Transcriptome analyses of amoebic gill disease-affected atlantic salmon (Salmo salar) tissues reveal localized host gene suppression

The transcriptome response of Atlantic salmon (Salmo salar) displaying advanced stages of amoebic gill disease (AGD) was investigated. Naïve smolt were challenged with AGD for 19 days, at which time all fish were euthanized and their severity of infection quantified through histopathological scoring. Gene expression profiles were compared between heavily infected and naïve individuals using a 17 K Atlantic salmon cDNA microarray with real-time quantitative RT-PCR (qPCR) verification. Expression profiles were examined in the gill, anterior kidney, and liver. Twenty-seven transcripts were significantly differentially expressed within the gill; 20 of these transcripts were down-regulated in the AGD-affected individuals compared with naïve individuals. In contrast, only nine transcripts were significantly differentially expressed within the anterior kidney and five within the liver. Again the majority of these transcripts were down-regulated within the diseased individuals. A down-regulation of transcripts involved in apoptosis (procathepsin L, cathepsin H precursor, and cystatin B) was observed in AGD-affected Atlantic salmon. Four transcripts encoding genes with antioxidant properties also were down-regulated in AGD-affected gill tissue according to qPCR analysis. The most up-regulated transcript within the gill was an unknown expressed sequence tag (EST) whose expression was 218-fold (± SE 66) higher within the AGD affected gill tissue. Our results suggest that Atlantic salmon experiencing advanced stages of AGD demonstrate general down-regulation of gene expression, which is most pronounced within the gill. We propose that this general gene suppression is parasite-mediated, thus allowing the parasite to withstand or ameliorate the host response. © 2008 Springer Science+Business Media, LLC.

Genetic diversity of Atlantic salmon (Salmo salar) and European whitefish (Coregonus lavaretus) in the Baltic Sea

We described the patterns and extent of microsatellite DNA variation in historical and present-day Atlantic salmon (Salmo salar L.) stocks in the Baltic Sea and neighbouring areas, and in European whitefish (Coregonus lavaretus) ecotypes, populations and run-timing types in Finland. Moreover, the amount and pattern of genetic diversity in historical salmon populations before human impact were described, and the proportion of diversity maintained in the present hatchery stocks evaluated. Salmon populations in the Baltic Sea were, on average, significantly less variable than eastern Atlantic populations, and the diversity of landlocked populations (Lakes Vänern, Saimaa, Onega and Ladoga) was in turn significantly lower than that of anadromous salmon populations in the Baltic Sea populations. Within the Baltic Sea, the anadromous populations of Atlantic salmon formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin) and southern (western Baltic Main Basin) regions. Based on microsatellite data, three salmon population groups in the Baltic Sea were considered potentially different colonization lineages. In short- and long-term breeding programmes of Atlantic salmon, the average observed rate of loss of alleles was 4.9% and 2.0% per generation and the average rate of loss of heterozygosity was 1.4% and 1% per generation, respectively. When comparing the genetic parameters of stocks before and after hatchery breeding of several successive generations (Rivers Iijoki and Oulujoki), statistically significant changes in allele frequencies were common, while large wild stock in the Teno River has remained temporally very stable over 56 years. Despite the observed losses of genetic diversity in broodstock breeding, a large proportion of the genetic resources of the extirpated stocks are still conserved in the broodstocks. Genetic differentiation among European whitefish ecotypes was generally low, thus giving support to the hypothesis of one native European whitefish species in Fennoscandia. Among the ecotypes, the northern, large sparsely rakered, bottom-dwelling whitefish was the most unique. The known genetic differences in quantitative traits have thus either developed independently of potential phylogenetic lineages, or the lineages have mixed and the quantitative traits of the ecotypes, like gill-raker number, have later changed according to environment and selection pressures. Overall, genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Wild whitefish populations studied had slightly higher allelic diversity than hatchery-reared populations in corresponding rivers.

Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Optimal management of conflicting species: Grey seal (Halichoerus grypus) and Atlantic salmon (Salmo salar) in the Baltic Sea

The objective of this thesis is to examine the economic effects in the conflict between grey seal population and the salmon fishery in the Baltic Sea. We will formulate a bioeconomic model which provides new insights on the optimal management of Atlantic salmon with respect to the effects brought about by the grey seal population. As the catch losses caused by seals have an effect on salmon fishery in Baltic, we will study how seal population affects the present value of the salmon fishery. The study considers the Finnish coastal trap net fishery. The bioeconomic model considers a scenario of sole salmon fishery and a scenario of salmon fishery affected by the grey seal population. On the basis of these scenarios, a seal compensation scheme is introduced. We can observe a significant economic seal-induced effect on the salmon fishery. The results suggest that the present seal compensation scheme emploid by the Finnish government is suboptimal. This thesis is part of the TARMO –project, in which the conflict between grey seal population and salmon fishery is studied using the methods of environmental economics.

