Salmon Hatchery Strategic Research Plan 2004

![](media/image1.png){width="2.1in" height="1.6298611111111112in"}

**Conservation Biology Division**

**Resource Enhancement and Utilization Technologies Division**

**Northwest Fisheries Science Center**

**National Oceanic and Atmospheric Administration**

**2725 Montlake Blvd. E.**

**Seattle, WA 98112**

**(206) 860-3234**

http://www.nwfsc.noaa.gov/research/divisions/cbd/index.cfm
<http://www.nwfsc.noaa.gov/research/divisions/reutd/index.cfm>

Executive Summary

This document provides an overview of both ongoing and planned hatchery
related research by the Conservation Biology (CB) and Resource
Enhancement and Utilization Technologies (REUT) Divisions of the
Northwest Fisheries Science Center (NWFSC), National Marine Fisheries
Service, National Oceanic and Atmospheric Administration
(NOAA-Fisheries). NWFSC hatchery research programs address needs to
develop and implement agency-related guidelines for both production and
conservation hatcheries. The programs focus on five primary research
themes: 1) determining the relative lifetime fitness of hatchery and
natural salmon, 2) assessing the ecological and genetic risks and
benefits of various types of hatchery programs, 3) improving fish
quality and health to achieve appropriate survival and fitness of salmon
after release from hatcheries and captive broodstock programs 4) testing
the effectiveness of supplementation in rebuilding depleted salmon
populations, and 5) identifying the scale of hatchery effects on natural
populations compared to habitat loss, harvest, and changes in ocean
productivity. Examples of priority areas for continuing and new research
over the next 3 to 5 years include the risk/benefit assessments of
hatchery programs, developing hatchery reform protocols to manage risk,
and effectiveness monitoring to determine if supplementation hatcheries
can rebuild natural populations. We shall update this plan and research
priorities on an annual basis.

# Introduction and Background

Artificial propagation of Pacific salmon and steelhead trout
(*Oncorhynchus* spp.) in hatcheries has proceeded for over a century
with the intent of enhancing fisheries and mitigating for loss of
habitat. Thus, augmenting fisheries was the major goal of conventional
(production) hatcheries. In recent times, the listing of multiple
species of Pacific salmon as threatened or endangered has mandated
changes in hatchery operations and management to rebuild native stocks,
or at least, do no harm to native stocks. The proposed new use of
artificial propagation to rebuild native stocks (conservation
hatcheries) is largely untested, and major uncertainties remain
regarding how and if hatcheries can be used to rebuild stocks to
self-sustaining levels. Knowing the benefits and risks of hatcheries is
a particularly important issue for the NOAA Fisheries, which is charged
with management of salmon and other marine and anadromous fishes under
the Endangered Species Act (ESA) and the Magnuson-Stevens Fisheries
Conservation and Management Act. Furthermore, the NOAA Fisheries draft
policy on salmon hatcheries considers some hatchery stocks as part of
the Evolutionarily Significant Units (ESUs), and must be included in
listing considerations.

Within the NWFSC Salmon Research Plan, the over-arching question focused
on hatchery research is: To what extent do hatchery operations of any
kind contribute to or mitigate the risk of extinction faced by wild
salmon populations?

Before hatcheries can be considered effective components of any recovery
strategy, key issues regarding hatcheries and natural populations must
be resolved. The major question is: can hatchery and natural production
be successfully integrated to conserve natural population vigor and
structure and allow sustainable fisheries? The framework for research is
contained in the report on Viable Salmonid Populations (VSP) and the
recovery of evolutionarily significant units. In this context, we must
determine how hatcheries affect population abundance, productivity,
spatial structure and diversity.

Unless substantial progress is made on these issues, it will be
difficult to recover many of the species already listed under the ESA,
prevent future listings, and build or maintain sustainable fisheries for
unlisted populations. Measuring, quantifying, and evaluating genetic and
ecological consequences of hatchery fish on wild populations are the
primary obstacles to assessing the conservation and sustainable
fisheries roles of hatcheries. At present, there is evidence that
hatchery programs can have both positive and negative effects on natural
populations, but low inferential power hinders our ability to predict
the nature or magnitude of these effects that will occur in any specific
situation. Despite the over 100 years of hatchery research and
technology development, there is a dearth of empirical evidence and
quantifiable data on genetic and ecological effects. There is a clear
sense of urgency in making progress on these questions---too many
populations are approaching extinction.

