DRAFT

NOAA Recovery Planning Hatchery Module

Reference: Hatchery sections of Shared Strategy Draft Puget Sound Recovery Plan, excerpted to be standalone document. Source: Volume I, Chapter 3, pp. 111-121 and Chapter 6, pp. 427-436

(1) From “The Effect of Hatcheries on Puget Sound Chinook, HoodCanal Summer chum, and Coastal/Puget Sound Bull Trout,”Vol 1, Ch. 3, pp. 111-121

Hatcheries were traditionally operated for two main purposes-to mitigate for the reduction of salmon runs due to the construction of dams and other habitat loss, and to increase the number of fish available for harvest.

The science and practice of hatchery operation has advanced significantly over the past 100 years, but hatchery intervention into salmon runs has created long term genetic and evolutionary consequences that may never be fully mended. Hatchery management today still seeks to provide opportunity for fishers where the negativeconsequences of artificial propagation can be minimized and isolated. Additionally, many hatchery programs are now utilized as tools to salvage the remaining salmon populations and help maintain them as they rebuild to self-sustaining and harvestable levels. Hatcheries alone cannot achieve this goal, and it is widely recognized that they must operate hand-in-hand with habitat restoration if future salmon are to find a home.

[Deleted: History of Hatchery Production in Puget Sound]

Hatchery Hazards and Risks

Concerns over the artificial propagation of salmondate back at least 150 years to the early days ofsalmon culture, when a Scottish critic calling himself“Salmo” harangued hatchery proponents as, “menof tanks and incubators... and feeble drivellers whohave voted [the salmon] incompetent to dischargethe functions which constitute the chief end andobject of her existence.” (Lichatowich, 1999) Theadvocates of hatcheries in the Pacific Northwest inthe late 19th century were highly optimistic aboutthe potential contribution hatcheries could maketo Northwest rivers, but recognized that the successfultransplant of salmon to other streamswould require similar river conditions and carefulmanagement.

Although hatcheries have significant roles inrecovering species and providing harvest opportunity,unless they are carefully managed a number ofpotential hazards stem from their operation (Busackand Currens, 1995):

  • Long lasting changes to the genetic compositionof salmon populations may occur due tothe large numbers of hatchery fish that arereleased, altering the proportion and flow ofgenes among wild populations.
  • Hatchery programs may lead to domesticationby unintentionally or intentionally selecting forphysical traits and behaviors that improve thechance of fish surviving in the hatchery environment.These characteristics have the potentialto lower the fitness of salmon populations tosurvive and reproduce successfully in the wild.
  • The physical layout and management of hatcheryfacilities themselves may create adverseeffects through the removal of stream flow,placement of structures in the flood plain andthe emission of effluent.
  • Ecological effects occur when hatchery fishcompete with naturally-spawned populationsfor territory and food, or when other hatchery-produced species prey upon threatenedpopulations.
  • The risk of disease is elevated in the highlydense hatchery environment, and can spreadto wild populations.
  • Hatchery production may increase the riskof overharvest of wild fish if harvest regimestarget areas where the threatened populationsare mixed in with hatchery runs, unless thesefisheries are carefully managed for the needsof wild fish.

Loss of Population Identity

Natural populations of salmon are negativelyaffected by “gene flow,” the transfer of genes fromhatchery populations to natural ones. Recent studieshave indicated that the greater the amount ofgene flow and the dissimilarity between the hatcheryand wild fish populations in a given watershed,the greater the negative genetic effects. Gene flowcan cause a loss in unique identity and traits amongnatural populations of salmon, and within individualpopulations that receive hatchery fish.

The reduction in diversity among natural populationscan result where a single hatchery stock ispropagated over a wide area, such as the commonpractice of using Green River Chinook eggs formany decades in Puget Sound.

Mass transfers of salmon between rivers disruptedthousands of years of reproductive isolation anddestroyed the adaptive relationship between thesalmon and their home stream. The newly hatchedfry, deposited in rivers distant from their natalstream, had to face a new set of survival challengesthat were not part of their revolutionary legacy. Theadvantages of local adaptation were lost...”(Lichatowich, 1999)

Similarly, changes in diversity can occur within individual populations receiving hatchery fish. “Areduction in diversity and the effective size of thewild population can result from ‘genetic swamping,’where a large number of hatchery fish fromrelatively few parents interbreed with wild fish,”(HSRG, 2004).

