Raphael Leblois
INRA Researcher (CR1)
Centre de Biologie pour la Gestion des Populations
Montpellier, France

Group "Population genetics and phylogeography"
Team "Inference Methods in Population Genetics"

I am doing theoretical population genetics and my work is essentially focussed on the inference of demographic parameters from genetic data. Most of my work concerns allelic data such a microsatellites or SNPs.

I am especially interested in realistic demographic models such as isolation by distance models. In this context, I tested the precision and robustness of a Fst-based method for the inference of density and dispersal parameters in continuous populations under isolation by distance (Rousset 1997's regression method). I tested the influence of demographic, mutational and sampling factor and showed that the regression method is precise and robust allowing precise inferences of present and local demographic parameters (see Leblois et al. 2003, Leblois et al. 2004). I also tested the influence of local isolation by distance structure on the detection of past reduction in population sizes and habitat contraction (Leblois et al. 2006). For all those simulation tests and others, I developped a special simulation programme based on a generation-by-generation coalescent algorithm. The program is very flexible so that many different models of isolation by distance could be considered, with various heterogeneities in space and time of the demographic parameters. It is implemented in the software package IBDSim (Leblois et al. 2008).

Recently, we developped a maximum likelihood method for the inference of demographic parameters based on Importance Sampling (IS) algorithms developped by R. Griffiths and collaborators. This work is published in DeIrio et al. 2006, Rousset & Leblois 2007, Rousset & Leblois 2012 and the inference method is implemented in the software package Migraine. Migraine is designed to make inferences about populations sizes, migration rates and/or dispersal parameters under various models : a one- or two-dimensional Isolation by distance model, two populations with migrations, a single panmictic population with past size variation and will soon be extended to other demographic models such as divergence and divergence with migration (IM).

Importance Sampling algorithms showed good performances and fast computations compared to alternative approaches. However, up to day, we only considered allelic type data (e.g. Microsatellites/SNPS/Allozymes) and few demographic models. I am currently working on the inference of past changes in population size (Leblois, Pudlo, Néron, Bertaux, Beeravolu, Vitalis & Rousset Submitted to MBE), and part of my futur work will be developing/adapting new algorithms and implementing new demographic and mutational models in the software package Migraine. To this aim, Champak Reddy Beeravolu is currently working with me as a Postdoc on a ANR/INRA contract.

Beside isolation by distance models, I am also interested in using/adapting population genetic tools to the study of recently diverging species. This lead me to work on DNA Barcoding (Frezal & Leblois 2008, Austerlitz et al. 2009, David et al. 2011) and I am currently developping maximum likelihood inferences under Isolation with Migration models (IM models, Beeravolu, Rousset & Leblois In Prep). All those implementations will soon be published and availlable in Migraine.

Postdoc and PhD opportunities :

Current Postdoc : Champak Reddy Beeravolu. Current PhD student: Coralie Merle.
I have currently no open postdoc or PhD position but several national and international funding bodies (Marie Curie, Human Frontiers, EMBO, AXA, INRA) provide fellowships for young researchers who wish to conduct a postdoc in France. Funding for PhD positions can be obtained with the INRA. So, if you are interested in applying for a PhD or a postdoc position and if your research interests are broadly similar to mine, do not hesitate to contact me (raphael.leblois@supagro.inra.fr)

Researcher (CR1) at the Center for Biology and Management of Populations, National Institute for Agronomical Research (CBGP - INRA), Montpellier, France

2006-2010 : Assistant Professor at the National Museum of Natural History of Paris (MNHN).

2005-2006 : PostDoc (CNRS grant) with Pr. Evelyne Heyer et Dr. Renaud Vitalis, Musée de l'Homme - MNHN, Paris, France.

2004-2005 : PostDoc (Lavoisier grant) with Pr. Montgomery Slatkin, University of California, Berkeley, United-States.

2000-2004 : PhD in Integrative Biology under the supervision of Dr. François Rousset and Dr. Arnaud Estoup. Montpellier Supagro – University of Montpellier II, France.

Complete CV can be downloaded here.

(Official distribution page)

IBDSim (Leblois et al. 2008) is a computer package for the simulation of genotypic data under general isolation by distance models.

