title: Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection.
abstract: Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions.
  
  
  
  In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13-15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals.
  
  
  
  Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation.
authors: Institute of Marine Research, Bergen, Norway. erikkj@imr.no.|Department of Biology, University of Bergen, Bergen, Norway. erikkj@imr.no.
authors: Erik
authors: E
authors: Kjærner-Semb
authors: Institute of Marine Research, Bergen, Norway.
authors: Fernando
authors: F
authors: Ayllon
authors: Institute of Marine Research, Bergen, Norway.
authors: Tomasz
authors: T
authors: Furmanek
authors: Institute of Marine Research, Bergen, Norway.
authors: Vidar
authors: V
authors: Wennevik
authors: Institute of Marine Research, Bergen, Norway.
authors: Geir
authors: G
authors: Dahle
authors: Natural Resources Institute Finland, Helsinki, Finland.
authors: Eero
authors: E
authors: Niemelä
authors: Kevo Subarctic Research Institute, University of Turku, Turku, Finland.
authors: Mikhail
authors: M
authors: Ozerov
authors: Kevo Subarctic Research Institute, University of Turku, Turku, Finland.|Association for Water and Environment of Western Uusimaa, Uusimaa, Finland.
authors: Juha-Pekka
authors: JP
authors: Vähä
authors: Institute of Marine Research, Bergen, Norway.|Department of Biology, University of Bergen, Bergen, Norway.
authors: Kevin A
authors: KA
authors: Glover
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors: Carl J
authors: CJ
authors: Rubin
authors: Institute of Marine Research, Bergen, Norway.
authors: Anna
authors: A
authors: Wargelius
authors: Institute of Marine Research, Bergen, Norway. rolfbe@imr.no.
authors: Rolf B
authors: RB
authors: Edvardsen
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics / Q000276:immunology; D000818:Animals; D017756:Aquaculture; D005075:Biological Evolution; D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics*; D005393:Fish Diseases / Q000235:genetics* / Q000276:immunology / Q000821:virology; D029941:Fish Proteins / Q000235:genetics / Q000276:immunology; D020440:Gene Duplication; D015870:Gene Expression; D014644:Genetic Variation; D016678:Genome; D055106:Genome-Wide Association Study; D020125:Mutation, Missense; D016328:NF-kappa B / Q000235:genetics / Q000276:immunology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D020317:Salmo salar / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000821:virology; D012641:Selection, Genetic; D057891:Tetraploidy
chemical_list: D029941:Fish Proteins; D016328:NF-kappa B
keywords: Adaptation; Aquaculture; GWAS; Immune system; Resequencing; SNPs; Salmo salar; Selective sweep; Whole genome duplication