Prevalence and genotypes of infectious salmon anaemia virus (ISAV) in returning wild Atlantic salmon (Salmo salar L.) in northern Norway

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Atlantic salmon and sea trout display synchronised smolt migration relative to linked environmental cues

Anadromous salmon and sea trout smolts face challenging migrations from freshwater to the marine environment characterised by high mortality. Therefore, the timing of smolt migration is likely to be critical for survival. Time-series comparing migration of Atlantic salmon and sea trout smolts in the same river, and their response to the same environmental cues, are scarce. Here, we analysed migration timing of ~41 000 Atlantic salmon and sea trout smolts over a 19-year period from the river Guddalselva, western Norway. Trout displayed a longer migration window in earlier years, which decreased over time to become more similar to the salmon migration window. On average, salmon migrated out of the river earlier than trout. Migration of both species was significantly influenced by river water temperature and water discharge, but their relative influence varied across the years. On average, body-length of smolts of both species overlapped, however, size differences were observed within the migration period and among the years. We conclude that salmon and trout smolts in this river are highly synchronised and migrate in response to the same range of linked environmental cues.publishedVersio

Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs

Background Many native Atlantic salmon populations have been invaded by domesticated escapees for three decades or longer. However, thus far, the cumulative level of gene-flow that has occurred from farmed to wild salmon has not been reported for any native Atlantic salmon population. The aim of the present study was to investigate temporal genetic stability in native populations, and, quantify gene-flow from farmed salmon that caused genetic changes where they were observed. This was achieved by genotyping historical and contemporary samples from 20 populations covering all of Norway with recently identified single nucleotide polymorphism markers that are collectively diagnostic for farmed and wild salmon. These analyses were combined with analysis of farmed salmon and implementation of Approximate Bayesian computation based simulations. Results Five of the populations displayed statistically significant temporal genetic changes. All five of these populations became more similar to a pool of farmed fish with time, strongly suggesting introgression of farmed fish as the primary cause. The remaining 15 populations displayed weak or non-significant temporal genetic changes. Estimated introgression of farmed fish ranged from 2-47% per population using approximate Bayesian computation. Thus, some populations exhibited high degrees of farmed salmon introgression while others were more or less unaffected. The observed frequency of escapees in each population was moderately correlated with estimated introgression per population R2 = 0.47 P < 0.001. Genetic isolation by distance existed within the historical and contemporary data sets, however, the among-population level of divergence decreased with time. Conclusions This is the first study to quantify cumulative introgression of farmed salmon in any native Atlantic salmon population. The estimations demonstrate that the level of introgression has been population-specific, and that the level of introgression is not solely predicted by the frequency of escapees observed in the population. However, some populations have been strongly admixed with farmed salmon, and these data provide policy makers with unique information to address this situation

Diet analysis of Atlantic salmon (Salmo salar) post-smolts after the ecological regime shift in the Northeast Atlantic

Transition from freshwater to saltwater presents multiple challenges for anadromous Atlantic salmon, and survival during this critical life-stage is thought to influence adult population abundance. Despite this, the role of feeding, which influences growth and therefore survival, is poorly studied. Here, we analyzed the diet of 580 post-smolts captured in four Norwegian fjords in 2018 and 2019. Post-smolt diet mainly consisted of fish larvae (Teleostei), krill (Euphasiidae), planktonic amphipods, and insects. However, diet varied among fjords and years. For example, post-smolts in Altafjord in northern Norway displayed a higher frequency of fish larvae in their diet compared to post-smolts from fjords in western Norway, although this effect was less clear in 2019 than in 2018. Post-smolts consuming fish larvae and/or krill displayed substantially higher feeding ratios, and these fish were on average 0.52 cm longer. This observation underpins results from earlier studies suggesting that consumption of fish larvae is important for marine growth and ultimately survival. The dietary observations reported here may therefore have implications for spatial and temporal patterns in Atlantic salmon marine survival rates in this region. Furthermore, we did not detect any clear differences in diet between post-smolts analyzed here in comparison with post-smolts collected in the same region approximately 20 years earlier. As there has been a well-documented ecological regime shift in the Northeast Atlantic between the present and earlier studies, we conclude that it has not had a large impact on post-smolt feeding conditions within Norwegian fjords. Diet Fish larvae Coastal ecosystem Migration EstuarypublishedVersio

Impacts of a Changing Ecosystem on the Feeding and Feeding Conditions for Atlantic Salmon During the First Months at Sea

During the last decades, many wild Atlantic salmon populations have declined dramatically. One hypothesis for an observed reduction in salmon marine growth and survival is reduced abundance of prey. However, the effect of spatial and temporal variation in marine prey abundance on post-smolt feeding conditions is poorly understood. Here we use stomach content data from 2572 salmon postsmolts sampled during 25 years in the Northeast Atlantic Ocean to examine spatial and temporal changes in diet and stomach fullness. Sandeel larvae west of Scotland and Ireland and in the northern North Sea, herring larvae in the eastern part of the Norwegian Sea, and amphipods in the western part of the Norwegian Sea were particularly important prey species. There was a reduction of fish larvae in the postsmolt stomachs over a large geographic area when comparing the period 1995–2004 to 2008–2019. This may be result of a bottom-up driven process, as increasing extent of Arctic Water masses and zooplankton abundance were positively correlated with postsmolt stomach fullness in the Norwegian Sea. Furthermore, the interspecific competition for fish larvae between post-smolts and mackerel may have increased with a larger mackerel stock expanding the feeding migrations northwards since 2007. Norwegian Sea, fish larvae, zooplankton, mackerel, oceanography, dietpublishedVersio