IBDSim can consider a large panel of subdivided population models representing discrete subpopulations as well as a large continuous population. Many dispersal distributions, with different tails, can be considered as well as various heterogeneities in space and time of the demographic parameters. For examples of various applications see Leblois et al. (2003), Leblois et al. (2004), Leblois et al. (2006), Rousset & Leblois (2007), Rousset & Leblois (2012).
The program runs on PC under Windows, Mac or Linux systems, and we provide the source code that can be easily compiled under any system using C++ ISO compiler.

Full distribution: (including documentation, sources, Windows executable) download IBDSimV2.0.zip
Documentation (Windows and Linux) : download IBDSimV2.0_UserGuide.pdf
Sources (ISO C++, ready to be compiled with g++) : download IBDSimV2.0_Sources.zip

See the documentation for all further information.

Old version (v1.4 ) full distribution: download IBDSimv1.4.zip
IBDSim © Raphael Leblois, François Rousset, Champak Reddy Beeravolu 2008-2012
IBDSim is freeware (i.e. you don't need to pay). It is free software covered by the CeCILL licence (GPL compatible), i.e. it can be used, copied, studied, modified, and redistributed in other free software (i.e. also covered by a GPL-compatible licence, with freely available source code, even if commercial software) provided the IBDSim source is acknowledged.

Migraine v0.4.1
(see Migraine distribution page to download this software package)

! Version 0.4 (December 20, 2013) includes inference of past population size variation (Leblois et al. 2014 MBE)!!!

Migraine implements coalescent algorithms for maximum likelihood analysis of population genetic data. Currently, only a limited set of models are implemented, as described in DeIorio et al. (2005), Rousset and Leblois (2007) and Rousset and Leblois (2011): essentially a model of isolation by distance in one or two dimension, including the island model as a sub-case; a two population mith migration model and a model of a single panmictic population. A new model of a single population with past size variation has now been released and can be used to detect and characterize past bottlenecks or expansions from microsatellite data (Leblois et al. (2014)). Typical analyses can be performed in seconds (in the one-parameter case) or overnight (in some three-parameter cases), and longer analyses can easily been split among different cores/computers. The data handled are allelic counts (e.g. microsatellite or allozyme data) and a beta version (availlable on demand) can analyse sequence data under the Infinitely many site model (ISM) for some demographic models. We plan to add more models in the future (e.g. Divergence, IM, Sequence and SNPS).

Master Biostatistique, University Montpellier II :
UE GMMA1 : Population genetics, 2013-2014-2015

Demographic inferences under the coalescent (MCMC & IS) 5H

Gene genealogies and the coalescent 2H

Genetic markers 1H

Master B2E "Biologie de l'Evolution et Ecologie", 2d year, University Montpellier II :
UE GMBE33A : Data analysis in population genetics, December 2010-2014

1 - Saptial population genetics: Isolation by distance, Landscape genetics 3H

2 - Clustering methods and multidimensional scaling methods for individual multilocus genotypes, cours 1H
TD : Clustering and multidimensional scaling methods for individual multilocus genotypes 2H
Associated virtual machine (VirtualBox) NOT READY...

3 - Likelihood-based demographic inference using the coalescent: MCMC & IS 2-4H

4 - Demographic inference using the coalescent with recombination: ARG & PSMC 1H

Erasmus Mundus Master Programme in Evolutionary Biology, University Montpellier II :
Genetic Data Analysis, 2011-2014

Likelihood-based demographic inference using the coalescent 3H

Demographic inference under isolation by distance 3H

Asignement and clustering algorithms for individual multilocus genotypes 3H

Likelihood-based demographic inference using the coalescent 3H
UE "population genetics", course "Genetic data analysis", MNHN

La théorie de la coalescence et ses applications
UE microbiologie

Génétique des populations : Dérive, migration, extinction et F-statistiques (2h-3h)
Module "Génétique des populations"

According to copyright laws, the following pdf files can be downloaded for personnal reading purpose only.

Vignaud T. M., J. Mourier, J. A. Maynard, R. Leblois, J. Spaet, E. Clua, V. Neglia, S. Planes. 2014. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range.
Molecular Ecology, 23: 5193-5207. doi : 10.1111/mec.12936

Laporte M., R. Leblois, A. Coulon, F. Bonhomme, P. Magnan, P. Berrebi. 2014.Genetic structure of a vulnerable species, the freshwater blenny (Salaria fluviatilis).
Conservation Genetics, In Press.

