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Raphael Leblois



**Raphaël Leblois E-mail : <>** **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<a name="_Toc132452540"></a><a name="_Toc132452446"></a><a name="_Toc124759601"></a><a name="_Toc124758305"></a><a name="_Toc124758178"></a><a name="_Toc124683779"></a> ORCHID : 0000-0002-3051-4497 idHAL : raphael-leblois **Present Position** Sept 2010 – Today**Researcher (CRCN)** at the Center for Biology and Management of Populations, National Institute for Agronomical Research (CBGP - INRA), Montpellier, France **Education &amp; Research Trainings &amp; 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. <a name="_Toc133317833"></a><a name="_Toc133308967"></a><a name="_Toc133298948"></a><a name="_Toc133298434"></a><a name="_Toc133298367"></a><a name="_Toc133140159"></a><a name="_Toc132692067"></a><a name="_Toc132692027"></a><a name="_Toc132691906"></a><a name="_Toc132632489"></a><a name="_Toc132632265"></a><a name="_Toc132625065"></a><a name="_Toc132452542"></a><a name="_Toc132452448"></a><a name="_Toc124759602"></a><a name="_Toc124758306"></a><a name="_Toc124758179"></a><a name="_Toc124683780"></a>Languages<a name="_Toc124759603"></a><a name="_Toc124758307"></a><a name="_Toc124758180"></a><a name="_Toc124683781"></a> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 &amp; 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 &amp; 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:** ***Mo****dern **H**uman installation in **M**orocco **I**nfluence on the small terrestrial vertebrate biodiversity and its **E**volution*”*.* 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 &amp; 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).


Combining RADseq and contact zone analysis to decipher cryptic diversification in reptiles: Insights from the Spiny‐footed Lizard (Reptilia, Lacertidae)

Paul Doniol-Valcroze , Loïs Rancilhac , José Carlos Brito , Aurélien Miralles , Philippe Geniez
Zoologica Scripta, inPress, ⟨10.1111/zsc.12628⟩
Journal articles hal-04202849v1

Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction

Bertrand Gauffre , Alexandre Boissinot , Vincent Quiquempois , Raphael Leblois , Pierre Grillet
Molecular Ecology, 2022, 31 (1), pp.119-133. ⟨10.1111/mec.16236⟩
Journal articles hal-03436626v1

Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

Emeline Charbonnel , Claire Daguin-Thiébaut , Lucille Caradec , Eléonore Moittié , Olivier Gilg
Heredity, 2022, 128 (5), pp.364-376. ⟨10.1038/s41437-022-00515-3⟩
Journal articles hal-03658284v1
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GSpace: an exact coalescence simulator of recombining genomes under isolation by distance

Thimothée Virgoulay , François Rousset , Camille Noûs , Raphaël Leblois
Bioinformatics, 2021, 37 (20), pp.3673-3675. ⟨10.1093/bioinformatics/btab261⟩
Journal articles hal-03229110v1
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From sympatry to parapatry: a rapid change in the spatial context of incipient allochronic speciation

Christian Burban , Susana Rocha , Raphaël Leblois , Jean-Pierre Rossi , Laure Saune
Evolutionary Ecology, 2020, 34 (1), pp.101-121. ⟨10.1007/s10682-019-10021-4⟩
Journal articles hal-02624010v1
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Sampling schemes and drift can bias admixture proportions inferred by structure

Ken S. Toyama , Pierre-André Crochet , Raphaël Leblois
Molecular Ecology Resources, inPress, ⟨10.1111/1755-0998.13234⟩
Journal articles hal-02924101v1

Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

Aurélien Miralles , Philippe Geniez , Menad Beddek , Daniel Mendez Aranda , José Carlos Brito
Zootaxa, 2020, 4747 (2), pp.302-326. ⟨10.11646/zootaxa.4747.2.4⟩
Journal articles hal-02524382v1
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Limited genetic structure and demographic expansion of the Brassicogethes aeneus populations in France and in Europe

Amandine Juhel , Corentin Barbu , Muriel Valantin-Morison , Bertrand Gauffre , Raphaël Leblois
Pest Management Science, 2019, 75 (3), pp.667-675. ⟨10.1002/ps.5162⟩
Journal articles hal-02619087v1
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Quaternary terrestrial microvertebrates from mediterranean northwestern Africa: State-of-the-art focused on recent multidisciplinary studies

Emmanuelle Stoetzel , Aude Lalis , Violaine Nicolas , Stéphane Aulagnier , Touria Benazzou
Quaternary Science Reviews, 2019, 224, pp.105966. ⟨10.1016/j.quascirev.2019.105966⟩
Journal articles hal-02380618v1
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Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

Orianne Tournayre , Jean-Baptiste Pons , Maxime Leuchtmann , Raphaël Leblois , Sylvain Piry
Ecology and Evolution, 2019, 9, pp.2272-12290. ⟨10.1002/ece3.5714⟩
Journal articles hal-02621425v1
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Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites

Danielle Macedo , Isabel Caballero , Mariana Mateos , Raphaël Leblois , Shelby Mccay
PeerJ, 2019, 7, pp.1-35. ⟨10.7717/peerj.7780⟩
Journal articles hal-02619696v1
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Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa

Raphaël Leblois , Mathieu Gautier , Audrey Rohfritsch , Julien Foucaud , Christian Burban
Molecular Ecology, 2018, 27 (1), pp.264-278. ⟨10.1111/mec.14411⟩
Journal articles hal-02626319v1

Crossing the Mid-Aegean Trench: vicariant evolution of the Eastern pine processionary moth, Thaumetopoea wilkinsoni (Lepidoptera: Notodontidae), in Crete

Dimitrios Petsopoulos , Raphaël Leblois , Laure Saune , Kahraman Ipekdal , Filippos A. Aravanopoulos
Biological Journal of the Linnean Society, 2018, 124 (2), pp.228-236. ⟨10.1093/biolinnean/bly041⟩
Journal articles hal-02621677v1
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Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations

Francois Rousset , Champak Reddy Beeravolu , Raphaël Leblois
Journal de la Société Française de Statistique, 2018, 159 (3), pp.142-166
Journal articles hal-01998088v1
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Measuring Genetic Differentiation from Pool-seq Data

Valentin Hivert , Raphael Leblois , Eric Petit , Mathieu Gautier , Renaud Vitalis
Genetics, 2018, 210 (1), pp.315-330. ⟨10.1534/genetics.118.300900⟩
Journal articles hal-01936905v1

Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: Implications for conservation plans in the Eastern Adriatic Sea

Jean-Baptiste Ledoux , Maša Frleta-Valić , Silvija Kipson , Agostinho Antunes , Emma Cebrian
Journal of Biogeography, 2018, 45 (12), pp.2645-2657. ⟨10.1111/jbi.13461⟩
Journal articles hal-02624223v1
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Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Anna Wereszczuk , Raphaël Leblois , Andrzej Zalewski
BMC Ecology, 2017, 17, ⟨10.1186/s12898-017-0156-6⟩
Journal articles hal-02625453v1

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Timothée Bonnet , Raphael Leblois , François Rousset , Pierre-André Crochet
Evolution - International Journal of Organic Evolution, 2017, 71 (9), pp.2140 - 2158. ⟨10.1111/evo.13296⟩
Journal articles hal-01801897v1
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Resampling: an improvement of Importance Sampling in varying population size models

Coralie Merle , Raphaël Leblois , François Rousset , Pierre Pudlo
Theoretical Population Biology, 2017, 114, pp.70 - 87. ⟨10.1016/j.tpb.2016.09.002⟩
Journal articles hal-01270437v1

Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times.

Cédric Lippens , A. Estoup , M.K. Hima , Anne Loiseau , Caroline Tatard
Heredity, 2017, 119 (2), pp.64-75. ⟨10.1038/hdy.2017.18⟩
Journal articles hal-01576202v1
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Demographic inference through approximate-Bayesian-computation skyline plots

Miguel Navascués , Raphaël Leblois , Concetta Burgarella
PeerJ, 2017, 5, pp.1-17. ⟨10.7717/peerj.3530⟩
Journal articles hal-01741290v1
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New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa

Aude Lalis , Raphaël Leblois , Sohaib Liefried , Ali Ouarour , Champak Beeravolu Reddy
Journal of Zoological Systematics and Evolutionary Research, 2016, 54 (1), pp.1 - 12. ⟨10.1111/jzs.12111⟩
Journal articles hal-02632927v1
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Phylogeography and demographic history of Shaw's Jird ( Meriones shawii complex) in North Africa

