Research projects

We aim to understand the genetic processes underlying adaptation and speciation in free-living populations and species. We also use the obtained knowledge as the basis for developing conservation and management guidelines which can be applied in a wide range of endangered and exploited populations and species. Research focusses on several study species and systems covering a range of ecosystems and geographic scales, including European grayling (Thymallus thymallus), Atlantic salmon (Salmo salar), Arctic charr (Salvelinus alpinus), and Ficedula flycatchers. Brief details of ongoing projects are listed under three sub-categories below.

1. Population Genetics

2. Ecological and Evolutionary Genomics

3. Evolutionary Applications

1. Population Genetics

We are conducting a number of projects aimed at determining the relative importance of mutation, migration, genetic drift and natural selection in shaping the population structure in a number of study systems over various geographic and temporal scales. We are increasingly moving towards a populaton genomics approach, where hunreds or thousands of markers are applied.

Examples of specific projects

Populations genetics of Atlantic salmon, Salmo salar, from northwest Russia

The effect of MHC variation on the occurrence of cataracts in wild and hatchery populations of Arctic charr

Temporal and spatial variation in the genetic structure of Atlantic salmon in the river Teno: implications for conservation


Example publications on the topic:

  • Vähä J-PK, Erkinaro J, Niemelä E, and Primmer CR (2007) Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Molecular Ecology 16: 2638-2654.
  • Ryynänen HJ, Tonteri A, Vasemägi A and Primmer CR A (2007) comparison of bi-allelic markers and microsatellites for the estimation of population and conservation genetic parameters in Atlantic salmon (Salmo salar). Journal of Heredity (in press).
  • Tonteri A, Veselov A, Titov S, Lumme J and Primmer CR (2007) The effect of migratory behavior on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon (Salmo salar L.) Journal of Fish Biology 70C: 381-398.
  • Primmer CR, Veselov AJ, Zubchenko A, Poututkin A, Bakhmet I & Koskinen MT (2006) Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia.Molecular Ecology (in press).
  • Vähä J-PK and Primmer CR (2006) Detecting hybridization between individuals of closely related populations - a simulation study to assess the efficiency of model-based Bayesian methods to detect hybrid individuals. Molecular Ecology 15: 63-72.
  • Koskinen MT, Haugen TO and Primmer CR. (2002) Contemporary fisherian life-history evolution in small salmonid populations. Nature 419: 826-830.
  • Koskinen MT, Piironen J and Primmer CR (2001) Deep inter-population divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation. Conservation Genetics 2: 133-143.
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    2. Ecological and Evolutionary Genomics

    Ecological and evolutionary genomics research in the group focuses on identifying genes underlying traits of ecological and evolutionary importance in non-model organisms such as salmonid fishes and passerine birds. Approaches used include hitchhiking mapping, linkage mapping, canadidate gene approaches as well as transripromics and proteomics. Many of these projects link closely to population genetic studies of the same systems.

    Examples of specific projects

    The molecular basis of speciation. Studies of hybridization in Fidecula flycatchers

    The molecular mechanisms and evolutionary significance of plumage colour variation in pied flycatchers

    Identification of genes involved in domestication in Atlantic salmon (Salmo salar)

    Identification of genes involved in local adaptation in European grayling (Thymallus thymallus)

    Example publications on the topic:

  • Vasemägi A and Primmer CR (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Invited Review in Molecular Ecology 14: 3623-3642.
  • Buggiotti L and Primmer CR (2006) Molecular evolution of the avian growth hormone gene and comparison with its mammalian counterpart. Journal of Evolutionary Biology 19: 844-854.
  • Ryynänen HJ and Primmer CR (2006) Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes. BMC Genomics 7: 192
  • Ryynänen H and Primmer CR. (2006) Varying signals of the effects of natural selection during teleost growth hormone gene evolution. Genome 49: 42-53.
  • Vasemägi A, Nilsson J and Primmer CR (2005) Expressed sequence tag (EST) linked microsatellites as a source of gene associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution 22: 1067-1076
  • Primmer CR, Borge T, Haavie J, and Sætre G-P. (2002) Single-nucleotide polymorphism (SNP) characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Molecular Ecology 11: 603-612.

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    3. Evolutionary Applications

    We also aim to use ecological and evolutionary genomic information as the basis for developing conservation and management guidelines which can be applied in a wide range of endangered and exploited populations and species. This is done in clocse c-operation with management organisations such as the Finnish Game and Fisheries Research Institute. I also lead the Centre of Evolutionary Applications- which conducts applied research projects for external clients.

    Examples of specific projects

    Temporal and spatial variation in the genetic structure of Atlantic salmon in the river Teno: implications for conservation

    The effect of MHC variation on the occurrence of cataracts in wild and hatchery populations of Arctic charr (Salvelinus alpinus)

    The effects of individual genetic diversity on fitness

    Mixed stock analysis of Lake Inari brown trout (Salmo trutta)


    Example publications on the topic:

  • Vähä J-PK, Erkinaro J, Niemelä E and Primmer CR (2008) Retrospective genetic monitoring of Atlantic salmon populations within a river system over two decades –implications for management. Evolutionary Applications (in press)
  • Johansson M, Primmer CR & Merilä J. (2007) Does habitat fragmentation reduce fitness and adaptability? A case study of the common frog (Rana temporaria). Molecular Ecology 16: 2693-2700.
  • Tiira K, Piironen J and Primmer CR (2006) Evidence for reduced genetic variation in severely deformed juvenile salmonids. Canadian Journal of Fisheries and Aquatic Sciences 63: 2700-2707.
  • Tiira K, Laurila A, Enberg K, Piironen J, Aikio S, Ranta E and Primmer CR (2006) Do dominants have higher heterozygosity? Social status and genetic variation in brown trout, Salmo trutta. Behavioral Ecology and Sociobiology 59: 657-665.
  • Tiira K, Laurila A, Peuhkuri N, Piironen J, Ranta E and Primmer CR. (2003) Aggressiveness is associated with genetic diversity in landlocked salmon, Salmo salar. Molecular Ecology 12: 2399-2407.
  • Primmer CR, Koskinen MT and Piironen J. (2000) The one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud. Proceedings of the Royal Society of London. Series B. 267: 1699-1704.

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