A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.) (original) (raw)
Related papers
BMC Genetics, 2010
Background Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. Results To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. Conclusions This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.
Molecular Ecology, 2001
Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5 -37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available.
Microsatellite Variation in Populations of Atlantic Salmon from North Europe
Environmental Biology of Fishes, 2000
Our aim was to investigate the level of genetic differentiation in northern European populations of Atlantic salmon, to establish the genetic relationship among major salmon populations in Russia and North Norway, and to compare these to populations from the western Atlantic lineage. Samples were collected along an east-west axis, from Pechora River in Russia to Restigouche River in Quebec, Canada. A total of 439 individual salmon were collected from seven rivers (sample sizes from 50 to 84 individuals). The samples were analysed for variation at four microsatellite loci; Ssa13.37, Ssa14, Ssa171 and Ssa171. Significant differences were found between most of the European populations, and the populations from the Tana and Pechora Rivers were most distinct. The samples from the Rivers Mezenskaya Pizhma and Emtsa in Arkhangelsk oblast in Russia were not significantly different from each other in an exact test of population differences. All other river pairs were significantly different. These results confirmed the deep genetic divergence between American and European salmon populations demonstrated in earlier studies, with alleles specific to continent found in three of the microsatellites.
Freshwater Biology, 2009
1. An important goal of conservation biology is to preserve the evolutionary potential of a species by maintaining natural levels of genetic diversity. Here, we assess the population differentiation in the Atlantic salmon, Salmo salar, listed in Annex II of the European Habitats Directive, to provide valuable information for its conservation in Normandy (France).2. Samples collected from 10 natural sites revealed that 13 of 14 microsatellite loci were polymorphic. Significant differentiation among populations was detected (FST = 0.054, P < 0.001), and all FST pairwise comparisons except one were significant. A genetic split was observed between populations inhabiting streams with limestone geology compared to those inhabiting streams with siliceous geology, which could reflect adaptative differences.3. Hatchery stocks used for the restocking of two rivers were genetically distinct from native stocks.4. Analysis of three stream habitats restored in 1995 showed that all were recolonized naturally by wild salmon from geographically close populations and no founder effects were detected. Allelic richness was similar between recolonized and wild populations.5. From a management perspective, our study revealed that restoration of habitat is very effective to recreate new populations in rivers from which salmon have disappeared and that natural recolonization can be fast and effective in terms of genetic diversity.
Rivers in Asturias (northern Spain) constitute the southern limit of the distribution of Atlantic salmon (Salmo salar L.) in Europe, a biological resource facing one of the more serious challenges for conservation today. In this work, eight microsatellite loci have been used to analyse samples collected in 1993 and 1999 from four Asturian rivers (Esva, Narcea, Sella, and Cares), obtaining information about the temporal and the spatial genetic variation in these populations and, in addition, estimations of their effective population sizes. The temporal analysis revealed a general decrease in all the estimated genetic variability parameters when samples from 1993 (mean A(1993) = 6.47, mean HO(1993) = 0.472, mean HE(1993) = 0.530) were compared with those obtained in 1999 (mean A(1999) = 6.16, mean HO(1999) = 0.460, mean HE(1999) = 0.490). This reduction was particularly notable for the case of the Esva river. Our results pointed to a pattern of spatial genetic differentiation inside the Asturian region (FST (1993) = 0.016 P\0.01; FST (1999) = 0.023 P\0.01). Using the standard Temporal Method we found estimates of Ne ^ (Esva) = 75.1 (33.2–267.2); Ne ^ (Cares) = 96.6 (40.0–507.5), Ne ^ (Sella) = 106.5 (39.1–9396.4) and Ne ^ (Narcea) = 113.9 (42.0–3693.3). The use of likelihood-based methods for the Ne ^ estimations improved the results (smaller CIs) for the Esva and Cares rivers (Ne ^ (Esva) = 63.9 (32.3–165.3); Ne ^ (Cares) = 76.4 (38.8–202.0) using a Maximum likelihood approach) and suggested the presence of larger populations for the Sella and Narcea rivers (Ne ^&200). These results showed that the Asturian Atlantic salmon populations (in particular Esva and Cares river populations) could be close to the conservation genetic borderline for avoiding inbreeding depression although we discuss some implications of the analysis of temporal genetic change in populations with overlapping generations.
Genetica, 2011
Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.
Microsatellite genotyping is a common DNAcharacterization technique in population, ecological andevolutionary genetics research. Since different alleles aresized relative to internal size-standards, different laboratoriesmust calibrate and standardize allelic designationswhen exchanging data. This interchange of microsatellitedata can often prove problematic. Here, 16 microsatelliteloci were calibrated and standardized for the Atlantic salmon,Salmo salar, across 12 laboratories. Althoughinconsistencies were observed, particularly due to differencesbetween migration of DNA fragments and actualallelic size ('size shifts'), inter-laboratory calibration wassuccessful. Standardization also allowed an assessment ofthe degree and partitioning of genotyping error. Notably,the global allelic error rate was reduced from 0.05 ± 0.01prior to calibration to 0.01 ± 0.002 post-calibration. Mosterrors were found to occur during analysis (i.e. when sizecallingalleles; the mean proportion of all errors that wereanalytical errors across loci was 0.58 after calibration). Noevidence was found of an association between the degreeof error and allelic size range of a locus, number of alleles,nor repeat type, nor was there evidence that genotypingerrors were more prevalent when a laboratory analyzedsamples outside of the usual geographic area theyencounter. The microsatellite calibration between laboratoriespresented here will be especially important forgenetic assignment of marine-caught Atlantic salmon,
Molecular Ecology Notes, 2005
Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise F ST , 0.12, was highly significant. These findings are consistent with patterns of continental-level differentiation observed previously using an alternate suite of microsatellite loci. Locus-by-locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure.
Canadian Journal of Fisheries and Aquatic Sciences, 1995
Atlantic salmon populations show Bow levels of genetic differentiation relative to other salmonid species, when surveyed by allozymes, and with mitochondrial DNA and nuclear ribosomal DNA markers. Here we report the application of three novel microsatellite VNTR loci to population differentiation in Atlantic salmon. A total of 232 microsatellites, cloned from Atlantic salmon, were classified as perfect. imperfect, and compound repeats. Microsatellite length, as in other teleosts, was significantly larger than published mammalian microsatellites. Primers for PCW amplification of three salmon microsatellites were designed. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for five populations from Nova Scotia, Canada, and from Europe. Nei's genetic distances of 0.02-0.9 were observed among populations. There was a clear discrimination between Canadian and European fish based on unique alleles present at two loci. These Atlantic salmon primers also amplify presumably homologous loci in nine other salmonid species. The polymorphic microsatellites loci reported here demonstrate great potential as genetic markers in population, breeding, and evolutionary studies.