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How hatcheries threaten wild salmon and steelhead recovery

When salmon and steelhead were listed in the late 1990s, the National Marine Fisheries Service created a regulation that permits hatcheries, which are run by various states and tribes. Hatcheries exist so Idaho can have a salmon and steelhead fishery (i.e., anglers can fish and keep the hatchery salmon and steelhead they catch). Hatcheries also exist to supplement fish for Pacific Northwest Tribes, whose land and primary food source the U.S. Government has stolen. However, science over the past decade has increasingly revealed how hatcheries can damage wild salmonids’ recovery potential.

Hatcheries may be integrated hatcheries, or they may be segregated hatcheries. Integrated hatcheries use broodstock (mature fish to breed the next generation) from the wild fish population. Even though integrated hatcheries are often aimed at conserving and recovering the fish species, they can negatively impact the genetics of the wild populations if not operated carefully for the same genetic reasons described below. Segregated hatcheries, however, use hatchery (not wild) broodstock, so fish are genetically distinct from their wild counterparts. Segregated hatcheries are intended to supplement rivers and streams with salmon and steelhead that recreational anglers can catch and keep. Most of the hatcheries in Idaho are segregated hatcheries. While either type of hatchery can injure the potential for wild fish to recover, segregated hatcheries have greater negative impacts.

Hatchery fish can ecologically and genetically threaten the survival of wild fish. Ecologically, if habitat is limited and hatcheries release too many fish, those hatchery fish will compete for the limited space and resources needed by vulnerable and recovering wild fish populations. High densities of fish can inhibit individual growth, cause premature emigration, increase competition for food, and cause increased mortality. Additionally, studies have found that hatchery fish are more aggressive or dominant juveniles, which is problematic if they are bigger than their wild counterparts when they are released into streams. Instead of a path to recovery where the offspring of wild fish outnumber their parents and survive to successfully reproduce, these pressures allow wild offspring to merely replace their parents. If succeeding wild populations cannot outnumber the parents, wild fish numbers can never grow, and population growth is critical to eventual recovery. Competition therefore suppresses the recovery of wild salmon or steelhead populations. But, hatchery fish pose more than just ecological risks to wild fish—there are genetic risks as well.

To appreciate how segregated hatchery fish and their genetics might adversely impact wild fish, it is useful to understand the concepts of “genetic fitness” and “genetic selection.” “Genetic fitness” is the reproductive success of an organism with a specific genetic makeup (a “genotype”); genetic fitness is how many offspring a genotype leaves behind that survive and reproduce. Offspring production can fail (and lead to reduced genetic fitness) at many points: when eggs do not hatch, when fish do not survive their early life stages, when fish do not return from the ocean, or when fish do not mate. “Genetic selection” is the process where certain traits become more prevalent in a species than other traits. Both genetic selection and genetic fitness inform why segregated-hatchery fish pose potentially significant risks to wild salmon and steelhead.

Researchers have found that genetic selection occurring in hatcheries favor different traits than genetic selection in the wild. Genetic selection in hatcheries produce fish that thrive in hatcheries, but perform poorly in natural stream environments. And, research has found that these underlying traits can be passed onto the next generation. This is a problem when returning hatchery fish escape anglers’ hooks, return to spawn in streams, and cross-breed with the genetically wild salmon and steelhead. Because hatcheries in Idaho transport many hatchery smolt to area streams to release them, returning adults return to either the hatchery or the stream where they were released. Returning hatchery fish migrate upstream at the same time that the wild fish do, so there is a risk that they will interbreed. A wild-hatchery hybrid or a stream-hatched offspring of two hatchery parents will look wild because it is not tagged or has a clipped adipose fin, which marks the hatchery fish. But, genetically this offspring will have reduced genetic fitness and its hatchery ancestry will reduce the ability of natural-born fish to survive and breed, even if those genetic variants will eventually be weeded out through generations of wild reproduction.

And of course, the larger the releases of hatchery fish or smaller the populations of wild fish, the above factors become increasingly potent. For example, we have recently seen some all-time lows for ESA-listed steelhead. In 2018, according to the Fish Passage Center, there were only 53,536 steelhead that passed Lower Granite Dam. Of that number, only 12,135 (roughly 23 percent) were unclipped; yet this fact does not reveal the genetic makeup those fish have.

Hatcheries, especially segregated hatcheries, are introducing significant ecological and genetic pressures that will suppress wild salmon and steelhead recovery. Recovering wild populations is unlikely without addressing correcting the threat from hatcheries.


A more thorough discussion of the science above can be found in the following academic papers:

* Araki et al. 2010. Is hatchery stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys. Aquaculture 308:S2-S11.

* Araki et al. 2009. Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild. Biology letters 5:621-624, doi:10.1098/rsbl.2009.0315.

* Araki et al. 2008. Fitness of hatchery-reared salmonids in the wild, Evolutionary Applications ISSN 1752-4571 (a synthesis).

* Araki et al. 2007 Genetic Effects of Captive Breeding Cause a Rapid, Cumulative Fitness Decline in the Wild, Science 318: 100-103.

* Christie et al. 2012. Genetic adaptation to captivity can occur in a single generation. Proceedings in the National Academy of Sciences, Vol 109(1): 238-242.

* Cook, Katrina V. Robert J. Lennox, Scott G. Hinch, Steven J. Cooke. 2015. Fish Out of Water: How Much Air is Too Much? Fisheries Volume 40 2015 – Issue 9 Published online

* Cooke, S. J., G. D. Raby, M.R. Donaldson, S. G. Hinch, C. M. O’Connor, R. Arlinghaus, A. J. Danylchuk, K. C. Hanson, T. D. Clark, and D. A. Patterson. 2013.The physiological consequences of catch-and-release angling: perspectives on experimental design, interpretation, extrapolation and relevance to stakeholders. Fisheries Management and Ecology 20: 268 – 287.

* Cooke, S.J. and C. D. Suski. 2005. Do we need species-specific guidelines for catch-and-release recreational angling to effectively conserve diverse fishery resources? Biodiversity and Conservation 14: 1195 – 1209.

* Ferguson, R. A. and B. L. Tufts. Physiological Effects of Brief Air Exposure in Exhaustively Exercised Rainbow Trout (Oncorhynchus mykiss): Implications for “Catch and Release” Fisheries Canadian Journal of Fisheries and Aquatic Sciences, 1992, Vol. 49, No. 6: pp. 1157-1162.

* Ford et al.2016. Broodstock history strongly influences natural spawning success in hatchery steelhead (Oncorynchus mykiss). Plos|One, DOI:10.1371/journal.pone.0164801

* Kostow 2009. Factors that contribute to the ecological risks of salmon and steelhead hatchery programs and some mitigating strategies, Rev. Fish Biol Fisheries 19:9-31.

* Richard, A., M. Dionne, J. Wang, and L. Bernatchez. 2013. Does catch and release affect the mating system and individual reproductive success of wild Atlantic salmon? Molecular Ecology 22: 187 – 200.

* Schreer J.F., Resch D., Gately M. & Cooke S.J. 2005. Swimming performance of brook trout following simulated catch-and release angling: looking for air exposure thresholds. North American Journal of Fisheries Management 25, 1513–1517.

* Twardek et al. 2018.  Consequences of catch-and-release angling on the physiology, behaviour and survival of wild steelhead Oncorhynchus mykiss in the Bulkley River, British Columbia.  Fisheries Research 206: 235-246.


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