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Notes: The feasibility of using genetic stock identification to analyse seasonal changes in stock compositions of Atlantic salmon catches in the Baltic Sea was examined. The analysis employed seven variable allozyme loci from most of the potentially contributing stocks (16) from Finland and Sweden. Catch samples were collected from Finnish salmon fisheries in the eastern Bothnian Sea during the 1992 fishing season. Simulation studies were used to evaluate the feasibility of identifying Baltic salmon stocks with allozyme data. Special attention was paid to analysing the wild production of salmon stocks. Clear seasonal differences in stock composition were found. The estimates were compared with smolt production and Carlin-tag data. The proportions of the Neva and Oulujoki river stocks could be estimated as individual stocks, whereas the contributions of the remaining stocks were estimated as four composite stock groups. One of the groups consisted of wild stocks from the rivers Kalixälven and Simojoki. Identification of this group, which could be used as an index of wild production in the catches, requires catch sample sizes 〉300 salmon if 〈15% error is required.

Notes: Electrophoretic studies of proteins remain a primary source of insight into genetic diversity in many species including the Atlantic salmon Salmo salar, one of the most culturally and economically important fish species of the North Atlantic region. Since 1966, 〉350 scientific papers on protein variation have been published encompassing 25 000+ salmon from over 400 locations in 〉200 river systems across the species’ distribution. Variation has been detected at 30% of the 110 protein loci screened, though most studies examine 〈40. The method has been applied largely to the investigation of population structure and differentiation, but work has also led to the systematic revision of the genus Salmo and remains the primary source of insight into hybridization in the wild with brown trout Salmo trutta. Spatial patterns of differentiation show temporal stability, both within and among river systems, and strongly support structuring of the species into river and tributary specific populations and the designation of European and North American populations as distinct sub-species. They also show widespread regional differentiation within both continents, beyond the marked subcontinental differences between Baltic Sea and Atlantic Ocean populations in Europe. Most of the differentiation probably reflects gene flow and founder events associated with colonization following the retreat of the glaciers from much of the species’ modern range. However, variation at MEP-2* shows strong correlations with environmental temperature, both within and among rivers, and associations with phenotypic performance. This suggests selection is acting on the locus and provides compelling evidence for the local adaptation of populations. Protein studies have led to more population centred management of the species and have been exploited in the discrimination of regional stocks in mixed stock analysis in high seas fisheries, particularly in the Baltic Sea, and as markers for the assessment of stocking success. They have also advanced insight into how the genetic character of populations can be changed in cultivation and the potential impact of salmon aquaculture and stocking on wild populations. The method has been largely superseded by DNA based analyses, but the results remain highly relevant to Atlantic salmon management and conservation and are an irreplaceable data set for studying genetic stability of populations over time.

Notes: The effective application of genetic information in fisheries management strategies implies political goal setting taking both conservation and fisheries management into account. The concept of sustainable use as set out by the Convention on Biological Diversity offers a valuable starting point in this respect, since the criterion for it is defined as the maintenance of genetic diversity within each species. However, strategic decisions are also needed on the practical level, where the actual genetic information can be taken into account. Genetic factors, such as glacial differentiation, the postglacial genetic structure of populations, gene flow levels and the probability of the existence of adaptive differences, have an effect on the formation of conservation and management units and on the long-term strategy for the sustainable use of aspecies. The Atlantic salmon (Salmo salar) in the Baltic Sea area is treated here as an example of a complicated management problem with a highly hierarchical genetic structure associated with marked loss of naturally reproductive stocks, extensive hatchery production and an effective international offshore fishery. The implications of genetic factors for the conservation and management strategy of the Baltic salmon is discussed in the light of the goals set by the Convention on Biological Diversity, the Straddling Fish Stocks and Highly Migratory Fish Stocks Agreement, the Habitats Directive of the European Union and the International Baltic Sea Fishery Commission.