Distribution and prevalence of the myxozoan parasite Tetracapsuloides bryosalmonae in northernmost Europe: analysis of three salmonid species

Global climate change is altering the abundance and spread of many aquatic parasites and pathogens. Proliferative kidney disease (PKD) of salmonids caused by the myxozoan Tetracapsuloides bryosalmonae is one such emerging disorder, and its impact is expected to increase with rising water temperature. Yet, the distribution and prevalence of T. bryosalmonae in Northern Europe remain poorly characterized. Here, we studied 43 locations in 27 rivers in northernmost Norway and Finland to describe T. bryosalmonae infection frequency and patterns in 1389 juvenile salmonids. T. bryosalmonae was discovered in 12 out of 27 rivers (44%) and prevalence ranged from 4.2 to 55.5% in Atlantic salmon and from 5.8 to 75% in brown trout among infected rivers. In sympatric populations, brown trout was more frequently infected with T. bryosalmonae than was salmon. Age-specific parasite prevalence patterns revealed that in contrast to lower latitudes, the infection of juvenile fish predominantly occurs during the second summer or later. Temperature monitoring over 2 yr indicated that the mean water temperature in June was 2.1 to 3.2°C higher in rivers containing T. bryosalmonae compared to parasite-free rivers, confirming the important role of temperature in parasite occurrence. Temporal comparison in T. bryosalmonae prevalence over a 10 yr period in 11 rivers did not reveal any signs of contemporary parasite spread to previously uninfected rivers. However, the wide distribution of T. bryosalmonae in rivers flowing to the Barents Sea indicates that climate change and heat waves may cause new disease outbreaks in northern regions.publishedVersio

Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)

Background: New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results: In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions: Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traitsEuropean Union, Kolarctic ENPI CBC project, Academy of Finland, Norwegian Directorate of Nature Management, Norwegian Research Council, Estonian Science Foundatio

Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations

Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlantic salmon produced in Norwegian aquaculture in the period 2007–2014. In contrast, the frequency of triploidy in wild salmon populations has not been studied thus far, and in wild populations of other organisms, it has been very rarely studied. In population genetic data sets, individuals that potentially display chromosome abnormalities, such as triploids with three alleles, are typically excluded on the premise that they may reflect polluted or otherwise compromised samples. Here, we critically re-investigated the microsatellite genetic profile of ~ 6000 wild Atlantic salmon sampled from 80 rivers in Norway and Russia, to investigate the frequency of triploid individuals in wild salmon populations for the first time.publishedVersio

Genetiske analyser av aure i Gloppenelva

I Gloppenelva ble det åpnet en laksetrapp i Eidsfossen i 1972, men trappen ble stengt i 2014 etter store skader under en flomhendelse, og det er ikke avklart om trappen skal restaureres. Inntil 1972 var Eidsfossen vandringshinder for anadrom fisk i Gloppenvassdraget. Det er ikke kjent om sjøaure vandret opp trappen og reproduserte oppstrøms i perioden 1971 til 2014, og det er ikke gjennomført kultivering med sjøaure oppstrøms Eidsfossen eller flyttet sjøaure forbi fossen. For å avklare om sjøaure har vandret opp og satt genetiske avtrykk i aurebestandene oppstrøms trappen i Eidsfossen ble det gjennomført genetiske analyser av aure på elvestrekningen mellom Eidsfossen og Trøselfossen som er neste vandringshinder oppstrøms, og i sideelva Ryssdalselva på denne strekningen.Genetiske analyser av aure i GloppenelvapublishedVersio

En vurdering av lakselusinfestasjonen i produksjonsområdene 2021 - Basert på data fra den nasjonale overvåkingen av lakselus på vill laksefisk (NALO)

For å estimere smittepresset i fjordene og langs kysten under smoltutvandringen, gjennomføres årlig en undersøkelse av lakselus på vill laksefisk basert på fangst av sjøørret og sjørøye med garn og ruse i alle de 13 produksjonsområdene. Det er i tillegg trålt i 4 sammenhengende uker under smoltutvandringen i Boknafjorden, Hardangerfjorden og Romsdalsfjorden, 5 sammenhengende uker i Sognefjorden og 8 sammenhengende uker i Trondheimsfjorden. For alle fjordene foruten Trondheimsfjorden er det også gjennomført genetiske analyser for å bestemme hvilken elv fisken har utvandret fra. Det også benyttet vaktbur hvor det settes ut oppdrettssmolt i Hardanger- og Boknafjorden.publishedVersio