Hatching Knowledge: A Case Study on the Hybridization of Local Ecological Knowledge and Scientific Knowledge in Small-Scale Atlantic Salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>) Cultivation in Norway

We investigate drivers of hybridization of local ecological knowledge (LEK) and scientific knowledge (SK) in small-scale Atlantic salmon (Salmo salar) fisheries in western Norway through a case study from the Ørsta River. We find three primary drivers of knowledge hybridization in local fishing groups as part of wild Atlantic salmon cultivation activities: facilitating intergenerational knowledge exchange, coping with regulatory change, and improving the perceived validity of local knowledge sets. We also identify three challenges to knowledge hybridization, and discuss how both drivers and challenges relate to once complementary SK and LEK sets that have diverged as SK has become more technical and complex. We examine the processes by which LEK and SK develop, evolve, and are used to facilitate wild salmon conservation in these fisheries and discuss the role hatcheries can play adapting and utilizing large-scale SK and salmon policy to the local environment through hybridization processes. We conclude with recommendations as to how reframing managerial views on hatcheries as facilitators of knowledge production and transfer may improve both the accessibility of SK to local communities and the integration of LEK into Norwegian wild salmon management.     

Climate and ecosystem linkages explain widespread declines in North American Atlantic salmon populations

North American Atlantic salmon (Salmo salar) populations experienced substantial declines in the early 1990s, and many populations have persisted at low abundances in recent years. Abundance and productivity declined in a coherent manner across major regions of North America, and this coherence points toward a potential shift in marine survivorship, rather than local, river‐specific factors. The major declines in Atlantic salmon populations occurred against a backdrop of physical and biological shifts in Northwest Atlantic ecosystems. Analyses of changes in climate, physical, and lower trophic level biological factors provide substantial evidence that climate conditions directly and indirectly influence the abundance and productivity of North American Atlantic salmon populations. A major decline in salmon abundance after 1990 was preceded by a series of changes across multiple levels of the ecosystem, and a subsequent population change in 1997, primarily related to salmon productivity, followed an unusually low NAO event. Pairwise correlations further demonstrate that climate and physical conditions are associated with changes in plankton communities and prey availability, which are ultimately linked to Atlantic salmon populations. Results suggest that poor trophic conditions, likely due to climate‐driven environmental factors, and warmer ocean temperatures throughout their marine habitat area are constraining the productivity and recovery of North American Atlantic salmon populations.     

Testing predictions of the critical period for survival concept using experiments with stocked Atlantic salmon

Two separate field experiments were performed in the U.S.A. and Norway with stocked Atlantic salmon Salmo salar . In the Norwegian experiment, the offspring of early‐spawning fish which had larger eggs and emerged a few days before offspring of later spawning fish had consistently higher survival rates. In the U.S.A. experiment, stream sections with higher proportions of favourable foraging locations during the critical period (the transition from dependence on maternally‐derived yolk reserves to independent feeding) had lower loss rates of fish stocked as unfed fry. These results provide support for the critical period concept (CPC) in Atlantic salmon, underscores the utility of a manipulative approach to achieve further advances in knowledge of Atlantic salmon ecology and provide additional guidance to management and restoration. A mechanistic, conceptual model for density dependence is presented to identify important knowledge gaps that remain to further evaluate the importance of the CPC for Atlantic salmon population regulation.     

Use of microsatellite data and pedigree information in the genetic management of two long-term salmon conservation programs

In this paper, we describe the utility of microsatellite data and genetic pedigree information to guide the genetic management of two long-term conservation programs for endangered populations of salmon: Snake River Sockeye Salmon, Oncorhynchus nerka, and inner Bay of Fundy Atlantic Salmon, Salmo salar. Both programs are captive broodstock (live gene banking) programs for endangered populations of salmon. In order for these programs to be successful for recovery efforts, genetic change, including accumulation of inbreeding, loss of genetic variation, and adaptation to captivity, must be minimized. We provide an overview of each program, describe broodstock selection and pairing for spawning, and discuss how pedigree data are being used to evaluate different management practices. While there are inherent species and programmatic differences, both of these programs use widely accepted genetic conservation strategies (minimize mean kinship, reduce variance in family size, minimize inbreeding in the next generation, maintain large census and effective population size) to potentially mitigate some unintended side-effects associated with the rearing of small populations in captivity. These case studies highlight the benefits and practical limitations of applying these strategies in the genetic management of salmon, and may be used to inform other conservation programs.     

