Sixty-four samples from 46 salmon populations totalling 2369 specimens were used for polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial ND1 region. The final analyses included 3095 specimens from 60 populations in Northern Europe. A subsample was analysed by RFLP of ND3/4/5/6. Representative RFLP haplotypes from different parts of the distribution area were sequenced and the phylogeny of European haplotypes and their relations to the North American lineage was described. The four common European haplotypes derive from the ancestral ND1-BBBA (rooting the European clade to the North American) by one-step substitutions: AAAA < AABA < BBBA > BBBB. The Swedish west-coast populations differ from the geographically close southern Baltic, indicating absence of inward and limited outward gene flow through the Danish straits during the last 8000 years. Within the Baltic Sea, only three ND1 haplotypes were detected and there was no variation for ND3/4/5/6. In the whole southern Baltic and in lakes Vänern, Ladoga and Onega the haplotype AABA dominated. Proposed postglacial colonization routes to the Baltic Sea are discussed in relation to the haplotype distribution pattern.

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.

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

Genetic homogenization has been recognized as a serious threat in an increasing number of species, including many salmonid fishes. We assessed the rate and impact of immigration from the main hatchery stocks of Atlantic salmon in the Gulf of Bothnia into one of the largest wild salmon populations in the Baltic Sea, the River Vindelä lven, within a temporal framework of 18 years (from 1985-2003). We provide genetic evidence based on mtDNA and microsatellite markers, using mixed-stock analysis, that a large proportion (66%) of fin-damaged spawners (n ¼ 181) caught in the Ume/ Vindelä lven during 1997-2003 originated from the hatcheries in the Rivers Å ngermanä lven, Luleä lven and Ljusnan. The maximum-likelihood estimate of immigration rate from these hatcheries into the wild Vindelä lven population was 0.068 (95% CI 0.021-0.128) over the studied time period (1985)(1986)(1987)(1988)(1989)(1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003) and reached up to a quarter (m ¼ 0.249, 95% CI 0.106-0.419) of the total population during 1993-2000. This resulted in significant (Po0.01) genetic homogenization trend between the wild Vindelä lven population and hatchery stocks of the Å ngermanä lven and Luleä lven. Our results demonstrate extensive straying from geographically distant hatchery releases into wild salmon population and emphasize the genetic risks associated with current large-scale stocking practices in the Baltic Sea. Heredity (2005) 95, 76-83.

BackgroundFor decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms.ResultsHere we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (Salmo salar) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment.ConclusionsThe INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.