NOAA Technical Memorandum NMFS-NWFSC-119

Genetic Risks Associated with 

Marine Aquaculture

September 2012

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Northwest Fisheries Science Center
NOAA Technical Memorandum

NMFS-NWFSC Series

The Northwest Fisheries Science Center of the National 

Marine Fisheries Service, NOAA, uses the NOAA Technical 

Memorandum NMFS-NWFSC series to issue scientific and 

technical publications. Manuscripts have been peer reviewed 

and edited. Documents published in this series may be cited 

in the scientific and technical literature.

The NMFS-NWFSC Technical Memorandum series of the 

Northwest Fisheries Science Center continues the NMFSF/NWC series established in 1970 by the Northwest & 

Alaska Fisheries Science Center, which has since been split 

into the Northwest Fisheries Science Center and the Alaska 

Fisheries Science Center. The NMFS-AFSC Technical 

Memorandum series is now used by the Alaska Fisheries 

Science Center.

Reference throughout this document to trade names does not 

imply endorsement by the National Marine Fisheries Service, 

NOAA.

This document should be referenced as follows:

Waples, R.S., K. Hindar, and J.J. Hard. 2012. Genetic risks 

associated with marine aquaculture. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-119, 149 p.
NOAA Technical Memorandum NMFS-NWFSC-119

Genetic Risks Associated with 

Marine Aquaculture

Robin S. Waples, Kjetil Hindar,* and Jeffrey J. Hard

Northwest Fisheries Science Center

2725 Montlake Boulevard East

Seattle, Washington 98112

*Norwegian Institute for Nature Research (NINA)

N-7485

Trondheim, Norway

September 2012

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Most NOAA Technical Memorandums

NMFS-NWFSC are available at the 

Northwest Fisheries Science Center

Web site, http://www.nwfsc.noaa.gov

Copies are also available from the

National Technical Information Service

5285 Port Royal Road

Springfield, VA 22161

Phone orders: 1-800-553-6847

E-mail orders: orders@ntis.fedworld.gov

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Table of Contents

List of Figures...............................................................................................................................................v

List of Tables..............................................................................................................................................vii

Foreword......................................................................................................................................................ix

Executive Summary.....................................................................................................................................xi

Acknowledgments.....................................................................................................................................xvii

Introduction...................................................................................................................................................1

Background...............................................................................................................................................1

Objectives of the NOAA Aquaculture Program .......................................................................................3

Objectives of this Document.....................................................................................................................4

Lessons Learned............................................................................................................................................5

General Lessons........................................................................................................................................5

Lessons from Salmon Aquaculture...........................................................................................................6

Joint Lessons from Salmon Aquaculture and Hatcheries .........................................................................8

Lessons from Marine Stock Enhancement..............................................................................................10

Lessons from Agriculture .......................................................................................................................11

Synthesis.................................................................................................................................................16

Characterizing Risks and Benefits..............................................................................................................18

Potential Benefits of Artificial Propagation for Natural Populations .....................................................18

Genetic Risks to Natural Populations from Aquaculture........................................................................19

Other Risk Factors..................................................................................................................................37

Risks to Natural Populations from other Anthropogenic Activities .......................................................38

Managing Risk............................................................................................................................................39

Fault Tree and Risk Assessment Pathway ..............................................................................................39

Aquaculture Genetics Management Plan................................................................................................39

State and Federal Guidelines ..................................................................................................................39

Atlantic Salmon in Maine .......................................................................................................................42

Genimpact...............................................................................................................................................43

Examples of Risk Assessment Tools......................................................................................................44

Risk Trade-offs.......................................................................................................................................45
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Monitoring ..............................................................................................................................................45

Opportunities for Research .....................................................................................................................48

Frequently Asked Questions.......................................................................................................................50

Example ......................................................................................................................................................54

Information from the AGMP ..................................................................................................................54

Analysis ..................................................................................................................................................57

Monitoring Performance Indicators........................................................................................................57

Comments...............................................................................................................................................60

Discussion...................................................................................................................................................61

Glossary ......................................................................................................................................................65

References...................................................................................................................................................69

Appendix A: In-depth Material...................................................................................................................89

Sources of Information ...........................................................................................................................89

Lessons Learned......................................................................................................................................90

Characterizing Risks and Benefits........................................................................................................117

Managing Risk......................................................................................................................................134

Appendix B: Aquaculture Genetic Management Plan (AGMP)...............................................................137

1. General Program Description...........................................................................................................137

2. Relationship of Program to other Management Objectives.............................................................140

3. Facilities...........................................................................................................................................140

4. Broodstock Origin and Identity........................................................................................................140

5. Broodstock Collection .....................................................................................................................141

6. Mating..............................................................................................................................................142

7. Incubation and Rearing....................................................................................................................143

8. Program Effects on Natural Populations..........................................................................................144

9. Monitoring and Evaluation of Performance Indicators....................................................................146

10. Research.........................................................................................................................................146

11. Attachments and Citations.............................................................................................................148

12. Certification Language and Signature of Responsible Party .........................................................148

Attachment 1: Definition of Terms Referenced in the AGMP Template .............................................149
v

List of Figures

Figure 1. Worldwide production from wild-capture fisheries and aquaculture............................................1

Figure 2. Fault tree of events leading to introgression of genes from escaping cultured fish into 

the gene pool of wild relatives....................................................................................................................12

Figure 3. Schematic diagram of the Ryman-Laikre effect, which can reduce overall effective 

population size in a combined captive/wild system....................................................................................24

Figure 4. Rate of increase in heterozygosity in natural populations after factors reducing Ne

are eliminated..............................................................................................................................................27

Figure 5. Estimated time to reach 50% of the equilibrium FST value, assuming that anthropogenic 

activities have completely eliminated population structure and that, at time 0, levels of migration 

are restored that will eventually produce the equilibrium FST.....................................................................31

Figure 6. Hypothetical relationship between fitness of a wild population and the degree of genetic 

similarity between the wild population and a captive population from which some individuals 

routinely escape ..........................................................................................................................................35

Figure 7. Pathway for conducting an assessment of gene flow .................................................................40

Figure 8. Recent aquaculture production of Atlantic salmon in New England..........................................43

Figure 9. Monitoring should focus on specific measurable end points in the cascade of potential 

changes that might result from escape and spread of cultured individuals.................................................46

Figure A-1. Farm Atlantic salmon escapes, official Norwegian records ...................................................95

Figure A-2. Farm rainbow trout escapes, official Norwegian records.......................................................95

Figure A-3. Farm Atlantic cod escapes, official Norwegian records.........................................................96

Figure A-4. Reported number of escaped farm Atlantic salmon by year from hatcheries and

grow-out farms in Norway..........................................................................................................................97

Figure A-5. Percent farm escaped Atlantic salmon by year in river fishing during summer and in 

experimental catches during autumn shortly before spawning in Norwegian rivers..................................98

Figure A-6. Changes in the proportional constitution of the Atlantic salmon population in the River 

Imsa following the release of native wild and farm spawners..................................................................100

Figure A-7. Simulation of the number of sea lice produced in Norwegian waters as a consequence 

of growth in the salmon farming industry.................................................................................................104

