk, Raphaël Leblois, Andrzej Zalewski. Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats. BMC Ecology, BioMed Central, 2017, 17, ⟨10.1186/s12898-017-0156-6⟩. ⟨hal-02625453⟩
  • Timothée Bonnet, Raphael Leblois, François Rousset, Pierre-André Crochet. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Evolution - International Journal of Organic Evolution, Wiley, 2017, 71 (9), pp.2140 - 2158. ⟨10.1111/evo.13296⟩. ⟨hal-01801897⟩
  • Coralie Merle, Raphaël Leblois, François Rousset, Pierre Pudlo. Resampling: an improvement of Importance Sampling in varying population size models. Theoretical Population Biology, Elsevier, 2017, 114, pp.70 - 87. ⟨10.1016/j.tpb.2016.09.002⟩. ⟨hal-01270437⟩
  • Cédric Lippens, A. Estoup, M.K. Hima, Anne Loiseau, Caroline Tatard, et al.. Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times.. Heredity, Nature Publishing Group, 2017, 119 (2), pp.64-75. ⟨10.1038/hdy.2017.18⟩. ⟨hal-01576202⟩
  • Miguel Navascués, Raphaël Leblois, Concetta Burgarella. Demographic inference through approximate-Bayesian-computation skyline plots. PeerJ, PeerJ, 2017, 5, pp.1-17. ⟨10.7717/peerj.3530⟩. ⟨hal-01741290⟩
  • Christian Burban, Mathieu Gautier, Raphaël Leblois, Julie Landes, Helena Santos, et al.. Evidence for low-level hybridization between two allochronic populations of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Biological Journal of the Linnean Society, Linnean Society of London, 2016, 119 (2), pp.311-328. ⟨10.1111/bij.12829⟩. ⟨hal-02633820⟩
  • Aude Lalis, Raphaël Leblois, Sohaib Liefried, Ali Ouarour, Champak Beeravolu Reddy, et al.. New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa. Journal of Zoological Systematics and Evolutionary Research, Wiley, 2016, 54 (1), pp.1 - 12. ⟨10.1111/jzs.12111⟩. ⟨hal-02632927⟩
  • Aude Lalis, Raphaël Leblois, Emmanuelle Stoetzel, Touria Benazzou, Karim Souttou, et al.. Phylogeography and demographic history of Shaw's Jird ( Meriones shawii complex) in North Africa. Biological Journal of the Linnean Society, Linnean Society of London, 2016, 118 (2), pp.262-279. ⟨10.1111/bij.12725⟩. ⟨hal-02401512⟩
  • S. Zenboudji, Marc Cheylan, Véronique Arnal, Albert Bertolero, Raphaël Leblois, et al.. Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography. Biological Conservation, Elsevier, 2016, 195, pp.279 - 291. ⟨10.1016/j.biocon.2016.01.007⟩. ⟨hal-02635013⟩
  • Karine Berthier, Madougou Garba, Raphael Leblois, Miguel Navascués, Caroline Tatard, et al.. Black rat invasion of inland Sahel: insights from interviews and population genetics in south-western Niger. Biological Journal of the Linnean Society, Linnean Society of London, 2016, 119 (4), pp.748-765. ⟨10.1111/bij.12836⟩. ⟨hal-01463818⟩
  • Bertrand Gauffre, Sophie Mallez, Marie Pierre Chapuis, Raphaël Leblois, Isabelle Litrico, et al.. Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape. Molecular Ecology, Wiley, 2015, 24 (8), pp.1713-1728. ⟨10.1111/mec.13152⟩. ⟨hal-01181310⟩
  • Martin Laporte, Raphaël Leblois, Aurélie Coulon, François Bonhomme, Pierre Magnan, et al.. Genetic structure of a vulnerable species, the freshwater blenny (Salaria fluviatilis). Conservation Genetics, Springer Verlag, 2015, 16 (3), pp.571 - 581. ⟨10.1007/s10592-014-0682-0⟩. ⟨hal-02633160⟩
  • Pierre-André Crochet, Raphaël Leblois, Julien Renoult. New reptile records from Morocco and Western Sahara.. Herpetology Notes, Societas Europaea Herpetologica (SEH), 2015, 8, pp.583-588. ⟨hal-02932241⟩
