title: Population genomic analyses of early-phase Atlantic Salmon (Salmo salar) domestication/captive breeding.
abstract: Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild Atlantic salmon (Salmo salarL.) populations are threatened by anthropogenic influences, and they are supplemented with captively bred fish. The Atlantic salmon is also widely used in selective breeding programs to increase the mean trait values for desired phenotypic traits. We analyzed a genomewide set of SNPs in three domesticated Atlantic salmon strains and their wild conspecifics to identify loci underlying domestication. The genetic differentiation between domesticated strains and wild populations was low (F ST < 0.03), and domesticated strains harbored similar levels of genetic diversity compared to their wild conspecifics. Only a few loci showed footprints of selection, and these loci were located in different linkage groups among the different wild population/hatchery strain comparisons. Simulated scenarios indicated that differentiation in quantitative trait loci exceeded that in neutral markers during the early phases of divergence only when the difference in the phenotypic optimum between populations was large. This study indicates that detecting selection using standard approaches in the early phases of domestication might be challenging unless selection is strong and the traits under selection show simple inheritance patterns.
authors: Division of Genetics and Physiology, Department of Biology, University of Turku Turku, Finland.
authors: Hannu
authors: H
authors: Mäkinen
authors: Division of Genetics and Physiology, Department of Biology, University of Turku Turku, Finland ; Department of Aquaculture, Estonian University of Life Sciences Tartu, Estonia.
authors: Anti
authors: A
authors: Vasemägi
authors: Aquaculture and Fisheries Development Centre, School of Biological, Earth, and Environmental Sciences, University College Cork Cork, Ireland ; Marine Institute, Furnace Newport, Co. Mayo, Ireland.
authors: Philip
authors: P
authors: McGinnity
authors: Aquaculture and Fisheries Development Centre, School of Biological, Earth, and Environmental Sciences, University College Cork Cork, Ireland.
authors: Tom F
authors: TF
authors: Cross
authors: Division of Genetics and Physiology, Department of Biology, University of Turku Turku, Finland.
authors: Craig R
authors: CR
authors: Primmer
keywords: adaptation; aquaculture; captive populations; ecological genetics; population genetics – empirical