In the following plan we outline a strategy for salmon hatchery
research, and identify specific research themes and questions. Our
objectives are to describe 1) our scientific approach to address
pressing needs, 2) our current and short-term research priorities (1-3
years), and 3) our long-term research plans (3-10 years). In doing so,
we strive to provide a document that will assist in coordination and
tracking of our research both within and outside the Center and Agency.

# Program Mission and Expertise

Scientists in the CB and REUT Divisions represent a broad range of
scientific disciplines including behavioral and physiological ecology,
physiology, chemistry, microbiology, molecular biology, pathology,
nutrition, risk analysis, genetics, evolutionary biology, ecology, and
population biology. The missions of the Divisions includes preserving
the biological diversity of aquatic organisms, increasing scientific
knowledge and developing technology to better serve agency priorities on
fisheries enhancement/culture, harvest and full utilization of
resources. Program scientists provide technical support to NOAA
Fisheries policy makers and regulatory staff, and collaborate with other
agencies, tribes, and educational institutions on research and education
related to the management of Pacific salmon and other species.

#### 

Current Research and Research Approach

The hatchery research program focuses on five major themes:

1)  Determining the relative lifetime fitness of hatchery and natural
    salmon

2)  Assessing the ecological and genetic risks and benefits of various
    types of hatchery programs

3)  Improving fish quality and health to achieve appropriate survival
    and fitness of salmon after release from hatcheries and captive
    broodstocks

4)  Testing the effectiveness of supplementation in rebuilding depleted
    salmon populations

5)  Identifying the scale of hatchery effects on natural populations
    compared to habitat loss, harvest, and changes in ocean
    productivity.

**1) Determining the relative lifetime fitness of hatchery and natural
salmon**

Most natural salmon populations contain some naturally spawning hatchery
fish, but their fitness relative to natural fish is rarely monitored. In
order to i) determine the effectiveness of hatcheries in rebuilding
depleted populations and ii) estimate the natural productivity of
ESA-listed populations, we conduct research to measure the relative
fitness of the naturally spawning hatchery fish compared to the natural
fish in the same stream. Estimation of annual average population growth
rates (lamdas) for ESA-listed salmon and steelhead populations are quite
sensitive to assumptions about the relative fitness of hatchery salmon.
Therefore, our research to quantify the relative lifetime fitness of the
hatchery fish is important for evaluating the viability of natural
populations.

Hatcheries have a variety of purposes, including mitigation for lost
habitat, harvest augmentation, supplementation of naturally spawning
populations, and conservation of genetic resources. Consequently,
broodstock sources, rearing and release practices, and genetic
management protocols vary widely. Broodstocks may be derived locally or
from an out-of-basin stock, and hatchery broodstocks may be comprised of
natural-origin adults, or adults from multi-generational hatchery
programs. We recently reviewed existing studies of the relative fitness
of hatchery fish, and found that gross differences in hatchery
broodstock management protocols appear to affect the relative fitness of
hatchery fish. However, the few published studies are heavily weighted
towards certain species and types of hatchery programs. Our research
plan is designed to fill major information gaps that exist for other
Pacific salmonids managed under other broodstock scenarios, such as
captive broodstocks and hatcheries incorporating broodstock of natural
origin.

**2) Assessing the ecological and genetic risks and benefits of various
types of hatchery programs**

Hatchery programs can be divided into two general categories, those that
exist primarily for harvest augmentation and habitat mitigation, and
those that exist for conservation and supplementation of wild
populations. The potential genetic and ecological risks of hatcheries on
wild populations is expected to vary according to species, broodstock
management, hatchery rearing and release protocols, and characteristics
of the receiving habitat. To accurately assess the risks and benefits of
hatchery programs, this plan focuses on coordinated research in the
fields of population genetics, population ecology, and behavioral
ecology.

