Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations

• Published in: Genetics Selection Evolution
• Main Authors: Rodríguez-Ramilo, Silvia Teresa, Baranski, Matthew, Moghadam, Hooman, Grove, Harald, Lien, Sigbjørn, Goddard, Mike E., Meuwissen, Theo H. E., Sonesson, Anna K.
• Other Authors: Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse ENSAT, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Norwegian University of Life Sciences (NMBU), University of Melbourne, Spanish Government CGL2012-39861-C02-02
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2019
• Subjects: viral nervous necrosis; stationary ecotype; read alignment; gene flow; differentiation; resistance; costal; vibriosis; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Arctic; Arctic cod; atlantic cod; Gadus morhua; Northeast Arctic cod
• Online Access: https://hal.science/hal-02344196; https://hal.science/hal-02344196/document; https://hal.science/hal-02344196/file/12711_2019_Article_503.pdf; https://doi.org/10.1186/s12711-019-0503-5

International audience Background: two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were to identify genomic islands of divergence and to propose an approach to quantify the strength of selection pressures using whole-genome single nucleotide polymorphism (SNP) data. After applying filtering criteria, information on 93 animals (9 CC individuals, 50 NEAC animals and 34 CC × NEAC crossbred individuals) and 3,123,434 autosomal SNPs were used.Results: Four genomic islands of divergence were identified on chromosomes 1, 2, 7 and 12, which were mapped accurately based on SNP data and which extended in size from 11 to 18 Mb. These regions differed considerably between the two populations although the differences in the rest of the genome were small due to considerable gene flow between the populations. The estimates of selection pressures showed that natural selection was substantially more important than genetic drift in shaping these genomic islands. Our data confirmed results from earlier publications that suggested that genomic islands are due to chromosomal rearrangements that are under strong selection and reduce recombination between rearranged and non-rearranged segments.Conclusion: Our findings further support the hypothesis that selection and reduced recombination in genomic islands may promote speciation between these two populations although their habitats overlap considerably and migrations occur between them