Aude Lalis , Raphaël Leblois , Emmanuelle Stoetzel , Touria Benazzou , Karim Souttou
Biological Journal of the Linnean Society, 2016, 118 (2), pp.262-279. ⟨10.1111/bij.12725⟩
Journal articles hal-02401512v1

Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography

S. Zenboudji , Marc Cheylan , Véronique Arnal , Albert Bertolero , Raphaël Leblois
Biological Conservation, 2016, 195, pp.279 - 291. ⟨10.1016/j.biocon.2016.01.007⟩
Journal articles hal-02635013v1

Evidence for low-level hybridization between two allochronic populations of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Christian Burban , Mathieu Gautier , Raphaël Leblois , Julie Landes , Helena Santos
Biological Journal of the Linnean Society, 2016, 119 (2), pp.311-328. ⟨10.1111/bij.12829⟩
Journal articles hal-02633820v1
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Black rat invasion of inland Sahel: insights from interviews and population genetics in south-western Niger

Karine Berthier , Madougou Garba , Raphael Leblois , Miguel Navascués , Caroline Tatard
Biological Journal of the Linnean Society, 2016, 119 (4), pp.748-765. ⟨10.1111/bij.12836⟩
Journal articles hal-01463818v1

Genetic structure of a vulnerable species, the freshwater blenny (Salaria fluviatilis)

Martin Laporte , Raphaël Leblois , Aurélie Coulon , François Bonhomme , Pierre Magnan
Conservation Genetics, 2015, 16 (3), pp.571 - 581. ⟨10.1007/s10592-014-0682-0⟩
Journal articles hal-02633160v1

Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape

Bertrand Gauffre , Sophie Mallez , Marie Pierre Chapuis , Raphaël Leblois , Isabelle Litrico
Molecular Ecology, 2015, 24 (8), pp.1713-1728. ⟨10.1111/mec.13152⟩
Journal articles hal-01181310v1

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Anne-Laure Ferchaud , Rémy Eudeline , Véronique Arnal , Marc Cheylan , Gilles Pottier
Molecular Ecology, 2015, 24 (1), pp.192-207. ⟨10.1111/mec.13011⟩
Journal articles hal-02630586v1
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New reptile records from Morocco and Western Sahara.

Pierre-André Crochet , Raphaël Leblois , Julien Renoult
Herpetology Notes, 2015, 8, pp.583-588
Journal articles hal-02932241v1
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Maximum-Likelihood Inference of Population Size Contractions from Microsatellite Data

Raphaël Leblois , Pierre Pudlo , Néron Joseph , François Bertaux , Champak Reddy Beeravolu
Molecular Biology and Evolution, 2014, 31 (10), pp.2805-2823. ⟨10.1093/molbev/msu212⟩
Journal articles hal-02087423v1

Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range

Thomas M. Vignaud , Johann Mourier , Jeffrey A. Maynard , Raphaël Leblois , Julia Spaet
Molecular Ecology, 2014, 23, pp.5193-5207. ⟨10.1111/mec.12936⟩
Journal articles hal-02631664v1

DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.

Jean-Marie Cornuet , Pierre Pudlo , Julien Veyssier , Alexandre Dehne-Garcia , Mathieu Gautier
Bioinformatics, 2014, 30 (8), pp.1187-1189. ⟨10.1093/bioinformatics/btt763⟩
Journal articles hal-01337243v1

Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

Thomas M. Vignaud , Jeffrey A. Maynard , Raphaël Leblois , Mark G. Meekan , Ricardo Vazquez-Juarez
Molecular Ecology, 2014, 23 (10), pp.2590-2601. ⟨10.1111/mec.12754⟩
Journal articles hal-02630929v1

Coalescent-Based DNA Barcoding: Multilocus Analysis and Robustness

Olivier David , Catherine Laredo , Raphaël Leblois , Brigitte Schaeffer , Nicolas Vergne
Journal of Computational Biology, 2012, 19 (3), pp.271-278
Journal articles hal-02642847v1

Effects of landscape features and demographic history on the genetic structure of Testudo marginata populations in the southern Peloponnese and Sardinia