Upon release, hatchery-produced salmonids interact ecologically with
wild fish. Competition for space and resources can affect growth,
survival and habitat use. Diseases can be transmitted between
populations, reducing the growth and survival of the susceptible
population. Hatchery releases can affect predator-prey relationships
with consequences ranging from cannibalism to increased predation risk
(e.g., predators are attracted to high densities of juvenile salmonids).
Hatchery smolt releases may also affect the migratory behavior of wild
salmonids. The magnitude of the risks associated with hatchery fish may
depend on both the hatchery release strategy (e.g., fry vs. smolts) and
the fish density in the receiving habitat. We conduct ecological and
behavioral experiments in the laboratory and field to determine the
mechanisms responsible for negative ecological interactions between
hatchery and wild fish, and how we can manipulate hatchery rearing and
release practices to minimize risk to wild salmonid populations.

We need to continue research evaluating the genetic impacts of hatchery
fish on natural populations. Genetic effects of hatcheries include
relaxation from natural selection, domestication, and inbreeding and
outbreeding depression. Studies on inbreeding and outbreeding depression
are on-going, critical and necessary for target species, although they
are major efforts because of the long generation time and complex life
cycle of Pacific salmon. Genetic modifications affect fitness, and it is
imperative that these effects be quantified and their reversibility be
determined. For captive broodstock programs, breeding schemes and
measures to minimize domestication must be developed to extend the
number of generations that fish can be kept in captivity before fitness
is lost.

**3)** **Improving fish quality and health to achieve appropriate
survival and fitness of salmon after release from hatcheries and captive
broodstocks**

We plan to continue conducting research on the quality and health of
fish produced from a variety of hatchery programs. Hatchery programs
range from those that spawn ocean-returning adults and release juvenile
offspring to captive broodstocks that rear salmon full-term to maturity
and release them or their offspring at various life-history stages.
Successful integration of hatchery fish into natural populations depends
on producing fish with desirable fitness traits. Assessment of
ecological risks and benefits of introduction of animals into the wild
identifies critical traits including juvenile survival, age of
smoltification, age of maturation, adult survival, mating success,
fertility and female fecundity. Hatcheries are intended to enhance
juvenile survival, but they may modify growth, development and behavior
of salmon, which may enhance or reduce their fitness. For segregated
hatcheries (production-type) the goal is to enhance juvenile and adult
survival, but limit reproductive success to minimize introgression into
the wild population. For integrated hatcheries (supplementation) the
goal is to enhance juvenile and adult survival and achieve an
appropriate level of natural reproduction to boost natural productivity.

For hatcheries that release juveniles prior to or during smoltification,
numerous rearing parameters can affect their post-release survival and
fitness in the natural environment. In general, salmon in hatcheries
grow faster than in the wild. This may lead to modified patterns of
smoltification and maturation, which may reduce survival and fitness.
Research is aimed at regulating seasonal growth patterns to achieve
appropriate age of smoltification and maturation as observed in the
target natural population. In captive broodstock and rearing programs,
the aim is to synchronize male and female reproduction and produce high
quality gametes.

Releases of juvenile salmon at sites that are remote from the main
hatchery facility are intended to achieve spatial distribution of adults
in supplementation programs. Accordingly it is important to understand
appropriate homing imprinting cues and timing for this strategy to work.
Research is aimed at determining factors responsible for homing
imprinting and homing behavior. Salmon homing imprinting studies are
also needed to understand natural stray rates and potential gene flow
between populations.

Research on improving fish health includes identifying mechanisms of
pathogenesis, improved disease diagnostics and disease control measures
such as antimicrobial therapeutics and vaccines. A major effort is
underway to sequence the genome of *Renibacterium salmoninarum*, the
causative agent of bacterial kidney disease and the major disease
concern in Pacific salmon hatcheries. Such genomic approaches will aid
efforts to develop novel diagnostics and disease control tools.

