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Aquapôle INRA

Inra Bordeaux-Aquitaine
Quartier Ibarron
64310 Saint-Pée-sur-Nivelle

tél : +33 (0) 5 59 51 59 51
fax : +33 (0) 5 59 54 51 52

Olivier Lepais

Research scientist

Olivier Lepais
Population Genetics & Ecological and Evolutionary Genomics

Contact | Research Activities | Projects | SoftwarePublications



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INRA Bordeaux - Aquitaine
Quartier Ibarron
F-64310 Saint Pée sur Nivelle
Tel: 0033 5 59 51 59 72

Research Activities

Academic achievements and Employment history

  • 2011-present: Research scientist, INRA, UMR 1224 ECOBIOP, France.
  • 2010-2011: Research Fellow of the Leverhulme Trust, Early Career Fellowship, School of Biological and Environmental Sciences, University of Stirling, UK.
  • 2008-2010: Postdoctoral Research Assistant, School of Biological and Environmental Sciences, University of Stirling, UK. Within the Bumblebee Behaviour and Ecology group headed by Pr D Goulson and then within the Restoration Genetics group headed by Dr CFE Bacles.
  • 2008: Teaching Fellow, Département Universitaire des Sciences d'Agen, Université Bordeaux I, France.
  • 2008: PhD in Evolutionary, Fonctional and Community Ecology, UMR 1202 BIOGECO, INRA & Université Bordeaux I, France. PhD dissertation: Dynamique d'hybridation dans le complexe d'espèces des chênes blancs européens (suppervised by Dr S. Gerber et Dr A. Kremer).
  • 2004: Master Plant Genetics and Developement, Université Bordeaux I et II, France.
  • 1998-2004: Full university curriculum in Biology and Geology, Université Bordeaux I, France.

Current research topics

As a population geneticist, I use molecular tools to help understanding the ecology and evolution history of populations and species.


With my fellow colleagues we are studying molecular marker variability within natural populations of salmonids (Atlantic salmon, Salmo salar and brown trout, Salmo trutta) to estimate the fitness of different behavioral strategies.

These studies aim at confirming theoretical models or suggesting new model to improve our general understanding of salmonid population functioning in order to improve management and conservation strategies for these threatened species.

A young Atlantic salmon parr

Recent and ongoing progresses of DNA sequencing technologies now allow applying powerful analytical methods that were until now confined to medical researches or limited to a few model species, to study ecological and evolutionary aspects of non model species. As a consequence, I am now starting to focus on ecological and evolutionary genomics making the most of these new technologies to better understand genic and genomic mechanisms involved in several salmonid behaviors. For instance, I am focusing on early male parr maturation determination in young Atlantic salmons.


Schematic representation of Atlantic salmon life cycle highlighting its shortening caused by early male parr maturation.

This reproductive behavior results in an early reproduction of some male at age 1 or 2 years, i. e. before their seaward migration. This phenomenon has important consequences for population functioning with for instance a shortening of average generation time and an increase in the effective population size. Environmental factors are likely to play an important role in the expression of this behavior as early maturing male can be common in populations located at the southern edge of the species distribution area (Iberia peninsula, south France) but is rarely observed in northern populations. One of my research objectives is to improve the understanding of the genetic determination of early male parr maturation and to study its genetic architecture and the evolution of this behavior through selection pressure in natural populations.

Research projects


   2012-2016: UE, Marie Curie Career Integration Grant (PCIG10-GA-2011-303526). GenEarly: Genetic determination of early male parr maturation in Atlantic salmon natural populations.


  • SimRAD: a R package to simulate and predict the number of loci expected in RAD and GBS approaches. This package provides a number of functions to simulate restriction enzyme digestion, library construction and fragments size selection to predict the number of loci expected from most of the Restriction site Associated DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD aims is to provide an estimation of the number of loci expected from a particular genome depending on the protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required. See the poster: "Genotyping by sequencing development for Salmo salar: a simulation-based predictive approach using the R package SimRAD", F1000Posters, 2014, 5:1187.

Selected publications

  • Lepais O, Weir JT. 2014. SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches. Molecular Ecology Resources, DOI: 10.1111/1755-0998.12273.
  • Lepais O, Muller SD, Saad-Limam SB, Benslama M, Rhazi L, Belouahem-Abed D, Daoud-Bouattour A, Mokhtar Gammar A, Ghrabi-Gammar Z, Bacles CFE. 2013. High genetic diversity and distinctiveness of rear-edge climate relicts maintained by ancient tetraploidisation for Alnus glutinosa. PLOS One, 8:e75029.
  • Lepais O, Roussel G, Hubert F, Kremer A, Gerber S. 2013. Strength and variability of postmating reproductive isolating barriers between four European white oak species. Tree Genetics & Genomes, 9:841-853.
  • Darvill B, Lepais O, Woodall LC, Goulson D. 2012. Triploid bumblebees indicate a direct cost of inbreeding in fragmented populations. Molecular Ecology, 21:3988-3995.
  • Lepais O, Bacles CFE. 2011. Comparison of random and SSR-enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimisation in Acacia harpophylla F. Muell. Ex Benth. Molecular Ecology Resources, 11:711-724.
  • Lepais O, Bacles CFE. 2011. De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing. Journal of Heredity, 102:622-626.
  • Lepais O, Gerber S. 2011. Reproductive patterns shape introgression dynamics and species succession within the European white oak species complex. Evolution, 65:156-170.
  • Lepais O, Darvill B, O’Connor S, Osborne J L, Sanderson R A, Cussans J, Goffe L, Goulson D. 2010. Estimation of bumblebee queen dispersal distances using sibship reconstruction method. Molecular Ecology 19:819-831.
  • Goulson D, Lepais O, O'Connor S, Osborne JL, Sanderson RA, Cussans J, Goffe L, Darvill B. 2010. Effects of land use at a landscape scale on bumblebee nest density and survival. Journal of Applied Ecology, 47:1207-1215.
  • Lepais O, Petit RJ, Guichoux E, Lavabre J, Alberto F, Kremer A, Gerber S. 2009. Species relative abundance and direction of introgression in oaks. Molecular Ecology 18:2228-2242.
Nuage de mots représentant ma recherche

"Word cloud computed on abstract of papers I have contributed in..