  • Anne-Laure Ferchaud, Rémy Eudeline, Véronique Arnal, Marc Cheylan, Gilles Pottier, et al.. Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard. Molecular Ecology, Wiley, 2015, 24 (1), pp.192-207. ⟨10.1111/mec.13011⟩. ⟨hal-02630586⟩
  • Raphaël Leblois, Pierre Pudlo, Néron Joseph, François Bertaux, Champak Reddy Beeravolu, et al.. Maximum-Likelihood Inference of Population Size Contractions from Microsatellite Data. Molecular Biology and Evolution, Oxford University Press (OUP), 2014, 31 (10), pp.2805-2823. ⟨10.1093/molbev/msu212⟩. ⟨hal-02087423⟩
  • Thomas M. Vignaud, Johann Mourier, Jeffrey A. Maynard, Raphaël Leblois, Julia Spaet, et al.. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range: Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range. Molecular Ecology, Wiley, 2014, 23, pp.5193-5207. ⟨10.1111/mec.12936⟩. ⟨hal-02631664⟩
  • Jean-Marie Cornuet, Pierre Pudlo, Julien Veyssier, Alexandre Dehne-Garcia, Mathieu Gautier, et al.. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.. Bioinformatics, Oxford University Press (OUP), 2014, 30 (8), pp.1187-1189. ⟨10.1093/bioinformatics/btt763⟩. ⟨hal-01337243⟩
  • Thomas M. Vignaud, Jeffrey A. Maynard, Raphaël Leblois, Mark G. Meekan, Ricardo Vazquez-Juarez, et al.. Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Molecular Ecology, Wiley, 2014, 23 (10), pp.2590-2601. ⟨10.1111/mec.12754⟩. ⟨hal-02630929⟩
  • Olivier David, Catherine Laredo, Raphaël Leblois, Brigitte Schaeffer, Nicolas Vergne. Coalescent-Based DNA Barcoding: Multilocus Analysis and Robustness. Journal of Computational Biology, Mary Ann Liebert, 2012, 19 (3), pp.271-278. ⟨hal-02642847⟩
  • Mélanie Perez, Raphaël Leblois, Barbara Livoreil, Roger Bour, Josie Lambourdière, et al.. Effects of landscape features and demographic history on the genetic structure of Testudo marginata populations in the southern Peloponnese and Sardinia. Biological Journal of the Linnean Society, Linnean Society of London, 2012, 105 (3), pp.591-606. ⟨10.1111/j.1095-8312.2011.01805.x⟩. ⟨hal-02931006⟩
  • Aude Lalis, Raphaël Leblois, Emilie Lecompte, Christiane Denys, Jan ter Meulen, et al.. The Impact of Human Conflict on the Genetics of Mastomys natalensis and Lassa Virus in West Africa. PLoS ONE, Public Library of Science, 2012, 7 (5), pp.e37068. ⟨10.1371/journal.pone.0037068⟩. ⟨hal-02931012⟩
  • François Rousset, Raphaël Leblois. Likelihood-Based Inferences under Isolation by Distance: Two-Dimensional Habitats and Confidence Intervals. Molecular Biology and Evolution, Oxford University Press (OUP), 2012, 29 (3), pp.957-973. ⟨10.1093/molbev/msr262⟩. ⟨hal-02651553⟩
  • Olivier David, Catherine Larédo, Raphael Leblois, Brigitte Schaeffer, Nicolas Vergne. Coalescent-based DNA barcoding: multilocus analysis and robustness. Journal of Computational Biology, Mary Ann Liebert, 2012, ⟨10.1089/cmb.2011.0122⟩. ⟨hal-02337205⟩
  • Fabrice Sagnard, Monique Deu, Dékoro Dembélé, Raphaël Leblois, Lassana Touré, et al.. Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region. TAG Theoretical and Applied Genetics, Springer Verlag, 2011, 123 (7), pp.1231-1246. ⟨10.1007/s00122-011-1662-0⟩. ⟨hal-02649865⟩
  • Christophe Girod, Renaud Vitalis, Raphaël Leblois, Hélène Fréville. Inferring population decline and expansion from microsatellite data: A simulation-based evaluation of the Msvar method. Genetics, Genetics Society of America, 2011, 188 (1), pp.165-179. ⟨10.1534/genetics.110.121764⟩. ⟨hal-02643411⟩
  • Raphaël Leblois, Katrin Kuhls, Olivier François, Gabriele Schönian, Thierry Wirth. Guns, germs and dogs: On the origin of Leishmania chagasi. Infection, Genetics and Evolution, Elsevier, 2011, 11 (5), pp.1091-1095. ⟨10.1016/j.meegid.2011.04.004⟩. ⟨hal-02931001⟩
