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Researcher identifiers

Number of documents


Pierre-Alexandre Gagnaire

Pierre-Alexandre Gagnaire


Born 07/02/1982


CNRS Researcher

UMR5554 – Montpellier Institute for Evolutionary Sciences, University of Montpellier, France



Research area

My research focuses on the evolutionary processes involved in adaptation and speciation, with a particular interest in the population genetic mechanisms underlying the build-up of reproductive isolation between divergent populations. Related interests concern the inference of the demographic history, the molecular evolution and the genetic architecture of phenotypic traits involved in local adaptation. My approaches are based on the analysis of population genomic data.


Previous positions

2013 ––, CNRS “Chargé de Recherches”, ISEM UMR5554, Montpellier

2011 –13, Post-doc ANR fellow, ISEM UMR5554, Montpellier

2009 –11, Post-doc fellow, Louis Bernatchez Lab, IBIS, Laval University, Canada



2009, PhD, Population genetics, UMR5554, Montpellier (Superviser Dr. Patrick Berrebi)

2006, MSc, Molecular and Cellular Biology, Ecole Nomale Supérieure de Lyon


Co-supervision of PhD students

2016–19, Maud Duranton [co-superviser F. Bonhomme]

2014–19, Clément Rougeux [co-superviser L. Bernatchez]

2015–18, Maeva Leitwein [co-superviser P. Berrebi & B. Guinand]

2014–16, Ahmed Soussi [co-superviser F. Bonhomme & Lilia Bahri-Sfar]



2011–, 2–5 hours per year at Master level, University of Montpellier

2007–09, 64 hours per year at Licence-Master level, University of Montpellier



2018–21, CoGeDiv project, ANR JCJC (307 kE)

2013–14, ArchiGen project, CNRS-INEE (15 kE)

2011–14, Labrad-Seq project, ANR « retour de postdoc » (210 kE)

2009–10, Post-Doc Fellowship, Canada Foreign Affairs, Trade and Development (32 k$)