Mélanie Perez , Raphaël Leblois , Barbara Livoreil , Roger Bour , Josie Lambourdière
Biological Journal of the Linnean Society, 2012, 105 (3), pp.591-606. ⟨10.1111/j.1095-8312.2011.01805.x⟩
Journal articles hal-02931006v1
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Coalescent-based DNA barcoding: multilocus analysis and robustness

Olivier David , Catherine Larédo , Raphael Leblois , Brigitte Schaeffer , Nicolas Vergne
Journal of Computational Biology, 2012, ⟨10.1089/cmb.2011.0122⟩
Journal articles hal-02337205v1
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Likelihood-Based Inferences under Isolation by Distance: Two-Dimensional Habitats and Confidence Intervals

François Rousset , Raphaël Leblois
Molecular Biology and Evolution, 2012, 29 (3), pp.957-973. ⟨10.1093/molbev/msr262⟩
Journal articles hal-02651553v1
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The Impact of Human Conflict on the Genetics of Mastomys natalensis and Lassa Virus in West Africa

Aude Lalis , Raphaël Leblois , Emilie Lecompte , Christiane Denys , Jan ter Meulen
PLoS ONE, 2012, 7 (5), pp.e37068. ⟨10.1371/journal.pone.0037068⟩
Journal articles hal-02931012v1

Inferring population decline and expansion from microsatellite data: A simulation-based evaluation of the Msvar method

Christophe Girod , Renaud Vitalis , Raphaël Leblois , Hélène Fréville
Genetics, 2011, 188 (1), pp.165-179. ⟨10.1534/genetics.110.121764⟩
Journal articles hal-02643411v1

Guns, germs and dogs: On the origin of Leishmania chagasi

Raphaël Leblois , Katrin Kuhls , Olivier François , Gabriele Schönian , Thierry Wirth
Infection, Genetics and Evolution, 2011, 11 (5), pp.1091-1095. ⟨10.1016/j.meegid.2011.04.004⟩
Journal articles hal-02931001v1

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region

Fabrice Sagnard , Monique Deu , Dékoro Dembélé , Raphaël Leblois , Lassana Touré
TAG Theoretical and Applied Genetics, 2011, 123 (7), pp.1231-1246. ⟨10.1007/s00122-011-1662-0⟩
Journal articles hal-02649865v1

Limited dispersal in mobile hunter-gatherer Baka Pygmies.

Paul Verdu , Raphaël Leblois , Alain Froment , Sylvain Théry , Serge Bahuchet
Biology Letters, 2010, 6 (6), pp.858-861. ⟨10.1098/rsbl.2010.0192⟩
Journal articles hal-00504086v1
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A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus

Ulrich Nübel , Janina Dordel , Kevin Kurt , Birgit Strommenger , Henrik Westh
PLoS Pathogens, 2010, 6 (4), pp.e1000855. ⟨10.1371/journal.ppat.1000855⟩
Journal articles hal-02944185v1

Genetic structure of the xerophilous bromeliad Pitcairnia geyskesii on inselbergs in French Guiana - a test of the forest refuge hypothesis

Marie-Catherine Boisselier-Dubayle , Raphaël Leblois , Sarah Samadi , Josie Lambourdière , Corinne Sarthou
Ecography, 2010, 33 (1), pp.175-184. ⟨10.1111/j.1600-0587.2009.05446.x⟩
Journal articles hal-02930847v1

Habitat continuity and geographic distance predict population genetic differentiation in giant kelp

Filipe Alberto , Peter Raimondi , Daniel Reed , Nelson Coelho , Raphaël Leblois
Ecology, 2010, 91 (1), pp.49-56. ⟨10.1890/09-0050.1⟩
Journal articles hal-02930859v1
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Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.

Giovanna Morelli , Yajun Song , Camila J Mazzoni , Mark Eppinger , Philippe Roumagnac
Nature Genetics, 2010, 42 (12), pp.1140-3. ⟨10.1038/ng.705⟩
Journal articles pasteur-00836130v1
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DNA barcode analysis: a comparison of phylogenetic and statistical classification methods.