  • Marie-Catherine Boisselier-Dubayle, Raphaël Leblois, Sarah Samadi, Josie Lambourdière, Corinne Sarthou. Genetic structure of the xerophilous bromeliad Pitcairnia geyskesii on inselbergs in French Guiana - a test of the forest refuge hypothesis. Ecography, Wiley, 2010, 33 (1), pp.175-184. ⟨10.1111/j.1600-0587.2009.05446.x⟩. ⟨hal-02930847⟩
  • Giovanna Morelli, Yajun Song, Camila J Mazzoni, Mark Eppinger, Philippe Roumagnac, et al.. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.. Nature Genetics, Nature Publishing Group, 2010, 42 (12), pp.1140-3. ⟨10.1038/ng.705⟩. ⟨pasteur-00836130⟩
  • Ulrich Nübel, Janina Dordel, Kevin Kurt, Birgit Strommenger, Henrik Westh, et al.. A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus. PLoS Pathogens, Public Library of Science, 2010, 6 (4), pp.e1000855. ⟨10.1371/journal.ppat.1000855⟩. ⟨hal-02944185⟩
  • Paul Verdu, Raphaël Leblois, Alain Froment, Sylvain Théry, Serge Bahuchet, et al.. Limited dispersal in mobile hunter-gatherer Baka Pygmies.. Biology Letters, Royal Society, The, 2010, 6 (6), pp.858-861. ⟨10.1098/rsbl.2010.0192⟩. ⟨hal-00504086⟩
  • Filipe Alberto, Peter Raimondi, Daniel Reed, Nelson Coelho, Raphaël Leblois, et al.. Habitat continuity and geographic distance predict population genetic differentiation in giant kelp. Ecology, Ecological Society of America, 2010, 91 (1), pp.49-56. ⟨10.1890/09-0050.1⟩. ⟨hal-02930859⟩
  • Raphaël Leblois, Arnaud Estoup, Francois Rousset. IBDSim: a computer program to simulate genotypic data under isolation by distance. Molecular Ecology Resources, Wiley/Blackwell, 2009, 9 (1), pp.107 - 109. ⟨10.1111/j.1755-0998.2008.02417.x⟩. ⟨halsde-00359920⟩
  • Frédéric Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, et al.. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods.. BMC Bioinformatics, BioMed Central, 2009, 10 Suppl 14 (Suppl 14), pp.S10. ⟨10.1186/1471-2105-10-S14-S10⟩. ⟨inserm-00663565⟩
  • Gilles Guillot, Raphaël Leblois, Aurélie Coulon, Alain Frantz. Statistical methods in spatial genetics. Molecular Ecology, Wiley, 2009, 18 (23), pp.4734-4756. ⟨10.1111/j.1365-294X.2009.04410.x⟩. ⟨hal-02930291⟩
  • Phillip, C. Watts, Francois Rousset, Ilik, J. Saccheri, Raphaël Leblois, Stephen, J. Kemp, et al.. Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of 'neighbourhood size' using a more precise estimator. Molecular Ecology, Wiley, 2008, 16 (4), pp.737 - 751. ⟨10.1111/j.1365-294X.2006.03184.x⟩. ⟨halsde-00321661⟩
  • Lise Frézal, Raphael Leblois. Four years of DNA barcoding: current advances and prospects.. Infection, Genetics and Evolution, Elsevier, 2008, 8 (5), pp.727-36. ⟨10.1016/j.meegid.2008.05.005⟩. ⟨mnhn-00392451⟩
  • Raphaël Leblois, Montgomery Slatkin. Estimating the number of founder lineages from haplotypes of closely linked SNPs. Molecular Ecology, Wiley, 2007, 16 (11), pp.2237-2245. ⟨10.1111/j.1365-294X.2007.03288.x⟩. ⟨hal-02929790⟩
  • Francois Rousset, Raphaël Leblois. Likelihood and Approximate Likelihood Analyses of Genetic Structure in a Linear Habitat: Performance and Robustness to Model Mis-Specification. Molecular Biology and Evolution, Oxford University Press (OUP), 2007, 24 (12), pp.2730-2745. ⟨10.1093/molbev/msm206⟩. ⟨halsde-00321541⟩
  • Raphaël Leblois, Arnaud Estoup, Rejane R. Streiff. Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?. Molecular Ecology, Wiley, 2006, 15 (12), pp.3601-3615. ⟨10.1111/j.1365-294X.2006.03046.x⟩. ⟨hal-02663496⟩