Research is well underway to develop methodologies to produce
artificially propagated juveniles similar to their wild cohorts in
behavior and morhpology. Laboratory research on enriching the hatchery
habitat (e.g., cover, structure, substrate) and behavioral modifiers
indicates that foraging efficiency, social behavior, predator avoidance,
and juvenile post-release survival can be enhanced through modification
of culture regimes. Habitat enrichment is currently being evaluated in
two ongoing smolt-to-adult survival studies. However, further
production-scale evaluations of these protocols and their interactions
are necessary to fully refine and validate concepts. Additionally,
research is being planned on engineering habitats to stabilize and
enhance natural stream-type rearing opportunities in urban environments.

Continued development and refinement of captive broodstock technology is
necessary to provide optimal mechanisms to stabilize ESA-listed salmon
populations until recovery actions succeed in addressing factors for
their decline. Captive broodstocks grown under current technologies
suffer from less than optimal culture environments that can affect
health, reproduction, behavior and survival. Our research focuses on
learning whether performance in culture and after release can be
improved by modifying rearing protocols, and identifying the underlying
mechanisms responsible for deficiencies. Our research program aims to
improve reintroduction success, olfactory imprinting and homing,
physiological development and maturation, in-culture survival through
prevention and treatment of disease, and evaluate effects of inbreeding
and inbreeding depression. We approach these goals through coordinated
studies on nutrition, physiology, microbiology, genetics, behavior, and
ecology.

**4) Testing the effectiveness of supplementation in rebuilding depleted
salmon populations**

There are a number of supplementation programs in the Columbia River
Basin and elsewhere that are designed to enhance imperiled salmon and
steelhead stocks, but the efficacy of hatchery supplementation to
recover salmon or steelhead populations has not been demonstrated. The
lack of examples of successful (or failed) supplementation programs is
at least partly due to the fact that virtually none have been adequately
monitored, which is a critical uncertainty. Our current research
includes evaluation of small-scale supplementation programs (i.e.,
individual populations). As indicated by the NWFSC's Recovery Science
Review Panel, it will be imperative that larger scale replicated
experiments be undertaken to adequately assess salmonid population
demographic and genetic responses to supplementation. We are
concurrently developing population abundance models that will predict
the effectiveness of supplementation under different assumptions of
habitat quality reproductive success, survival, genetic fitness, and
harvest. Data from items 1-3 above will be used to parameterize
population abundance models and improve the accuracy short- and
long-term predictions.

**5) Identifying the scale of hatchery effects on natural populations
compared to habitat loss, harvest, and changes in ocean productivity.**

There are several potential mechanisms by which hatchery releases could
impact the dynamics of natural populations, such as predation,
competition for food or space, infectious disease transmission, or
genetic changes. The existence of these mechanisms can be demonstrated
by laboratory or field experiments outlined in the first four research
themes. However, in order to quantify the effect that hatchery programs
have on natural population growth rates (lamdas) and compare these
effects to factors such as habitat degradation, it is necessary to
conduct experiments or analyses on a landscape scale. The most powerful
way to address this issue is through experimentation that involves
manipulating hatchery operations on a large spatial scale. While this
may be the ideal approach to answering this question, the scale and
implication of such work requires a strong *a priori* demonstration of
its relevance. In order to design good experiments, it will also be
necessary to have a good understanding of the patterns of hatchery
releases and natural population growth rates prior to experimental
manipulations. Therefore, before undertaking large scale experimental
manipulations of hatchery operations, a thorough exploration and
analysis of existing hatchery and natural population data are warranted.

The questions we seek to answer include:

-At what spatial and temporal scales do hatchery operations impact
natural populations?

-How large are the impacts of hatcheries compared to other factors, such
as habitat loss, harvest, and changes in ocean productivity?

-How do different types of hatcheries impact natural population?

-What are the optimal experimental designs to measure the impacts of
hatcheries?

Through the recent ESA Status Review Update and Technical Recovery Team
efforts, reasonably complete data sets of hatchery releases and natural
population abundance of anadromous salmonids in the Northwest have been
compiled. The Cumulative Risk Initiative (CRI) will assess the
applicability of these data to analyses of ecological impacts of
artificial production on natural populations. Where the data
quality/quantity are appropriate, this group will use
statistical/analytical tools to answer the four questions outlined
above. Where the current data quality/quantity are not sufficient to
support analysis, CRI staff will develop guidelines for monitoring
artificial production operations such that future assessments will be
possible.