Population and size-specific distribution of Atlantic salmon Salmo salar in the Baltic Sea over five decades

Population-specific assessment and management of anadromous fish at sea requires detailed information about the distribution at sea over ontogeny for each population. However, despite a long history of mixed-stock sea fisheries on Atlantic salmon, Salmo salar, migration studies showing that some salmon populations feed in different regions of the Baltic Sea and variation in dynamics occurs among populations feeding in the Baltic Sea, such information is often lacking. Also, current assessment of Baltic salmon assumes equal distribution at sea and therefore equal responses to changes in off-shore sea fisheries. Here, we test for differences in distribution at sea among and within ten Atlantic salmon Salmo salar populations originating from ten river-specific hatcheries along the Swedish Baltic Sea coast, using individual data from >125,000 tagged salmon, recaptured over five decades. We show strong population and size-specific differences in distribution at sea, varying between year classes and between individuals within year classes. This suggests that Atlantic salmon in the Baltic Sea experience great variation in environmental conditions and exploitation rates over ontogeny depending on origin and that current assessment assumptions about equal exploitation rates in the offshore fisheries and a shared environment at sea are not valid. Thus, our results provide additional arguments and necessary information for implementing population-specific management of salmon, also when targeting life stages at sea.     

Alternative mating strategies in Atlantic salmon and brown trout

By screening variable number of tandem repeat (VNTR) loci, multiple paternity within clutches has been found in wild populations of southern European Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). For Atlantic salmon, we determined the relative contribution of alternative male phenotypes to the next generation. Individual males that are morphologically juvenile yet sexually mature fertilized a large proportion of eggs, and they thereby contributed to an increase of genetic variability in wild populations via (1) balancing the sex ratio, (2) increasing outbreeding, and (3) enlarging the effective population size, in part a consequence of (1) and (2). In addition, these precocious males ensured that interspecific spawns involving Atlantic salmon females and brown trout males (a fairly common occurrence in southern Europe where the two species are sympatric) resulted mostly in Atlantic salmon progeny. For brown trout, preliminary genetic results indicated that multiple paternity, when present, was not due to alternative mating strategies by males, but rather to successive fertilizations by adult suitors.     

Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon

The extent and effect of disease interaction and pathogen exchange between wild and farmed fish populations is an ongoing debate and an area of research that is difficult to explore. The objective of this study was to investigate pathogen transmission between farmed and wild Atlantic salmon (Salmo salar L.) populations in Norway by means of molecular epidemiology. Piscine reovirus (PRV) was selected as the model organism as it is widely distributed in both farmed and wild Atlantic salmon in Norway, and because infection not necessarily will lead to mortality through development of disease. A matrix comprised of PRV protein coding sequences S1, S2 and S4 from wild, hatchery-reared and farmed Atlantic salmon in addition to one sea-trout (Salmo trutta L.) was examined. Phylogenetic analyses based on maximum likelihood and Bayesian inference indicate long distance transport of PRV and exchange of virus between populations. The results are discussed in the context of Atlantic salmon ecology and the structure of the Norwegian salmon industry. We conclude that the lack of a geographical pattern in the phylogenetic trees is caused by extensive exchange of PRV. In addition, the detailed topography of the trees indicates long distance transportation of PRV. Through its size, structure and infection status, the Atlantic salmon farming industry has the capacity to play a central role in both long distance transportation and transmission of pathogens. Despite extensive migration, wild salmon probably play a minor role as they are fewer in numbers, appear at lower densities and are less likely to be infected. An open question is the relationship between the PRV sequences found in marine fish and those originating from salmon.     

Statistical analysis on otolith data of anadromous fishes

Stable oxygen and carbon isotope (δ¹⁸O and δ¹³C) analyses of otoliths are becoming increasingly common in fisheries science and management. However, little is known about the statistical properties of isotopic data and few attempts have been made to explore appropriate statistical methods that could be used for otolith data analysis. In this paper, we present a pilot study on δ¹⁸O and δ¹³C data from otoliths of two anadromous fish species, Atlantic salmon (Salmo salar) and Pacific sockeye salmon (Oncorhynchus nerka). The results indicated that the salmon otolith data were not normally distributed, so that linear discriminant function analysis and commonly-used statistical tests such as ANOVA and the t-test may not be appropriate. Using non-parametric k-sample nearest neighbor discriminant analysis, we were able to discriminate with high accuracy among five hatcheries for Atlantic salmon and the origins of wild and hatchery sockeye salmon. Analyses also indicated that the sample sizes required to estimate δ¹⁸O and δ¹³C means based on the different sources of variability (between group or within group) and precision levels (≤ ±5.0 %) were not large. These results and conclusions not only address the statistical considerations of isotopic data from otoliths, but also have practical importance for fisheries management as well.     