  • M. de Iorio, R. Griffiths, Raphaël Leblois, Francois Rousset. Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models. Theoretical Population Biology, Elsevier, 2005, 68 (1), pp.41-53. ⟨10.1016/j.tpb.2005.02.001⟩. ⟨halsde-00325236⟩
  • Raphaël Leblois, Francois Rousset, Arnaud Estoup. Influence of Spatial and Temporal Heterogeneities on the Estimation of Demographic Parameters in a Continuous Population Using Individual Microsatellite Data. Genetics, Genetics Society of America, 2004, 166 (2), pp.1081-1092. ⟨10.1093/genetics/166.2.1081⟩. ⟨halsde-00326841⟩
  • Carine Brouat, Florent Sennedot, Philippe Audiot, Raphaël Leblois, Jean-Yves Rasplus. Fine‐scale genetic structure of two carabid species with contrasted levels of habitat specialization. Molecular Ecology, Wiley, 2003, 12 (7), pp.1731-1745. ⟨10.1046/j.1365-294X.2003.01861.x⟩. ⟨hal-02929781⟩
  • Raphaël Leblois, Arnaud Estoup, Francois Rousset. Influence of Mutational and Sampling Factors on the Estimation of Demographic Parameters in a "Continuous" Population Under Isolation by Distance. Molecular Biology and Evolution, Oxford University Press (OUP), 2003, 20 (4), pp.491-502. ⟨10.1093/molbev/msg034⟩. ⟨halsde-00333631⟩
  • Raphaël Leblois, François Rousset, Dani Tikel, Craig Moritz, Arnaud Estoup. Absence of evidence for isolation by distance in an expanding cane toad ( Bufo marinus ) population: an individual-based analysis of microsatellite genotypes. Molecular Ecology, Wiley, 2000, 9 (11), pp.1905-1909. ⟨10.1046/j.1365-294x.2000.01091.x⟩. ⟨hal-02929761⟩
  • D. Tikel, D. Paetkau, M. Cortinas, Raphaël Leblois, Craig Moritz, et al.. Polymerase chain reaction primers for polymorphic microsatellite loci in the invasive toad species Bufo marinus. Molecular Ecology, Wiley, 2000, 9 (11), pp.1927-1929. ⟨10.1046/j.1365-294x.2000.01074-6.x⟩. ⟨hal-02929768⟩

Conference papers30 documents

  • Orianne Tournayre, J. B. Pons, M. Leuchtmann, Raphaël Leblois, Sylvain Piry, et al.. Population genetics as a tool for conservation biology: defining management units for the greater horseshoe bat. 8. European Congress of Mammalogy, Sep 2019, Warsaw, Poland. ⟨hal-02790960⟩
  • Carole Kerdelhue, Christian Burban, Susana Rocha, Martin Godefroid, Jean-Pierre Rossi, et al.. Allochronic differentiation in the pine processionary moth: possible impacts of past and future climate changes. International Processionary Meeting, Dec 2018, Hammamet, Tunisia. ⟨hal-02788464⟩
  • Orianne Tournayre, J. B. Pons, M. Leuchtmann, J. Duhayer, Maxime Galan, et al.. Conservation et écologie du Grand rhinolophe: Que nous apprennent les analyses moléculaires?. 17. Rencontre Nationale des Chauves-Souris, Mar 2018, Bourges, France. ⟨hal-02785155⟩
  • Thimothee Virgoulay, Raphaël Leblois. Développement et optimisation d’un outils de simulation en c++ de données génomique en populations spécialisés. Printemps de Baillarguet, Institut National de Recherche Agronomique (INRA). UMR Centre de Biologie pour la Gestion des Populations (1062)., May 2018, Montferrier sur Lez, France. ⟨hal-02735977⟩
  • A. Miralles, Philippe Geniez, José Carlos Brito, P. Sorouille, D. Mendez-Aaranda, et al.. Taxonomie des Acanthodactyles à queue rouge (Acanthodactylus erythrurus, Squamata) : une approche intégrative révèle la diversité cryptique dans l’Atlas marocain. Co-meeting: 6. Congrès Franco-Tunisien de Zoologie, 6. Congrès Franco-Maghrébin de Zoologie et 119. Journées Annuelles de la Societé Zoologique de France, Nov 2018, Paris, France. ⟨hal-02786568⟩