# Programmatic Organization

The Center's hatchery research is organized in five programs across two
divisions; the Conservation Biology (CB) Division and the Resource
Enhancement and Utilization Technologies (REUT) Division (figure 1). The
Divisions are separately organized based, in part, on scientific
disciplines in biology. CB Division houses geneticists and mathematical
biologists, whereas the REUT Division houses ecologists, behaviorists,
physiologists, and microbiologists. All of the research themes are
interdisciplinary, interrelated and require coordination among teams.
Moreover, interdisciplinary and broad-scale research of this nature
cannot be conducted without cooperation and collaboration from other
divisions within the Center and other agencies and organizations
throughout the region. Coordination is achieved through reviews and
discussions involving the Center's Salmon Science Coordinator and the
salmon science Division Directors, in addition to Program Managers, Team
Leads and scientific staff.

> > Figure 1. Organizational structure of the Hatchery Research Program.
> > This includes only the government employees. In addition, the
> > Program includes approximately 15 non-government employees
> > (contractors, graduate students, and interns) who are instrumental
> > in conducting our research and day-to-day business.

## Prioritizing Research and Allocating Resources {#prioritizing-research-and-allocating-resources .unnumbered}

The prioritization of key research needs and questions under each of the
five research themes and teams requires periodic meetings with both
regulators and scientists within and outside the agency. We have gone
through an extensive planning and development effort to define pressing
research needs including meeting with NOAA Fisheries regulatory staff
and with stakeholders to define our research direction over the next
several years. Prioritization also involves attending key workshops and
professional meetings to report and promote our scientific research.
Moreover, we continue to meet with the Regional office and our
constituents to update our short-term research plans and objectives and
to assure that we are focusing our efforts on the most pressing applied
research questions.

Based on these periodic meetings, we prioritized our current and
proposed future research in one of three categories:

-   High (Priority 1), the most pressing needs for NOAA Fisheries
    science in the next 3 to 5 years

-   Medium (Priority 2), important needs for which some information
    exists, or where we can leverage funds from other agencies

-   Low (Priority 3), those needs for which some information currently
    exists but additional information is required to reduce uncertainty.

> Table 1. Draft timeline for initiation and completion of Watershed
> Program major research areas and projects. Base funding represents
> annual funding from NOAA Fisheries. Other funding represents outside
> funds or short-term grants received from within NOAA. Priorities 1, 2,
> and 3 are high, medium, and low, respectively. Dark gray shading
> indicates fully funded projects and light gray partially funded
> projects. Asterisks indicate research area or projects that are a
> priority in the next 3-5 years.

  ----------------- ------------------ -------------- ---------- ----------- ---------- ---------- ---------- ---------- ------- ------- -------- --------
                                       **Research**   **FY03                 **Fiscal                                                             
                                                      Funds**                Year**                                                               

  **Research                           **Priority**   **NOAA**   **Other**   **4**      **5**      **6**      **7**      **8**   **9**   **10**   **11**
  Area/Project**                                                                                                                                  

  **1. Estimating                                                                                                                                  
  relative                                                                                                                                        
  fitness**                                                                                                                                       

                    1a. Little Sheep   1                         95          190        204        210        217                                  
                    Creek                                                                                                                         

                    1b. Minter Creek   1              42         100         142                                                                   

                    1c. Wenatchee      1                                     415        415                                                        
                    River                                                                                                                         

                    1d. Lostine River  1\*                       130         91         94         96                                              

                    1e. Catherine                                130         91         94         96                                              
                    Creek                                                                                                                         

  **2A. Assessing                      1                                                                                                           
  genetic risk**                                                                                                                                  

                    2Aa. Snake River   1                         170         75         77         80         82                                   
                    Monitoring                                                                                                                    

                    2Ab. Life history  1                                                                                                           
                    evolution                                                                                                                     

                    2Ac. Inbreeding    1                         146         154                                                                   
                    depression                                                                                                                    

