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Performance and limitations of linkage-disequilibrium-based methods for inferring the genomic landscape of recombination and detecting hotspots: a simulation study
Marie Raynaud
,
Pierre-Alexandre Gagnaire
,
Nicolas Galtier
Article dans une revue
hal-03879740v1
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Age-specific survivorship and fecundity shape genetic diversity in marine fishes
Pierre Barry
,
Thomas Broquet
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-03443785v2
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Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha
Jade Castel
,
Stéphane Hourdez
,
Florence Pradillon
,
Claire Daguin-Thiébaut
,
Marion Ballenghien
Article dans une revue
hal-03771381v1
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Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei
Adrien Tran Y. Lu
,
Stephanie Ruault
,
Claire Daguin-Thiébaut
,
Jade Castel
,
Nicolas Bierne
Article dans une revue
hal-03669635v1
|
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Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?
Christelle Fraïsse
,
Alan Le Moan
,
Camille Roux
,
Guillaume Dubois
,
Claire Daguin-Thiébaut
Article dans une revue
hal-03817700v1
|
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Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish
Israel Guerrero-Cózar
,
Jessica Gomez-Garrido
,
Concha Berbel
,
Juan Martinez-Blanch
,
Tyler Alioto
Article dans une revue
hal-03443762v1
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Speciation history of European (Anguilla anguilla) and American eel (A. rostrata), analysed using genomic data
Natacha Nikolic
,
Shenglin Liu
,
Magnus W Jacobsen
,
Bjarni Jónsson
,
Louis Bernatchez
Article dans une revue
hal-03065758v1
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Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream
Carine Rey
,
Audrey M. Darnaude
,
Franck Ferraton
,
Bruno Guinand
,
François Bonhomme
Article dans une revue
hal-02887670v1
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Genetic characterization of cupped oyster resources in Europe using informative single nucleotide polymorphism (SNP) panels
Sylvie Lapègue
,
Serge Heurtebise
,
Florence Cornette
,
Erwan Guichoux
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-03065752v1
|
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Comparative genomics approach to evolutionary process connectivity
Pierre-Alexandre Gagnaire
Article dans une revue
hal-03065737v1
|
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Spatial gradients of introgressed ancestry reveal cryptic connectivity patterns in a high gene flow marine fish
Tony Robinet
,
Valérie Roussel
,
Karine Cheze
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-02925509v1
|
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The contribution of ancient admixture to reproductive isolation between European sea bass lineages
Maud Duranton
,
François Allal
,
Sophie Valière
,
Olivier Bouchez
,
François Bonhomme
Article dans une revue
hal-03065745v1
|
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Using Haplotype Information for Conservation Genomics
Maeva Leitwein
,
Maud Duranton
,
Quentin Rougemont
,
Pierre-Alexandre Gagnaire
,
Louis Bernatchez
Article dans une revue
hal-02395119v1
|
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The spatial scale of dispersal revealed by admixture tracts
Maud Duranton
,
François Bonhomme
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-02395949v1
|
|
Model‐based demographic inference of introgression history in European whitefish species pairs'
Clément Rougeux
,
Pierre-Alexandre Gagnaire
,
Louis Bernatchez
Article dans une revue
hal-02395921v1
|
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Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages
Florentine Riquet
,
Cathy Liautard‐haag
,
Lucy Woodall
,
Carmen Bouza
,
Patrick Louisy
Evolution - International Journal of Organic Evolution, 2019, 73 (4), pp.817-835. ⟨10.1111/evo.13696⟩
Article dans une revue
hal-02395914v1
|
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Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics
Keoni Saint-Pé
,
Maeva Leitwein
,
Laurence Tissot
,
Nicolas Poulet
,
Bruno Guinand
Article dans une revue
hal-02395980v1
|
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Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex
Clément Rougeux
,
Pierre-Alexandre Gagnaire
,
Kim Praebel
,
Ole Seehausen
,
Louis Bernatchez
Article dans une revue
hal-02395961v1
|
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The role of recombination on genome‐wide patterns of local ancestry exemplified by supplemented brook charr populations
Maeva Leitwein
,
Hugo Cayuela
,
Anne‐laure Ferchaud
,
Eric Normandeau
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-02395970v1
|
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Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L.