Figure A-8. Simulation of the infection pressure of sea lice at different target levels of the number 

of sea lice per fish in fish farms................................................................................................................104

Figure A-9. Illustration of the Ryman-Laikre effect and consequences for effective population size.....122

Figure A-10. Time to reach migration-drift equilibrium in two groups of 10 subpopulations with 

different effective sizes.............................................................................................................................127

Figure A-11. Schematic representation of expected effects of increasing exploitation rate on several 

biological indicators of population and ecosystem health ........................................................................132
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List of Tables

Table 1. Contrasting goals of stock enhancement and aquaculture..............................................................5

Table 2. Comparison of biological and aquaculture-relevant characteristics of Atlantic salmon 

and marine fish species considered for genetic impact studies in Europe by the European Union 

Genimpact project.......................................................................................................................................13

Table 3. Key terms that quantify the Ryman-Laikre effect........................................................................23

Table 4. Results of applying equation 1 to various combinations of parameter values for the proposed 

aquaculture program for Species X, under two different options for sourcing broodstock ........................59

Table A-1. Compilation of genetic changes between cultured and wild salmonid populations in 

phenotypic traits..........................................................................................................................................99

Table A-2. Lifetime successes of wild, farm, and hybrid groups of Atlantic salmon in the Burrishoole 

system, Ireland, averaged over several cohorts where available...............................................................108

Table A-3. Examples of the Ryman-Laikre effect for some scenarios that involve relatively small 

fractional contributions from escapes.......................................................................................................123

Table A-4. Hypothetical examples showing how the Ryman-Laikre effect can result in an increase 

in NeT compared to what it would have been without a captive program, provided the Ne / N ratio is 

substantially higher in captivity than in the wild. .....................................................................................123

Table B-1. Example of performance standards........................................................................................138

Table B-2. Estimated natural fish take levels by aquaculture activity .....................................................147
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Foreword

The National Marine Fisheries Service (NMFS) Office of Aquaculture and scientists at 

NMFS fisheries science centers are leading the agency’s efforts to increase scientific knowledge 

in support of its regulatory and management missions pertaining to marine aquaculture. Critical 

scientific uncertainties need to be addressed to guide research, provide and communicate 

knowledge, and inform policy and regulatory decisions. There is a range of genetic issues in 

marine aquaculture, including genetic stock improvement for commercial culture, genetic risks 

to natural populations, management strategies for mitigating genetic risks, and development of 

tools to assess relative and acceptable risk. NMFS is sponsoring a series of white papers to 

address these genetic issues. This technical memorandum, Genetic Risks Associated with 

Marine Aquaculture, one such paper, is intended to provide an overview of potential genetic risks 

from a conservation perspective. It is a state-of-the-art summary, identifying areas where 

additional studies are needed, providing a framework for balancing risks, and supplying 

examples of how adequate monitoring and evaluation might be done. Additional papers will 

address genetic improvement, risk mitigation, and a risk assessment modeling effort.

This report is intended for a broad audience, including researchers, natural resource 

managers, policy makers, the aquaculture and fishing industries, the recreational fishing 

community, and the public. Accordingly, it is written in a style that should be readable by a 

broad but informed audience. Genetic terms are defined, complex genetic principles are 

described, and scientific jargon is avoided or moved to appendices.

The authors are experts in finfish genetics, particularly in conservation of genetic 

resources of salmonid populations and the interaction of natural and hatchery-reared populations. 

They have a global perspective and have drawn from the experience of a similar effort in Europe 

with the development of best management practices for genetic guidelines in aquaculture.

Walton Dickhoff

Director, Resource Enhancement and Utilization Technologies Division, Northwest Fisheries 

Science Center, Seattle, Washington

Michael Rubino

Director, Office of Aquaculture, National Marine Fisheries Service, Silver Spring, Maryland
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Executive Summary

Introduction

This technical memorandum is intended to provide managers with a better understanding 

of the genetic effects of marine aquaculture on natural populations, so that these factors can more 

effectively be incorporated into informed decisions pertaining to federal marine aquaculture 

policy and regulatory decisions. We do not attempt an exhaustive literature review of scientific 

information regarding this complex topic. Instead, in the main body of this report we attempt to 

synthesize relevant information in an accessible way, providing key references; interested readers 

can find more detailed treatments in Appendix A. Furthermore, the document does not provide a 

detailed treatment of ecological factors such as waste discharge/assimilation, competition, and 

disease, as those factors are considered elsewhere. We focus on commercial aquaculture of 

marine finfish, but also consider information for salmon hatcheries and marine stock 

enhancement.

Aquaculture is used to produce aquatic species for food and other human uses. Hatcheryproduced stocks are also used to replenish or supplement wild stocks of importance to 

recreational and commercial fishing, restore threatened or endangered species, or rebuild habitat 

such as oyster or coral reefs (referred to as enhancement or restoration aquaculture undertaken by 

public agencies). The global harvest of wild fish and shellfish has leveled off, but demand for 

protein from aquatic species continues to grow. As a consequence, aquaculture has been a fastgrowing system of food production worldwide during the past two decades (although not for the 

past 5 years in the United States). The last two to three decades have also seen a growing 

recognition of the importance of conserving natural populations and the profound ways in which 

anthropogenic changes to natural ecosystems can affect biodiversity. The paradigm of 

sustainable development emerged and is now widely applied to natural resources management. 

The Brundtland Commission report, Our Common Future (1987), defined sustainable 

development as “development that meets the needs of the present without compromising the 

ability of future generations to meet their own needs.” Applied to aquaculture, the concept of 

sustainable development raises an important question: How can global aquaculture production 

continue to increase without compromising long-term viability and sustainability of natural 

populations and the ecosystems on which they depend?

In the United States, the National Marine Fisheries Service (NMFS) has diverse and 

potentially competing responsibilities with respect to marine aquaculture:

1. Enable and support the growth of sustainable seafood production in the United States by 

aquaculture, including stock enhancement activities and commercial production.

2. Ensure that such growth is compatible with NMFS’stewardship responsibility for living 

marine resources.
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3. Encourage marine aquaculture activities that complement and support sustainable marine 

fisheries.

4. Protect and restore threatened or endangered species and habitats.

5. Develop a scientific framework to assist in permitting and regulating aquaculture and in 

making public policy decisions about commercial and replenishment aquaculture.

6. Develop a research program that takes advantage of opportunities provided by

aquaculture operations to address critical uncertainties and to educate the public about the 

benefits and risks of aquaculture.

This technical memorandum is intended to assist the agency in meeting some of these

responsibilities. Numerous marine species are already the subjects of commercial and 

enhancement aquaculture in the United States, and NMFS must make regulatory and policy 

decisions about aquaculture that are consistent with the agency’s stewardship responsibility for 

living marine resources. These decisions must consider a complex range of factors from the 

natural and the social sciences.

We begin by summarizing what has been learned over the past several decades from 

experience in three major arenas: salmon (Salmonidae) aquaculture and hatcheries, propagation 

of marine species, and agriculture. Important points include the following:

1. The most reliable way to ensure long-term sustainability is to conserve a diverse array 

of natural populations.

