The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction‐site‐associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout ( Salmo trutta ) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST , was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half‐ and full‐siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual‐level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual‐level genotype information, such as quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

No abstract

The genetic structure and isolation pattern of the Atlantic salmon (Salmo salar) throughout its range in the Baltic Sea were examined as a starting point for a conservation strategy for the species in this area. The allozyme variation in seven polymorphic loci was studied in 5125 salmon from 24 rivers in four countries. A clear dichotomy was observed between stock groups from southeastern (Russia, Estonia, Latvia, southern Sweden) and northwestern (northern Finland, northern Sweden) drainage regions, corresponding to the postglacial colonisation of the Baltic Sea by two phylogeographic lineages, one from the east (the Ice Lake lineage) and one from the west (the Atlantic lineage). The geographical and genetic distances between stocks fit the one-dimensional "isolation-by-distance" model (p < 0.001). The estimated gene flow ranged from 0 to10 migrants per generation. The total diversity of hatchery stocks was 72% of that of the wild stocks. Genetically similar stock groups, phylogeographic lineages, and drainage regions are recommended for use as genetic management units in addition to stock level.

The genetic structure and phylogeography of Atlantic salmon (Salmo salar) across the Baltic Sea basin and neighbouring areas (eastern Atlantic Ocean, North Sea, Barents Sea, White Sea, and two Russian lakes, Onega and Ladoga) were studied to resolve the partly contradictory hypotheses of the species' postglacial colonization history. Thirty-eight populations (total of 2180 individuals) were studied for nine DNA microsatellite loci. Within the Baltic Sea, the anadromous populations formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin), and southern regions (western Baltic Main Basin). The genetic differences among these three groups were clearly greater (G GB 5.6%; G GB being the proportion of diversity components between regions within basins) than were those among population groups in the eastern Atlantic Ocean (G GB 2.2%) from Ireland to the White Sea. The isolation-by-distance model explained part of the differentiation within, but not between, the regions. The results strongly indicate colonization of the Baltic Sea by at least three glacial lineages. Potential refugium areas for each lineage are proposed.Résumé : Nous avons étudié la structure génétique et la phylogéographie du saumon atlantique (Salmo salar) de part en part du bassin de la Baltique et dans les régions avoisinantes (est de l'Atlantique, mer de Barents, mer Blanche et deux lacs russes, les lacs Onega et Ladoga) pour résoudre les hypothèses en partie contradictoires sur l'histoire de la colonisation postglaciaire de l'espèce. Nous avons analysé neuf locus ADN microsatellites chez 2180 individus appartenant à 38 populations. Au sein de la Baltique, les populations anadromes forment trois groupes distincts qui correspondent aux régions du nord (golfe de Bothnie), de l'est (golfe de Finlande et bassin principal de l'est de la Baltique) et du sud (bassin principal de l'ouest de la Baltique). Les différences génétiques entre ces trois groupes sont nettement plus importantes (G GB 5,6 %; G GB représente la proportion d'éléments de diversité entre les régions à l'intérieur des bassins) que celles qui existent entre les groupes de populations de l'est de l'Atlantique (G GB 2,2 %), de l'Irlande à la mer Blanche. Le modèle de l'isolement en fonction de la distance explique une partie de la différentiation au sein des régions, mais non entre elles. Nos résultats indiquent fortement une colonisation de la Baltique par au moins trois lignées glaciaires. Nous proposons des zones possibles de refuge pour chaque lignée.[Traduit par la Rédaction] Säisä et al. 1904

No abstract

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 000þ 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 †Author to whom correspondence should be addressed. Tel.: þ44 (0) 796 472060; fax: þ44 (0) 1796 473523; # 2005 Crown copyright 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. # 2005 Crown copyright

Mixture modeling is shown to outperform classical individual assignments for both estimating stock composition and identifying individuals' sources in a case study of an eight-locus DNA microsatellite database from 26 Atlantic salmon (Salmo salar) stocks of the Baltic Sea. Performance of the estimation methods was compared using selfassignment tests applied to each of the baseline samples and using independent repeat samples from two of the baseline stocks. The different theoretical underpinnings, hypothesis testing versus decision theory, of the methods explain their estimation capacities. In addition, actual catch samples from three northern Baltic Sea sites in 2000 were analysed by mixture modeling, and estimated compositions were consistent with previous knowledge. Baltic main basin and Gulf of Finland stocks were each minor components (<1% at any site), and three groups of Gulf of Bothnia stocks, wild (36%-43% among sites), Finnish hatchery (15%-49%), and Swedish hatchery (11%-41%), were each important with the two hatchery contributions trending geographically.Résumé : Dans une étude de cas comportant une banque de données sur des microsatellites ADN à huit locus provenant de 26 stocks de saumons atlantiques (Salmo salar) de la Baltique, nous montrons qu'un modèle de mélange fonctionne mieux que les assignations individuelles classiques, tant pour estimer la composition des stocks que pour identifier les origines des individus. Nous avons comparé la performance des méthodes d'estimation à celle des tests d'auto-assignation appliqués à chacun des échantillons de base et à des échantillons répétées indépendants des deux stocks de base. Les différents fondements théoriques, évaluation d'hypothèse ou théorie de décision, des méthodes expliquent leur capacité d'estimation. De plus, nous avons analysé des échantillons réels de récoltes en 2000 dans trois sites du nord de la Baltique à l'aide de modèles de mélange; les compositions estimées que nous avons obtenues concordent avec nos connaissances antérieures. Les stocks du bassin principal de la Baltique et du golfe de Finlande sont tous deux des composantes mineures (<1 % à tous les sites) et trois groupes de stocks du golfe de Bothnie, stocks sauvages (36-43 % parmi les sites), stocks finlandais de pisciculture (15-49 %) et stocks suédois de pisciculture (11-41 %), sont tous importants; les deux contributions des piscicultures suivent des gradients géographiques.[Traduit par la Rédaction] Koljonen et al. 2158

DNA-level information from an eight-loci microsatellite baseline database of 32 Atlantic salmon (Salmo salar) stocks was used with a Bayesian estimation method to assess the stock and stock group proportions of Finnish salmon catches in the Baltic Sea area. The proportions of seven stock groups, important to fisheries management, were assessed in catch samples taken between 2000 and 2005. In the Gulf of Bothnia area, the proportion of wild fish in catches showed an increasing trend in all areas until 2003, mainly because of the decrease in total catches caused by the relatively greater mortality of hatchery-reared fish compared with wild fish. In 2004, the total number of wild fish caught had also increased, indicating an increase in the abundance of wild stocks. In catches from the Åland Sea, the proportion of wild fish increased from 44% in 2000 to 70% in 2004, while the catch during the same period increased from 4628 to 7329 fish. In the Gulf of Finland, the local Neva salmon stock, which is released by Estonia, Finland, and Russia, made the largest contribution. In the western part of the Gulf of Finland, fish originating in the Baltic Main Basin also made a substantial contribution to catches. The threatened eastern Estonian and Russian wild stocks were recorded only in the western part of the Gulf of Finland, where the proportion of wild fish increased from 9% in 2003 to 19% in 2004.