The role of hatcheries in the decline of Lake Ontario Atlantic Salmon

Lake Ontario Atlantic Salmon were one of the first species of fish to be cultured in Canada. Their story goes from abundance in the 1700s to protective legislation in 1807, then hatchery culture in 1866 and finally ends in extirpation in 1898. The standard narrative is that Samuel Wilmot’s hatchery efforts briefly staved off their loss from the Lake Ontario basin. However, that story is replete with inaccurate assumptions, unfounded faith in technological solutions, and a belief that numbers of fish released was an accurate measure of success. We challenge the narrative around the perceived benefits of these hatchery efforts and suggest instead that they contributed to the decline of Atlantic Salmon in Lake Ontario through the mining of wild gametes, transferring eggs out of basin, mixing locally-adapted populations across streams, and the negative genetic effects of releasing hatchery fish.

Diary of Wimpy Fish: How to Grow Up in a Conservation Hatchery and Survive in the Real World

Conservation hatcheries are like luxury fish hotels that raise threatened and endangered fish that are nearing extinction in the wild. Raising fish in the controlled environment of the conservation hatchery usually takes away the issues that caused the population to dwindle in the first place. However, there is one problem: the fish get used to the conservation hatchery and become wimpy, meaning they become domesticated and do not do as well as wild fish in if they are returned to the natural environment. Managing the genes of hatchery fish is one way to block domestication and raise fish that are as close as possible to wild fish. In the San Francisco Estuary watershed, there are conservation hatcheries for the endangered delta smelt and winter-run Chinook salmon. Read on to learn about how these conservation hatcheries help hatchery fish be as tough as possible and survive in the wild.

Determining salmon provenance with automated otolith reading

Synthetic otolith marks are used at hundreds of hatcheries throughout the Pacific Rim to record the release location of salmon. Each year, human readers examine tens of thousands of otolith samples to identify the marks in salmon that are caught. The data inform dynamic management practices that maximize allowable catch while preserving populations, and guide hatchery investments. However, the method is limited by the time required to process otoliths, the inability to distinguish between wild and un-marked hatchery fish, and in some cases classification processes are limited by the subjective decisions of human readers. Automated otolith reading using computer vision has the potential to improve on all three of these limitations. Our work advances the field of automated otolith reading through a novel otolith classification algorithm that uses two neural networks trained with an adversarial algorithm to achieve 93% classification accuracy between four hatchery marks and unmarked otoliths. The algorithm relies on hemisection images of the otolith exclusively: no additional biological data are needed. Our work demonstrates a novel technique with modest training requirements that achieves unprecedented accuracy. The method can be easily adopted in existing otolith labs, scaled to accommodate additional marks, and does not require tracking additional information about the fish that the otolith was retrieved from.

Field assessments of heart rate dynamics during spawning migration of wild and hatchery-reared Chinook salmon

During spawning, adult Pacific salmonids ( Oncorhynchus spp . ) complete challenging upriver migrations during which energy and oxygen delivery must be partitioned into activities such as locomotion, maturation and spawning behaviours under the constraints of an individual's cardiac capacity. To advance our understanding of cardiac function in free-swimming fishes, we implanted migrating adult Chinook salmon ( Oncorhynchus tshawytscha ) collected near the mouth of the Sydenham River, Ontario, with heart rate ( f H ) biologgers that recorded f H every 3 min until these semelparous fish expired on spawning grounds several days later. Fundamental aspects of cardiac function were quantified, including resting, routine and maximum f H , as well as scope for f H (maximum−resting f H ). Predictors of f H were explored using generalized least-squares regression, including water temperature, discharge, fish size and fish origin (wild versus hatchery). Heart rate was positively correlated with water temperature, which aligned closely with daily and seasonal shifts. Wild fish had slower resting heart rates than hatchery fish, which led to significantly higher scope for f H . Our findings suggest that wild salmon may have better cardiac capacity during migration than hatchery fish, potentially promoting migration success in wild fish. This article is part of the theme issue ‘Measuring physiology in free-living animals (Part I)’.