Journal articles48 documents

  • Tony Robinet, Valérie Roussel, Karine Cheze, Pierre-Alexandre Gagnaire. Spatial gradients of introgressed ancestry reveal cryptic connectivity patterns in a high gene flow marine fish. Molecular Ecology, Wiley, 2020, ⟨10.1111/mec.15611⟩. ⟨hal-02925509⟩
  • Carine Rey, Audrey Darnaude, Franck Ferraton, Bruno Guinand, François Bonhomme, et al.. Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream. Genes, MDPI, 2020, 11 (4), pp.398. ⟨10.3390/genes11040398⟩. ⟨hal-02887670⟩
  • Maeva Leitwein, Maud Duranton, Quentin Rougemont, Pierre-Alexandre Gagnaire, Louis Bernatchez. Using Haplotype Information for Conservation Genomics. Trends in Ecology and Evolution, Elsevier, 2019, ⟨10.1016/j.tree.2019.10.012⟩. ⟨hal-02395119⟩
  • Clément Rougeux, Pierre-Alexandre Gagnaire, Kim Praebel, Ole Seehausen, Louis Bernatchez. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Molecular Ecology, Wiley, 2019, 28 (19), pp.4388-4403. ⟨10.1111/mec.15226⟩. ⟨hal-02395961⟩
  • Maeva Leitwein, Hugo Cayuela, Anne‐laure Ferchaud, Eric Normandeau, Pierre-Alexandre Gagnaire, et al.. The role of recombination on genome‐wide patterns of local ancestry exemplified by supplemented brook charr populations. Molecular Ecology, Wiley, 2019, 28 (21), pp.4755-4769. ⟨10.1111/mec.15256⟩. ⟨hal-02395970⟩
  • Sara Faggion, Marc Vandeputte, Béatrice Chatain, Pierre-Alexandre Gagnaire, François Allal. Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L.. Heredity, Nature Publishing Group, 2019, 122 (5), pp.612-621. ⟨10.1038/s41437-018-0157-z⟩. ⟨hal-02395931⟩
  • Keoni Saint-Pé, Maeva Leitwein, Laurence Tissot, Nicolas Poulet, Bruno Guinand, et al.. Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-5958-9⟩. ⟨hal-02395980⟩
  • M. Vandeputte, P.-A. Gagnaire, F. Allal. The European sea bass: a key marine fish model in the wild and in aquaculture. Animal Genetics, Wiley-Blackwell, 2019, 50 (3), pp.195-206. ⟨10.1111/age.12779⟩. ⟨hal-02395941⟩
  • Maud Duranton, François Bonhomme, Pierre-Alexandre Gagnaire. The spatial scale of dispersal revealed by admixture tracts. Evolutionary Applications, Blackwell, 2019, 12 (9), pp.1743-1756. ⟨10.1111/eva.12829⟩. ⟨hal-02395949⟩
  • Clément Rougeux, Pierre-Alexandre Gagnaire, Louis Bernatchez. Model‐based demographic inference of introgression history in European whitefish species pairs'. Journal of Evolutionary Biology, Wiley, 2019, 32 (8), pp.806-817. ⟨10.1111/jeb.13482⟩. ⟨hal-02395921⟩
  • Florentine Riquet, Cathy Liautard‐haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, et al.. Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. Evolution, Wiley, 2019, 73 (4), pp.817-835. ⟨10.1111/evo.13696⟩. ⟨hal-02395914⟩
  • Maud Duranton, François Allal, Christelle Fraïsse, Nicolas Bierne, François Bonhomme, et al.. The origin and remolding of genomic islands of differentiation in the European sea bass. Nature Communications, Nature Publishing Group, 2018, 9 (1), ⟨10.1038/s41467-018-04963-6⟩. ⟨hal-01825457⟩
  • Maeva Leitwein, Pierre-Alexandre Gagnaire, Erick Desmarais, Patrick Berrebi, Bruno Guinand. Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts. Molecular Ecology, Wiley, 2018, 27 (17), pp.3466 - 3483. ⟨10.1111/mec.14816⟩. ⟨hal-01922616⟩
  • Pierre-Alexandre Gagnaire, Jean-Baptiste Lamy, Florence Cornette, Serge Heurtebise, Lionel Degremont, et al.. Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2018, 10 (9), pp.2518-2534. ⟨10.1093/gbe/evy194⟩. ⟨hal-02395878⟩
  • Christelle Fraïsse, Camille Roux, Pierre-Alexandre Gagnaire, Jonathan Romiguier, Nicolas Faivre, et al.. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies. PeerJ, PeerJ, 2018, 6, ⟨10.7717/peerj.5198⟩. ⟨hal-01882981⟩
  • Ahmed Souissi, François Bonhomme, Manuel Manchado, Lilia Bahri-Sfar, Pierre-Alexandre Gagnaire. Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.). Heredity, Nature Publishing Group, 2018, 121 (6), pp.579-593. ⟨10.1038/s41437-018-0079-9⟩. ⟨hal-02395886⟩
  • Charles Babin, Pierre-Alexandre Gagnaire, Scott Pavey, Louis Bernatchez. RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata). Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2017, 9 (11), pp.2974-2986. ⟨10.1093/gbe/evx226⟩. ⟨hal-02395860⟩
  • Maeva Leitwein, Bruno Guinand, Juliette Pouzadoux, Erick Desmarais, Patrick Berrebi, et al.. A Dense Brown Trout ( Salmo trutta ) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3, Genetics Society of America, 2017, 7 (4), pp.1365 - 1376. ⟨10.1534/g3.116.038497⟩. ⟨hal-01922619⟩