Frédéric Austerlitz , Olivier David , Brigitte Schaeffer , Kevin Bleakley , Madalina Olteanu
BMC Bioinformatics, 2009, 10 Suppl 14 (Suppl 14), pp.S10. ⟨10.1186/1471-2105-10-S14-S10⟩
Journal articles inserm-00663565v1

IBDSim: a computer program to simulate genotypic data under isolation by distance

Raphaël Leblois , Arnaud Estoup , Francois Rousset
Molecular Ecology Resources, 2009, 9 (1), pp.107 - 109. ⟨10.1111/j.1755-0998.2008.02417.x⟩
Journal articles halsde-00359920v1

Statistical methods in spatial genetics

Gilles Guillot , Raphaël Leblois , Aurélie Coulon , Alain Frantz
Molecular Ecology, 2009, 18 (23), pp.4734-4756. ⟨10.1111/j.1365-294X.2009.04410.x⟩
Journal articles hal-02930291v1

Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of 'neighbourhood size' using a more precise estimator

Phillip, C. Watts , Francois Rousset , Ilik, J. Saccheri , Raphaël Leblois , Stephen, J. Kemp
Molecular Ecology, 2008, 16 (4), pp.737 - 751. ⟨10.1111/j.1365-294X.2006.03184.x⟩
Journal articles halsde-00321661v1
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Four years of DNA barcoding: current advances and prospects.

Lise Frézal , Raphael Leblois
Infection, Genetics and Evolution, 2008, 8 (5), pp.727-36. ⟨10.1016/j.meegid.2008.05.005⟩
Journal articles mnhn-00392451v1
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Likelihood and Approximate Likelihood Analyses of Genetic Structure in a Linear Habitat: Performance and Robustness to Model Mis-Specification

Francois Rousset , Raphaël Leblois
Molecular Biology and Evolution, 2007, 24 (12), pp.2730-2745. ⟨10.1093/molbev/msm206⟩
Journal articles halsde-00321541v1

Estimating the number of founder lineages from haplotypes of closely linked SNPs

Raphaël Leblois , Montgomery Slatkin
Molecular Ecology, 2007, 16 (11), pp.2237-2245. ⟨10.1111/j.1365-294X.2007.03288.x⟩
Journal articles hal-02929790v1

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Raphaël Leblois , Arnaud Estoup , Rejane R. Streiff
Molecular Ecology, 2006, 15 (12), pp.3601-3615. ⟨10.1111/j.1365-294X.2006.03046.x⟩
Journal articles hal-02663496v1

Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models

M. de Iorio , R. Griffiths , Raphaël Leblois , Francois Rousset
Theoretical Population Biology, 2005, 68 (1), pp.41-53. ⟨10.1016/j.tpb.2005.02.001⟩
Journal articles halsde-00325236v1

Influence of Spatial and Temporal Heterogeneities on the Estimation of Demographic Parameters in a Continuous Population Using Individual Microsatellite Data

Raphaël Leblois , Francois Rousset , Arnaud Estoup
Genetics, 2004, 166 (2), pp.1081-1092. ⟨10.1093/genetics/166.2.1081⟩
Journal articles halsde-00326841v1
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Influence of Mutational and Sampling Factors on the Estimation of Demographic Parameters in a "Continuous" Population Under Isolation by Distance

Raphaël Leblois , Arnaud Estoup , Francois Rousset
Molecular Biology and Evolution, 2003, 20 (4), pp.491-502. ⟨10.1093/molbev/msg034⟩
Journal articles halsde-00333631v1

Fine‐scale genetic structure of two carabid species with contrasted levels of habitat specialization

Carine Brouat , Florent Sennedot , Philippe Audiot , Raphaël Leblois , Jean-Yves Rasplus
Molecular Ecology, 2003, 12 (7), pp.1731-1745. ⟨10.1046/j.1365-294X.2003.01861.x⟩
Journal articles hal-02929781v1

Absence of evidence for isolation by distance in an expanding cane toad ( Bufo marinus ) population: an individual-based analysis of microsatellite genotypes

Raphaël Leblois , François Rousset , Dani Tikel , Craig Moritz , Arnaud Estoup
Molecular Ecology, 2000, 9 (11), pp.1905-1909. ⟨10.1046/j.1365-294x.2000.01091.x⟩
Journal articles hal-02929761v1

Polymerase chain reaction primers for polymorphic microsatellite loci in the invasive toad species Bufo marinus

D. Tikel , D. Paetkau , M. Cortinas , Raphaël Leblois , Craig Moritz
Molecular Ecology, 2000, 9 (11), pp.1927-1929. ⟨10.1046/j.1365-294x.2000.01074-6.x⟩
Journal articles hal-02929768v1

Population genetics as a tool for conservation biology: defining management units for the greater horseshoe bat

Orianne Tournayre , J. B. Pons , M. Leuchtmann , Raphaël Leblois , Sylvain Piry
8. European Congress of Mammalogy, Sep 2019, Warsaw, Poland
Conference papers hal-02790960v1

Conservation et écologie du Grand rhinolophe: Que nous apprennent les analyses moléculaires?