  • Orianne Tournayre, Anne Loiseau, M. Galan, J.B. Pons, M. Leuchtmann, et al.. Population genetics of the greater horseshoe bat (R. ferrumequinum) in Western France. 14. European Bat Research Symposium, Aug 2017, San Sebastian, Spain. ⟨hal-02785519⟩
  • Orianne Tournayre, Anne Loiseau, Maxime Galan, J. B. Pons, M. Leuchtmann, et al.. Landscape population genetics of the greater horse-shoe bat (R. ferrumequinum) in West-Eastern France. 14. European Bat Research Symposium, Aug 2017, San Sebastian, Spain. ⟨hal-02786746⟩
  • Timothée Bonnet, Raphaël Leblois, François Rousset, Pierre-André Crochet. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Approche Interdisciplinaire en Évolution, GDR 3765 AIEM, Nov 2016, Saint-Martin-de-Londres, France. ⟨hal-02932428⟩
  • Coralie Merle, Raphaël Leblois, Jean-Michel Marin, François Rousset. Detecting past contraction in population size using runs of homozygosity. 48èmes Journées de Statistique de la SFdS, May 2016, Montpellier, France. ⟨hal-02932426⟩
  • Aude Lalis, Violaine Nicolas, Annemarie Ohler, Aurélien Miralles, Pierre André Crochet, et al.. Comparative phylogeography and population genetic structure of 10 widespread small vertebrate species in Morocco. 6.Congrès international Barcode of Life, Aug 2015, Guelph, Canada. pp.1. ⟨hal-02743116⟩
  • Aude Lalis, Emmanuelle Stoetzel, Raphaël Leblois, Touria Benazzou, Karim Souttou, et al.. Histoire géographique et démographique de l’espèce de rongeur Meriones shawii en Afrique du Nord. Approche Intégrative de la 6ème Extinction (Restitution du projet ANR MOHMIE), Apr 2014, Paris, France. ⟨hal-03025617⟩
  • Raphaël Leblois, Aude Lalis, Violaine Nicolas, Champak Beeravolu Reddy, François Rousset. Inference of past changes in population size from genetic data : Test of a new method and application to real data. Congress ”Integrative study of the 6th extinction”, MNHN, Apr 2014, Paris, France. ⟨hal-02932421⟩
  • Raphaël Leblois, Champak Beeravolu Reddy, François Rousset. The Migraine project : A user- friendly software for likelihood-based inferences of spatial structure and demographic history from genetic data. Summer Research School "Software and Statistical methods for population genetics", Jun 2013, Aussois, France. ⟨hal-02803141⟩
  • Julie Pisano, Raphaël Leblois, H Hennttonen, Maxime Galan, Nathalie Charbonnel, et al.. Nuclear genetic structure of the bank vole (Myodes glareolus) in Fennoscandia with an emphasis on the mitochondrial contact zones – Preliminary results. EDENext 2013, Mar 2013, Bellaterra, Spain. ⟨hal-02932410⟩
  • Julie Landes, Christian Burban, Mathieu Gautier, Helena Santos, Manuela Branco, et al.. Incipient allochronic speciation in the pine processionary moth: molecular analysis of a divergent population. Congress of the European Society for Evolutionary Biology, Aug 2013, Lisbon, Portugal. ⟨hal-02932411⟩
  • Julie Pisano, Raphaël Leblois, Nathalie Charbonnel, Heikki Henttonen, Maxime Galan, et al.. Nuclear genetic structure of the bank vole (Myodes glareolus) in Fennoscandia with an emphasis on the mitochondrial contact zones. The 11th International Mammalogical Congress, Aug 2013, Belfast, Ireland. ⟨hal-02932418⟩
  • Raphaël Leblois, François Rousset. Likelihood-based inférence under spatial structure and demographic changes: the Migraine project. Mathematical and Computational Evolutionnary Biology 2012, Jun 2012, Montpellier, France. ⟨hal-02932404⟩