Lagerversuch von frischem bzw. tief gefrorenen gelagerten kalt geräuchertem Atlantischem Lachs (Salmo salar) in 200-g-Fertigpackungen mit sensorischer Beurteilung in Abhängigkeit von der Lagerzeit

After 4 months frozen storage at –18 °C cold smoked Atlantic salmon in consumer packages can hardly be differentiated from the freshly smoked product by sensory assessment by an expert panel and cannot be differentiated by consumers.

Das M74-Syndrom des Ostseelachses (Salmo salar): Symptome, Verbreitung und Ursachen

An overview is presented on the M74-Syndrome of Baltic salmon which is known since 1974 and which, since 1992, has caused considerable losses of artificially produced yolk-sac larvae in Swedish and Finnish hatcheries responsible for compensatory salmon stocking programmes. The syndrome only affects offspring of wild salmon ascending the rivers for spawning and not offspring derived from salmon broodstocks permanently kept in hatcheries. The syndrome seems to be restricted to the Baltic Sea where it has been recorded in all of the remaining Swedish (except the west coast) and Finnish salmon rivers as well as in populations of Estonian rivers and the Russian River Neva. In Sweden and in Finland, the syndrome has been recorded in recent years in offspring of up to 80 % of female salmon used for spawning and resulted in a larval mortality of up to 90 %. A nutrition-associated thiamine (vitamin B1) deficiency is considered as primary cause. However, other environmental factors seem to be involved in addition. There is concern that the syndrome constitutes a major threat with respect to the survival of the few still naturally reproducing populations of Baltic salmon.

Regulation of the fitness of Atlantic salmon (Salmo salar) by intra-specific competition amongst the juveniles

Factors affecting the fitness of juvenile salmon are discussed. Although fitness from the genetic point of view is defined as the relative capacity of carriers of a given genotype to transmit their genes to the gene pool of the following generations, growth and survival of individuals are also components of fitness, and are influenced by responses to competition, which is the major topic of this article including implications for management. In order to better understand the relationships of density-dependent survival in Newfoundland, egg depositions were manipulated experimentally in the Freshwater River. Figures demonstrate the relationship between stock (number of eggs per 100 m2 of river) and recruitment (number of smolts per l00 m2 of Atlantic salmon, and also the percentage survival from egg to smolt stage related to potential egg depositions.

Review of NRA tracking projects on salmon, Salmo salar L., and sea trout, Salmo trutta L

The report briefly outlines the programme of the National Rivers Authority (NRA), placing the Fisheries programme in the context of the work of the NRA as a whole, and viewing the tracking work against the broader requirements of the NRA Fisheries research programme. All regions of England and Wales are considered. Two techniques currently exist for studying the detailed timing and extent of movements of adult salmon: tracking of individually identifiable fish, and counting the numbers of fish moving past a fixed point in the river. The development of tracking techniques and the integrated use of tracking and fish counters is briefly reviewed in Section 3. Further details of these techniques are given in Appendices. Section 4 summarises and assesses completed and current NRA tracking studies. Section 5 discusses the scientific content of these studies in relation to similar work carried out elsewhere in the UK. The NRA programme of tracking studies is evaluated in Section 6. Section 7 discusses future fisheries projects and Section 8 details the future development of tracking techniques. Finally, recommendations arising out of this review are summarised in Section 9.

An evaluation of the survival of Atlantic salmon (Salmo salar L.)fry stocked in eight streams in the North West of England.

Eight streams from the North West of England were stocked with Atlantic salmon (Salmo salar L.) fed fry at densities ranging from 1 to 4/m2 over a period of up to three years to evaluate survival to the end of the first an d second growing periods and hence assess the value of stocking as a management practice. Survival to the end of the first growin g period (mean duration of 108 days) was found to vary between 7.8 and 41.3% with a mean of 22% and CV of 0.44. Survival from the end of the first growing period to the end of the second growing period (mean duration of 384 days) ranged from 19.9 to 34.1% with a mean of 26.3% and CV of 0.21. Survival was found to be positively related to 0+ trout density (P < 0.05) and negatively related to altitude (P < 0.05). A comparison of the raw survival data (non standardised with respect to duration of experiments) with that from other studies in relation to stocking densities revealed a negative relationship between fry survival and stocking density (P < 0.05). Densities in excess of 5/m2 tended to result in lower levels of survival. Post stocking fry dispersal patterns were examined for the 1991 data. On average 86.7% of the number of fry surviving remained within the stocked zone by the end of the first growing period. With the exception of one stream there was little in the way of dispersal beyond the stocked zone. The dispersal pattern approximated to the normal distribution (P < 0.05). It was estimated that stocking can result in a net gain of fish to a river system compared with natural productivity, however the numerical significance of this gain and its cost effectiveness need to be determined on a river specific basis.

Use of biological reference points for the conservation of atlantic salmon (Salmo salar L.)in the River Lune, North West England.