Orianne Tournayre , J. B. Pons , M. Leuchtmann , J. Duhayer , Maxime Galan
17. Rencontre Nationale des Chauves-Souris, Mar 2018, Bourges, France
Conference papers hal-02785155v1

Allochronic differentiation in the pine processionary moth: possible impacts of past and future climate changes

Carole Kerdelhue , Christian Burban , Susana Rocha , Martin Godefroid , Jean-Pierre Rossi
International Processionary Meeting, Dec 2018, Hammamet, Tunisia
Conference papers hal-02788464v1

Taxonomie des Acanthodactyles à queue rouge (Acanthodactylus erythrurus, Squamata) : une approche intégrative révèle la diversité cryptique dans l’Atlas marocain

A. Miralles , Philippe Geniez , José Carlos Brito , P. Sorouille , D. Mendez-Aaranda
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
Conference papers hal-02786568v1

Développement et optimisation d’un outils de simulation en c++ de données génomique en populations spécialisés

Thimothee Virgoulay , Raphaël Leblois
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
Conference papers hal-02735977v1

Landscape population genetics of the greater horse-shoe bat (R. ferrumequinum) in West-Eastern France

Orianne Tournayre , Anne Loiseau , Maxime Galan , J. B. Pons , M. Leuchtmann
14. European Bat Research Symposium, Aug 2017, San Sebastian, Spain
Conference papers hal-02786746v1

Population genetics of the greater horseshoe bat (R. ferrumequinum) in Western France

Orianne Tournayre , Anne Loiseau , M. Galan , J.B. Pons , M. Leuchtmann
14. European Bat Research Symposium, Aug 2017, San Sebastian, Spain
Conference papers hal-02785519v1

Detecting past contraction in population size using runs of homozygosity

Coralie Merle , Raphaël Leblois , Jean-Michel Marin , François Rousset
48èmes Journées de Statistique de la SFdS, May 2016, Montpellier, France
Conference papers hal-02932426v1

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Timothée Bonnet , Raphaël Leblois , François Rousset , Pierre-André Crochet
Approche Interdisciplinaire en Évolution, GDR 3765 AIEM, Nov 2016, Saint-Martin-de-Londres, France
Conference papers hal-02932428v1

Comparative phylogeography and population genetic structure of 10 widespread small vertebrate species in Morocco

Aude Lalis , Violaine Nicolas , Annemarie Ohler , Aurélien Miralles , Pierre André Crochet
6.Congrès international Barcode of Life, Aug 2015, Guelph, Canada. pp.1
Conference papers hal-02743116v1

Histoire géographique et démographique de l’espèce de rongeur Meriones shawii en Afrique du Nord

Aude Lalis , Emmanuelle Stoetzel , Raphaël Leblois , Touria Benazzou , Karim Souttou
Approche Intégrative de la 6ème Extinction (Restitution du projet ANR MOHMIE), Apr 2014, Paris, France
Conference papers hal-03025617v1

Inference of past changes in population size from genetic data : Test of a new method and application to real data

Raphaël Leblois , Aude Lalis , Violaine Nicolas , Champak Beeravolu Reddy , François Rousset
Congress ”Integrative study of the 6th extinction”, MNHN, Apr 2014, Paris, France
Conference papers hal-02932421v1

Nuclear genetic structure of the bank vole (Myodes glareolus) in Fennoscandia with an emphasis on the mitochondrial contact zones

Julie Pisano , Raphaël Leblois , Nathalie Charbonnel , Heikki Henttonen , Maxime Galan
The 11th International Mammalogical Congress, Aug 2013, Belfast, Ireland
Conference papers hal-02932418v1