2. Some genetic change associated with artificial propagation is inevitable and can be 

desirable from a production standpoint; however, it is not inevitable that changes to 

cultured populations will have substantial genetic effects on natural populations.

3. A certain level of escapes probably cannot be avoided, particularly when production

is scaled to increase profitability; therefore, risk assessments should accept this reality 

and account for potential effects on natural populations.

4. However, to make a genetic impact, escapes must survive and reproduce successfully 

in the wild. The capability of escaped fish to do this can vary widely, depending on a 

variety of factors. In general, fitness in the wild of captively reared individuals 

decreases with number of generations in captivity.

5. Some genetic risks are inversely correlated, such that reducing one risk 

simultaneously increases another. For example, creating a genetically divergent 

aquaculture population might reduce the chances that escapes can survive and 

reproduce, but those that do can pass on maladapted genes to the natural population.

6. An effective monitoring component is important but cannot compensate for failure to 

implement risk-averse strategies. Even ambitious monitoring programs might have 

low power to detect adverse effects before serious harm is caused.

Characterizing Risks and Benefits

Informed decisions about appropriate use of marine aquaculture are best made following 

a comprehensive assessment of potential risks and benefits. The major genetic risks of 
xiii

aquaculture include loss of genetic diversity within populations, loss of genetic diversity among 

populations, and loss of fitness. These risks have been known and characterized for several 

decades and their potential effects on natural populations are increasingly well documented, if 

not always easy to predict. The genetic risks discussed in this document should be considered in 

conjunction with ecological risks discussed elsewhere.

Potential benefits are of two types: benefits to society and benefits to natural populations. 

Evaluating societal benefits (economic, social, political) involves a host of normative 

considerations and is not attempted here, but this is a crucial component of any comprehensive 

risk-benefit analysis. Of the potential benefits of artificial propagation for natural populations, 

reducing short-term extinction risk by maintaining a gene pool in captivity is best supported by 

empirical evidence. Artificial propagation also has been used successfully for some terrestrial or 

freshwater species to facilitate reintroduction into formerly occupied habitat. Neither of these 

activities is typically a goal of commercial marine aquaculture. However, two types of indirect 

benefits of aquaculture for natural populations might be applicable in some situations: 1) 

abundant aquaculture products can sometimes help alleviate fishing pressure on wild 

populations, and 2) biological information obtained through aquaculture operations can 

potentially aid species conservation.

Loss of Diversity within Populations

Genetic variability within populations provides the raw material for evolution and 

populations with low levels of genetic variability have less capacity to respond to changes in 

their environments. Levels of genetic variability within populations are determined largely by 

effective population size (Ne), which can be influenced by many factors, including aquaculture. 

Effective population size strongly influences levels of genetic diversity and the capacity to adapt 

to environmental change; Ne is typically lower—and in marine species, often substantially 

lower—than the population’s census size. Marine species are particularly susceptible to loss of 

within-population variability, because high fecundity and high survival during early life stages in 

captivity make it theoretically possible for just a few adults to contribute a large fraction of the 

genes to the natural population. In general, risks increase when Ne in the captive population is 

much lower than in the wild and when the fraction of natural spawners that are of captive origin 

is relatively high.

Loss of Diversity among Populations

Genetic diversity among populations confers resilience to natural systems on a variety of 

temporal and spatial scales. On an equivalent spatial scale, marine species generally show lower 

levels of molecular genetic differentiation among populations than do anadromous or freshwater 

species. However, several recent studies show surprisingly strong evidence for local adaptations 

among populations of marine species, including mobile and highly fecund fishes such as Atlantic 

cod (Gadus morhua). The major concern regarding loss of among-population diversity is that 

widespread escapes from one or a few aquaculture broodstocks will lead to replacement of 

existing patterns of locally adapted populations with a smaller number of relatively 

homogeneous ones. In many marine species, diversity among populations has evolved over 

many hundreds to thousands of years and cannot easily be regenerated once lost.
xiv

Loss of Fitness

Domestication is a process by which populations become better adapted to artificial 

environments. Because of the profound differences in selective regimes and mortality patterns 

between wild and aquaculture environments, domestication will occur to some extent when 

animals are reared under controlled conditions over several generations. Note that domestication 

does not require (nor generally involve) genetic change to or modification of individual fish; 

rather, it occurs across generations as certain individuals and their associated genotypes survive 

and reproduce at different rates than they would in the wild.

Although some level of domestication is probably essential in a profitable aquaculture 

operation, domesticated individuals are less fit in the wild, and if they reproduce successfully 

their progeny can depress fitness and compromise viability of the wild population. A related 

phenomenon, outbreeding depression, is the loss of fitness that occurs when individuals from 

two genetically divergent populations interbreed. Outbreeding depression can be facilitated by 

aquaculture operations that import nonlocal stocks that escape and interbreed with local 

populations. Use of local broodstocks will not avoid domestication, but it will avoid losses of 

fitness arising from translocation and subsequent interbreeding of genetically divergent 

populations. Some aquaculture operations will involve both factors (broodstock derived from a 

nonlocal source and strong domestication for market-related reasons).

Managing Risk

We discuss several tools that might be used to help manage genetic risks associated with 

marine aquaculture. We developed a framework for an Aquaculture Genetics Management Plan; 

this is based on a tool developed for hatchery salmon programs in the U.S. Pacific Northwest by 

the Hatchery Science Review Group, but modified here to better reflect particular issues 

associated with marine aquaculture programs. We also review Florida’s Genetic Policy for the 

Release of Finfishes in Florida, recent developments involving aquaculture and endangered 

Atlantic salmon (Salmo salar) in Maine, and Genimpact, a project supported by the European 

Union to evaluate the genetic impact of aquaculture activities on wild fish populations. An 

example using information for a permit application for a hypothetical marine aquaculture 

operation is used to illustrate some of the issues involved with assessing and managing genetic 

risks. A section on frequently asked questions addresses some specific topics that arise 

repeatedly in considering genetic consequences of artificial propagation. A number of riskaverse strategies can be employed to manage risk, including the use of triploid or sterile fish, 

shore-based systems, site selection, and improved containment technology, among others.

Discussion

Although marine aquaculture is a relatively new enterprise, artificial propagation of fish 

populations has been conducted for centuries, and the major genetic risks associated with salmon 

hatcheries and marine stock enhancement (loss of fitness, loss of diversity within and among 

natural populations) have been characterized for several decades. A key feature of these genetic 

risks is that they are proportional to the fraction of successful spawners in nature that were 

produced in captivity. Each of the major genetic concerns associated with these 

hatchery/enhancement programs is also a potential risk of marine aquaculture. However, 
xv

important differences also exist between marine aquaculture and hatchery/enhancement 

programs that can affect the likelihood that genetic effects will materialize. For this to occur, 

three conditions must be met: 1) captively reared individuals must enter the marine environment; 

2) some of these individuals must survive to sexual maturity, and 3) some of the mature adults 

must successfully reproduce, including some level of interbreeding with wild fish. For salmon 

hatcheries and marine stock enhancement programs, all three conditions are commonly met: 

captive individuals are intentionally released into the wild in the hope that at least some will 

survive long enough to be harvested at a substantially larger size, and those that aren’t harvested 

often reproduce in natural habitat (sometimes by design). The goals of marine aquaculture are 

quite different, as each of the three conditions leads to undesirable outcomes: escapes are 

economically costly and therefore unintentional, and survival and reproduction of escapes 

increases regulatory scrutiny while providing no economic benefits.

