Natural Salmon Populations Research Articles

A Review of Pacific Salmon Hatcheries in British Columbia, Canada, and Interactions With Natural Populations

Pacific salmon Oncorhynchus spp. hatcheries in British Columbia (BC) have been the major activity of the Salmonid Enhancement Program since 1977. However, the present diminished abundance of Pacific salmon and loss of fisheries in BC called for a review of hatchery effectiveness. The Pacific Salmon Foundation conducted a review resulting in 15 reports publicly available on the Pacific Salmon Foundation marine science website. The review includes evaluations of effectiveness of hatchery production, evidence of interactions with natural salmon populations (including rebuilding natural populations with hatchery‐produced salmon), and future opportunities via genomics. Beyond the estimation of juvenile production and contribution to catches and spawning escapements, the ability to assess effectiveness was limited. The assessments of interactions provided a few examples of positive outcomes, but most were negative. The lack of comparative assessments in purely wild populations seriously limits interpretations of hatchery–wild interactions. Future evaluations of the hatchery effectiveness require more quantitative and integrated assessments of hatchery and wild salmon, open data sharing for public review or research, and related studies could benefit from application of new genomic technologies. This paper presents recommendations to address these needs and calls for regularized reviews of the Salmonid Enhancement Program and its net value to sustainability of BC's Pacific salmon.

Experiences from targeted removal of farmed Atlantic salmon from Norwegian rivers

Abstract Farmed salmon escaping from aquaculture and interbreeding with wild conspecifics pose a significant threat to the genetic integrity of natural salmon populations. Despite advancements in aquaculture security, escape incidents persist, prompting the need for effective mitigation strategies. This study summarizes experiences from efforts to remove escaped farmed salmon over a 12-year period in 63 western Norwegian rivers, using either (1) spearfishing during snorkelling by trained personnel or (2) traditional fishing methods employed by local groups. Recaptured farmed salmon ranged widely in size and included both spawners as well as immature fish, demonstrating that farmed fish entering rivers comprise fish of different ages and escape histories. Traditional fishing by locals recaptured the highest number of farmed fish, while removal during snorkelling in general captured larger and mature fish. On average, 53% of the farmed salmon observed during snorkelling were recaptured. This efficacy was influenced by the number of farmed fish present and the size of the farmed fish. In addition, efficacy increased over time, indicating that the removal team became more efficient. The study underscores that active removal, when executed judiciously, contributes to reducing the ecological risks associated with escaped farmed fish, complementing broader strategies for sustainable aquaculture.

Most of the escaped farmed salmon entering a river during a 5-year period were infected with one or more viruses.

Disease interactions between farmed and wild populations have been poorly documented for most aquaculture species, in part due to the complexities to study this. Here, we tested 567 farmed Atlantic salmon escapees, captured in a Norwegian river during 2014-2018, for five viral infections that are prevalent in global salmonid aquaculture. Over 90% of the escapees were infected with one or more viruses. Overall prevalences were: 75.7% for piscine orthoreovirus (PRV-1), 43.6% for salmonid alphavirus (SAV), 31.2% for piscine myocarditis virus (PMCV), 1.2% for infectious pancreatic necrosis virus (IPNV) and 0.4% for salmon anaemia virus (ISAV). A significantly higher prevalence of PMCV infection was observed in immature compared to mature individuals. The prevalence of both SAV and PMCV infections was higher in fish determined by fatty acid profiling to be 'recent' as opposed to 'early' escapees that had been in the wild for a longer period of time. This is the first study to establish a time-series of viral infection status of escapees entering a river with a native salmon population. Our results demonstrate that farmed escapees represent a continuous source of infectious agents which could potentially be transmitted to wild fish populations.

Ecological implications of changing hatchery practices for Chinook salmon in the Salish Sea

AbstractFor over a century, hatchery programs have been used to subsidize natural salmon populations in order to increase fisheries opportunities and, more recently, to conserve declining natural populations. While an extensive literature has described the impacts of large‐scale hatchery operations on freshwater ecosystems, less attention has been given to ecosystem interactions within the marine environment. We analyzed records of hatchery‐released Chinook salmon in the Salish Sea to assess temporal and spatial changes in hatchery practices since 1950, with the goal of identifying potential implications for ecosystem dynamics and conservation efforts in the region. Over the past 65 yr, we found significant changes in the size and time at which juvenile salmon are released, resulting in decreased diversity of these traits. Research suggests that predation on juvenile salmon by other fish, avian, and marine mammal species could be size‐dependent, and our results indicate that current hatchery practices are releasing Chinook salmon in the size range preferred by these predators. With current marine survival rates at chronically low levels, and increasing demand for hatchery subsidies, it is important to consider how modifying existing hatchery programs intended to reduce homogenization may promote more natural marine food web dynamics, with potential benefits to both hatchery and natural Chinook populations.