                    2Ad. Outbreeding   1              165                    245                                                                   
                    depression (Hard)                                                                                                             

                    2Ae. Response to   2                                                                                                           
                    Selection                                                                                                                     

                                                                                                                                                   

                                                                                                                                                   

  **2B. Assessing                                                                                                                                  
  ecological risk**                                                                                                                               

                    2Ba. Foraging and  1              100        150         250        250        250        250                                  
                    behavior (Riley)                                                                                                              

                    2Bb. Density,      1              100        200         300        300        300        300                                  
                    social behavior,                                                                                                              
                    habitat use                                                                                                                   
                    (Riley)                                                                                                                       

                    2Bc. Steelhead     1              100        150         250        250        250                                             
                    competition                                                                                                                   
                    (Berejikian)                                                                                                                  

                    2Bd. Competition   1              0          500         500        500                                                        
                    of hatchery& wild                                                                                                             
                    offspring                                                                                                                     
                    (Berejikian)                                                                                                                  

                    2Be. Hatchery      1              100        300         250        250        250                                             
                    spawner density                                                                                                               
                    (Berejikian)                                                                                                                  

                                                                                                                                                   

                                                                                                                                                   

                                                                                                                                                  

  **3. Fish quality                                                                                                                                
  and health**                                                                                                                                    

                    **Physiology**                                                                                                                

                    3a.. Reproductive  1              50         250         300        300        300        300                                  
                    performance of                                                                                                                
                    salmon (Swanson).                                                                                                             

                    3b. Smolt quality  1              100        350         450        450        450        450                                  
                    and precocious                                                                                                                
                    maturation of                                                                                                                 
                    Chinook salmon                                                                                                                
                    (Larsen)                                                                                                                      

                    3c. New measure of 2              0          100         100                                                                   
                    growth rate                                                                                                                   
                    (Beckman)                                                                                                                     

                    3d. Growth rate    1              50         350         350        350        350        350                                  
                    and early male                                                                                                                
                    maturation                                                                                                                    
                    (Swanson)                                                                                                                     

                                                                                                                                                  

                    3e. Virulence      1              100        100         200        200        200        200                                  
                    factors of                                                                                                                    
                    bacterial                                                                                                                     
                    pathogens (Rhodes,                                                                                                            
                    Strom)                                                                                                                        

                    3f. Vaccines for   1              50         125         175                                                                   
                    BKD control                                                                                                                   
                    (Rhodes, Strom)                                                                                                               

                    3g. Molecular ID   1              40         0           40                                                                    
                    of R. sal. Strains                                                                                                            
                    (Strom)                                                                                                                       

                    3h. Genome         1              0          450         450        50                                                        
                    sequencing of R.                                                                                                              
                    sal. (Strom)                                                                                                                  

                    3i. Anti-predator  1              0          220         220        220                                                        
                    conditioning                                                                                                                  
                    (Berejikain)                                                                                                                  

                    3j. Minimize       1              100        300         300        300                                                        
                    straying (Dittman)                                                                                                            

                    3k. Homing         1              50         0           300        300        300                                             
                    fidelity of                                                                                                                   
                    satellite                                                                                                                     
                    acclimation                                                                                                                   
                    (Dittman)                                                                                                                     

                    3l. Hatchery       1              400        500         500        500        500                                             
                    environment                                                                                                                   
                    (Maynard)                                                                                                                     

                                                                                                                                                   

  **4                                                                                                                                              
  Supplementation                                                                                                                                 
  effectiveness**                                                                                                                                 

                                                                                                                                                   

  **5. Large scale                                                                                                                                 
  analysis**                                                                                                                                      

                    CRI hatchery       1              100        200                                                                               
                    research                                                                                                                      

                                                                                                                                                   

                                                                                                                                                   

                                                                                                                                                   

                                                                                                                                                   

  **Total                                             **1647**   **5016**    **6338**   **5104**   **3632**   **2149**   **0**   **0**   **0**    **0**
  (thousands                                                                                                                                      
  \$\'s)**                                                                                                                                        
  ----------------- ------------------ -------------- ---------- ----------- ---------- ---------- ---------- ---------- ------- ------- -------- --------