These considerations indicate that successful containment of genetic risks associated with 

marine aquaculture should focus on two general strategies: 1) prevent escapes and 2) ensure that 

individuals that do escape have a low probability of surviving to reproduce in the wild. The 

magnitude of genetic effects of marine aquaculture is determined primarily by how effective 

programs are at these two control points. Regarding the first point, a variety of methods can be 

used to reduce the probability of escapes, but it is generally recognized that no marine 

containment system will be 100% effective. The realized genetic effects of marine aquaculture 

on natural populations, therefore, will depend heavily on the subsequent fate of individuals that 

escape into natural habitats. According to one view, significant genetic introgression due to 

escapes from aquaculture is unlikely, because stocks used for aquaculture will either be sterile or 

so highly domesticated that survival and reproduction in nature is greatly compromised. The 

extent to which (and time frame over which) this actually occurs, however, is likely to vary 

considerably among species.

Currently, marine aquaculture is experimenting (or contemplating experimenting) with a 

wide variety of slightly domesticated and not-yet-domesticated species. Eventually, attention 

might focus on a relatively few, highly domesticated species, as occurs with terrestrial grain 

production and animal husbandry. If this happens, it might be the case that escaped individuals 

would have minimal success in the wild. In the interim, however, it seems likely that at least 

some marine aquaculture operations will use stocks that have an appreciable probability of 

surviving and reproducing in the wild, and in these cases the effectiveness of the first control 

point (preventing escapes in the first place) becomes increasingly crucial. Because no 

aquaculture system in the marine environment is perfect, it is important to consider program 

scale and duration in developing strategies to provide adequate safeguards for natural 

populations.

An alternative strategy for dealing with the consequences of escapes is to minimize 

domestication in the aquaculture broodstock, with the goal of minimizing the deleterious genetic 

effects of captive-wild interbreeding events that do occur. This strategy is widely used, for 

example, in hatchery supplementation programs for salmon that have a goal of improving the 

conservation status of a natural population. However, the differences between the captive and 

wild environments are so substantial that some erosion of fitness is impossible to avoid, even in 

the most enlightened programs; furthermore, this strategy will generally enhance survival and 

reproduction of aquaculture escapes and lead to elevated rates of introgression. Therefore, 
xvi

although development of locally derived broodstocks might have a role to play in the early stages 

of development of marine aquaculture, it is not a panacea.

Although the genetic risks posed by marine aquaculture are well understood in a general 

sense, considerable uncertainty is associated with predicting the exact consequences of any 

particular program. Furthermore, risks will vary according to biological attributes of the target 

species, but relatively little is known about the basic biology of many marine species that might 

be used in aquaculture. As a consequence, it is important for scientists, managers, and policy 

makers to discuss how to deal with uncertainty and what is an appropriate way to assign burden 

of proof. Should proposed operations be allowed to go forward unless it can be convincingly 

demonstrated that they will cause serious harm? Or should proposed operations not be allowed 

to proceed unless it can be demonstrated with a high degree of certainty that adverse effects will 

not occur?

These questions will repeatedly arise in considering the most appropriate ways to 

implement marine aquaculture. They cannot be answered by science alone, but how they are 

answered can have a profound effect on the nature and magnitude of aquaculture programs that 

are considered permissible. The same general questions, it should be noted, are relevant to 

assessing the consequences of other anthropogenic actions that affect marine populations (such 

as fishing or habitat modification), as well as the consequences of propagation programs that 

release large numbers of individuals of other taxa into the wild (e.g., birds, insects, trees).

Two critical uncertainties merit particular attention for focused research efforts. First, the 

factors that determine how likely escaped fish are to spawn naturally are diverse and poorly 

understood, but have a strong influence on actual genetic risks posed by marine aquaculture. 

Therefore, achieving a better understanding of how escapes function in the wild should be an 

important research priority. Second, the relative genetic consequences for natural populations of 

using local, lightly domesticated versus nonlocal, strongly domesticated broodstocks are 

complicated to assess. The first strategy will reduce divergence between captive and wild 

populations and hence the severity of interbreeding events that do occur, but will also generally 

lead to more captive-wild genetic interactions. The second strategy should reduce survival or 

reproductive capacity of escapes, but each interbreeding event that does occur is more likely to 

be deleterious. More research is needed to determine the conditions under which each strategy is 

more consistent with sustainability of natural populations.
xvii

Acknowledgments

For encouraging and supporting this project since its inception, we thank Michael 

Rubino, National Marine Fisheries Service (NMFS) Office of Aquaculture, and Walt Dickhoff, 

Northwest Fisheries Science Center (NWFSC). For useful discussions and sharing valuable 

information, we are grateful to Marissa Baskett, University of California Davis; David Bean, 

NMFS Protected Resources Division; Barry Berejikian, Bill Fairgrieve, Tom Flagg, Phil Levin, 

Conrad Mahnken (ret.), Mike Rust, and Nat Scholz, NWFSC; and Lars Mobrand, Hatchery 

Scientific Review Group. This document was considerably improved as a result of comments by 

David Alves, NMFS Northeast Regional Office; Kevin Amos, Lorenzo Juarez, and Michael 

Rubino, NMFS Office of Aquaculture; Suzanne Bolton and Kenric Osgood, NMFS Office of 

Science and Technology; Theo Brainerd, Southeast Fisheries Science Center; Chris Brown, 

Northeast Fisheries Science Center; Walt Dickhoff, Bill Fairgrieve, and Bob Iwamoto (ret.), 

NWFSC; Jennifer Ferdinand and Jeff Guyon, Alaska Fisheries Science Center; Stew Grant,

Alaska Department of Fish and Game; Lorenz Hauser and Fred Utter, University of Washington;

Dennis Hedgecock, University of Southern California; Kristen Koch, NMFS; Jeff Silverstein,

USDAAgricultural Research Service; Mike Tringali, Florida Fish and Wildlife Conservation 

Commission; Tim Tynan, NMFS Northwest Regional Office; and several anonymous reviewers 

on earlier drafts. This work was supported in part by funds from the NOAA Aquaculture 

Program.
xviii
Introduction

Background

Aquaculture (farming of aquatic organisms) has a long history in freshwater and marine 

systems. In the United States, scientists from the National Marine Fisheries Service (NMFS) or 

its precursor agencies have played a role in development and evaluation of marine aquaculture 

since the late 1800s (e.g., Earll 1880). But two recent developments have generated a new wave 

of interest in aquaculture. First, continued rapid growth of the global human population 

generates increasing demand for high-protein food sources, a trend expected to continue into the 

foreseeable future. However, for the last two decades, worldwide harvest of wild fish and 

shellfish has leveled off at around 80–90 million metric tons annually. In contrast, over this 

period aquaculture has been a fast-growing system of food production, increasing at a rate of 

nearly 9% per year (Figure 1). Aquaculture is widely viewed as becoming increasingly 

important in the future in helping to lessen the gap between worldwide demand for and 

production of protein, at least if it can do so without compromising the sustainable production of 

protein from fisheries. Nearly half of the fish consumed worldwide is now farmed, compared to 

9% in 1980, with most of the current farmed production involving freshwater species. Estimated 

aquaculture production would have to nearly double by 2050 to keep up with current per-capita 

consumption levels (FAO 2006).

