title: European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation.
abstract: The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation.
authors.affiliation: 1] Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany [2] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [3].
authors.forename: Mbaye
authors.initials: M
authors.lastname: Tine
authors.affiliation: 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [2].
authors.forename: Heiner
authors.initials: H
authors.lastname: Kuhl
authors.affiliation: 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France [3].
authors.forename: Pierre-Alexandre
authors.initials: PA
authors.lastname: Gagnaire
authors.affiliation: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal.
authors.forename: Bruno
authors.initials: B
authors.lastname: Louro
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France.
authors.forename: Erick
authors.initials: E
authors.lastname: Desmarais
authors.affiliation: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal.
authors.forename: Rute S T
authors.initials: RS
authors.lastname: Martins
authors.affiliation: 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [2] BCRT, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, D-13353 Berlin, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Hecht
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Knaust
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France.
authors.forename: Khalid
authors.initials: K
authors.lastname: Belkhir
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Klages
authors.affiliation: Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Dieterich
authors.affiliation: Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany.
authors.forename: Kurt
authors.initials: K
authors.lastname: Stueber
authors.affiliation: Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-49, 08003 Barcelona, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Piferrer
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Guinand
authors.affiliation: 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bierne
authors.affiliation: Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium.
authors.forename: Filip A M
authors.initials: FA
authors.lastname: Volckaert
authors.affiliation: Dipartimento di Biomedicina Comparata e Alimentazione, Università di Padova, I-35124 Padova, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bargelloni
authors.affiliation: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal.
authors.forename: Deborah M
authors.initials: DM
authors.lastname: Power
authors.affiliation: 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France.
authors.forename: François
authors.initials: F
authors.lastname: Bonhomme
authors.affiliation: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal.
authors.forename: Adelino V M
authors.initials: AV
authors.lastname: Canario
authors.affiliation: 1] Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany [2] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D001267:Atlantic Ocean; D001492:Bass / Q000235:genetics* / Q000502:physiology; D002874:Chromosome Mapping; D049810:Genetic Speciation; D014644:Genetic Variation; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny