Intra- and Interspecific Competition in Hatchery Landlocked Salmon and Brown Trout in Semi-Natural Streams

I studied inter- and intraspecific competition in two hatchery stocks: landlocked salmon with long-hatchery background and a heterogenic brown trout stock. These species are potential competitors in the natural environment when landlocked salmon is being restored to wild by stocking hatchery juveniles. Behavioural responses were studied in four indoor laboratory flumes (400 cm long and 37 cm wide) and habitat use in six semi-natural outdoor streams (26 m long and 1.5 m long). Video recordings were used to monitor fish behaviour and electrofishing for fish positioning in the outdoor channels. The study design included five treatments: two densities of brown trout and salmon in solitary and both species together. The results of the study demonstrated that juvenile brown trout changed their behaviour in laboratory streams in response to presence of the landlocked salmon and the density of the conspecifics also tended to alter the habitat use by brown trout in semi-natural streams. Landlocked salmon juveniles showed no response to treatments. I conclude that possible poor adaptive ability to conditions outside hatchery by the hatchery salmon together and more competitive brown trout stocks may limit the success of management action in restoring landlocked salmon back to their natural streams of stocking.     

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.     

Temporal patterns in adult salmon migration timing across southeast Alaska

Pacific salmon migration timing can drive population productivity, ecosystem dynamics, and human harvest. Nevertheless, little is known about long‐term variation in salmon migration timing for multiple species across broad regions. We used long‐term data for five Pacific salmon species throughout rapidly warming southeast Alaska to describe long‐term changes in salmon migration timing, interannual phenological synchrony, relationships between climatic variation and migratory timing, and to test whether long‐term changes in migration timing are related to glaciation in headwater streams. Temporal changes in the median date of salmon migration timing varied widely across species. Most sockeye populations are migrating later over time (11 of 14), but pink, chum, and especially coho populations are migrating earlier than they did historically (16 of 19 combined). Temporal trends in duration and interannual variation in migration timing were highly variable across species and populations. The greatest temporal shifts in the median date of migration timing were correlated with decreases in the duration of migration timing, suggestive of a loss of phenotypic variation due to natural selection. Pairwise interannual correlations in migration timing varied widely but were generally positive, providing evidence for weak region‐wide phenological synchrony. This synchrony is likely a function of climatic variation, as interannual variation in migration timing was related to climatic phenomenon operating at large‐ (Pacific decadal oscillation), moderate‐ (sea surface temperature), and local‐scales (precipitation). Surprisingly, the presence or the absence of glaciers within a watershed was unrelated to long‐term shifts in phenology. Overall, there was extensive heterogeneity in long‐term patterns of migration timing throughout this climatically and geographically complex region, highlighting that future climatic change will likely have widely divergent impacts on salmon migration timing. Although salmon phenological diversity will complicate future predictions of migration timing, this variation likely acts as a major contributor to population and ecosystem resiliency in southeast Alaska.     

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.     

Isolation and characterization of variable (GT)n repetitive sequences from Atlantic salmon, Salmo salar L.

Microsatellites are islands of long repeats of mono-, di- or trinucleotides evenly distributed in the eukaryotic genome with an average distance of 50–100 kb. They display a high degree of length polymorphism and heterozygosity at individual loci, making them highly useful as markers in the development of genomic maps of eukaryotes. In the present work, we examined the dinucleotide repeat motif (dG-dT)_n in the Atlantic salmon, Salmo salar L., genome. The frequency of (dG-dT)_n microsatellites in salmon correlates well with earlier published estimations. Cloning and sequencing of 45 salmon microsatellites revealed perfect and imperfect repeats, but no compound microsatellites. The distribution of number of repeat units in salmon microsatellites differ significantly from that of higher vertebrates. Salmon tends to have more long repeat stretches and less intermediate length repeats.     

Atlantic salmon (Salmo salar) serum albumin: cDNA sequence, evolution, and tissue expression

Atlantic salmon serum albumin is one of the most abundant proteins in salmon liver, representing 1.6% of all clones in a cDNA library made from salmon liver RNA. The DNA from a number of clones was sequenced to reveal an open reading frame of 1,827 bases encoding a 608-amino-acid protein. The sequenced 5' untranslated region is 69 bases long and the 3' untranslated region contains two putative polyadenylation signals and poly(A) tail. Sequence analysis of different clones indicates the presence of a second cDNA for salmon serum albumin. Multiple alignments of salmon serum albumin deduced amino acid sequence with Xenopus laevis, rat, bovine, and human serum albumins shows significant conservation of cysteine residues. The triple domain structure of serum albumin proteins is maintained. Unlike mammalian systems where serum albumin expression appears to be specific to liver only, salmon serum albumin is expressed in muscle also.     