Figure 1. Worldwide production from wild-capture fisheries and aquaculture. Data from FAO 2010.
2

A second major development over the last 2–3 decades has been growing recognition of 

the importance of biodiversity conservation and the profound ways in which anthropogenic 

changes to natural ecosystems can affect biodiversity (e.g., the Convention on Biological 

Diversity that emerged from the 1992 U.N. Conference on Environment and Development). On 

a global scale, the most pervasive anthropogenic changes to natural ecosystems involve loss and 

degradation of habitat, overharvest, and species introductions (Diamond 1989, Hilton-Taylor 

2000, Mace and Reynolds 2001). Potential effects of agriculture (including aquaculture) on 

biodiversity are also substantial, even when they are not dependent on introduced species. 

Aquaculture and stock enhancement generally involve direct intervention in growth and 

reproduction of target species; in many cases, intentional selection for production-related traits 

also occurs. These evolutionary changes in cultured species can have profound consequences for 

natural populations when cultured and wild individuals interact (Costa-Pierce 2002, Bert 2007). 

Wild progenitors of most domesticated animals have long since disappeared from the natural 

landscape, but that is not the case with the vast majority of species subject to aquaculture.

Not surprisingly, these two developments have generated a certain amount of tension, and 

as a result, a new and challenging problem has been identified: How can global aquaculture 

production continue to increase at a rapid pace without compromising long-term viability and 

sustainability of natural populations and the ecosystems on which they depend? In the United 

States, legislative and policy events over the past decade have focused attention on the promise 

and risks of aquaculture and broadened NOAA’s involvement in marine aquaculture (commercial 

and enhancement). Some of the key events include:

1. The Department of Commerce Aquaculture Policy (1999) set the following goals for 

2025:

• Increase the value of domestic aquaculture production (freshwater and marine) from 

$900 million annually to $5 billion.

• Develop aquaculture technologies and methods not only to improve production but 

also to safeguard the environment.

• Enhance depleted wild fish stocks through aquaculture.

2. The Final Report of the U.S. Commission on Ocean Policy (2004) called on the Secretary 

of Commerce to:

• Design and implement national policies for environmentally and economically 

sustainable marine aquaculture.

• Develop a comprehensive, environmentally sound permitting, leasing, and regulatory 

program for marine aquaculture.

• Expand marine aquaculture research.

3. In June 2005, the Marine Fisheries Advisory Committee asked NOAA to prepare a plan 

to support development of marine aquaculture in the United States. In response to this 

request, NOAA (2007) produced a “10-year Plan for Marine Aquaculture” that identifies 

four goals:

• A comprehensive regulatory program for marine aquaculture.
3

• Development of commercial marine aquaculture and replenishment of wild stocks.

• Public understanding of marine aquaculture.

• Increased collaboration and cooperation with international partners.

4. The Aquaculture Act of 1980 was reauthorized in the 2008 Farm Bill. The act calls on 

the departments of Agriculture, Commerce, and Interior to develop U.S. aquaculture.

5. The Magnuson-Stevens Reauthorization Act of 2006 calls for the end of overfishing, 

rebuilding of wild stocks managed by the federal government, and attention to the effects 

of fisheries regulations on coastal communities (e.g., alternative or supplemental 

employment).

6. NOAA (with other agencies) continues to administer the U.S. Endangered Species Act

(ESA), the Marine Mammal Protection Act, the National Environmental Policy Act, and 

other laws aimed at the conservation and protection of marine species and the marine 

environment.

7. In June 2011, following public comment, the U.S. Department of Commerce Aquaculture 

Policy and the NOAA Marine Aquaculture Policy were released. Potential competitive 

and genetic effects of aquaculture on wild species were among the identified 

environmental challenges to be addressed.

Several marine species are already subjects of commercial aquaculture in the United 

States, including Atlantic cod (Gadus morhua), cobia (Rachycentron canadum), striped bass 

(Morone saxatilis), pompano (Trachinotus spp.), yellowtail jack (Seriola lalandi), moi (Pacific 

threadfin, Polydactylus sexfilis), kahala (greater amberjack, Seriola dumerili), American lobster 

(Homarus americanus), Pacific oyster (Crassostrea gigas), hard clam (Meretrix lusoria), 

goeduck (Panopea abrupta), abalone (Haliotis spp.), and others. On a regular basis, NMFS must

make decisions about the nature of aquaculture programs that are consistent with the agency’s 

stewardship responsibility for living marine resources. These decisions must consider a complex 

range of factors from the natural and the social sciences. This technical memorandum is 

intended to provide managers with a better understanding of the potential genetic effects of 

marine aquaculture for natural populations, so that these factors can be incorporated more 

effectively into informed decisions about the appropriate role of marine aquaculture.

Objectives of the NOAA Aquaculture Program

It is clear from the material reviewed above that NOAA has several responsibilities with 

respect to marine aquaculture:

1. Facilitate and support the growth of sustainable seafood production in the United States

by aquaculture, including stock enhancement activities and commercial production.

2. Ensure that such marine aquaculture that comes under NOAA’s legal and regulatory 

mandates is compatible with NOAA’s stewardship responsibility for living marine 

resources.

3. Develop a scientific framework to assist in permitting and regulating aquaculture.
4

4. Develop a research program that takes advantage of opportunities provided by 

aquaculture operations to address critical uncertainties and educate the public about the 

benefits and risks of aquaculture.

Objectives of this Document

This report is intended to assist the agency in meeting some of the above responsibilities. 

We do not attempt an exhaustive literature review of scientific information regarding this 

complex topic; rather, we synthesize and summarize the relevant information and identify 

references that treat these topics in more detail for interested readers. Furthermore, the document 

will not consider ecological factors (such as waste discharge/assimilation, competition, and 

disease), except insofar as they might have evolutionary consequences for natural populations; 

ecological factors are treated elsewhere (e.g., Naylor et al. 2005, Ford and Myers 2008, Diana 

2009, Duarte et al. 2009). We will focus on commercial aquaculture of marine finfish (which is

typically designed to rear individuals in net pen cages that are intended to be self-contained) but 

will also consider information for marine stock enhancement (in which individuals are 

intentionally released into the wild for growth and maturity). Although the focus will be marine 

finfish, we also draw on the extensive literature for freshwater and anadromous species, as well 

as examples from aquaculture of marine invertebrates.

