Salmon hatcheries by Andy Ferguson

With declining populations of salmon (and sea trout), it is understandable that many anglers and fishery owners see hatcheries as something tangible and practical that they can do to boost populations. In this article, Andy Ferguson looks at why supplementary stocking with hatchery reared Atlantic salmon younger than smolts is rarely successful in increasing the number of returning fish and can instead result in a reduction.

More information on resident brown trout stocking, click here.

The experience of hatcheries in the USA in this film: Artifishal’.

Andy Ferguson is Professor Emeritus at Queen’s University Belfast and advisor to the Wild Trout Trust.


Salmo salar eggs

Salmon hatcheries

Stocking, the release of hatchery or farm reared individuals into the wild, is probably the most controversial topic in trout and salmon fisheries management right now. Stocking can be used to restore extinct populations, to provide a fishery in waters with little or no natural spawning, or, most commonly, to try to supplement a natural population where the numbers of fish are considered to be insufficient to meet angling or conservation needs. The latter is known as supplementary stocking and is also referred to as enhancement stocking or supportive breeding, and it includes mitigation for impacts such as dams. Hatchery broodstock can be from the same population being stocked (native) or from a different population (non-native) and can be taken directly from wild fish each generation or a separate strain can be maintained over multiple generations. Offspring can be released to the wild at any stage from eyed egg to adult. This diversity of practices, and failures to compare like with like, has resulted in many unfounded conclusions. 

Even with supplementary stocking, the Atlantic salmon is still declining at an alarming rate in many of our rivers because of widespread degradation of freshwater environments and increasingly challenging conditions at sea. Salmon hatcheries have been in use for nearly 150 years and for almost as long their value in supplementing wild stocks has been questioned. Indeed, some have suggested that hatcheries are an example of human techno-arrogance”, based on the delusion that we can degrade our rivers and seas as much as we like and solve the problems arising by technology. Others have suggested that, given its record of failure, the hatchery myth requires an almost idolatrous faith” to persist. 

So why then have we continued to use hatcheries? The argument for artificial rearing is that it overcomes the high mortality occurring in the wild. Typically, survival from fertilised egg to first autumn can be 10-fold higher in the hatchery, less for earlier stages, and greater from egg to smolt. The implicit, although incorrect, assumption is that these hatchery reared individuals will perform as well, post release, as wild individuals of the same age. In spite of much discussion on the potential negative impacts of hatcheries, the fundamental questions — can hatcheries work to increase adult runs and offspring in subsequent generations, and, if so, under what conditions — have largely been ignored by fishery managers and scientists. Demonstration that some stocked fish return as adults is irrelevant. Stocking is only of value if more adult salmon return, and more offspring are produced, compared to the broodstock having been left to breed naturally, this effect being compounded over generations. Thus, it is the overall life cycle survival together with the contribution to the next generation that matters (both combined are referred to as biological fitness, henceforth fitness), not simply the increased survival during the period in the hatchery. The crux of the lack of success of much stocking is that on release from the protected hatchery environment, stocked individuals have substantially lower fitness than naturally produced equivalents. 

Surprisingly, given the long-term debate on stocking, no complete assessments have been carried out for Atlantic salmon to determine the fitness of hatchery reared fish, stocked at different ages, relative to naturally produced offspring. However, some partial studies have been published. Hatchery reared Atlantic salmon, stocked as 0+ and 1+ parr, have been shown to have significantly reduced relative survival to adult return (only 2.5% to 12.5%). For salmon stocked as smolts the relative survival to adult return has ranged from 7% to 50%. Even for the much revered West Ranga ranching operation, hatchery reared smolts have shown only 18% survival to return compared to wild smolts elsewhere in Iceland. For salmon released at fed fry or parr stages a relative reproductive success from 45% to 71% has been shown. For release as smolts this falls to 20% to 42%. Studies of several North American salmonids with life cycles comparable to Atlantic salmon have shown a similar picture of much reduced fitness. For example, first generation hatchery reared steelhead (the rainbow trout equivalent of our sea trout) spawning in wild produced only 2.4% to 11% of the adult offspring produced by wild fish. 