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

AbstractAtlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Farmed salmon represent a limited number of wild source populations that have been exposed to ≥12 generations of domestication. Consequently, farmed and wild salmon differ in many traits including molecular‐genetic polymorphisms, growth, morphology, life history, behaviour, physiology and gene transcription. Field experiments have demonstrated that the offspring of farmed salmon display lower lifetime fitness in the wild than wild salmon and that following introgression, there is a reduced production of genetically wild salmon and, potentially, of total salmon production. It is a formidable task to estimate introgression of farmed salmon in wild populations where they are not exotic. New methods have revealed introgression in half of ~150 Norwegian populations, with point estimates as high as 47%, and an unweighted average of 6.4% across 109 populations. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population‐specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long‐term consequences of introgression is expected to lead to changes in life‐history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts.

The ecological profile of Atlantic salmon escapees entering a river throughout an entire season: diverse in escape history and genetic background, but frequently virus-infected

In 2014, 129 farmed salmon escapees captured in an upstream-migration trap located in the river Etne, western Norway, were investigated for viral infections, age at escape, size, and genetic composition. The frequency of escapees positive for salmonid alphavirus (SAV), piscine orthoreovirus (PRV), and infectious salmon anaemia virus (ISAV) was 12, 79, and <1%, respectively. Fatty acid analysis demonstrated that the individuals had escaped from farms at different stages of the production cycle, although the majority had probably escaped from farms in the same year as their capture in the river. Genetic analyses demonstrated that the escapees originated from multiple farms. This was also supported by the distribution of fish size and timing of entry into the river. A combination of genetic, fatty acid and viral infection analyses showed that in the river Etne in 2014: (i) most of the fish entering the river were infected with one or more viruses, (ii) the majority of them had escaped in the same year that they entered the river, (ii) they originated from multiple farm sources, and (iv) two of the identified genetic groups likely originated from two recent and distinct escape events. This is the first study to integrate results from multiple analytical methods in order to reveal the ecological and genetic diversity of escaped farmed fish entering a river with native salmon population throughout an entire season.

Juvenile life-history diversity and population stability of spring Chinook salmon in the Willamette River basin, Oregon

Migratory and rearing pathways of juvenile spring Chinook salmon (Oncorhynchus tshawytscha) were documented in the Willamette River basin to identify life histories and estimate their contribution to smolt production and population stability. We identified six primary life histories that included two phenotypes for early migratory tactics: fry that migrated up to 140–200 km shortly after emergence (movers) and fish that reared for 8–16 months in natal areas (stayers). Peak emigration of juvenile salmon from the Willamette River was in June–July (subyearling smolts), March–May (yearling smolts), and November–December (considered as “autumn smolts”). Alternative migratory behaviors of juvenile salmon were associated with extensive use of diverse habitats that eventually encompassed up to 400 rkm of the basin, including tributaries in natal areas and large rivers. Juvenile salmon that reared in natal reaches and migrated as yearlings were the most prevalent life history and had the lowest temporal variability. However, the total productivity of the basin was increased by the contribution of fish with dispersive life histories, which represented over 50% of the total smolt production. Life-history diversity reduced the variability in the total smolt population by 35% over the weighted mean of individual life histories, providing evidence of a considerable portfolio effect through the asynchronous contributions of life histories. Protecting and restoring a diverse suite of connected habitats in the Willamette River basin will promote the development and expression of juvenile life histories, thereby providing stability and resilience to native salmon populations.

Genetic introgression of farmed salmon in native populations: quantifying the relative influence of population size and frequency of escapees

Farmed escapees may threaten the genetic integrity of native salmon populations through interbreeding. However, introgression requires survival until maturation, successful reproduction and successful early development. These traits are often compromised in domesti- cated animals selected for high performance in captivity. This makes it difficult to predict intro- gression levels in native populations. A recent study estimated genetic introgression of farmed escaped Atlantic salmon Salmo salar in 20 Norwegian rivers and found highly population-specific levels of introgression. The underlying causes of these patterns, however, remain unknown. Here, using a modeling approach on empirical and demographic data, we demonstrated that a combi- nation of the observed relative frequency of escaped farmed salmon and the average annual angling catch weights for rivers, provides a significantly better predictor for cumulative introgres- sion of farmed salmon in wild populations than the frequency of farmed salmon alone. Our results suggest that the demography of the native population is a significant factor influencing the rela- tive success of farmed salmon in the wild.