Nuclear genetic structure of the bank vole (Myodes glareolus) in Fennoscandia with an emphasis on the mitochondrial contact zones – Preliminary results

Julie Pisano , Raphaël Leblois , H Hennttonen , Maxime Galan , Nathalie Charbonnel
EDENext 2013, Mar 2013, Bellaterra, Spain
Conference papers hal-02932410v1

Incipient allochronic speciation in the pine processionary moth: molecular analysis of a divergent population

Julie Landes , Christian Burban , Mathieu Gautier , Helena Santos , Manuela Branco
Congress of the European Society for Evolutionary Biology, Aug 2013, Lisbon, Portugal
Conference papers hal-02932411v1
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The Migraine project : A user- friendly software for likelihood-based inferences of spatial structure and demographic history from genetic data

Raphaël Leblois , Champak Beeravolu Reddy , François Rousset
Summer Research School "Software and Statistical methods for population genetics", Jun 2013, Aussois, France
Conference papers hal-02803141v1

Likelihood-based inférence under spatial structure and demographic changes: the Migraine project

Raphaël Leblois , François Rousset
Mathematical and Computational Evolutionnary Biology 2012, Jun 2012, Montpellier, France
Conference papers hal-02932404v1

Empirical likelihood for Bayesian inference in population genetics

Pierre Pudlo , Raphaël Leblois , Christian Robert
Mathematical and Computational Evolutionnary Biology 2012, Jun 2012, Montpellier, France
Conference papers hal-02932407v1

Allochronic differentiation of a pine processionary moth population in Portugal: evolutionary scenario based on neutral markers

Raphaël Leblois , Christian Burban , Helena Santos , Julie Landes , Maria Rosa Paiva
MEDINSECT3, Jun 2012, Hammamet, Tunisia
Conference papers hal-02932402v1

Processus neutres et introgression cyto-nucléaire discordante

Timothée Bonnet , Raphaël Leblois , François Rousset , Pierre-André Crochet
34. Réunion annuelle du Groupe d’Etude de Biologie et Génétique des Populations (Petit Pois Déridé 2012), Aug 2012, Avignon, France
Conference papers hal-02748562v1

Inference of demographic parameters from genetic data using importance sampling algorithm on coalescent histories

Raphaël Leblois , François Rousset
Congress « Statistiques du Sud », Jun 2010, Mèze, France
Conference papers hal-02932394v1

Likelihood-based inference of dispersal rates from patterns of genetic diversity

Raphaël Leblois , François Rousset
38th Congress if the Canadian Statistical Society, Jun 2010, Québec, Canada
Conference papers hal-02932398v1

Guns, Germs and Dogs: on the origin of Leishmania chagasi

Thierry Wirth , Raphaël Leblois , Katrin Kuhls , Gabriele Schönian
4th international symposium on Leishmania, Feb 2009, Lucknow, India
Conference papers hal-02932433v1

Demographic inferences under isolation by distance: Why some methods are more robust than others?

Raphaël Leblois , François Rousset
Dispersion day (École Nationale du Génie Rural des Eaux et des Forêts), Apr 2008, Paris, France
Conference papers hal-02932392v1

Comparing phylogenetic and statistical classification methods for DNA barcoding

Frédéric Austerlitz , Olivier David , Brigitte Schaeffer , Kevin Bleakley , Madalina Olteanu
In Second International Barcode of Life Conference. Consortium for the Barcode of Life, Sep 2007, Taipei, Taiwan
Conference papers hal-02757822v1

Why isolation by distance is a realistic model for spatial population genetics

Raphaël Leblois
International "Conservation genetics Symposium" at the American Museum of Natural History, Dec 2007, New-York, United States
Conference papers hal-02932434v1

What is the molecular signature of speciation events

Raphaël Leblois , Michel Veuille
International EMBO Workshop on “Molecular Biodiversity and DNA Barcode”, May 2007, Rome, Italy
Conference papers hal-02932389v1

DNA Barcode analysis in nascent species : comparing phylogenetic and statistical classification methods

Michel Veuille , Frédéric Austerlitz , Olivier David , Brigitte Schaeffer , Kevin Bleakley
DNA Barcoding in Europe European Distributed Institute of Taxonomy, Oct 2007, Leiden, Netherlands. 1 p
Conference papers hal-02822639v1