Although there is considerable variability among estimates as would be expected from distinct conditions in different rivers and hatcheries, taking average values for relative survival and relative reproductive success gives a fitness for hatchery reared salmon of only 8% of that of naturally reared fish. Thus, for stocking to be of value in increasing runs, under current hatchery practices, hatchery survival must, on average, be substantially more than 12.5 times greater than equivalent wild salmon. The caveat is that this is an average value so in some cases it will be less, in others more. However, it emphasises that hatchery survival must be substantially greater than in the wild to compensate for lowered fitness after release. Such relative survival is only generally seen when rearing to the smolt stage. There is no point stocking to end up with the same return as from wild rearing, or only marginally better. Worse still, in many cases, release at earlier stages is likely to cause a reduction in returning salmon, and fewer offspring in the next generation, than would have been the case had the broodstock used been left to breed naturally! 

Many supporters still regard hatcheries as an unqualified success. The problem of assessing the impact of hatchery supplementation is that it often takes place alongside environmental and other improvements, or increases in fishing effort, resulting in spurious correlations to hatchery intervention. An often-cited case is the River Tyne, which has currently the best salmon run in England. It has a hatchery so ipso facto that must be the cause, many argue. The Tyne is probably the worst example that could be used as tagging data are available that refute the claim! The Tyne was almost certainly the most important of the English salmon rivers in the 19th Century. However, industrial and sewage pollution of the lower river led almost to the extinction of salmon by the mid-20th Century. Following environmental improvements, natural salmon runs increased again from 1960. Twenty years later a hatchery was established to mitigate for loss of some 6 – 8% of the spawning habitat due to the construction of the Kielder Dam. Stocking has mainly involved first (0+) and second year (1+) parr. Estimates based on returns from tagged parr in the 1980 to 2000 runs indicated an average hatchery contribution of 6% (range 3% — 14%) to the annual Tyne rod catch. However, this does not take account of the less than 50% relative reproductive success of hatchery-reared salmon. Reduced fitness of hatchery reared salmon was not taken account of in determining the number of parr required for mitigation. Thus, it is debatable if the hatchery has fulfilled its mitigation mission in terms of lost recruitment, still less contributed to the restoration of the entire Tyne salmon stock to its former glory! 

Why do hatchery reared salmon, even in the first generation, perform so poorly compared to natural fish from the same river? A key issue is the choice of broodstock and making crosses. Fishery managers frequently treat stocks within a river system as if they are homogeneous and fully mixing, an assumption that is generally untrue for larger systems. Many of these have genetically distinct sub-populations of salmon spawning in separate tributaries or at different times. This is a particular problem if broodstock are taken in the mainstem of these rivers as they can be a mixture of distinct sub-populations, with the offspring of such mixed crosses showing reduced fitness. In some rivers farm salmon escapees may be present and may not be readily identifiable if they escaped at an early age. Again, interbreeding with these farm fish results in substantially reduced fitness. In Norway there is mandatory testing to ensure that broodstock used in supplementary stocking have no farm genes. Hatchery procedures cannot accurately reproduce the total patterns of sexual selection, mating and other aspects of reproduction that occur under natural conditions. Female salmon make active mate choices (except for sneaking parr) and can recognise relatives and non-relatives of different levels of genetic distinctness by smell”, whereas in the hatchery inappropriate forced matings can occur. 