We begin with a summary of lessons that have been learned over the past several decades 

of experience with artificial propagation (including aquaculture) of anadromous and marine 

species. The next section, Characterizing Risks and Benefits, explores in detail the potential 

benefits and risks posed by commercial aquaculture and outlines the factors that should be 

included in a comprehensive risk-benefit assessment of a proposed aquaculture operation. In 

Managing Risk, we outline general and specific tools that can be used to help assess and manage 

risks. This section also includes discussion of methods for monitoring genetic consequences of 

marine aquaculture and identifies some critical uncertainties that merit additional research. We 

follow this with a section that includes answers to frequently asked questions about artificial 

propagation and its effects on natural populations. Finally, we include a worked example to 

show how the principles discussed here can be used to make decisions about appropriate use of 

marine aquaculture.

It is important to clarify our use of the word risk. Some authors (e.g., Currens and 

Busack 1995) have used the term to apply only to the probability that an event will occur. We 

use the term risk in the broader sense of “a factor, thing, element, or course involving uncertain 

danger”1 because this usage facilitates the discussion of risks and benefits. In the Glossary, we 

provide definitions of other key terms used in this document, particularly those that might not be 

familiar to nongeneticists. To allow a briefer and (hopefully) more readable treatment in the 

main text, detailed supporting material and many additional references have been moved to 

Appendix A. A reader looking for more information on a particular topic can look at the material 

under the same heading in this appendix.

 1 American Heritage Dictionary, third edition.
5

Lessons Learned

In this section, we synthesize and summarize what has been learned over the past several 

decades from experience in three major arenas: salmon aquaculture and hatcheries, propagation 

of marine species, and agriculture. More details and references on these topics can be found in 

Appendix A.

General Lessons

Expect the Unexpected

Unanticipated events inevitably occur during the course of a program or operation; this is 

particularly true for those working with new species or populations recently brought into culture. 

In most cases, these unexpected events lead to higher rather than lower risks to natural 

populations. This means that risk analyses that do not explicitly account for such events 

probably will underestimate risks and the potential for adverse effects on natural populations.

Program Goals

Risks and benefits are best evaluated in the context of program goals. The goals of stock 

enhancement and captive aquaculture are substantially different in terms of intended interactions 

with natural populations; this will influence how risks and benefits are monitored and managed

(Table 1). Stock enhancement programs generally incorporate wild individuals into the 

broodstock to minimize divergence from the wild population and intentionally release 

individuals into the wild, with the goal of enhancing harvest, the naturally spawning population, 

or both. In contrast, any interactions of aquaculture and wild fish are incidental and intended to 

be minimized. See the Characterizing Risks and Benefits section for more on this topic.

Adaptive Management

Lessons about effects on natural populations are often slowly learned from experience. 

The major types of genetic effects of cultured fish on natural populations have been known since 

Table 1. Contrasting goals of stock enhancement and aquaculture.

Stock enhancement Aquaculture

Incorporation of wild 

individuals into broodstock

Yes Sometimes

Release of cultured individuals 

into the wild

Intentional Accidental

Reproduction of cultured 

individuals in the wild

Intentional To be minimized
6

the early 1980s and are, for example, outlined by Allendorf and Ryman (1987), Hindar et al.

(1991), and Waples (1991). In subsequent years, these effects on natural populations have been 

increasingly well documented (Araki and Schmid 2010). However, it was a long time before 

attempts to address these concerns were made in many fishery management arenas, and even 

today these issues are commonly neglected in the fields of forestry and game management. 

Laikre et al. (2010) offer some possible explanations for this neglect; perhaps the most important 

is that potential benefits of stock enhancement are easy to visualize, while appreciation of longterm effects on natural populations requires a more nuanced understanding of biological systems. 

With respect to the current interest in taking advantage of potential benefits of marine 

aquaculture while providing adequate safeguards for natural biodiversity, the most effective 

approach will be to accept the reality of genetic risks and focus attention on understanding how 

the risks interact with key features of the marine environment, life histories of the species 

involved, and particular aspects of individual aquaculture programs.

Diversity of Natural Populations

Conservation of a diverse array of natural populations or native land races is the most 

reliable way to ensure long-term sustainability. This point has been made repeatedly by a long 

series of science panels that have reviewed this topic in recent decades (e.g., NRC 1996, NOU 

1999, Myers et al. 2004, NASCO at http://www.nasco.int).

Monitoring

An effective monitoring component is important but cannot compensate for failure to 

implement risk-averse strategies. Monitoring is necessary to estimate the magnitude of effects of 

a particular aquaculture or enhancement program on natural populations, as well as to provide 

adaptive management information that can be applied more broadly to other programs. 

However, even ambitious monitoring programs often have low power to detect adverse effects 

before they have long-lasting consequences (Hard 1995b).

Lessons from Salmon Aquaculture

Artificial propagation involves direct intervention in the reproduction and survival of the 

target species. Because some leakage from the cultured to the wild population is almost 

inevitable, propagation programs also involve, either directly or indirectly, intervention in 

survival and reproduction of associated natural populations. Here are a few of the practical 

realities that can be expected as part of an aquaculture operation, starting with those that apply 

equally to captive commercial aquaculture and enhancement of natural populations.

Escapes

A certain level of escapes from marine cages (net pens) is almost inevitable, except 

perhaps for secure land-based operations. Key questions arise. How many individuals will 

escape and how often? What life stages will escape? How will they interact with wild 

populations?
7

Recapture of Escaped Fish

Efforts to recapture fish that have escaped from culture have had limited success. This 

means that managers cannot rely on mop-up operations and containment efforts are more 

effective when they focus on prevention of escapes in the first place.

Postescape Survival

Although many escaped individuals do not survive, because they are eaten by predators 

or are not conditioned to foraging for food, some do. Captively reared fish that do survive can 

disperse over large areas. As a consequence, wild populations at some distance from culture 

sites can be affected by escaped captively reared individuals.

Marking

Although efficient aquaculture operations keep close track of inventory and will generally 

notice any sizeable number of escapes, fish that do escape can be hard to detect and distinguish 

in the wild unless they are marked and monitoring is sufficiently frequent and adequate in spatial 

scale. This reality complicates efforts to control the effects of escaped fish (by targeting 

collection of marked fish), as well as efforts to monitor the consequences of escapes for natural 

populations.

Reproduction of Escaped Individuals

Reproductive capabilities of captively reared fish in the wild vary across species, life 

stages of release/escape, geographic locations, and other factors. If survival and reproduction in 

the wild are poor, the genetic consequences of escapes could be much less than might be 

suggested by their absolute numbers. Generally, individuals escaping at an early life stage have 

a lower probability of surviving to reproduce than do escapes that are nearly mature, and a higher 

reproductive success if they reach maturity after having spent most of their life in the wild. 

However, escapes at any life stage can lead to successful reproduction in the wild, and if large 

numbers escape at early life stages, the probability that at least some will survive to reproduce 

could be high.

Containment Effectiveness

Indices of containment effectiveness (e.g., the fraction of cultured individuals that 

escape) must be evaluated in the context of program scale. Although escapes cannot be 

eliminated, they can be controlled to some extent with sufficient experience, efficiency, and 

financial motivation. However, even if the fraction of escaping fish declines over time, the net 

effects of escapes on wild populations can continue to increase if overall production is also 

increasing. This pattern has been observed for Atlantic salmon (Salmo salar) in Norway.
8

Joint Lessons from Salmon Aquaculture and Hatcheries

Long-term Sustainability

Empirical results show that, in many cases, artificial propagation can maintain 

populations for several decades or fish generations. However, little evidence exists to show that 

artificial propagation can improve the long-term sustainability of natural populations. These 

results suggest that potential conservation benefits of artificial propagation might be largely 

limited to short-term efforts to prevent extinction. Long-term effects of artificial propagation are 

essentially unknown; even the longest-running programs have lasted only a tiny fraction of the 

time over which most aquatic species have persisted in the wild.