Juvenile salmon in estuaries: comparisons between North American Atlantic and Pacific salmon populations

All anadromous fishes, including juvenile salmon, encounter estuarine habitats as they transition from riverine to marine environments. We compare the estuarine use between juvenile Atlantic salmon (Salmo salar) in the Penobscot River estuary and Pacific salmon (Oncorhynchus spp.) in the Columbia River estuary. Both estuaries have been degraded by anthropogenic activities. Atlantic and Pacific salmon populations in both basins rely heavily on hatchery inputs for persistence. Pacific salmon, as a group, represent a continuum of estuarine use, from species that move through rapidly to those that make extensive use of estuarine habitats. While Atlantic salmon estuarine use is predominantly similar to rapidly moving Pacific salmon, they can exhibit nearly the entire range of Pacific salmon estuarine use. Both slow and rapidly migrating Atlantic and Pacific salmon actively feed in estuarine environments, consuming insect and invertebrate prey. Interactions between juvenile salmon and estuarine fish communities are poorly understood in both estuaries, although they experience similar avian and marine mammal predators. Estuaries are clearly important for Atlantic and Pacific salmon, yet our understanding of this use is currently insufficient to make informed judgments about habitat quality or overall estuary health. This review of salmonid migration through and residency within estuaries identifies actions that could hasten restoration of both Atlantic and Pacific salmon populations.     

Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon (Salmo salar) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.     

Genetic markers in population studies of Atlantic salmon Salmo salar L.: karyotype characters and allozymes

The review, which consist of two parts, summarizes literature data on all genetic markers used in population studies of Atlantic salmon. The first part of the review concerns karyotype features and allozyme markers of Salmo salar. The latter are effectively used for distinguishing populations and subpopulations of Atlantic salmon, as well as for genetic monitoring of its populations. It is shown that the distribution of alleles of some allozymes may be related to selection for resistance to certain environmental conditions.     

Cytogenetic studies of Atlantic salmon, Salmo salar L., in Scotland

Chromosome numbers for Atlantic salmon, Salmo salar L., from ten populations in Scotland were ascertained. The majority of fish had 2n = 58, NF = 74 karyotypes, and no polymorphisms between populations were found. The findings suggest that Atlantic salmon in Scotland are cytogenetically homogeneous.     

Genetic markers in population studies of Atlantic salmon Salmo salar L.: Karyotype characters and allozymes

The review, which consist of two parts, summarizes literature data on all genetic markers used in population studies of Atlantic salmon. The first part of the review concerns karyotype features and allozyme markers of Salmo salar. The latter are effectively used for distinguishing populations and subpopulations of Atlantic salmon, as well as for genetic monitoring of its populations. It is shown that the distribution of alleles of some allozymes may be related to selection for resistance to certain environmental conditions.     

Otolith shape discriminates between juvenile Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L.

Otoliths of Atlantic salmon, Salmo salar L., are more slender than the otoliths of brown trout, Salmo trutta L. Discriminant analysis on otolith measurements of juvenile Atlantic salmon and brown trout from four river systems revealed a discriminant function which distinguished more than 94% of the cases. This function was tested by using data from a fifth river with cohabiting Atlantic salmon and brown trout: all Atlantic salmon and 91 % of the brown trout were correctly classified.     

A review of genetic variation in Atlantic salmon, Salmo salar L., and its importance for stock identification, enhancement programmes and aquaculture

The increasing exploitation of Atlantic salmon as a food source and sport fish demands a better understanding of salmon genetics and the dynamics of Atlantic salmon populations. Surveys of salmon populations for protein electrophoretic variation reveal that the average heterozygosity in Salmo salar is low and that four gene loci account for more than 95% of the total electrophoretically detectable variation. Populations that have been studied by this means fall into one of three groups: Western Atlantic, Eastern Atlantic or Baltic. However, biochemical genetics involving starch gel electrophoresis cannot be used routinely to identify the continent of origin of an Atlantic salmon, let alone its native river. The mitochondrial genome can be used to identify North American or European salmon with the aid of restriction endonucleases that have six base pair recognition sites. Restriction endonucleases that recognize four base pairs appear to be able to identify salmon from a particular river system. There has been a move from protein variation to mitochondrial DNA variation and this will inevitably lead to more extensive studies on the nuclear genome. Chromosomal studies suggest differences between salmon from Europe and North America but these have been hampered by lack of good banding procedures. Preliminary studies using cloned segments of salmonid genomes suggest that repeated sequences such as the genes for ribosomal RNA will be most useful for identifying specific stocks of Atlantic salmon. The need for continued genetic studies on the Atlantic salmon and the relevance and importance of the results of this research for stock identification, enhancement programmes, aquaculture and basic science are discussed.     