Sara Faggion
,
Marc Vandeputte
,
Béatrice Chatain
,
Pierre-Alexandre Gagnaire
,
François Allal
Article dans une revue
hal-02395931v1
|
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The European sea bass: a key marine fish model in the wild and in aquaculture
Marc Vandeputte
,
P.-A. Gagnaire
,
F. Allal
Article dans une revue
hal-02395941v1
|
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The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies
Christelle Fraïsse
,
Camille Roux
,
Pierre-Alexandre Gagnaire
,
Jonathan Romiguier
,
Nicolas Faivre
Article dans une revue
hal-01882981v1
|
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Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)
Ahmed Souissi
,
François Bonhomme
,
Manuel Manchado
,
Lilia Bahri-Sfar
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-02395886v1
|
|
The origin and remolding of genomic islands of differentiation in the European sea bass
Maud Duranton
,
François Allal
,
Christelle Fraïsse
,
Nicolas Bierne
,
François Bonhomme
Article dans une revue
hal-01825457v1
|
|
Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata
Pierre-Alexandre Gagnaire
,
Jean-Baptiste Lamy
,
Florence Cornette
,
Serge Heurtebise
,
Lionel Degremont
Article dans une revue
hal-02395878v1
|
|
Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts
Maeva Leitwein
,
Pierre-Alexandre Gagnaire
,
Erick Desmarais
,
Patrick Berrebi
,
Bruno Guinand
Article dans une revue
hal-01922616v1
|
|
RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata)
Charles Babin
,
Pierre-Alexandre Gagnaire
,
Scott Pavey
,
Louis Bernatchez
Article dans une revue
hal-02395860v1
|
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Introgressive hybridization and morphological transgression in the contact zone between two Mediterranean Solea species
Ahmed Souissi
,
Pierre-Alexandre Gagnaire
,
François Bonhomme
,
Lilia Bahri-Sfar
Article dans une revue
hal-02395842v1
|
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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
Maeva Leitwein
,
Bruno Guinand
,
Juliette Pouzadoux
,
Erick Desmarais
,
Patrick Berrebi
Article dans une revue
hal-01922619v1
|
|
Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)
Clément Rougeux
,
Louis Bernatchez
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-02395854v1
|
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Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes
Quentin Rougemont
,
Pierre-Alexandre Gagnaire
,
Charles Perrier
,
Clémence Genthon
,
Anne-Laure Besnard
Article dans une revue
hal-01606314v1
|
|
Candidate gene variation in gilthead sea bream reveals complex spatiotemporal selection patterns between marine and lagoon habitats
B. Guinand
,
C. Chauvel
,
M. Lechene
,
J. Tournois
,
C.S. Tsigenopoulos
Article dans une revue
hal-03046445v1
|
|
Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits
M. Szulkin
,
P.-A. Gagnaire
,
N. Bierne
,
A. Charmantier
Article dans une revue
hal-02326694v1
|
|
Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact
A. Le Moan
,
P.-A. Gagnaire
,
F. Bonhomme
Article dans une revue
hal-02395752v1
|
|
Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations
M. Leitwein
,
P. Gagnaire
,
E. Desmarais
,
S. Guendouz
,
Marine Rohmer
Article dans une revue
hal-01922655v1
|
|
Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches
Pierre-Alexandre Gagnaire
,
Oscar Gaggiotti
Article dans une revue
hal-02395790v1
|
|
Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era
Pierre-Alexandre Gagnaire
,
Thomas Broquet
,
D. Aurelle
,
Frédérique Viard
,
Ahmed Souissi
Article dans une revue
hal-01187735v1
|
|
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
Martin Laporte
,
Sean Rogers
,
Anne-Marie Dion-Côté
,
Eric Normandeau
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-02395342v1
|
|
Biodiversity and distribution of leptocephali west of the Mascarene Plateau in the southwestern Indian Ocean
Michael J. Miller
,
Eric Feunteun
,
Jun Aoyama
,
Shun Watanabe
,
Mari Kuroki
Article dans une revue
hal-01192848v1
|
|
Do North Atlantic eels show parallel patterns of spatially varying selection?
Malene G Ulrik
,
José Martín Pujolar
,
Anne-Laure Ferchaud
,
Magnus W Jacobsen
,
Thomas D Als
Article dans une revue
hal-02395323v1
|
|
European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation
Mbaye Tine
,
Heiner Kuhl
,
Pierre-Alexandre Gagnaire
,
Bruno Louro
,
Erick Desmarais
Article dans une revue
hal-01922671v1
|
|
THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING
Pierre-Alexandre Gagnaire
,
Scott Pavey
,
Eric Normandeau
,
Louis Bernatchez
Evolution - International Journal of Organic Evolution, 2013, 67 (9), pp.2483-2497. ⟨10.1111/evo.12075⟩
Article dans une revue
hal-02395314v1
|
|
Nonparallelism in MHCIIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish ( Coregonus clupeaformis ) species pairs as revealed by next-generation sequencing
Scott Pavey
,
Maelle Sevellec
,
William Adam
,
Eric Normandeau
,
Fabien Lamaze
Article dans une revue
hal-02395312v1
|
|
The geography of introgression in a patchy environment and the thorn in the side of ecological speciation
Nicolas Bierne
,
Pierre-Alexandre Gagnaire
,
Patrice David
Article dans une revue
hal-02395293v1
|
|
Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)
Pierre-Alexandre Gagnaire
,
Eric Normandeau
,
Scott Pavey
,
Louis Bernatchez
Article dans une revue
hal-02395307v1
|
|
Population genetics of the American eel ( Anguilla rostrata ): F ST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species
Caroline Côté
,
Pierre-Alexandre Gagnaire
,
Vincent Bourret
,
Guy Verreault
,
Martin Castonguay
Article dans une revue
hal-02395299v1
|
|
Present and past genetic connectivity of the Indo-Pacific tropical eel Anguilla bicolor
Yuki Minegishi
,
Pierre-Alexandre Gagnaire
,
Jun Aoyama
,
Pierre Bosc
,
Eric Feunteun
Article dans une revue
hal-02395267v1
|
|
Comparative Genomics Reveals Adaptive Protein Evolution and a Possible Cytonuclear Incompatibility between European and American Eels
Pierre-Alexandre Gagnaire
,
Eric Normandeau
,
Louis Bernatchez
Article dans une revue
hal-02395279v1
|
|
The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel ( Anguilla rostrata )
Pierre-Alexandre Gagnaire
,
Eric Normandeau
,
Caroline Côté
,
Michael Møller Hansen
,
Louis Bernatchez
Article dans une revue
hal-02395275v1
|
|
RNA/DNA ratios in American glass eels ( Anguilla rostrata ): evidence for latitudinal variation in physiological status and constraints to oceanic migration?
