Conservation Genetics

, Volume 11, Issue 2, pp 571–582 | Cite as

Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon

  • Sten Karlsson
  • Thomas Moen
  • Kjetil Hindar
Research Article


Levels of genetic variability at 12 microsatellite loci and 19 single nucleotide polymorphisms in mitochondrial DNA were studied in four farm strains and four wild populations of Atlantic salmon. Within populations, the farm strains showed significantly lower allelic richness and expected heterozygosity than wild populations at the 12 microsatellite loci, but a significantly higher genetic variability with respect to observed number of haplotypes and haplotype diversity in mtDNA. Significant differences in allele- and haplotype-frequencies were observed between farm strains and wild populations, as well as between different farm strains and between different wild populations. The large genetic differentiation at mitochondrial DNA between wild populations (FST = 0.24), suggests that the farm strains attained a high mitochondrial genetic variability when created from different wild populations seven generations ago. A large proportion of this variability remains despite an expected lower effective population size for mitochondrial than nuclear DNA. This is best explained by the particular mating schemes in the breeding programmes, with 2–4 females per male. Our observations suggest that for some genetic polymorphisms farm populations might currently hold equal or higher genetic variability than wild populations, but lower overall genetic variability. In the short-term, genetic interactions between escaped farm salmon and wild salmon might increase genetic variability in wild populations, for some, but not most, genetic polymorphisms. In the long term, further losses of genetic variability in farm populations are expected for all genetic polymorphisms, and genetic variability in wild populations will be reduced if escapes of farm salmon continue.


Atlantic salmon Salmo salar Farm salmon Wild salmon Mitochondrial DNA Microsatellite Captive breeding 



We gratefully acknowledge SalmoBreed and Aqua Gen for providing samples from farm strains, Gunnel Østborg (NINA), Paul Berg, Arne Roseth (Cigene), and Hege Munck (Nofima) for technical assistance. We also want to thank two anonymous referees for their help in improving this paper. This paper is a contribution from the project “Genomics as a tool for detecting selection in farm Atlantic salmon and interactions between escaped and farm wild salmon” funded by the Research Council of Norway (NFR FUGE grant no. 175130).


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.NOFIMAÅsNorway
  2. 2.Aqua Gen ASPirsenteretTrondheim
  3. 3.CIGENEÅsNorway
  4. 4.Norwegian Institute for Nature Research (NINA)TrondheimNorway

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