Genetic changes associated with artificial propagation are inevitable. Selective regimes 

and mortality profiles differ so dramatically between natural and cultured populations that some 

genetic change cannot be avoided—and from the aquaculture perspective, such changes might be 

desirable if they increase profitability. For the purposes of this paper, the key questions are: How 

much genetic change will occur and what will be the consequences for natural populations with 

which they might interact?

Fitness

Fitness of captively reared fish in the wild decreases with the number of generations in 

captivity. A large body of empirical information now documents reduced fitness of cultured fish 

in nature compared to their wild counterparts, and the fitness reductions increase as a function of 

the number of generations in captivity. Reduced fitness has also been documented among the 

wild-born descendants of captively reared fish (Araki et al. 2009). These fitness reductions 

become a concern when escaped fish interbreed with natural populations.

Genetic Risks

Genetic risks associated with fish culture can be reduced but not eliminated entirely 

except in a completely closed system. This is true even for state-of-the-art programs. Many 

risks are negatively correlated, such that reducing one inevitably increases another (see Waples 

and Drake 2004). For example, creating a genetically divergent aquaculture population might

reduce the chances that escapes can survive and reproduce, but those that do can pass on very 

maladapted genes to the natural population.

Direct Effects

The consequences for natural populations of interbreeding with cultured fish depend in a 

complex way on a variety of factors. The factors that determine whether invasion and 

introgression are initially successful are difficult to predict (Drake and Lodge 2006, Hayes and 

Barry 2008). The factors that subsequently influence the consequences of introgression include 

the rate and duration of interbreeding and the magnitude of genetic differences between cultured 

and wild populations. Some conclusions are straightforward: 1) effects are cumulative across 

generations, so all else being equal, interbreeding is more detrimental the longer it occurs; 2) for 

a given level of population divergence, interbreeding is more harmful if it occurs at a higher 
9

frequency; and 3) for a given rate of interbreeding, the consequences are worse if the cultured 

population is strongly diverged from the wild population. However, in other cases firm 

predictions are difficult because of inherent trade-offs (see Frequently Asked Questions section 

below).

Indirect Effects

Reduced population size and other indirect genetic effects have been associated with fish 

culture. Effects on survival or abundance of wild fish populations have been linked to 

aquaculture production of the same or a closely related species. Moreover, stock recruitment 

analyses have shown reduced recruitment for the same stock size when part of the spawning 

stock has a cultured background.

Genetic Effects

Genetic effects have occurred in native populations following invasion of intentionally or 

accidentally released cultured fish. The genetic effects that have been found in wild populations 

receiving cultured fish include changes in molecular genetic diversity and changes in fitness 

traits that have a genetic component. When genetic effects on fitness traits have been detected, 

they are generally negative in comparison with unaffected native populations (Hindar et al.

1991).

Substantial genetic effects are not inevitable, even when large numbers of captively

reared fish are released into the wild. For example, some enhancement programs for salmon

have operated for many years without detectable genetic effects on natural populations (reviewed 

by Hindar et al. 1991). This does not prove that these programs have had no genetic 

consequences, since the power to detect effects might have been limited by sampling constraints 

and fitness has seldom been evaluated directly. However, this result does illustrate the difficulty 

in making quantitative predictions about consequences of any particular program.

Genetic Technologies

Breeding programs and application of genetic technologies have been developed for 

relatively few aquaculture species, and the potential consequences of escaped cultured fish for 

wild populations have not yet been carefully evaluated. Until recently, breeding programs in 

aquaculture have been limited to a few species such as salmon and trout (Salmonidae spp.), 

tilapia (e.g., Tilapia, Oreochromis, Sarotherodon spp.), seabass (e.g., Morone spp.), sea bream

(e.g., Pagrus major, Acanthopagrus schlegeli schlegeli), catfish (e.g., Ictalurus punctatus), 

oysters, shrimp, and other invertebrates. In comparison to programs for terrestrial agricultural 

species, breeding programs for most aquaculture species have been ongoing for only a few years 

or decades. Consequently, knowledge of the phenotypic and genetic parameters of many 

economically important traits of interest to marine aquaculturists is limited. This is an important 

gap in knowledge, because this information might also be helpful in determining how 

interbreeding between escaped cultured and wild individuals might affect natural population 

structure and viability in the marine environment.
10

Lessons from Marine Stock Enhancement

A large number of marine species have been targets for marine stock enhancement or 

restoration (sometimes also called sea ranching, which entails intentional release of juveniles 

into the wild), but only a small fraction have been studied in detail. Lorenzen et al. (2010) 

provide an updated discussion of responsible approaches to marine stock enhancement programs. 

It is an open question whether the strong empirical record for salmonids provides a good 

indication of the likely effects in marine systems that can be affected by cultured populations. 

On the one hand, all the genetic and ecological concerns identified for salmonids also apply in 

theory to marine species. On the other hand, some (e.g., Bonhomme 2007) argue that most 

marine species with high fecundity and large population sizes should be less susceptible to at 

least some genetic risks.

Here are some factors associated with marine species that should be kept in mind in 

extrapolating from the lessons learned from anadromous species.

Biology of Marine Species

Much less is known about the basic biology of most marine species compared to salmon. 

As a consequence, except for a relatively few well-studied species, more uncertainty will be 

associated with all aspects of marine aquaculture programs. However, collectively marine 

species have a greater diversity of life history strategies and fill a greater range of ecological 

roles than do salmonids. This observation suggests that novel cultured/wild interactions are 

likely to occur in some marine species and that the lessons learned from salmonid systems will 

need to be supplemented based on experience with marine systems.

Population Differentiation

In general, on an equivalent spatial scale, marine species show lower levels of molecular 

genetic differentiation among populations than do anadromous or freshwater species. 

Presumably this arises from larger population sizes (for which random genetic changes are 

considerably reduced) and reduced barriers to dispersal.

Local Adaptations in Marine Species

Despite the previous point, several recent studies show surprisingly strong evidence for 

local adaptations in populations of marine species. This result emphasizes the empirical 

observation that molecular (and presumably selectively neutral) genetic variation is generally a 

poor predictor of the degree of adaptive genetic differentiation (Hard 1995a, Lynch 1996, Naish

and Hard 2008).

Spawning in Net Pens or Cages

At least some marine species can successfully spawn in net pens or cages. This reality 

presents special challenges for managing aquaculture programs for marine species: even if 

managers are 100% successful in controlling escapes of cultured individuals, gametes or 
11

fertilized eggs produced by cultured adults can leave net pen cages and might lead to 

introgression with wild populations.