Three Decades of Farmed Escapees in the Wild: A Spatio-Temporal Analysis of Atlantic Salmon Population Genetic Structure throughout Norway

Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world’s largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15–30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970–2010. Based upon the analysis of 22 microsatellites, individual admixture, FST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global FST = 0.038) and contemporary data sets (global FST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global FST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population.

Managed metapopulations: do salmon hatchery 'sources' lead to in-river 'sinks' in conservation?

Maintaining viable populations of salmon in the wild is a primary goal for many conservation and recovery programs. The frequency and extent of connectivity among natal sources defines the demographic and genetic boundaries of a population. Yet, the role that immigration of hatchery-produced adults may play in altering population dynamics and fitness of natural populations remains largely unquantified. Quantifying, whether natural populations are self-sustaining, functions as sources (population growth rate in the absence of dispersal, λ>1), or as sinks (λ<1) can be obscured by an inability to identify immigrants. In this study we use a new isotopic approach to demonstrate that a natural spawning population of Chinook salmon, (Oncorhynchus tshawytscha) considered relatively healthy, represents a sink population when the contribution of hatchery immigrants is taken into consideration. We retrieved sulfur isotopes (34S/32S, referred to as δ34S) in adult Chinook salmon otoliths (ear bones) that were deposited during their early life history as juveniles to determine whether individuals were produced in hatcheries or naturally in rivers. Our results show that only 10.3% (CI = 5.5 to 18.1%) of adults spawning in the river had otolith δ34S values less than 8.5‰, which is characteristic of naturally produced salmon. When considering the total return to the watershed (total fish in river and hatchery), we estimate that 90.7 to 99.3% (CI) of returning adults were produced in a hatchery (best estimate = 95.9%). When population growth rate of the natural population was modeled to account for the contribution of previously unidentified hatchery immigrants, we found that hatchery-produced fish caused the false appearance of positive population growth. These findings highlight the potential dangers in ignoring source-sink dynamics in recovering natural populations, and question the extent to which declines in natural salmon populations are undetected by monitoring programs.

Erratum to: An overview of salmon enhancement and the need to manage and monitor natural spawning in Hokkaido, Japan

The chum and pink salmon catches in Hokkaido, Japan have increased dramatically since the 1970s and the 1990s, respectively. In contrast, masu salmon catches have been steadily decreasing. Despite intensive hatchery development in Hokkaido, naturally spawning salmon populations persist based on results from a recent river survey. This paper focuses on the challenges of maintaining hatchery salmon populations while protecting natural chum, pink and masu salmon populations in Hokkaido. Two important initiatives related to meeting this ambitious goal are managing hatcheries in a way that minimizes negative interactions between natural and hatchery salmon populations, and initiating new efforts at restoring and rehabilitating degraded freshwater habitats. In addition, in order to maintain a balance of demand and supply in the domestic market through the exportation of extra salmon, Hokkaido has decided to enter full assessment to gain Marine Stewardship Council (MSC) certification of the Hokkaido chum salmon trap net fishery. This would involve a fundamental shift in fisheries management as practiced in Japan, specifically elevating the importance of managing the fishery in a way that conserves natural salmon populations. A key component of a new salmon management strategy is the establishment of a zone management framework based on the designation of stream units to spatially separate natural salmon from hatchery salmon to minimize negative effects of hatchery fish and to utilize effectively hatchery salmon for commercial fisheries. This effort is allied with similar initiatives in other Pacific Rim countries that are focusing on management reform to restore natural ecosystem function and maintain the coexistence of wild and hatchery salmon.