This paper deals with the development and use of biological reference points for salmon conservation on the River Lune, England. The Lune supports recreational and net fisheries with annual catches in the region of 1,000 and 1356 salmon respectively. Using models transported from other river systems, biological reference points exclusive to the Lune were developed; specifically the number of eggs deposited and carrying capacity estimates for age 0+ and 1+ parr. The conservation limit was estimated at 11.9 million eggs and between 1989 and 1998 was exceeded in two years. Comparison of juvenile salmon densities in 1991 and 1997 with estimates of carrying capacity indicated that 0+ and 1+ parr densities were at around 60 % of carrying capacity and may relate to the number of eggs deposited in 1990 and 1996 being approximately 70% of the target value. The paper discusses the management actions taken in order to ensure that the management target of the conservation limit being met four years out of five is delivered. It also discusses the balance between conservation and exploitation and the socio-economic decisions made in order to ensure parity of impacts on the rod and net fisheries. The regulations have been enforced since 1999 and the paper concludes with an assessment of the actions taken to deliver the management targets, over the last five years.

Use of telemetric tracking to examine environmental influences on catch/effort indices. A case study of Atlantic Salmon (Salmo salar L.)in the R. Tywi, S. Wales

A case study of Atlantic Salmon runs into the R. Tyvi (S. Wales) is presented. Radio tracking of over 200 salmon in 1988 and 1989 has demonstrated that flow is an important factor in modifying both run timing and migratory success. Entry of salmon into the river is typically in response to flow events, and periods of low falling flows delay entry and may directly result in reduced runs into the river. Delayed entry may also increase the proportion of the run migrating after the end of both rod and net fishing seasons. The implications of these results for net and rod catch and catch/effort data are discussed, using both statutory reported catch data and data from specific catch/effort studies. Flow is demonstrated to be a dominant factor in determining the within-season distribution of rod catch and catch/effort during low-flow years. Estuarial seine net catch and catch/effort tend to be controlled more by time of return than by flow although low flows may delay runs. Annual reported rod catch is correlated with flow, which controls in season availability, catchability and consequently the amount of fishing effort. Use of catch or catch/effort data should take account of inter-year variations in flow and other environmental factors. Although catch and catch/effort are valuable indicators of fishery performance, they are inadequate to represent changing stock levels.

Evaluation of bioelectrical impedance analysis and Fulton’s condition factor as nonlethal techniques for estimating short-term responses in postsmolt Atlantic salmon (Salmo salar) to food availabili

We evaluated measures of bioelectrical impedance analysis (BIA) and Fulton’s condition factor (K) as potential nonlethal indices for detecting short-term changes in nutritional condition of postsmolt Atlantic salmon (Salmo salar). Fish reared in the laboratory for 27 days were fed, fasted, or fasted and then refed. Growth rates and proximate body composition (protein, fat, water) were measured in each fish to evaluate nutritional status and condition. Growth rates of fish responded rapidly to the absence or reintroduction of food, whereas body composition (% wet weight) remained relatively stable owing to isometric growth in fed fish and little loss of body constituents in fasted fish, resulting in nonsignificant differences in body composition among feeding treatments. The utility of BIA and Fulton’s K as condition indices requires differences in body composition. In our study, BIA measures were not significantly different among the three feeding treatments, and only on the final day of sampling was K of fasted vs. fed fish significantly different. BIA measures were correlated with body composition content; however, wet weight was a better predictor of body composition on both a content and concentration (% wet weight) basis. Because fish were growing isometrically, neither BIA nor K was well correlated with growth rate. For immature fish, where growth rate, rather than energy reserves, is a more important indicator of fish condition, a nonlethal index that reflects shortterm changes in growth rate or the potential for growth would be more suitable as a condition index than either BIA measures or Fulton�

Diurnal and nocturnal temperatures for Atlantic salmon postsmolts (Salmo salar L.) during their early marine life

Data storage tags (DSTs) were applied to Atlantic salmon (Salmo salar L.) smolts during their seaward migration in the spring of 2002 at a fish counting fence on Campbellton River, Newfoundland. Our objectives were to discover whether or not salmon smolts could carry DSTs and survive, whether or not useful data on thermal habitat could be obtained and interpreted, and whether or not salmon smolts moved vertically in the water column. Data were downloaded from 15 of the recovered tags and revealed the hourly water temperatures experienced by the fish for periods of 3 to 71 days. The data on the DSTs were analyzed for temperature patterns in relation to migration behavior and diurnal movement of the fish. While in the sea, the DSTs recorded night temperatures of 12.5°C, which were higher than day temperatures of 11.6°C; the record from moored recorders, however, indicated that sea temperatures actually declined at night. It is hypothesized that posts-molts avoid avian predators during daylight hours by positioning themselves deeper in the water column and that they were pursuing prey during the deeper vertical descents or ascents noted during the periods of more rapid changes in temperature.