Conditions in the hatchery often differ considerably from those in the native river resulting in behavioural, structural, physiological, genetic and epigenetic differences between hatchery reared and wild fish. Hatchery tanks provide much simpler physical conditions than in the river in relation to substrate variety, cover, water depth, and flow. Depending on the source of water for the hatchery, there may be differences in its chemistry and temperature. Higher temperature during egg incubation has been shown to result in later adult return. Generally, artificial food is given to the hatchery fish from above with the quantity and timing of delivery, and nutritional composition of the food being very different from the wild. Fish are generally kept at much greater densities than in the wild and thus social interactions are different and stress much higher. Predators and competitors are excluded. There is generally treatment for diseases and parasites. Not surprisingly then hatchery-reared salmon, even if kept in the hatchery for only a short time, differ considerably from wild ones and this has a lasting effect on their survival and breeding. It has been found that the deeper bodies and smaller fins of hatchery-reared Atlantic salmon increased their energy requirements by up to 30% in turbulent flow and they had reduced swimming ability. Many behavioural changes have been shown between hatchery-reared and wild salmon, including changes in aggression, reduced ability to find food, altered sheltering behaviour, reduced risk-awareness of predators and altered mating behaviour. Hatchery-reared fish can have problems in learning to forage wild prey. Fish conditioned to a hatchery environment are naïve with respect to predators and often show their highest mortality immediately after release when they are most vulnerable. Hatchery fish being easier prey for predators can also attract predators to an area and may increase predation on wild fish. Stocked salmon have also been shown to stay nearer to the surface than wild fish and associate surface disturbance with food, increasing their vulnerability to predators. In North America, herons apparently have learned to mimic hatchery feeding by sprinkling water on the surface to encourage the stocked salmon to come up! Hatchery reared salmon can also be naïve with respect to taking.

shelter from increased flow rates. Thus, in one study it was found that when a severe flood occurred a couple of weeks after stocking, subsequent electrofishing found few hatchery salmon parr (marked) but no obvious decline in wild fish of the same age. Salmon, in common with humans, have a complex mixture of intestinal bacteria. This microbiome has important influences on many aspects of digestion and metabolism and plays a critical role in the immune system. Hatchery reared salmon have been shown to possess gut microbial communities different from those of wild fish. 

Hatchery conditions inevitably result in genetic changes relative to the wild population. This can occur due to inappropriate crossing. Even with the relatively high survival in the hatchery there is still some selective mortality that can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild. This results in domestication even if reared individuals are kept in captivity for only a small part of their life cycle. This domestication is much increased if returning stocked individuals are subsequently used as broodstock. Following stocking out natural selection is intensified due to high mortality but the individuals that survive can be different from those wild fish that survive, again leading to genetic differences.

We now know that much more important than genetic changes are epigenetic changes. Although epigenetics is now widely referred to in the media, since the term may not be familiar to all, some explanation is warranted. Salmon, as with other organisms, have tens of thousands of genes only a small proportion of which are active, i.e. expressed, at any one time. For example, during development different genes are expressed in separate tissues resulting in their differentiation into muscle, liver, brain etc. Such differentiation is controlled by other genes. However, gene expression can also be altered by different environmental conditions such as those found in the hatchery compared to the natural environment. Changes in gene expression are brought about by adding chemical tags to the genes, which switch the genes on or off. Since the DNA sequence comprising the genes doesn’t change, these tags that alter gene expression are referred to as epigenetic changes, literally meaning upon” genes. Epigenetic tags are one reason why the same DNA genotype can produce different salmon phenotypes (i.e. the observable characteristics) as a result of environmental interactions. Many epigenetic tags are set early in development and even if the environment changes, the signals may continue into adulthood. Epigenetic modifications induced by captive rearing are now seen as a significant cause of reduced fitness in hatchery reared salmon. Thus, when hatchery reared salmon are stocked out, even at the eyed egg or unfed fry stages, gene expression suitable for the hatchery environment can continue resulting in maladaptation and reduced survival. Although most epigenetic tags are wiped at reproduction, some may be inherited and so the maladaptation continues into the next generation – epigenetic inheritance. When stocked salmon interbreed with wild fish, epigenetic and genetic differences can result in lower fitness of the wild population, requiring continually increasing stocking to compensate. However, this problem has sometimes been overstated due to failure to differentiate between findings from native versus non-native, and first generation versus multigeneration, broodstock. 