Vignaud T.M., J.A. Maynard, R. Leblois, M.G. Meekan, R. Vazquez-Juarez, D. Ramirez-Macias, S.J. Pierce, D. Rowat, M.L. Berumen, C. Beeravolu, S. Baksay, S. Planes. 2014. Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline.
Molecular Ecology 23: 2590-2601. doi : 10.1111/mec.12754

Leblois R., P. Pudlo, F. Bertaux, J. Néron, C. R. Beeravolu, R. Vitalis, F. Rousset. 2014. Maximum likelihood inference of population size contractions from microsatellite data.
Molecular Biology and Evolution 31: 2805-2823. doi: 10.1093/molbev/msu212

Cornuet J.-M., P. Pudlo, J. Veyssier, A. Dehne-Garcia, M. Gautier, R. Leblois, J.-M. Marin, A. Estoup. 2014. DIYABC v2.0: a software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data.
Bioinformatics 30 : 1187-1189. Doi : 10.1093/bioinformatics/btt763

Perez M., R. Leblois, B. Livoreil, R. Bour, J. Lambourdiere, S. Samadi, M.C. Boisselier. 2012. 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 105 : 591-606. doi:10.1111/j.1095-8312.2011.01805.x

Lalis A.*, R. Leblois*, E. Lecompte*, C. Denys, J. Ter Meulen, T. Wirth. 2012. The Impact of Human Conflict on the Genetics of Mastomys natalensis and Lassa Virus in West Africa.
PLoS One, 7 : e37068. doi:10.1371/journal.pone.0037068

Rousset F., R. Leblois. 2012. Likelihood-based inferences under a coalescent model of isolation by distance: two-dimensional habitats and confidence intervals.
Molecular Biology and Evolution : doi:10.1093/molbev/msr262.

David O., C. Laredo, R. Leblois, B. Shaeffer, N. Vergne. 2012. Coalescent-based DNA barcoding: multilocus analysis and robustness.
Journal of Computationnal Biology 19: 271-278. doi: 10.1089/cmb.2011.0122.

Deu, M., F. Sagnard, D. Dembélé, R. Leblois, L. Touré, M. Diakité, C. Calatayud, M. Vaksmann, S. Bouchet, Y. Mallé, S. Togola, P. Traoré. 2011. Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region.
Theoretical Applied Genetics : doi: 10.1007/s00122-011-1662-0.

Leblois R, K. Kuhls, O. Francois, G. Schönian, T. Wirth. 2011. Guns, germs and dogs: On the origin of Leishmania chagasi.
Infections, Genetics and Evolution 188: 165-179.

Girod C., R. Vitalis, R. Leblois, H. Fréville. 2011. Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the MSVAR method.
Genetics 188: 165-179.

Morelli G., Y. J. Song, C. J. Mazzoni, M. Eppinger, P. Roumagnac, D. M. Wagner, M. Feldkamp, B. Kusecek, A. J. Vogler, Y. J. Li, Y. J. Cui, N. R. Thomson, T. Jombart, R. Leblois, P. Lichtner, L. Rahalison, J. M. Petersen, F. Balloux, P. Keim, T. Wirth, J. Ravel, R. F. Yang, E. Carniel, M. Achtman. 2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.
Nature Genetics 42: 1140.

Verdu P., R. Leblois, A. Froment, S. Thery, S. Bahuchet, F. Rousset, E. Heyer, R. Vitalis. 2010. Limited dispersal in mobile hunter-gatherer Baka Pygmies.
Biology Letters 6: 858-861.

Nubel U., J. Dordel, K. Kurt, B. Strommenger, H. Westh, S. K. Shukla, H. Zemlickova, R. Leblois, T. Wirth, T. Jombart, F. Balloux, W. Witte. 2010. A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus.
Plos Pathogens 6: e1000855.

Alberto F., P. T. Raimondi, D. C. Reed, N. C. Coelho, R. Leblois, A. Whitmer, E. A. Serrão. 2010. Habitat continuity and geographic distance predict population genetic differentiation in giant kelp.
Ecology 91: 49-56.