Transmission dynamics of parasitic sea lice from farm to wild salmon

Marine salmon farming has been correlated with parasitic sea lice infestations and concurrent declines of wild salmonids. Here, we report a quantitative analysis of how a single salmon farm altered the natural transmission dynamics of sea lice to juvenile Pacific salmon. We studied infections of sea lice (Lepeophtheirus salmonis and Caligus clemensi) on juvenile pink salmon (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) as they passed an isolated salmon farm during their seaward migration down two long and narrow corridors. Our calculations suggest the infection pressure imposed by the farm was four orders of magnitude greater than ambient levels, resulting in a maximum infection pressure near the farm that was 73 times greater than ambient levels and exceeded ambient levels for 30 km along the two wild salmon migration corridors. The farm-produced cohort of lice parasitizing the wild juvenile hosts reached reproductive maturity and produced a second generation of lice that re-infected the juvenile salmon. This raises the infection pressure from the farm by an additional order of magnitude, with a composite infection pressure that exceeds ambient levels for 75 km of the two migration routes. Amplified sea lice infestations due to salmon farms are a potential limiting factor to wild salmonid conservation.     

Warming Ocean Conditions Relate to Increased Trophic Requirements of Threatened and Endangered Salmon

The trophic habits, size and condition of yearling Chinook salmon (Oncorhynchus tshawytscha) caught early in their marine residence were examined during 19 survey years (1981–1985; 1998–2011). Juvenile salmon consumed distinct highly piscivorous diets in cold and warm ocean regimes with major differences between ocean regimes driven by changes in consumption of juvenile rockfishes, followed by several other fish prey, adult euphausiids and decapod larvae. Notable, Chinook salmon consumed 30% more food in the warm versus cold ocean regime in both May and June. Additionally, there were about 30% fewer empty stomachs in the warm ocean regime in May, and 10% fewer in warm June periods. The total prey energy density consumed during the warmer ocean regime was also significantly higher than in cold. Chinook salmon had lower condition factor and were smaller in fork length during the warm ocean regime, and were longer and heavier for their size during the cold ocean regime. The significant increase in foraging during the warm ocean regime occurred concurrently with lower available prey biomass. Adult return rates of juvenile Chinook salmon that entered the ocean during a warm ocean regime were lower. Notably, our long term data set contradicts the long held assertion that juvenile salmon eat less in a warm ocean regime when low growth and survival is observed, and when available prey are reduced. Comparing diet changes between decades under variable ocean conditions may assist us in understanding the effects of projected warming ocean regimes on juvenile Chinook salmon and their survival in the ocean environment. Bioenergetically, the salmon appear to require more food resources during warm ocean regimes.     

Determination of polymorphism of the cytochrome b gene fragment of mitochondrial DNA of chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> (Walbaum) from the Ola River (northern Coast of the Sea of Okhotsk)

Sequencing of 395 bp long fragments of cytochrome b gene occupying the 15396–15790 bp positions of mtDNA, the data on the structure and variability of the studied region in chum salmon from the Ola River (northern coast of the Sea of Okhtosk) were obtained for the first time. Nine haplotype variants and four protein modifications were obtained. The medial net was built reflecting the variability and phylogenetic relationships of haplotypes in the gene pool of the studied population of the chum salmon from the Ola River. Comparative analysis of the published and original data showed that the Ola chum salmon differs from the Canadian salmon ninth genotypically (in structure of cytochrome b gene) and in the amino acid sequence of the studied site of the enzyme.     

Long‐term zooplankton responses to nutrient and consumer subsidies arising from migratory sockeye salmon (Oncorhynchus nerka)

Migratory animals, such as Pacific salmon, can significantly shape communities in recipient habitats both by altering the flux of resources, and changing community composition and subsequent trophic interactions. Here we mainly used paleoecological records from natural sockeye salmon nursery lakes to quantify the response of plankton communities to the influx of salmon‐derived nutrients and consumers (juvenile salmon). Our long‐term data show that increases in the density of spawning salmon often elevated influx of nutrients, and, in turn, zooplankton production over the past few centuries. In contrast, significant correlations were not detected in two lakes with extremely low or high average spawner densities (i.e. 1.5 and 34.7 × 10³ spawners km^?2 year^?1 respectively). With increasing spawner densities across lakes, analysis of the size structure of subfossils in sediments revealed a strong decrease in body size of a main juvenile salmon prey item (Eubosmina longispina; r²= 0.36, p < 0.001, n = 67), consistent with an overriding effect of predation in lakes with high salmon densities. These long‐term data not only highlight the key role of salmon‐derived nutrients in stimulating plankton communities, but also suggest that the relative effect of nutrient and consumer subsidies varies along gradients of lake production, despite a single ultimate causal mechanism (migrating fish).     