  • Raphaël Leblois, Christian Burban, Helena Santos, Julie Landes, Maria Rosa Paiva, et al.. Allochronic differentiation of a pine processionary moth population in Portugal: evolutionary scenario based on neutral markers. MEDINSECT3, Jun 2012, Hammamet, Tunisia. ⟨hal-02932402⟩
  • Pierre Pudlo, Raphaël Leblois, Christian Robert. Empirical likelihood for Bayesian inference in population genetics. Mathematical and Computational Evolutionnary Biology 2012, Jun 2012, Montpellier, France. ⟨hal-02932407⟩
  • Timothée Bonnet, Raphaël Leblois, François Rousset, Pierre-André Crochet. Processus neutres et introgression cyto-nucléaire discordante. 34. Réunion annuelle du Groupe d’Etude de Biologie et Génétique des Populations (Petit Pois Déridé 2012), Aug 2012, Avignon, France. ⟨hal-02748562⟩
  • Raphaël Leblois, François Rousset. Inference of demographic parameters from genetic data using importance sampling algorithm on coalescent histories. Congress « Statistiques du Sud », Jun 2010, Mèze, France. ⟨hal-02932394⟩
  • Raphaël Leblois, François Rousset. Likelihood-based inference of dispersal rates from patterns of genetic diversity. 38th Congress if the Canadian Statistical Society, Jun 2010, Québec, Canada. ⟨hal-02932398⟩
  • Thierry Wirth, Raphaël Leblois, Katrin Kuhls, Gabriele Schönian. Guns, Germs and Dogs: on the origin of Leishmania chagasi. 4th international symposium on Leishmania, Feb 2009, Lucknow, India. ⟨hal-02932433⟩
  • Raphaël Leblois, François Rousset. Demographic inferences under isolation by distance: Why some methods are more robust than others?. Dispersion day (École Nationale du Génie Rural des Eaux et des Forêts), Apr 2008, Paris, France. ⟨hal-02932392⟩
  • Raphaël Leblois, Michel Veuille. What is the molecular signature of speciation events. International EMBO Workshop on “Molecular Biodiversity and DNA Barcode”, May 2007, Rome, Italy. ⟨hal-02932389⟩
  • Raphaël Leblois. Why isolation by distance is a realistic model for spatial population genetics. International "Conservation genetics Symposium" at the American Museum of Natural History, Dec 2007, New-York, United States. ⟨hal-02932434⟩
  • Frédéric Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, et al.. Comparing phylogenetic and statistical classification methods for DNA barcoding. In Second International Barcode of Life Conference. Consortium for the Barcode of Life, Sep 2007, Taipei, Taiwan. ⟨hal-02757822⟩
  • Michel Veuille, Frédéric Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, et al.. DNA Barcode analysis in nascent species : comparing phylogenetic and statistical classification methods. DNA Barcoding in Europe European Distributed Institute of Taxonomy, Oct 2007, Leiden, Netherlands. 1 p. ⟨hal-02822639⟩
  • Raphaël Leblois. Inference of demographic parameters : isolation by distance, maximum likelihood and bayesian approaches. International Workshop on „Advances in molecular evolutionary ecology: statistical tools to unravel evolutionary processes in natural populations“, Nov 2006, Munich, Germany. ⟨hal-02932436⟩
  • Raphaël Leblois, Maria de Iorio, Robert Griffiths, Arnaud Estoup, François Rousset. Inference of demographic parameters under isolation by distance: what can we do now. 2nd International Congress on DNA Polymorphisms in Human Populations, Dec 2003, Paris, France. ⟨hal-02932438⟩

Poster communications12 documents

  • Thimothee Virgoulay, Raphaël Leblois, Alexandre Dehne Garcia, François David Collin. Développement et optimisation d’un outil de simulation en C++ de données génomiques en populations spatialisées. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2018), Jul 2018, Marseille, France. 366 p., 2018, Journées Ouvertes en Biologie, Informatique et Mathématiques : JOBIM 2018 Abstracts. ⟨hal-02733797⟩