The loss of genetic diversity may result in adecrease of the viability of a local salmon populationin two ways: 1) Loss of adaptation may occurwhen genes that evolved in a non-local environmentreplace those that were locally adapted; and2) hybridization results in recombinations of setsof genes that were favorable to a local population,leading to loss of individual performance andpopulation productivity that may not show up for ageneration or more.

Loss of Fitness

Loss of fitness can occur because of domestication,which is the change in the genetic compositionof a population as a result of selection for anartificial, captive environment (Busack and Currens,1995). Fish rearing in a hatchery for all or a portionof their life experience very different environmentsthan fish living in the wild. Fish with genetic traitsthat allow them to perform well in the wild may notsurvive as well in hatchery environments.Conversely,fish with genetic traits that allow them tosurvive better in the hatchery environments oftenperform more poorly in the wild. Hatchery environmentstend to select for fish that do well in thehatchery environment.

Because hatcheries can successfully producelarge numbers of fish, this can change the overallgenetic composition of the population. Over time,if fish adapted to the hatchery return to spawn inthe wild or natural-origin fish are used to producefish in the hatchery, the population is forced toadapt to two different environments, whichlowers the overall performance or fitness of thepopulation.

Effects of Hatchery Facilities

Most hatcheries withdraw water from segmentsof a stream as the water passes throughthe hatchery facilities and is then returned further downstream. In some cases, diminished flow canbe severe enough to affect migration and spawningbehavior. Injuries and mortalities can occur at thescreens where water is withdrawn. Hatchery effluentcan change water temperatures as well as otherchemical and nutrient levels.

Hatcheries that are utilized to incubate or rearthreatened populations also present special risks, asthe concentration of a large number of these preciouseggs in a single “basket” raises the possibilityof a catastrophic loss if equipment breaks downor water lines freeze. Restoration hatchery programsalso run the risk of “mining” the broodstockpopulation if they are unable to produce as manysuccessful returning spawners as the remaining wildcomponent of the population. Recent plans andreform initiatives have identified a number of potentiallyadverse impacts at Puget Sound hatcheries.Specific recommendations and actions to upgradehatchery facilities and operations to reduce the riskto threatened populations have been incorporatedinto Hatchery Genetic Management Plans and localwatershed plans, and implementation has commencedin many locations.

Ecological Effects

Ecological effects of hatchery fish include predationand competition for food and space. Hatchery-origin fish may prey upon juvenile wild Chinookin freshwater and estuarine areas, or compete forlimited food supplies and territory. A large mass ofmigrating hatchery fish may also attract concentrationsof birds, fish and seals, which contribute topredation on wild populations as well. A number ofprocedural changes have been incorporated by theco-managers in the operation of hatchery programsto minimize the risks to threatened populations,including alterations in the number, timing and locationof releases of hatchery-produced fish.

Potential threats to HoodCanal summer chumsalmon from negative interactions with hatcheryfish (late-timed Chinook, coho, pink, and fall chumsalmon) through predation, competition, behaviormodification or disease transfer were identified bythe NMFS Chum Biological Review Team (2003).However, NMFS indicated that specific mitigationmeasures for hatchery programs which presenteda risk to summer chum had been identified andlargely implemented by 2000. Continued evaluationand reporting on hatchery threats to summerchum is conducted by WDFW and the Point NoPoint Treaty Tribes through the Summer ChumConservation Initiative (WDFW, PNPTT; 2000 andupdates).

Disease Transfer

Although the pathogens responsible for fishdiseases are present in both hatchery and naturalpopulations, hatchery-origin fish may have anincreased risk of carrying fish disease pathogens becausethe higher densities of rearing in the hatcherymay stress fish and lower immune responses. Asalmonid disease control policy was adopted byPuget Sound co-managers in 1998 to specify minimumfish health standards and conditions and proceduresfor egg and fish transfers, health inspectionand communication (NWIFC & WDFW, 1998). Thedisease control policy emphasizes the importanceof assessing the pathogen history of the fish, watersupply and watershed prior to release or transfers.