Habitat use by the Formosan landlocked salmon Oncorhynchus masou formosanus

The critically endangered Formosan landlocked salmon Oncorhynchus masou formo- sanus is one of the southernmost natural salmon populations in the world, which only occurs in Chichiawan Stream and its tributaries in the Wuling basin of subtropical Taiwan. We examined habi- tat uses by different size classes of the Formosan salmon and the sympatric shovelmouth minnow Varicorhinus barbatulus, and identified the relative importance of environmental variables, biotic components and seasonal effects in explaining the variance in the relative occurrences of fish at the catchment scale. After removing seasonal effects, 74.9% of the variation in the relative occurrence of fish was explained by the measured environmental variables and biotic components. Habitat uses by the Formosan salmon and shovelmouth minnow were distinct. The shovelmouth minnow occurred more frequently at sites with a high concentration of NH3-N and high proportions of gravel and rif- fles, while the Formosan salmon utilized sites at high elevations. Habitat uses by Formosan salmon of different size classes varied slightly. Juvenile and subadult salmon inhabited sites with lower temper- atures and current velocities, but adult salmon occurred more frequently with large-grain-sized sub- stratum. Our study showed that variations in the relative occurrence of fish in the Wuling basin were best explained by physicochemical parameters (38.8%), followed by substratum composition (11.4%). The variations exclusively explained by mesohabitat composition, seasonal effects, and biotic components were not significant. This conclusion has important consequences for local man- agers and conservationists.

Do native species limit survival of reintroduced Atlantic salmon in historic rearing streams?

Reintroduction of extirpated populations creates a unique context that can exacerbate the effects of interactions among species. Thus, reintroduced populations may be particularly vulnerable to predators and competitors, including native species with which they historically coexisted. In this study, we evaluated the effect of native fishes on survival of reintroduced Atlantic salmon ( Salmo salar) in the Connecticut River basin, where the native salmon population is extinct. Juvenile salmon are stocked annually in many Connecticut River tributaries. We sampled salmon reintroduction sites across tributaries with different fish communities to determine whether native fish reduce the success of salmon reintroductions ( N = 19 site-years). Increased density of slimy sculpin ( Cottus cognatus), a native generalist predator, was associated with reduced recruitment of reintroduced salmon. Salmon first-summer survival declined with increased sculpin density across sites, and low first-summer survival led to reduced densities of overyearling salmon the subsequent year. Hierarchical partitioning analysis showed that the negative relationship between sculpin and salmon was independent of potentially confounding variation in other fish community or habitat characteristics. Negative effects of native, historically-sympatric species, particularly generalist predators, can impede restoration of extirpated populations.

Analysis of gene associated tandem repeat markers in Atlantic salmon (Salmo salar L.) populations: implications for restoration and conservation in the Baltic Sea

Patterns of genetic diversity and differentiation among five wild and four hatchery populations of Atlantic salmon in the Baltic Sea were assessed based on eight assumedly neutral microsatellite loci and six gene-associated markers, including four expressed sequence tag (EST) linked and two major histocompatibility complex (MHC) linked tandem repeat markers (micro- and mini-satellites). The coalescent simulations based on the method of Beaumont and Nichols (1996, Proc. R. Soc. Lond. Ser. B – Biol. Sci., 263, 1619–1626) indicated that two loci (MHCIIα and Ssa171, with the lowest and highest overall FST estimates, respectively) exhibited significant departures (P<0.05) from the neutral expectations. Another coalescent-based test for selective neutrality (Vitalis et al. 2001, Genetics, 158, 1811–1823) further supported the outlier status of the Ssa171 microsatellite locus but not of the MHCIIα linked minisatellite. In addition, actin related protein linked microsatellite locus was identified with this test as an outlier in six pairwise population comparisons. All genetic diversity estimates revealed more genetic variation in hatchery stocks than in the small wild salmon populations from the Gulf of Finland. However, the wild populations possessed alleles at gene-associated markers (e.g. MHCI and IGF) not found in the hatchery stocks, which together with moderate genetic differentiation and distinctive environmental conditions justifies the special conservation measures for the last remaining native salmon populations in the Gulf of Finland.

Rapid communication / Communication rapide Invasion of transgenes from salmon or other genetically modified organisms into natural populations

In recent years, there has been widespread concern about the ecological and genetic effects of genetically modified organisms. In salmon and other fishes, transgenic growth hormone genes have been shown to have large effects on size and various traits related to fitness. In this paper, I have shown by using a deterministic model that if such a transgene has a male-mating advantage and a general viability disadvantage, then the conditions for its invasion in a natural population are very broad. More specifically, for 66.7% of the possible combinations of the possible mating and viability parameters, the transgene increases in frequency, and for 50% of the combinations, it goes to fixation. In addition, by this increase in the frequency of the transgene, the viability of the natural population is reduced, increasing the probability of extinction of the natural population. These findings provide independent confirmation of previous concerns about the inherent risks of transgenic organisms, especially for native salmon populations potentially affected by commercial salmon production using transgenic stocks.

Lifetime success and interactions of farm salmon invading a native population.

