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Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.

Freshwater Atlantic salmon (Salmo salar L.) populations are a living example of adaptation to the changing conditions caused by glacial cycles. The uniqueness of these populations is emphasized by almost complete resistance to the dangerous parasite Gyrodactylus salaris. In Europe, freshwater salmon populations occur primarily in north-western Russia in the republic of Karelia. These systems include Lakes Ladoga and Onega, the two largest lakes in Europe, each of which harbours a number of freshwater salmon spawning rivers. We used microsatellite markers to study the genetic structure and temporal stability of 11 freshwater salmon populations in Russian Karelia. Populations clustered according their region of origin. Although temporal variation in allele frequencies was observed in the majority of temporal comparisons, various lines of evidence demonstrated that this influence was relatively minor compared to spatial variation that explained eight times more of the variability than temporal variation. Temporal stability tended to occur in populations from rivers with a higher linear lake coefficient. The high level of genetic structuring observed in both lake systems and the apparent low level of migration between populations suggests that treating each river as a separate management unit is recommended. In addition, as the number of populations is large, the best strategy for such fine scale management would be to ensure that the level of natural reproduction in each river is sufficient to sustain the population. A prioritization strategy for population conservation based on estimating the relative roles of different evolutionary forces shaping the gene pools highlighted a number of populations where further monitoring is warranted and also identified populations which could be prioritized for conservation as living gene banks in the event that conservation resources are limited. This prioritization agreed well with the occurrence of temporal (in)stability.

An important issue for designing any conservation programme aimed at preserving genetic diversity is estimation of the scale at which genetic structuring occurs. Additional relevant factors include distinguishing whether or not population structuring is expected to be stable as predicted by the member-vagrant hypothesis, or alternatively, whether populations are more prone to local extinction-recolonization processes, as predicted by the metapopulation evolutionary model. In this study, the population genetic structure of Atlantic salmon from 11 locations within or nearby the Varzuga River tributary system was assessed using 17 microsatellites. Mantel tests and spatial autocorrelation analyses revealed a significant isolation-by-distance signal within the tributary system as well as a negative association between the level of genetic diversity and waterway distance from the river mouth, indicating that dispersal is less likely to occur to populations deep in the tributary system. Individual-level spatial autocorrelation analyses indicated that the majority of migration occurred between populations situated within 20 km of each other. The relatively high level of genetic structuring and significant isolation-by-distance signal observed in the Varzuga tributaries are concordant with the predictions of the member-vagrant evolutionary model. However, one subpopulation in particular revealed signs of instability which may be due to its location in the tidal zone, or due to the fact that it is more affected by human impacts. The results suggest that preservation of a number of spawning sites spaced throughout the tributary system is recommendable for ensuring sustainable fishing tourism in the river.