Assigning individual fish to populations using microsatellite DNA markers

Authors

  • Michael M. Hansen,

    Corresponding author
    1.  Danish Institute for Fisheries Research, Department of Inland Fisheries, Vejlsøvej 39, DK–8600 Silkeborg, Denmark, and
      *Correspondence: Michael M. Hansen, Danish Institute for Fisheries Research, Department of Inland Fisheries, Vejlsøvej 39, DK–8600 Silkeborg, Denmark Tel.: + 45 89 213100 Fax: + 45 89 213150 E-mail:mmh@dfu.min.dk
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  • Ellen Kenchington,

    1.  Department of Fisheries & Oceans, Bedford Institute of Oceanography, 1 Challenger Drive, PO Box 1006, Dartmouth, Nova Scotia, Canada B2Y 4A2
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  • Einar E. Nielsen

    1.  Danish Institute for Fisheries Research, Department of Inland Fisheries, Vejlsøvej 39, DK–8600 Silkeborg, Denmark, and
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*Correspondence: Michael M. Hansen, Danish Institute for Fisheries Research, Department of Inland Fisheries, Vejlsøvej 39, DK–8600 Silkeborg, Denmark Tel.: + 45 89 213100 Fax: + 45 89 213150 E-mail:mmh@dfu.min.dk

Abstract

New statistical developments combined with the use of highly polymorphic microsatellite DNA markers enable the determination of the population of origin of single fish, resulting in numerous new research possibilities and applications in practical management of fish populations. We first describe three main categories of methods available, i.e. (i) assignment tests and related methods, (ii) discriminant function analysis and (iii) artificial neural networks. In all these, individuals can be assigned to the population from which their multilocus genotypes are most likely to be derived. Assignment tests are based on calculations of the likelihood of multilocus genotypes in populations, based on allele frequencies. Discriminant function analysis is based on multivariate statistics, whereas artificial neural networks formulate predictions through exposure to correct solutions. Assignment tests are the methods of choice when considering genetic data alone, whereas discriminant function analysis and artificial neural networks may be useful when genetic data are combined with, for instance, morphological and ecological data. Assignment tests can be used to assess the genetic distinctness of populations, for discriminating among closely related species and to directly identify immigrants or individuals of immigrant ancestry, and thereby study patterns of dispersal among populations, including sex-biased dispersal. In a conservation context, assignment tests can be used to assess the genetic impact of domesticated fish on wild populations and for determining if extant fish populations are in fact indigenous or descendants from stocked fish or strayers, and they can be applied in forensics, for instance to reveal poaching. Assignment tests are at present most useful for studies of freshwater and anadromous fishes owing to stronger genetic differentiation among populations than in marine fishes. However, some genetically divergent populations of marine fishes have been discovered, which could be used as natural laboratories for studying dispersal and gene flow. It is foreseen that ongoing developments in statistical methods, combined with improved techniques for screening large numbers of loci, will permit assignment methods to become standard tools in studies on the biology of fishes.

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