Molecular Ecology (2000) 9, 583–594 © 2000 Blackwell Science Ltd Blackwell Science, Ltd Microsatellite and mitochondrial DNA polymorphism reveals life-history dependent interbreeding between hatchery and wild brown trout (Salmo trutta L.) MICHAEL M. HANSEN, DANIEL E. RUZZANTE, EINAR E. NIELSEN and KAREN-LISE D. MENSBERG Danish Institute for Fisheries Research, Department of Inland Fisheries, Population Genetics Laboratory, Vejlsøvej 39, DK-8600 Silkeborg, Denmark Abstract The effects of stocking hatchery trout into wild populations were studied in a Danish river, using microsatellite and mitochondrial DNA (mtDNA) markers. Baseline samples were taken from hatchery trout and wild trout assumed to be unaffected by previous stocking. Also, samples were taken from resident and sea trout from a stocked section of the river. Genetic differentiation between the hatchery strain and the local wild population was modest (microsatellite F ST = 0.06). Using assignment tests, more than 90% of individuals from the baseline samples were classified correctly. Assignment tests involving samples from the stocked river section suggested that the contribution by hatchery trout was low among sea trout (< 7%), but high (46%) among resident trout. Hybrid index analysis and a high percentage of mtDNA haplotypes specific to indigenous trout observed among resident trout that were assigned to the hatchery strain suggested that interbreeding took place between hatchery and wild trout. The latter result also indicated that male hatchery trout contributed more to interbreeding than females. We suggest that stronger selection acts against stocked hatchery trout that become anadromous compared to hatchery trout that become resident. As most resident trout are males this could also explain why gene flow from hatchery to wild trout appeared to be male biased. The results show that even despite modest differentiation at neutral loci domesticated trout may still perform worse than local populations and it is important to be aware of differential survival and reproductive success both between life-history types and between sexes. Keywords: assignment test, gene flow, microsatellite, mitochondrial DNA, Salmo trutta, stocking Received 2 September 1999; revision received 24 November 1999; accepted 24 November 1999 Introduction The advent of molecular markers, in particular microsatellite DNA, is fuelling the development of numerous new research possibilities in population and conservation genetics (Estoup & Angers 1998; Beaumont & Bruford 1999), including the development of new statistical techniques that allow identification of immigrants and their descendants (Rannala & Mountain 1997; Waser & Strobeck 1998), a subject of critical importance for monitoring gene flow or detecting introgression. Genetic interactions between wild and domes- ticated fish (Hindar et al. 1991a) is one area of conserva- tion genetics where microsatellite markers are expected to be particularly useful, as in many instances the limited resolution power of traditionally used markers, such as allozymes and mitochondrial DNA (mtDNA), has not allowed for the detection of interbreeding and introgression and for the tracing of the fate of stocked fish in the wild. Many important insights into the dynamics of gene flow from domesticated fish into wild fish populations have been gained using allozyme markers (Chilcote et al. 1986; Taggart & Ferguson 1986; Largiadèr & Scholl 1996). However, in most cases the resolution power of allozymes has only allowed the genetic discrimination of domestic- ated and wild populations that are genetically strongly divergent, such as those derived from different phylogeo- graphic lineages (Largiadèr & Scholl 1996). In cases where hatchery strains have been founded from populations in Correspondence: Michael M. Hansen. Fax: + 45 89 213150; E-mail: mmh@dfu.min.dk