  • Quentin Rougemont, Pierre-Alexandre Gagnaire, Charles Perrier, Clémence Genthon, Anne-Laure Besnard, et al.. Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Molecular Ecology, Wiley, 2017, 26 (1), pp.142-162. ⟨10.1111/mec.13664⟩. ⟨hal-01606314⟩
  • Clément Rougeux, Louis Bernatchez, Pierre-Alexandre Gagnaire. Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis). Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2017, 9 (8), pp.2057-2074. ⟨10.1093/gbe/evx150⟩. ⟨hal-02395854⟩
  • Ahmed Souissi, Pierre-Alexandre Gagnaire, François Bonhomme, Lilia Bahri-Sfar. Introgressive hybridization and morphological transgression in the contact zone between two Mediterranean Solea species. Ecology and Evolution, Wiley Open Access, 2017, 7 (5), pp.1394-1402. ⟨10.1002/ece3.2533⟩. ⟨hal-02395842⟩
  • M. Szulkin, P.-A. Gagnaire, N. Bierne, A. Charmantier. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Molecular Ecology, Wiley, 2016, 25 (2), pp.542-558. ⟨10.1111/mec.13486⟩. ⟨hal-02326694⟩
  • A. Le Moan, P.-A. Gagnaire, F. Bonhomme. Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact. Molecular Ecology, Wiley, 2016, 25 (13), pp.3187-3202. ⟨10.1111/mec.13627⟩. ⟨hal-02395752⟩
  • Pierre-Alexandre Gagnaire, Oscar Gaggiotti. Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Current zoology, Institute of zoology, Chinese academy of sciences, 2016, 62 (6), pp.603-616. ⟨10.1093/cz/zow088⟩. ⟨hal-02395790⟩
  • M. Leitwein, P. Gagnaire, E. Desmarais, S. Guendouz, Marine Rohmer, et al.. Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations. Journal of Fish Biology, Wiley, 2016, 89 (6), pp.2717 - 2734. ⟨10.1111/jfb.13131⟩. ⟨hal-01922655⟩
  • Martin Laporte, Sean Rogers, Anne-Marie Dion-Côté, Eric Normandeau, Pierre-Alexandre Gagnaire, et al.. RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs. G3, Genetics Society of America, 2015, 5 (7), pp.1481-1491. ⟨10.1534/g3.115.019067⟩. ⟨hal-02395342⟩
  • Pierre-Alexandre Gagnaire, Thomas Broquet, D. Aurelle, Frédérique Viard, Ahmed Souissi, et al.. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evolutionary Applications, Blackwell, 2015, 8 (8), pp.769-786. ⟨10.1111/eva.12288⟩. ⟨hal-01187735⟩
  • Michael J. Miller, Eric Feunteun, Jun Aoyama, Shun Watanabe, Mari Kuroki, et al.. Biodiversity and distribution of leptocephali west of the Mascarene Plateau in the southwestern Indian Ocean. Progress in Oceanography, Elsevier, 2015, 137, pp.84-102. ⟨10.1016/j.pocean.2015.05.026⟩. ⟨hal-01192848⟩
  • Mbaye Tine, Heiner Kuhl, Pierre-Alexandre Gagnaire, Bruno Louro, Erick Desmarais, et al.. European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation. Nature Communications, Nature Publishing Group, 2014, 5 (1), ⟨10.1038/ncomms6770⟩. ⟨hal-01922671⟩
  • Nicolas Bierne, Pierre-Alexandre Gagnaire, Patrice David. The geography of introgression in a patchy environment and the thorn in the side of ecological speciation. Current zoology, Institute of zoology, Chinese academy of sciences, 2013, 59 (1), pp.72 - 86. ⟨10.1093/czoolo/59.1.72⟩. ⟨hal-02395293⟩
  • Caroline Côté, Pierre-Alexandre Gagnaire, Vincent Bourret, Guy Verreault, Martin Castonguay, et al.. Population genetics of the American eel ( Anguilla rostrata ): F ST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species. Molecular Ecology, Wiley, 2013, 22 (7), pp.1763-1776. ⟨10.1111/mec.12142⟩. ⟨hal-02395299⟩
  • Pierre-Alexandre Gagnaire, Eric Normandeau, Scott Pavey, Louis Bernatchez. Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Molecular Ecology, Wiley, 2013, 22 (11), pp.3036-3048. ⟨10.1111/mec.12127⟩. ⟨hal-02395307⟩
  • Scott Pavey, Maelle Sevellec, William Adam, Eric Normandeau, Fabien Lamaze, et al.. Nonparallelism in MHCIIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish ( Coregonus clupeaformis ) species pairs as revealed by next-generation sequencing. Molecular Ecology, Wiley, 2013, 22 (14), pp.3833-3849. ⟨10.1111/mec.12358⟩. ⟨hal-02395312⟩
  • Pierre-Alexandre Gagnaire, Scott Pavey, Eric Normandeau, Louis Bernatchez. THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING. Evolution, Wiley, 2013, 67 (9), pp.2483-2497. ⟨10.1111/evo.12075⟩. ⟨hal-02395314⟩
  • Simon Laflamme, Caroline Côté, Pierre-Alexandre Gagnaire, Martin Castonguay, Louis Bernatchez. RNA/DNA ratios in American glass eels ( Anguilla rostrata ): evidence for latitudinal variation in physiological status and constraints to oceanic migration?. Ecology and Evolution, Wiley Open Access, 2012, 2 (5), pp.875-884. ⟨10.1002/ece3.212⟩. ⟨hal-02395286⟩