Simon Laflamme
,
Caroline Côté
,
Pierre-Alexandre Gagnaire
,
Martin Castonguay
,
Louis Bernatchez
Article dans une revue
hal-02395286v1
|
|
Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata
Lamya Chaoui
,
Pierre-Alexandre Gagnaire
,
Bruno Guinand
,
Jean-Pierre Quignard
,
Costas Tsigenopoulos
Article dans une revue
hal-01922723v1
|
|
WITHIN-POPULATION STRUCTURE HIGHLIGHTED BY DIFFERENTIAL INTROGRESSION ACROSS SEMIPERMEABLE BARRIERS TO GENE FLOW IN ANGUILLA MARMORATA
Pierre-Alexandre Gagnaire
,
Yuki Minegishi
,
Saliha Zenboudji
,
Pierre Valade
,
Jun Aoyama
Article dans une revue
hal-02395262v1
|
|
Multiplex PCR assay to discriminate four neighbouring species of the Calliptamus genus (Orthoptera: Acrididae) from France
E. Blanchet
,
L. Blondin
,
Pierre-Alexandre Gagnaire
,
A. Foucart
,
J.M. Vassal
Article dans une revue
hal-02395257v1
|
|
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
Benjamin Genovesi
,
Mi-Sun Shin-Grzebyk
,
Daniel Grzebyk
,
Mohamed Laabir
,
Pierre-Alexandre Gagnaire
Article dans une revue
hal-00632294v1
|
|
Ocean currents drive secondary contact between Anguilla marmorata populations in the Indian Ocean
Pierre-Alexandre Gagnaire
,
Y. Minegishi
,
J. Aoyama
,
Elodie Reveillac
,
Tony Robinet
Article dans une revue
halsde-00372244v1
|
|
Natural selection influences AFLP intraspecific genetic variability and introgression patterns in Atlantic eels
Pierre-Alexandre Gagnaire
,
V. Albert
,
B. Jónsson
,
Louis Bernatchez
Article dans une revue
halsde-00373273v1
|
|
Development of a key using morphological characters to distinguish south-western Indian Ocean anguillid glass eels
Elodie Reveillac
,
Pierre-Alexandre Gagnaire
,
Raymonde R. Lecomte-Finiger
,
Patrick Berrebi
,
Tony Robinet
Article dans une revue
halsde-00420526v1
|
|
New clues for freshwater eels (Anguilla spp.) migration routes to eastern Madagascar and surrounding islands
Tony Robinet
,
Elodie Réveillac
,
M. Kuroki
,
J. Aoyama
,
K. Tsukamoto
Article dans une revue
halsde-00284449v1
|
|
Co-occurence of two Alexandrium species in Thau Lagoon
Benjamin Genovesi
,
Estelle Masseret
,
M.S. Shin-Grzebyk
,
Daniel Grzebyk
,
Patrick Berrebi
Harmful Agae News An IOC Newsletter on toxic algae and algal blooms, 2008, 37, pp.1-2
Article dans une revue
halsde-00451663v1
|
|
Anguilla marmorata larval migration plasticity as revealed by otolith microstructural analysis
Elodie Reveillac
,
Eric Feunteun
,
Patrick Berrebi
,
Pierre-Alexandre Gagnaire
,
Raymonde R. Lecomte-Finiger
Canadian Journal of Fisheries and Aquatic Sciences, 2008, 65 (10), pp.2127-2137. ⟨10.1139/F08-122⟩
Article dans une revue
halsde-00367277v1
|
|
RFLP and semi-multiplex PCR-based identification of four eel species from the south-western Indian Ocean region
Pierre-Alexandre Gagnaire
,
K. Tsukamoto
,
J. Aoyama
,
Y. Minegishi
,
P. Valade
Article dans une revue
halsde-00300254v1
|