Restitution and genetic differentiation of salmon populations in the southern Baltic genotyped with the Atlantic salmon 7K SNP array

Abstract

BackgroundNative populations of Atlantic salmon in Poland, from the southern Baltic region, became extinct in the 1980s. Attempts to restitute salmon populations in Poland have been based on a Latvian salmon population from the Daugava river. Releases of hatchery reared smolts started in 1986, but to date, only one population with confirmed natural reproduction has been observed in the Slupia river. Our aim was to investigate the genetic differentiation of salmon populations in the southern Baltic using a 7K SNP (single nucleotide polymorphism) array in order to assess the impact of salmon restitution in Poland.MethodsOne hundred and forty salmon samples were collected from: the Polish Slupia river including wild salmon and individuals from two hatcheries, the Swedish Morrum river and the Lithuanian Neman river. All samples were genotyped using an Atlantic salmon 7K SNP array. A set of 3218 diagnostic SNPs was used for genetic analyses.ResultsGenetic structure analyses indicated that the individuals from the investigated populations were clustered into three groups i.e. one clade that included individuals from both hatcheries and the wild population from the Polish Slupia river, which was clearly separated from the other clades. An assignment test showed that there were no stray fish from the Morrum or Neman rivers in the sample analyzed from the Slupia river. Global FST over polymorphic loci was high (0.177). A strong genetic differentiation was observed between the Lithuanian and Swedish populations (FST = 0.28).ConclusionsWild juvenile salmon specimens that were sampled from the Slupia river were the progeny of fish released from hatcheries and, most likely, were not progeny of stray fish from Sweden or Lithuania. Strong genetic differences were observed between the salmon populations from the three studied locations. Our recommendation is that future stocking activities that aim at restituting salmon populations in Poland include stocking material from the Lithuanian Neman river because of its closer geographic proximity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0121-9) contains supplementary material, which is available to authorized users.

Baltic Sea genetic biodiversity: Current knowledge relating to conservation management

“…Genetic differences between brackish and freshwater populations are also present and have been documented for grayling ( Thymallus thymallus ; Swatdipong, Vasemägi, Koskinen, Piironen, & Primmer, ) and northern pike (Bekkevold, Jakobsen, et al, ). Management advice presented in the scientific literature include identification of the size of management units of pike (Laikre, Miller, et al, ), identification of cod stocks in the eastern Baltic Sea and hybrid zones between stocks in the eastern and western Baltic Sea (Nielsen et al, ; Poćwierz‐Kotus et al, ), genetic differentiation among demersal and pelagic spawners in flounder (Florin & Höglund, ) genetically distinct populations of salmon and trout in separate rivers (and areas within rivers) warranting management of each river flowing into the Baltic Sea separately (Ståhl, ; Ozerov et al, ), and low, but detectable, differentiation among stocks of herring, which promotes management on a more local level than currently applied (Barrio et al, ; Bekkevold, Heylar et al, ; Teacher, André, Jonsson, & Merilä, ). Of specific conservation interest is the identification of sturgeon ( Acipenser oxyrinchus ) populations from Canada suggested as the most suitable source populations for reintroduction programmes in Poland and Germany of the extinct sturgeon (Popović et al, ).…”

“…Genetic differences between brackish and freshwater populations are also present and have been documented for grayling (Thymallus thymallus;Swatdipong, Vasemägi, Koskinen, Piironen, & Primmer, 2009) and northern pike(Bekkevold, Jakobsen, et al, 2015). Management advice presented in the scientific literature include identification of the size of management units of pike(Laikre, Miller, et al, 2005), identification of cod stocks in the eastern Baltic Sea and hybrid zones between stocks in the eastern and western Baltic SeaPoćwierz- Kotus et al, 2015), genetic differentiation among demersal and pelagic spawners in flounder(Florin & Höglund, 2008) genetically distinct populations of salmon and trout in separate rivers (and areas within rivers) warranting management of each river flowing into the Baltic…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…It has been suggested that such demographic processes in the native population as spawning success and survival of the offspring influence the relative success of farmed salmon in the wild (Heino et al, 2015). Hatchery released and native extirpated salmon populations were identified in Poland using an Atlantic salmon array (Pocwierz-Kotus et al, 2015;Bernas et al, 2016). Understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes (Pritchard et al, 2016).…”

Recent genetic changes in enhanced populations of sea trout (Salmo truttam.trutta) in the southern Baltic rivers revealed with SNP analysis

“…These enhancements have included releases of artificially reared stocks or escapes of large numbers of individuals characterized by lower fitness (Satake and Araki 2011;Baskett et al 2013;Milot et al 2013;Naish et al 2013) and lower genetic diversity have been reported for some species, including Adriatic sturgeon (Boscari and Congiu 2014), Korean starry flounder ) and black sea bream in Japan (Blanco Gonzalez and Umino 2009). Other effects have been introductions of nonindigenous populations, such as salmon in Poland (Poćwierz-Kotus et al 2015a;Bernaś et al 2016); or alien populations of the same species and their subsequent hybridization a Corresponding author: rwenne@iopan.gda.pl with local native populations, as with salmon and brown trout in Bulgaria (Chelenkova et al 2012), Norway (Thaulow et al 2012), Hungary (Horváth et al 2013) and in Spain (Madeira et al 2005), pikeperch in Finland (Salminen et al 2012); unintentional escapes from hatcheries as red sea bream in Japan (Blanco Gonzalez et al 2015), salmon in Norway (Liu et al 2013) and Canada (Fraser et al 2008). Accidental or deliberate introductions of exotic and invasive species to new environments, often beneficial economically, causes distortions in the functioning of local ecosystems and can threaten native populations of fish and shellfish, as in the case of brown trout in Japan (Hasegawa and Maekawa 2008), Patagonia (Vigilano et al 2007;Young et al 2010) and in North America (Turek et al 2016), mussel Mytilus in Europe and South Africa (Kijewski et al 2009;McQuaid et al 2015 and oyster Crassostrea gigas (Carlton 1979;Meehan et al 1989;Miller et al 2012;Lallias et al 2015).…”