Inference of demographic parameters : isolation by distance, maximum likelihood and bayesian approaches

Raphaël Leblois
International Workshop on „Advances in molecular evolutionary ecology: statistical tools to unravel evolutionary processes in natural populations“, Nov 2006, Munich, Germany
Conference papers hal-02932436v1

Inference of demographic parameters under isolation by distance: what can we do now

Raphaël Leblois , Maria de Iorio , Robert Griffiths , Arnaud Estoup , François Rousset
2nd International Congress on DNA Polymorphisms in Human Populations, Dec 2003, Paris, France
Conference papers hal-02932438v1
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Measuring genetic differentiation from pooled population samples

Valentin Hivert , Raphaël Leblois , Eric Petit , Mathieu Gautier , Renaud Vitalis
2. Joint Congress on Evolutionary Biology (EVOLUTION 2018), Aug 2018, Montpellier, France. 2018
Conference poster hal-02785674v1

Développement et optimisation d’un outil de simulation en C++ de données génomiques en populations spatialisées

Thimothee Virgoulay , Raphaël Leblois , Alexandre Dehne Garcia , François David Collin
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
Conference poster hal-02733797v1
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Detecting past contraction in population size using haplotype homozygosity

C Merle , Jean-Michel Marin , F. Rousset , Raphaël Leblois
Mathematical and Computational Evolutionnary Biology 2016, Jun 2016, Montpellier, France.
Conference poster hal-02932275v1
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A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Timothée Bonnet , Raphaël Leblois , Francois Rousset , Pierre-André Crochet
Conférence Jacques Monod : Coalescence des approches théoriques et expérimentales en génomique évolutive et biologie des systèmes, Oct 2016, Roscoff, France
Conference poster hal-02932269v1
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Resampling : an improvement in varying population size models

Coralie Merle , Raphaël Leblois , Pierre Pudlo
Mathematical and Computational Evolutionnary Biology 2015, Jun 2015, Porquerolles, France. , 2015
Conference poster hal-02932290v1
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Testing the presence of a barrier to nuclear gene flow between two distant mitochondrial lineages of the bank vole (Myodes glareolus) in central finland

Julie Pisano , Raphaël Leblois , Jean-François Cosson , Nathalie Charbonnel , Maxime Galan
GERI 2015 « Genes, Ecosystems, and risk of infection », Apr 2015, Heraklion, Greece. , 2015
Conference poster hal-02932297v1
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Acceleration of important sampling methods for the calculation of likelihood in population genetics

Coralie Merle , Raphaël Leblois , J.-M Marin , P Pudlo , F. Rousset
Day of The Institute for Computational Biology (IBC), May 2014, Montpellier, France. 2014
Conference poster hal-02932305v1

Demographic inference from genetic data : consideration of an epidemiological model and a combinaition of different types of markers

Raphaël Leblois , Pierre Pudlo , Champak Reddy Beeravolu , François Rousset
Summer Research School "Software and Statitsical methods for population genetics", Jun 2013, Aussois, France
Conference poster hal-02933715v1

Demographic inference from genetic data : consideration of an epidemiological model and a combinaition of different types of markers

Raphaël Leblois , Pierre Pudlo , Champak Reddy Beeravolu , François Rousset
Mathematical and Computational Evolutionnary Biology 2013, May 2013, Montpellier, France
Conference poster hal-02933720v1
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Maximum likelihood inference comparing sequence and allelic markers in a population of variable size: an Importance Sampling approach

Champak Beeravolu Reddy , Francois Rousset , Pierre Pudlo , Raphaël Leblois
Mathematical and Computational Evolutionnary Biology 2012, Jun 2012, Montpellier, France. , 2012
Conference poster hal-02932322v1
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Past demographic history of Astrocaryum sciophilum: chloroplast genetic structure and restricted seed dispersal

Christophe Girod , Raphaël Leblois , Bernard Riera , Hélène Fréville
Frugivores and seed dispersal, Jun 2010, Montpellier, France. 2010
Conference poster hal-02932338v1
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Inference of demographic parameters using importance sampling on coalescence history

Raphaël Leblois , M. de Iorio , R. Griffiths , François Rousset
SMBE 2008, Jun 2008, Barcelona, Spain. 2008
Conference poster hal-02932346v1