Farm Atlantic salmon escape and invade rivers throughout the North Atlantic annually, which has generated growing concern about their impacts on native salmon populations. A large-scale experiment was therefore undertaken in order to quantify the lifetime success and interactions of farm salmon invading a Norwegian river. Sexually mature farm and native salmon were genetically screened, radio tagged and released into the River Imsa where no other salmon had been allowed to ascend. The farm fishes were competitively and reproductively inferior, achieving less than one-third the breeding success of the native fishes. Moreover, this inferiority was sex biased, being more pronounced in farm males than females, resulting in the principal route of gene flow involving native males mating with farm females. There were also indications of selection against farm genotypes during early survival but not thereafter. However, evidence of resource competition and competitive displacement existed as the productivity of the native population was depressed by more than 30%. Ultimately, the lifetime reproductive success (adult to adult) of the farm fishes was 16% that of the native salmon. Our results indicate that such annual invasions have the potential for impacting on population productivity, disrupting local adaptations and reducing the genetic diversity of wild salmon populations.

Genetic divergence and interactions in the wild among native, farmed and hybrid Atlantic salmon

There is concern that the progeny resulting from the spawnings of escaped farmed Atlantic salmon may compete with and disrupt native salmon populations. This study compared, both in the hatchery and in the wild, fitness‐related traits and examined interactions among farmed, native and hybrid 0+ parr derived from controlled crosses and reared under common conditions. The farmed salmon were seventh‐generation fish from the principal commercial strain in Norway and native salmon were from the rivers Imsa and Lone, Norway. In the hatchery, farmed salmon were more aggressive than both native populations and tended to dominate them in pairwise contests. Farmed salmon were also more prone to risk, leaving cover sooner after a simulated predator attack, and had higher growth rates than native fish. Interbreeding between farmed and native fish generally resulted in intermediate expression of the above traits. There was, however, evidence of hybrid vigour in Lone/farmed crosses which were able to dominate both pure Lone and farmed parr in pairwise contests. In the wild, observations of habitat use and diet suggested that the populations compete for territory and food, and both farmed fish and hybrids expressed higher growth rates than native fish. Our results suggest that these innate differences in behaviour and growth, that probably are linked closely to fitness, will threaten native populations through competition and disruption of local adaptations.

Allozyme variation in natural populations of Atlantic salmon in Asturias (northern Spain)

This study describes the genetic variation (based on analysis of 24 protein-coding genes) within and between two natural salmon populations of Asturian rivers. Information on the genetic structure of populations at the southern distribution limit of Salmo salar in Europe is provided. In the natural populations, five of 24 protein-coding loci were polymorphic ( Aat-2, Idh-3, Mdh-3,4, Sdh-1 and Sdh-2). Non-significant allele frequency differences were found between populations. At the Mdh-3,4 locus the frequency of the 87 allele is much higher than the values given for other European populations. The mean heterozygosity in these samples (based on 24 loci investigated) was 2.18%. Nevertheless, the amount of variability in Asturian natural populations is somewhat lower than the average estimated in the Atlantic salmon population.

Predictability of the Consequences of the Kemano Hydroelectric Proposal for Natural Salmon Populations

The Aluminum Company of Canada, Limited (Alcan) has proposed completion of its hydroelectric developments to increase aluminum smelting capacity in north-central B.C. The project was started in 1950 and included the Kenney Dam on the Nechako River in the Fraser catchment area, the creation of the Nechako Reservoir, and the construction of facilities for generating power at the Kemano River on the west coast. Completion of development (Kemano Completion Proposal), at a cost of over $2 billion, would divert 84 percent of the initial mean annual discharge of the Nechako River, and 62 percent of the mean annual discharge of the Nanika River in the Skeena catchment area, to the Kemano River. The proposal offers discharges that are intended to protect Pacific salmon stocks, or, where this is not possible, mitigation of losses. This paper identifies the more obvious effects of abstraction and regulation on salmon populations and their habitat. These include interference with migration of adults, changes in the q...

The regulation of stock characteristics in a simulated Atlantic salmon population

A computer simulation model is developed for a hypothetical salmon population. Mortality during the fry to smolt stage follows the model derived for R. Wye salmon by Gee et al. (1978a). Compensatory mortality during the freshwater phase regulates the abundance of the adult stock both when other mortality rates are constant and when these fluctuate randomly. In the absence of perturbing forces, oscillations in adult abundance are minimal but follow an approximate 10-year cycle when marine mortality is variable. If sea-age composition is assumed to have some genetic basis, exploitation, acting selectively on salmon of older sea-ages, results not only in an increase in the relative but also in the absolute abundance of fish of younger sea-age. The relevance of these simulations in assessing changes in natural salmon populations is discussed.