Boisselier-Dubayle M. -C., R. Leblois, M. I. Khodabux, S. Samadi, J. Lambourdière, C. Sarthou. 2010. Genetic structure of a xerophilious bromeliad in a fragmented habitat and the forest refuge hypothesis: Pitcairnia geyskeysii on inselbergs in French Guyana.
Ecography 33 : 175-184

Guillot G., R. Leblois, A. Coulon, A. C. Frantz . 2009. Statistical methods in spatial genetics.
Molecular Ecology 18: 4734-4756.

Austerlitz F., O. David, B. Schaeffer, K. Bleakley, M. Olteanu, R. Leblois, M. Veuille, C. Laredo. 2009. Comparing phylogenetic and statistical classification methods for DNA barcoding.
BMC Bioinformatics 10: Suppl. 14: S10.

Leblois, R., A. Estoup, F. Rousset. 2009. IBDSim: a computer package for coalescent simulations under isolation by distance with temporal and spatial heterogeneities.
Molecular Ecology Resources 9: 107–109.

Frezal L., R. Leblois. 2008. 4 years of DNA barcoding: current advances and prospects.
Infection, Genetics & Evolution 8: 727–736.

Rousset, F., R. Leblois. 2007. Likelihood and approximate likelihood analyses of genetic structure in a linear habitat: performance and robustness to model mis-specification.
Molecular Biology and Evolution. 24:2730–2745.

Leblois, R., M. Slatkin. 2007. Estimating the number of founder lineages from haplotypes of closely linked SNPs.
Molecular Ecology 16: 2237-2245.

Watts P.C., F. Rousset, I.J. Saccheri, R. Leblois, S.J. Kemp, D.J. Thompson. 2007. Compatibility of genetic and demographic estimates of 'neighborhood size' in insect populations: analysis of Coenagrion mercuriale (Odonata: Zygoptera) using an improved estimator of genetic divergence.
Molecular Ecology 16: 737–751.

Leblois, R., Estoup, A., Streiff, R. 2006. Habitat contraction and reduction in population size: Does isolation by distance matter?
Molecular Ecology 15: 3601–3615.

De Iorio M., Griffiths R., Leblois R., Rousset F. 2005. Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models.
Theoretical Population Biology 68: 41-53.

Leblois R., Rousset F., Estoup A. 2004. Influence of spatial and temporal heterogeneities on the estimation of demographic parameters in a continuous population from microsatellite data.
Genetics 166: 1081-1092

Brouat C., Sennedot F., Audiot P., Leblois R., Rasplus J. -Y. 2003. Fine-scale genetic structure of two carabid species with contrasted levels of habitat specialization.
Molecular Ecology 12: 1731 - 1745.

Leblois R., Estoup A., Rousset F. 2003. Influence of mutational and sampling factors on the estimation of demographic parameters in a continuous population under isolation by distance.
Molecular Biology and Evolution. 20: 491-502

Tikel D., Peatkau D., Cortinas N., Leblois R., Moritz C., Estoup A. 2000. Microsatellite loci in the invasive toad species Bufo marinus.
Molecular Ecology 9 : 1927-1929.

Leblois R.., Rousset F., Tikel D., Moritz C., Estoup A. 2000. Absence of evidence for isolation by distance in an expanding cane toad (Bufo marinus) population: an individual-based analysis of microsatellite genotypes.
Molecular Ecology 9: 1905-1909.

Leblois, R. 2004. Estimation de paramètres de dispersion en populations structurées à partir de données génétiques.
PhD thesis (Montpellier SupAgro), 233 pp.

Leblois, R. 2000. Etude par simulation de l'influence de facteurs mutationnels et démographiques sur l'estimation de paramètres démographiques à partir de génotypes individuels.
Master Thesis (DEA Biologie de l'Evolution et Ecologie, Montpellier SupAgro et Université Montpellier II). 30pp.

• 2013-2014: IBC (Institute of Computationnal Biology, Montpellier) , with P. Pudlo, "Utilisation des longueurs d'haplotype et du déséquilibre de liaison pour l'inférence de l'histoire démographique populationnelle à partir de données génomique.". 10 k€

• 2010-2014: ANR (french national agency for research funding), 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 Biodiversity, with P. Grandcolas et al., "BioNeoCal: Endemism in New Caledonia: phylogenetic and population study of its emergence". 940 k€