Use of population viability analysis models for Atlantic and Pacific salmon recovery planning

Uncertainty and risk abound in making natural resource management decisions. Population viability analysis (PVA) includes a variety of qualitative or quantitative analyses to predict the future status of a population or collection of populations and to predict the risk of extinction (or quasi-extinction) over time given some assumptions of the factors driving population dynamics. In this paper, we review the various PVA models applied to Atlantic and Pacific salmon for determination of listing under the Endangered Species Act and in planning recovery actions. We also review the numerous cautions involved in developing PVA models and in interpreting their results. There have been a larger number of PVA models applied to Pacific salmon compared to Atlantic salmon due to the greater geographic range and number of species of Pacific salmon. Models for both Atlantic and Pacific salmon have ranged from simple models that view populations as simply a number of organisms to complex age- or stage-structured models depending on the purpose of the model and available data for model parameterization. The real value of PVA models to salmon conservation is not in making absolute predictions of the risk of extinction, but rather in evaluating relative effects of management alternatives on extinction risk and informing decision making within an adaptive management framework. As computing power, quantitative techniques, and knowledge of mechanistic linkages between terrestrial, freshwater, and marine environments advance, PVA models will become an even more powerful tool in conservation planning for salmon species.     

Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

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.     

The effect of migratory behaviour on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon Salmo salar

The genetic diversity of anadromous and freshwater Atlantic salmon ( Salmo salar ) populations from north-west Russia and other north European locations was compared using microsatellite variation to evaluate the importance of anadromous migration, population size and population glacial history in determining population genetic diversity and divergence. In anadromous Atlantic salmon populations, the level of genetic diversity was significantly higher and the level of population divergence was significantly lower than among the freshwater Atlantic salmon populations, even after correcting for differences in stock size. The phylogeographic origin of the populations also had a significant effect on the genetic diversity characteristics of populations: anadromous populations from the basins of the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than anadromous populations from the Baltic Sea basin. Among the freshwater populations, the result was the opposite: the Baltic freshwater populations were more variable. The results of this study imply that differences in the level of long-term gene flow between freshwater populations and anadromous populations have led to different levels of genetic diversity, which was also evidenced by the hierarchical analysis of molecular variance. Furthermore, the results emphasize the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash. Hence, high conservation status is warranted in order to ensure the long-term survival of the limited number of European populations with this life-history strategy.     

Effects of species, culture history, size and residency on relative competitive ability of salmonids

The relative competitive ability of juvenile farm and wild salmonids was investigated to provide insight into the potential effects of introduction of cultured salmon on wild Pacific salmonid ( Oncorhynchus ) species. Aquarium experiments involving equal contests ( i.e. size matched, simultaneously introduced individuals) indicated that two wild coho salmon Oncorhynchus kisutch populations were competitively equal to a farm coho salmon population. In equal contests between farm Atlantic salmon Salmo salar (Mowi strain) and these wild coho salmon populations or coastal cutthroat trout Oncorhynchus clarki clarki , Atlantic salmon were subordinate in all cases. When Atlantic salmon were given a residence advantage, however, they were competitively equal to both wild coho salmon populations, but remained subordinate to coastal cutthroat trout. When Atlantic salmon were given a 10–30% length advantage, they were competitively equal to one wild coho salmon population but remained subordinate to the other. In equal contests in semi-natural stream channels, both wild coho and farm Atlantic salmon grew significantly more in the presence of the other species than when alone. It appears that coho salmon obtain additional food ration by out competing Atlantic salmon, whereas Atlantic salmon were stimulated to feed more in the presence of coho salmon competitors. These results suggest that wild coho salmon and cutthroat trout should out compete farm Atlantic salmon of a similar size in nature. As the relative competitive ability of Atlantic salmon improves when they have a size and residence advantage, should feral populations become established, they may exist on a more equal competitive footing owing to the long freshwater residence of Atlantic salmon.