Surface water with more natural temperatures promotes physiological and endocrine changes in landlocked Atlantic salmon smolts

Hatchery salmonid smolts are often reared using groundwater with elevated temperatures to maximize growth. Previous work has shown that rearing hatchery smolts in surface water with a more natural thermal regime resulted in increased return rates of adult landlocked Atlantic salmon (Salmo salar). We evaluated whether landlocked Atlantic salmon reared in surface water with a natural temperature regime have altered physiological smolt characteristics compared with fish reared in groundwater with elevated winter temperatures. Hatchery fish were sampled three consecutive years from January to May. Additional fish were released as smolts, recaptured, and compared with fry-stocked smolts. Surface water smolts had earlier peaks of plasma T4, lower T3 levels, later peak cortisol, and lower gill Na+/K+-ATPase activity as compared with groundwater smolts. After release and recapture, surface water fish had elevated plasma T4 and gill Na+/K+-ATPase activity compared with groundwater fish, but less than stream-reared fish. Elevated plasma T4 in surface water fish in the hatchery and after release may have promoted imprinting and other aspects of smolt development, contributing to the higher adult return rates of a cohort reared in surface water.

Can we identify wild-born salmon from parentage assignment data? A case study in the Garonne-Dordogne rivers salmon restoration programme in France

Parentage assignment with genomic markers provides an opportunity to monitor salmon restocking programs. Most of the time, it is used to study the fate of hatchery-born fish in those programs, as well as the genetic impacts of restocking. In such analyses, only fish that are assigned to their parents are considered. In the Garonne-Dordogne river basin in France, native salmon have disappeared, and supportive breeding is being used to try to reinstate a self-sustained population. It is therefore of primary importance to assess the numbers of wild-born returning salmon, which could appear as wrongly assigned or not assigned, depending on the power of the marker set and on the size of the mating plan. We used the genotypes at nine microsatellites of the 5800 hatchery broodstock which were used from 2008 to 2014, and of 884 upstream migrating fish collected from 2008 to 2016, to assess our ability to identify wild-born salmon. We simulated genotypes of hatchery fish and wild-born fish and assessed how they were identified by the parentage assignment software Accurassign. We showed that 98.7% of the fish assigned within the recorded mating plan could be considered hatchery fish, while 93.3% of the fish in other assignment categories (assigned out of the mating plan, assigned to several parent pairs, not assigned) could be considered wild-born. Using a Bayesian approach, we showed that 31.3% of the 457 upstream migrating fish sampled from 2014 to 2016 were wild-born. This approach is thus efficient to identify wild-born fish in a restoration program. It remains dependent on the quality of the recording of the mating plan, which we showed was rather good (<5% mistakes) in this program. To limit this potential dependence, an increase in the number of markers genotyped (17 instead of 9) is now being implemented.

Postrelease exploration and diel activity of hatchery, wild, and hybrid strain brown trout in seminatural streams

Behaviour that is adaptive in captivity may be maladaptive in the wild and compromise postrelease survival of hatchery fish. The understanding of behavioural variation displayed immediately after release could help to improve hatchery protocols and development of behavioural tests for assessing the fitness of fish reared for releases. We characterized the postrelease behaviour of common-garden-raised offspring of wild resident, captive-bred migratory, and hybrid brown trout (Salmo trutta) in two experiments: in small artificial channels and in high and low densities in seminatural streams. The results from seminatural streams showed that hatchery fish were more likely to disperse downstream from the initial stocking site compared with hybrid and wild strain fish. The small-scale experiment did not reveal this ecologically pivotal difference in postrelease performance among strains, and individual responses were inconsistent between the experiments. Circadian activity patterns did not differ among strains. These detailed observations of postrelease behaviour reveal important intrinsic differences in dispersal traits among brown trout strains and suggest that selective breeding and crossbreeding can substantially affect these traits.

Post-release exploration and diel activity of hatchery, wild and crossbred strain brown trout in semi-natural streams

Behaviours that are adaptive in captivity may be maladaptive in the wild and hence compromise after-release survival of hatchery fish. Understanding behavioural differences displayed straight after the release could help improving hatchery protocols and developing behavioural tests for assessing the fitness of fish reared for releases. We characterized the post-release behaviour in two experiments using parr from wild, hatchery and crossed strains of brown trout (Salmo trutta): in small-scale channels and in high and low densities in mesocosm streams. Our results show that hatchery fish were more likely to disperse downstream from the natal stocking site compared to crossbred and wild fish. Small-scale experiment was not sufficient in discovering this ecologically pivotal difference in post-release performance between strains, and individual responses were inconsistent between experiments. Circadian activity patterns were not found to remarkably differ between strains. This detailed empirical evidence of post-release behaviour improves our understanding of the low success of captive-reared fish in the wild. Mixing locally adapted wild fish in the broodstock could rapidly mitigate some of the behavioural effects of hatchery selection.