Given the problems of reduced survival and reproductive success of hatchery reared salmonids, and potential negative impacts of stocking on wild populations, numerous studies have been undertaken in attempts to improve these aspects. One North American study on steelhead reported successful supplementation by taking eyed eggs from natural redds, incubating them in a hatchery and stocking as smolts. As inappropriate forced matings are seen by some as one of the key factors in reduced fitness of hatchery reared salmon this approach allows natural mate choice as well as potentially allowing early epigenetic tags to be set for natural rather than hatchery conditions. 

Several studies have shown that survival of hatchery-reared salmonids can be considerably increased by life skills training’ prior to release. The natural environment can be simulated through providing more structure in the tanks, irregular changes in water levels, velocities, and direction, under-water food delivery, and virtual predators. Results from such hatchery enrichment have been encouraging although not always consistent among studies. Significantly better foraging success of salmon on release was found following pre-release training involving exposure to live prey items in the presence of previously trained fish. Survival of salmon smolts while migrating down a large river in Finland was doubled by rearing in an enriched environment, although these still had only 67% survival relative to wild smolts. 

Optimum procedures for carrying out crosses have been known for some time but are not yet implemented in all hatcheries. Milt from different males should not be mixed but fertilisation carried out on a 1:1 basis. Mixing milt can result in one male fertilising all or most of the eggs. In the wild the eggs of a female salmon are often fertilised by up to five males, including mature male parr, and individual males may fertilise eggs from more than one female. This can be replicated to some extent in the hatchery by factorial crossing. That is, the eggs and milt from each parent are split into five or more batches. Thus, for example, for each set of five females and five males 25 crosses, on a 1:1 basis, are produced. Once fertilisation has occurred the crosses can be mixed prior to incubation. 

Before any supplementary stocking is undertaken it is essential to establish where the bottlenecks to survival occur in that river and no stocking should be permitted until that has been done. Mortality in juvenile salmon is density dependant, that is, as the number of juveniles in an area increases this is accompanied by an increase in deaths, sometimes exponentially. More eggs and juveniles will not necessarily result in more smolts. Thus, if reduced numbers of salmon are due to lower availability of habitat or food, then adding more fish can result in increased competition and lower survival overall, likely giving fewer fish at the end of the day than if stocking had not been carried out. For that reason, stocking of juvenile salmon should only be undertaken into areas of the river with suitable rearing habitat where there is little or no natural spawning. It has been suggested that translocating naturally produced fry from areas of high density to such areas is a valuable technique to increase juvenile survival, doesn’t require hatchery facilities, and avoids the problems associated with inappropriate crosses and hatchery rearing. Growth is often better under hatchery conditions. When stocked these larger fish can displace the smaller wild ones resulting in death of the latter. Subsequently the poor survival of the stocked salmon means that they do not compensate for the loss of displaced natural fish resulting in a lower overall return. In an experimental stocking with farm salmon offspring, due to competitive displacement from these larger fish the overall adult return was just 45% of what it would have been had only the wild fish been present. 

The age at which stocking is undertaken is important as this needs to be after the time of the bottleneck(s). However, given that there are multiple bottlenecks throughout the freshwater part of the life cycle, and reduced fitness of hatchery-reared individuals, stocking prior to the smolt stage is unlikely to be of value in most cases. There is no evidence to support the often-stated advice to keep the hatchery period as short as possible and it seems to be based simply on the assumption that shorter must be better. The main hatchery induced changes noted above will be present by the 0+ parr stage. Some have advocated the stocking of eyed eggs and unfed fry to avoid changes brought about by rearing. However, even these stages involve forced unnatural matings and some epigenetic changes, and such stocking may be just as damaging to the wild population as that with later stages. Thus, a few days after fertilisation some 20% of epigenetic changes that persist into adulthood will have taken place. There is also no evidence that stocking with eyed eggs or unfed fry are effective in supplementation except where there are issues with spawning habitat quality or accessibility. It is for good reason that hatcheries in the American Pacific North West stock most of their billions of salmonids at stages appropriate for direct life in the ocean, which for species with life cycles similar to Atlantic salmon is the smolt stage. In a study of chinook salmon, using wild native broodstock, returning adult offspring from stocked smolts was approximately five times that of naturally spawning parents in the first generation. For coho salmon, stocking with smolts resulted in an 80 times greater adult return compared to stocking unfed fry. Given high relative hatchery survival from unfed fry to smolt, this represents a considerable boost to population numbers. In Scandinavia most Atlantic salmon stocking is as smolts. Given that survival at sea is now one of the main bottlenecks in overall Atlantic salmon life cycle survival, experiments are being carried out on capturing wild migrating smolts, rearing them in cages until maturity and then releasing them for natural spawning. Similarly, captive kelt reconditioning can be used in an attempt to improve their survival. Again, such interventions are not without potential problems. 