Salmon ocean migration models suggest a variety of population-specific strategies

Many species of salmon around the world migrate to open ocean environments for multiple years and then return to their natal rivers to spawn. How exactly salmon are able to execute these long distance migrations, and the impact of environmental conditions on migration behavior, is not well understood. Individual based modeling is one tool that has been used to explore salmon migration in the ocean. Although models are usually not able to confirm whether a particular behavior is used, they can rule out some behaviors as unrealistic. An extensive review of published literature suggests that there is no universal migration behavior. Behaviors that fish use to navigate depend on where they are in the ocean relative to where they are going, as well as the ocean flows and conditions along the way. Future models of salmon migration should be flexible and at an appropriate scale to capture variable oceanographic conditions and fish responses.     

Moon phase and nocturnal density of Atlantic salmon parr in the Sainte‐Marguerite River, Québec

Nocturnal underwater counts of Atlantic salmon Salmo salar parr were made on four consecutive occasions (two lunar cycles, samplings at both the full and new moon) at four 40 m long sites in the Sainte‐Marguerite River, Québec, Canada, between 30 June and 14 August 2003. Atlantic salmon parr counts did not differ significantly between moon phases. Cloud cover ranged from 0 to 100% during the study, and had no significant effect on parr counts. There were significantly more Atlantic salmon parr in the near shore than in the midstream areas. The findings of this study suggest that the sampling strategy of summer studies aimed at assessing population abundance or developing habitat quality models can be designed without taking moon phase or cloud cover into consideration, but it should account for the higher relative abundance of Atlantic salmon parr in the near shore areas as compared to areas closer to the middle of streams.     

Nucleotide sequence analysis of the cloned salmon preproinsulin cDNA

A cDNA library was constructed using polyadenylated RNA from salmon (Oncorhynchus keta) Brockmann bodies, plasmid vector pBR322, and in vitro recombinant DNA techniques. Insulin-related clones were identified with a cDNA probe generated from the same RNA and enriched for insulin sequences. Two recombinants were shown to contain the nucleotide sequence of the entire coding region and parts of the 5' and 3' untranslated regions. The salmon preproinsulin mRNA is about 760 nucleotides long, 315 of which code for the protein, while about 190 and 200 nucleotides belong to the 5' and 3' flanking regions, respectively. Comparison of the nucleotide sequences of salmon insulin mRNA with those from other species reveals that sequence conservation is limited to the regions coding for the B and A peptides and two segments of the signal peptide. The C-peptide region exhibits no significant sequence homology with the C-peptides of other vertebrates. The 5' and 3' untranslated regions of the salmon preproinsulin mRNA are homologous only with the anglerfish mRNA, whereas there is no evident homology with those of birds and mammals. In addition to establishing the sequence of the preproinsulin mRNA, cloned salmon insulin cDNA provides a specific probe for the analysis and isolation of genomic DNA fragments containing insulin genes.     

Redistribution of juvenile salmonid fishes after localized catastrophic depletion

Juvenile Atlantic salmon and brown trout were depleted at three sites ( c . 108–380 m²) of a natural stream during the summer months of 1991 and 1992. Local population changes and movements of fish marked in sections adjacent to each depleted area were monitored thereafter. There was very little movement of marked salmon parr into the central regions of the depleted areas following the immediate post-marking period. Upstream movement by young-of-the-year fish from high density sections in mid-late summer was noted for trout but not salmon. Unmarked 1-year-old salmon parr immigrated into depleted areas in June 1992, and the pattern of recolonization was consistent with migration upstream from the adjoining river. It is concluded that resident salmon were very strongly site-attached and resource tracking was of no functional significance as a compensatory mortality mechanism. The occurrence of a long distance migratory component in the population during early-mid summer indicates that this, rather than local resource tracking, constitutes a potential compensatory mechanism.     

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.     

Stomach analyses of Baltic salmon from 1959–1962 and 1994–1997: possible relations between diet and yolk-sac-fry mortality (M74)

In recent years, Baltic Sea salmon Salmo salar have suffered high larval mortality (M74) which can be cured by thiamine treatment. Analyses of long term mortality records (1928–1998) from two salmon hatcheries suggest that before the 1970s M74 did not occur, or was less frequent. This indicates that varying M74 did not cause the long-term fluctuations of Baltic salmon catches in this period. The frequency of M74 has been correlated positively to the abundance of the salmon's primary prey, sprat Sprattus sprattus. Sprat, herring Clupea harengus and three-spined stickleback Gasterosteus aculeatus dominated the diet in both the periods of study, 1959–1962 and 1994–1997. The mean size of consumed sprat was significantly smaller in 1994–1997 compared with 1959–1962. Herring and, to a lesser extent, three-spined stickleback increased in the diet of salmon, while sprat appeared to constitute a smaller part of the diet in 1994–1997. The cause of M74 and the thiamine deficiency involved remains unknown, but is thought to be related to changes in thiamine or thiaminase content in forage fish, winter-feeding of salmon or general changes in the pelagic food web, caused by overfishing or eutrophication.