  • Lamya Chaoui, Pierre-Alexandre Gagnaire, Bruno Guinand, Jean-Pierre Quignard, Costas Tsigenopoulos, et al.. Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata. Molecular Ecology, Wiley, 2012, 21 (22), pp.5497 - 5511. ⟨10.1111/mec.12062⟩. ⟨hal-01922723⟩
  • Pierre-Alexandre Gagnaire, Eric Normandeau, Caroline Côté, Michael Møller Hansen, Louis Bernatchez. The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel ( Anguilla rostrata ). Genetics, Genetics Society of America, 2012, 190 (2), pp.725-736. ⟨10.1534/genetics.111.134825⟩. ⟨hal-02395275⟩
  • Yuki Minegishi, Pierre-Alexandre Gagnaire, Jun Aoyama, Pierre Bosc, Eric Feunteun, et al.. Present and past genetic connectivity of the Indo-Pacific tropical eel Anguilla bicolor. Journal of Biogeography, Wiley, 2012, 39 (2), pp.408-420. ⟨10.1111/j.1365-2699.2011.02603.x⟩. ⟨hal-02395267⟩
  • Pierre-Alexandre Gagnaire, Eric Normandeau, Louis Bernatchez. Comparative Genomics Reveals Adaptive Protein Evolution and a Possible Cytonuclear Incompatibility between European and American Eels. Molecular Biology and Evolution, Oxford University Press (OUP), 2012, 29 (10), pp.2909-2919. ⟨10.1093/molbev/mss076⟩. ⟨hal-02395279⟩
  • Pierre-Alexandre Gagnaire, Yuki Minegishi, Saliha Zenboudji, Pierre Valade, Jun Aoyama, et al.. WITHIN-POPULATION STRUCTURE HIGHLIGHTED BY DIFFERENTIAL INTROGRESSION ACROSS SEMIPERMEABLE BARRIERS TO GENE FLOW IN ANGUILLA MARMORATA. Evolution, Wiley, 2011, 65 (12), pp.3413-3427. ⟨10.1111/j.1558-5646.2011.01404.x⟩. ⟨hal-02395262⟩
  • Benjamin Genovesi, Mi-Sun Shin-Grzebyk, Daniel Grzebyk, Mohamed Laabir, Pierre-Alexandre Gagnaire, et al.. ASSESSMENT OF CRYPTIC SPECIES DIVERSITY WITHIN BLOOMS AND CYST BANK OF THE ALEXANDRIUM TAMARENSE COMPLEX (DINOPHYCEAE) IN A MEDITERRANEAN LAGOON FACILITATED BY SEMI-MULTIPLEX PCR. Journal of Plankton Research, Oxford University Press (OUP), 2010, ⟨10.1093/plankt/FBQ127⟩. ⟨hal-00632294⟩
  • Pierre-Alexandre Gagnaire, V. Albert, B. JÓnsson, Louis Bernatchez. Natural selection influences AFLP intraspecific genetic variability and introgression patterns in Atlantic eels. Molecular Ecology, Wiley, 2009, 18 (8), pp.1678 - 1691. ⟨10.1111/j.1365-294X.2009.04142.x⟩. ⟨halsde-00373273⟩
  • Pierre-Alexandre Gagnaire, Y. Minegishi, J. Aoyama, Elodie Reveillac, Tony Robinet, et al.. Ocean currents drive secondary contact between Anguilla marmorata populations in the Indian Ocean. Marine Ecology Progress Series, Inter Research, 2009, 379, pp.267-278. ⟨10.3354/meps07895⟩. ⟨halsde-00372244⟩
  • Elodie Reveillac, Pierre-Alexandre Gagnaire, Raymonde Lecomte-Finiger, Patrick Berrebi, Tony Robinet, et al.. Development of a key using morphological characters to distinguish south-western Indian Ocean anguillid glass eels. Journal of Fish Biology, Wiley, 2009, 74 (9), pp.2171-2177. ⟨10.1111/j.1095-8649.2009.02284.x⟩. ⟨halsde-00420526⟩
  • Benjamin Genovesi, Estelle Masseret, M.S. Shin-Grzebyk, Daniel Grzebyk, Patrick Berrebi, et al.. Co-occurence of two Alexandrium species in Thau Lagoon. Harmful Agae News An IOC Newsletter on toxic algae and algal blooms, 2008, pp.1-2. ⟨halsde-00451663⟩
  • Elodie Reveillac, Eric Feunteun, Patrick Berrebi, Pierre-Alexandre Gagnaire, Raymonde Lecomte-Finiger, et al.. Anguilla marmorata larval migration plasticity as revealed by otolith microstructural analysis. Canadian Journal of Fisheries and Aquatic Sciences, NRC Research Press, 2008, 65 (10), pp.2127-2137. ⟨10.1139/F08-122⟩. ⟨halsde-00367277⟩
  • Tony Robinet, Elodie Réveillac, M. Kuroki, J. Aoyama, K. Tsukamoto, et al.. New clues for freshwater eels (Anguilla spp.) migration routes to eastern Madagascar and surrounding islands. Marine Biology, Springer Verlag, 2008, 154, pp.453-463. ⟨10.1007/s00227-008-0938-7⟩. ⟨halsde-00284449⟩
  • Pierre-Alexandre Gagnaire, K. Tsukamoto, J. Aoyama, Y. Minegishi, P. Valade, et al.. RFLP and semi-multiplex PCR-based identification of four eel species from the south-western Indian Ocean region. Journal of Fish Biology, Wiley, 2007, pp.279-287. ⟨10.1111/j.1095-8649.2007.01605.x⟩. ⟨halsde-00300254⟩

Preprints, Working Papers, ...2 documents

  • Florentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, et al.. Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. 2018. ⟨hal-01869948⟩
  • B Guinand, C Chauvel, M Lechene, J Tournois, Costas S Tsigenopoulos, et al.. Candidate gene variation in gilthead sea bream reveals complex spatiotemporal selection patterns between marine and lagoon habitats. 2016. ⟨hal-01370327⟩