In conclusion, based on scientific studies to date and current practices, supplementary stocking with younger stages than smolts is unlikely to result in increased Atlantic salmon runs and can indeed by counterproductive. There are likely to be specific issues that can be mitigated by release of earlier life stages, but these need to be established on an individual river basis. Since stocking can undoubtedly have adverse impacts on wild populations, irrespective of what life stage is used, it is only worth the risk where is a significant increase in the adult run, i.e. where the decline in fitness in the population is more than offset by the increased numbers. In other words, if there is the possibility of some pain it should only be done where there is a probability of a good gain! A similar maxim applies to playing the stock markets. Smolts should be marked prior to release. Such individuals can then be avoided when subsequent broodstock are taken otherwise multigeneration hatchery domestication can occur. In that respect it is important to differentiate between smolt ranching and supplementary stocking with smolts. In the former returning adults are used as broodstock to develop a strain adapted to ranching as, for example, has been done at Burrishoole in western Ireland. Under this ranching scenario all returning adults resulting from smolt release need to be captured to prevent their interbreeding with the wild population. At Burrishoole angling for such adults takes place on the brackish Lough Furnace, which is downstream of permanent traps where all further adults resulting from 

smolt releases can be removed. For supplementation, on the other hand, returning adults must be excluded from the next hatchery broodstock although they can naturally interbreed with wild salmon. Since much of the loss of fitness from hatchery rearing is likely to result from epigenetic changes, and not genetic ones as previously thought, these changes will be reset after one generation of natural reproduction. The main problem with stocking smolts is the increased cost and facilities required. In Scotland, for example, low marine survival and low ate of rod capture potentially results in a very low realised return. Some have argued that the greater straying of hatchery reared smolts compared to wild ones potentially presents a genetic threat to neighbouring populations. However, given the lower reproductive success of hatchery ones the actual gene exchange may not be any greater, which is all that matters. 

The above comments should not be taken as advocating smolt stocking but rather that, where supplementary stocking is deemed absolutely essential in the short term, it is the only approach that is likely to result in an increased adult run to sustain the population until longer term restoration measures are put in place. Even at its best supplementary stocking will never be more than a sticking-plaster” and should be the approach of last resort. Until we accept that we need to return our aquatic ecosystems to something closer to their natural state, Atlantic salmon, as a species exploited for angling, is probably doomed in many rivers. With an ever-growing human population and demands on the environment from hydropower generation, fish farming, agriculture, water abstraction, and rural development this is increasingly difficult to achieve both actually and politically. Multiple studies have shown that river habitat and environmental restoration always pay much greater dividends than hatchery intervention except where a very specific irremovable bottleneck is being targeted by the latter. In Denmark, contrary to the trend elsewhere, Atlantic salmon populations have increased in three targeted rivers, reaching greater numbers than ever previously recorded. This followed a major shift in the management in the early 2000s when, after many years of unsuccessful stocking this was abandoned as the primary solution, effort was concentrated on habitat improvements. A key focus was the removal of barriers to movement, or the installation of bypass channels suitable for both up and downstream movements. Major habitat restoration was undertaken in the rivers including the addition of stones and gravel to create extensive new spawning grounds. Controls on estuary netting, salmon farming and predators were also introduced. Many salmon rivers in Britain and Ireland would likely benefit from similar attention.

Andy Ferguson 

April 2020