Hatchery Production and Harvest Management

The presence of large numbers of hatcheryproducedfish in ocean and Puget Sound fisheriesis thought to have exacerbated the risk to threatenedpopulations in the past, due to the harvestof mixed populations of wild and hatchery fish.Naturally-spawning populations, many of whichare low in abundance and productivity, are mixedin with populations from other river systems andwith hatchery fish, and may be overfished whereharvest rates were set high enough to take advantageof the hatchery production. However, currentharvest management plans carefully control thesemixed stock fisheries for the needs of wild fish.

Additionally, managers use tools, such as time-andareamanagement and mark-selective fisheries toconcentrate harvest on fish produced by hatcherieswithout exceeding allowable harvest rates for wildfish. As a result, some recreationaland net fisheries have been maintainedwhile harvest rates on mostwild Chinook stock have been greatlyreduced over the past 10 years (seeFigure 3.32).

Until the development of “codedwire-tags” in the 1970’s, fisheriesmanagers lacked tools to assessthe fate of fish once they left thehatchery. The coded tags, 1 mm inlength, are inserted into the nose ofjuvenile salmon prior to release. Tagsare recovered from fish harvestedin commercial and sport fisheries as well as thecarcasses of adults that have spawned in naturalareas or at hatcheries. The tags help managersobtain data on specific populations, providing cluesto the proportional relationship between hatcheryand natural origin fish and where, when and howthe fish are caught.

Hatchery Threats to Bull Trout

Bull trout have not been extensively culturedin any part of the species’ range, thus limitingthe potential genetic and biological risks associatedwith hatcheries. Extensive supplementationprograms are not considered to be necessary, andthe potential use of hatcheries has generally beenlimited to genetic reserves and restoration restockingin watersheds where a population has beenextirpated. The operation of hatchery facilities suchas weirs and water intakes may have some impactsto bull trout, and correction of these threats is intendedto be integrated with other hatchery reformefforts (USFWS, 2004). Although the interaction ofhatchery species of salmon, steelhead or cutthroattrout with bull trout are cited as a potential threat,it is unclear whether these species serve primarilyas prey for the bull trout, or whether they increasecompetitive pressure.

Hatchery Reform

Although fish rearing practices have continuallyimproved in hatcheries over the last 100 yearsbecause of advancements in science, the developmentof the Puget Sound Salmon ManagementPlan in 1985 provided support to fundamentallychange the direction of hatchery operations inWashingtonState. Tribal and state co-managersdeveloped and implemented several important productionguidelines and policies, including guidelinesfor fish transfers and spawning operations to minimizegenetic loss, a salmonid disease control policywhich limited the exchange of fish among watershedsto help prevent the spread of fish pathogens,and broodstock spawning protocols. Hatcherymanagers in the 1990s were also required toprepare detailed operations plans and completepermit requirements under the National PollutionDischarge Elimination System for producing healthyhatchery salmon populations and minimizing theireffects on wild salmon. The Wild Stock RestorationInitiative began in 1991 with a comprehensiveassessment of the status of local salmon andsteelhead stocks by the co-managers, known as theSalmon and Steelhead Stock Inventory (WDF et al.,1993) which continues to be updated on a regularbasis. Further efforts by the co-managers haveincluded an assessment of management practicesand proposed changes, and the development ofthe Wild Salmonid Policy (WDFW, 1997).

More recently, efforts toward hatchery reformrelated to threatened species have occurred on twointerrelated tracks. The Hatchery Scientific ReviewGroup, an independent panel of scientists, was convenedby the US Congress to evaluate Puget Soundhatcheries; and the State of Washington and PugetSound Treaty Tribes have prepared comprehensiveChinook resource management plans for harvestand hatchery management in response to thestatus of the Chinook populations and the requirementsof the Endangered Species Act.

Hatchery Scientific Review Group

In 1999 the US Congress convened an independentpanel of scientists called the Hatchery ScientificReview Group (HSRG) to evaluate Puget Soundhatcheries and provide recommendations for howhatcheries can accomplish two objectives:

1) Conserve naturally spawning salmon andsteelhead populations; and

2) Support sustainable fisheries.

The evaluation process occurred from 2000to 2003 and a written report, Hatchery Reform: Principles and Recommendations, was issued bythe HSRG in 2004. In addition to the two primaryobjectives, the hatchery reform project was requiredto consider the relationship of artificial productionprograms to several legal mandates, including:

  • Treaty fishing rights and co-management statusof Puget Sound Indian tribes;
  • The US/Canada Salmon Treaty;
  • Applicable laws and responsibilities of the Stateof Washington; and
  • The US Endangered Species Act.

