Journal of Fish Biology (1996) 49, 411–429 Minisatellite DNA variation and stock identification of coho salmon T. D. B, K. M. M  R. E. W Department of Fisheries and Oceans, Pacific Biological Station, Nanaimo, BC, Canada, V9R 5K6 (Received 15 August 1995, Accepted 11 January 1996) Geographic variation in minisatellite DNA variation was examined in 18 stocks of coho salmon Oncorhynchus kisutch from British Columbia and three stocks from Kamchatka or Western Alaska. Genomic DNA was restricted with MboI or HaeIII and hybridized with two minisatellite probes (pSsa-A34, OtsPBS-1). Allele frequencies and DNA band counts derived from the two probes were combined with band counts from the probe Ssa1 to show a regional stock structure. In British Columbia, stocks from the Fraser River were distinct from those on Vancouver Island, and all were differentiated from those on the mainland of British Columbia. Average heterozygosity at the Ssa-A34 locus was 71%. Compared with a previous study of British Columbia coho salmon population structure in which variation at 26 allozyme loci was examined, greater population differentiation and higher heterozygosity were observed at minisatellite loci. Estimated stock compositions of simulated mixtures of fishery samples from British Columbia stocks were accurate and precise, with the potential of identifying stocks within the drainage basin of a major river, the Fraser River. Minisatellite DNA variation may provide accurate and precise estimates of stock composition in actual fishery applications, and has the potential of identifying individual fish to region or stock of origin.  1996 The Fisheries Society of the British Isles Key words: fisheries management; molecular genetics; population structure. INTRODUCTION Stock identification techniques based upon genetic differentiation among con- tributing stocks have been applied extensively to estimation of stock composition in selected Pacific salmon fisheries (Beacham et al., 1987; Wood et al., 1989). Genetic variation has been surveyed primarily with protein electrophoresis, in which genetic variation at protein-coding loci is examined indirectly by analysis of variation in the proteins (enzymes) produced. Specific applications of protein electrophoresis to discrimination of coho salmon Oncorhynchus kisutch (Walbaum) stocks have been limited generally to population structure (Bartley et al., 1992) with some potential for stock identification (Milner, 1993), but low levels of variation are observed typically (Wehrhahn & Powell, 1987). As protein-coding regions comprise only a very small portion of the genome, additional discrimination among stocks based on genetic differentiation will probably be observed by direct analysis of DNA variation. Population structure analysis based upon direct surveys of DNA variation has been undertaken for a number of fish species (Wilson et al., 1987; Palva et al., 1989; Bernatchez et al., 1992; Stevens et al., 1993; Taylor et al., 1994). Recent analysis of variation in minisatellite DNA variation has indicated that many populations of Pacific salmon are genetically distinct (Taylor et al., 1994; 411 0022–1112/96/090411+19 $25.00/0  1996 The Fisheries Society of the British Isles