  • Valentin Hivert, Raphaël Leblois, Eric Petit, Mathieu Gautier, Renaud Vitalis. Measuring genetic differentiation from pooled population samples. 2. Joint Congress on Evolutionary Biology (EVOLUTION 2018), Aug 2018, Montpellier, France. 2018. ⟨hal-02785674⟩
  • Timothée Bonnet, Raphaël Leblois, Francois Rousset, Pierre-André Crochet. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Conférence Jacques Monod : Coalescence des approches théoriques et expérimentales en génomique évolutive et biologie des systèmes, Oct 2016, Roscoff, France. ⟨hal-02932269⟩
  • C Merle, Jean-Michel Marin, F. Rousset, Raphaël Leblois. Detecting past contraction in population size using haplotype homozygosity. Mathematical and Computational Evolutionnary Biology 2016, Jun 2016, Montpellier, France. ⟨hal-02932275⟩
  • Coralie Merle, Raphaël Leblois, Pierre Pudlo. Resampling : an improvement in varying population size models. Mathematical and Computational Evolutionnary Biology 2015, Jun 2015, Porquerolles, France. 2015. ⟨hal-02932290⟩
  • Julie Pisano, Raphaël Leblois, Jean-François Cosson, Nathalie Charbonnel, Maxime Galan, et al.. Testing the presence of a barrier to nuclear gene flow between two distant mitochondrial lineages of the bank vole (Myodes glareolus) in central finland. GERI 2015 « Genes, Ecosystems, and risk of infection », Apr 2015, Heraklion, Greece. 2015. ⟨hal-02932297⟩
  • Coralie Merle, Raphaël Leblois, J.-M Marin, P Pudlo, F. Rousset. Acceleration of important sampling methods for the calculation of likelihood in population genetics. Day of The Institute for Computational Biology (IBC), May 2014, Montpellier, France. 2014. ⟨hal-02932305⟩
  • Raphaël Leblois, Pierre Pudlo, Champak Reddy Beeravolu, François Rousset. Demographic inference from genetic data : consideration of an epidemiological model and a combinaition of different types of markers. Summer Research School "Software and Statitsical methods for population genetics", Jun 2013, Aussois, France. ⟨hal-02933715⟩
  • Raphaël Leblois, Pierre Pudlo, Champak Reddy Beeravolu, François Rousset. Demographic inference from genetic data : consideration of an epidemiological model and a combinaition of different types of markers. Mathematical and Computational Evolutionnary Biology 2013, May 2013, Montpellier, France. ⟨hal-02933720⟩
  • Champak Beeravolu Reddy, Francois Rousset, Pierre Pudlo, Raphaël Leblois. Maximum likelihood inference comparing sequence and allelic markers in a population of variable size: an Importance Sampling approach. Mathematical and Computational Evolutionnary Biology 2012, Jun 2012, Montpellier, France. 2012. ⟨hal-02932322⟩
  • Christophe Girod, Raphaël Leblois, Bernard Riera, Hélène Fréville. Past demographic history of Astrocaryum sciophilum: chloroplast genetic structure and restricted seed dispersal. Frugivores and seed dispersal, Jun 2010, Montpellier, France. 2010. ⟨hal-02932338⟩
  • Raphaël Leblois, M. de Iorio, R. Griffiths, François Rousset. Inference of demographic parameters using importance sampling on coalescence history. SMBE 2008, Jun 2008, Barcelona, Spain. 2008. ⟨hal-02932346⟩

Reports1 document

  • Christiane Denys, Violaine Nicolas, Stephane Aulagnier, Annemarie Ohler, Francois-Joseph Lapointe, et al.. Rapport final du projet MOHMIE (ANR-09-PEXT-0004 - 2009) (dir. C. Denys). [Contrat] Museum National d'Histoire Naturelle (MNHN). 2014. ⟨hal-02982066⟩