The Hatchery Scientific Review Group issueda number of system-wide recommendations forhatchery reform, along with approximately 1,000program-specific recommendations across theregion. These conclusions and recommendationsmay be viewed at TheHSRG also noted that a number of successfulhatchery programs are already operational, whichare helping to recover and conserve naturallyspawning populations, supporting sustainablefisheries, and/or providing other benefits such aseducation.

In addition to the scientific evaluation process,the US Congress appropriated funding for relatedresearch grants, implementation of early actionreform projects, and designated Long Live the Kings(a private, non-profit organization) as the facilitationand communications team for the project. TheHSRG and regional co-managers are continuing towork on monitoring and evaluation programs.

Comprehensive Chinook Salmon ResourceManagement Plan: Hatchery Component

The draft hatchery component of the PugetSound Comprehensive Chinook Salmon ResourceManagement Plan was jointly developed by theWashington Department of Fish and Wildlife andthe Puget Sound treaty tribes as part of the WildStock Restoration Initiative and completed in 2004.In response to ESA, it expands the biological assessmentof tribal hatchery programs submittedby the Bureau of Indian Affairs as a requirement ofSection 7 of the Endangered Species Act to all stateand tribal hatcheries. It also incorporates managementalternatives developed by the tribes and theNational Marine Fisheries Service, and draws fromthe recommendations of the Hatchery ScientificReview Group.

Several general principles guide the plan, includingthe following:

Hatchery programs need to assess and managethe ecological and genetic risks to naturalpopulations.

Hatchery programs need to coordinate withfishery management programs to maximizebenefits and minimize biological risks so thatthey do not compromise overall plans to conservepopulations.

Hatchery programs need protocols to managerisks associated with fish health, broodstockcollection, spawning, rearing, and release of juveniles;disposition of adults; and catastropheswithin the hatchery.

Benefits and risks from each artificial productionprogram for Chinook salmon in Puget Sound wereevaluated in multiple ways, resulting in a numberof improvements and commitments to Chinooksalmon programs in the region. The plan emphasizesthe use of indigenous broodstock, the reductionof egg and juvenile transfers between watersheds,the timing and location of hatchery releasesto avoid competition and predation, and a processof adaptive management. The plan also calls for anumber of net pen and other production programsto be terminated or reduced. State-of-the-art fishhealth monitoring, facility disinfecting and diseasemanagement procedures are established for theoperation of Puget Sound hatcheries. Specific facilitiesupgrades for screening, rearing or incubationare identified in some cases. The plan also calls fora number of research, monitoring and evaluationprograms to mark fish and to determine the effectsof competition and predation between hatcheryand natural fish.

The specific details for each hatchery programare contained in 42 Hatchery Genetic and ManagementPlans developed by state and tribal fisheriesmanagers. A Draft Environmental Impact Statementfor the implementation of the hatchery componentof the Comprehensive Puget Sound ChinookManagement Plan is presently in process and isexpected to be released in the summer of 2005.

NMFS Policy on the Consideration ofHatchery-Origin Fish in ESA ListingDeterminations of Pacific Salmon

On June 3, 2004, the National Marine FisheriesService issued a proposed policy to address therole of hatchery produced Pacific salmon in listingdeterminations under the Endangered Species Act(ESA) (69 FR 31354-31359). This policy supersededan interim policy on the artificial propagationof salmon under the ESA that was issued in 1993.In the past, NMFS had focused on whether thenaturally spawned fish are, by themselves, self-sustainingin their natural ecosystems when makinglisting determinations. Generally NMFS did notexplicitly consider the contribution of hatchery fishto the viability of threatened populations of salmon,and the potential that the hatchery fish couldreduce the risk of extinction. A 2001 decision bythe U.S. District Court in Alsea Valley Alliance v.Evans, 161 F. Supp. 2ad 1154 (D. Or. 2001) led tochanges in how NMFS considered hatchery fish inpopulation viability and extinction risk assessments.In that ruling, U.S. District Judge Michael Hoganfound that the ESA listing for the Oregon Coastalcoho salmon Evolutionarily Significant Unit (ESU)was invalid because the federal government did nottake into account genetically similar hatchery fishwith wild coastal coho in determining listing status.Judge Hogan did not determine how hatchery fishshould be taken into consideration, but he did holdthat they must be considered.