The high fecundity of many marine species means that relatively few individual breeders 

can have a large genetic impact on natural populations. This can potentially lead to an extreme 

example of the Ryman-Laikre effect, where the wild population is swamped by genes derived 

from a few captive individuals. This in turn can reduce levels of genetic variability and increase 

levels of inbreeding in natural populations.

Evaluation

Detecting and evaluating the genetic effects of cultured marine species on natural 

populations is extremely challenging and involves a number of linked steps. A fault tree of the 

chain of events necessary for introgression of genes from escaped cultured fish into the wild 

(Figure 2) describes the key events and what to look for.

Despite some obvious differences between marine species and salmonids, many 

important features of the marine species considered by the European Union project Genimpact

are similar to those of Atlantic salmon, as illustrated in Table 2.

Lessons from Agriculture

In the previous two subsections, we focused on lessons that are relevant to consideration 

of potential effects on natural populations. These factors have not been primary considerations 

during the development of the agriculture and aquaculture industries. Agriculture has long relied 

on the incredible genetic and phenotypic diversity available in natural populations to develop 

cultured stocks that can be altered through control of breeding and environmental variation. The 

primary considerations in these industries are the cost-effective production of safe and highquality products (see Gjedrem 2005). Breeding programs in agriculture have applied a 

combination of inbreeding, selection, and crossbreeding to develop strains with desirable 

characteristics that improve the efficiency of agricultural production. Chief among these 

characteristics are stage-specific survival, rapid growth, high tissue quality for consumption, ease 

of culture, rapid maturity, and improved resistance to pathogens. Here we briefly outline how 

these considerations help to shape the nature and types of agriculture programs that are 

implemented.

Selective Breeding

Agriculture can efficiently produce plants and animals with desirable marketable 

phenotypes through careful broodstock selection, intensive selective breeding, and judicious use 

of arable land. Agricultural operations have grown in efficiency with technological advances and 

more efficient use of land, but major advances have also been made by genetically improving 

stocks through the concerted application of stock selection, inbreeding, and crossbreeding. The 

combination of selective breeding, calculation of breeding values based on an individual’s 

performance and that of its relatives, and breeding to maximize genetic gain can rapidly increase 

the frequency of desirable phenotypes for market.
12 

Figure 2. Fault tree of events leading to introgression of genes from escaping cultured fish into the gene pool of wild relatives. The fault tree 

should be read from the bottom to the top. Gray background = event leading to entry of sexually mature cultured fish into a breeding wild 

population. White background = postentry event leading to introgression. F1 = first-generation hybrids from cultured and wild fish 

matings. BC1 = first-generation backcrosses between F1 hybrids and wild relatives. Additional lower level events could contribute to 

events in rectangular boxes but they are not shown for clarity. (Adapted with permission from Kapuscinski et al. 2007, copyright Centre 

for Agricultural Bioscience International.)
13 

Table 2. Comparison of biological and aquaculture-relevant characteristics of Atlantic salmon and marine fish species considered for genetic 

impact studies in Europe by the European Union Genimpact project (Svåsand et al. 2007) and in Asia (i.e., large yellow croaker, Liu et al. 

2008). FW = freshwater, LC = least concern, LR = low risk, V = vulnerable, E = endangered, and NE = not evaluated.

Species Range Ecology

Population 

genetics

Wild

harvest Breeding and culture

Interaction 

studies

IUCN 

status Reference

Atlantic salmon North Atlantic 

Ocean and 

freshwater; 

72°N to 37°N, 

77°W to 37°E

Anadromous, some FW; 

river spawning; long 

migration with homing; 

feeds on invertebrates 

and fish; spends 1–6 yr 

FW; 1–4 yr sea; 

sexually mature M 10–

140 cm and 0.01–35 kg, 

F 40–120 cm and 1–20 

kg; annual to biannual 

spawning; eggs 2,000–

20,000, 6 mm diameter, 

benthic; max 150 cm, 

45 kg, 13 yr

Moderate to 

strong genetic 

structure; global 

FST = 0.366 

allozymes; E. 

Atlantic, W. 

Atlantic 

subspecies; 

empirical 

evidence for 

local adaptations

1,700 t (2008), 

declining 80% 

from 1970–

1980s; extinct 

from many 

rivers in North 

America and 

Europe

1.3 M t; 300-fold 

increase since 1980; 

hatching and juvenile 

rearing in FW tanks 

0.5–1.5 yr; growth in 

seawater cages 1–2 yr; 

large-scale selective 

breeding programs 

(since 1970s) for 

growth, age at maturity, 

disease resistance, flesh 

quality; thousands of 

single nucleotide 

polymorphism (SNP) 

markers

This report LR Genimpacta

FishBaseb

FishStat Plusc

Ward et al. 

1994

Verspoor et al. 

2007

Atlantic cod North Atlantic 

Ocean; 35–

80°N, 95°W–

61°E; cont. 

shelves and 

banks

Marine; epibenthic 

pelagic; long migration, 

localized spawning 

sites; feeds on 

invertebrates and fish; 

sexually mature 30–100 

cm, 3–15 yr; annual 

spawning; eggs 1,000s 

to 30 M, 1 mm 

diameter, pelagic; max 

200 cm, 96 kg, 25 yr

Low to moderate 

structure; global 

FST = 0.076 

allozymes; 

stationary and 

migratory 

population 

segments; 

empirical 

evidence for 

local adaptations

1M t (2004); 

declining 70% 

since 1960s; 

major stock 

collapses

10,000 t; 5-fold 

increase since 2000; 

larvae production 

difficult and partly 

relying on live feed; 

mature 2 yr, some 

growth in sea cages, 

partly from wild-caught 

juveniles; selective 

breeding programs 

(since 1990s) for 

growth, delayed 

maturity, disease 

resistance; genome 

sequenced 2009

Genetic marking 

in sea ranching 

experiments; 

spawning in sea 

cages

V Genimpact

FishBase

Ward et al. 

1994
14 

Table 2 continued. Comparison of biological and aquaculture-relevant characteristics of Atlantic salmon and marine fish species considered for 

genetic impact studies in Europe by the European Union Genimpact project (Svåsand et al. 2007) and in Asia (i.e., large yellow croaker, 

Liu et al. 2008). FW = freshwater, LC = least concern, LR = low risk, V = vulnerable, E = endangered, and NE = not evaluated. 

Species Range Ecology

Population 

genetics

Wild

harvest Breeding and culture

Interaction 

studies

IUCN 

status Reference

Atlantic halibut 

(Hippoglossus 

hippoglossus) 

North Atlantic 

Ocean; 79°N–

36°N, 77°W–

55°E

Marine; demersal, 

occasionally pelagic; 

migratory; depth range 

50-2,000 m; feeds on 

invertebrates and fish; 

batch spawner; sexually 

mature M 55 cm, 4.5 yr, 

F 110 cm, 7 yr; eggs 1 

M or more, small, deep, 

pelagic; larval 

metamorphosis; max M 

470 cm, 320 kg, F 300 

cm, 50 yr

Low genetic 

structure; FST = 

0.012 allozymes; 

unclear if local 

adaptations 

occur

European 

catches 10-

15K t (1950–

1965), 

declined to 

2,000 t (2004)

500 t; eggs stripped 

from wild-caught 

individuals; life-cycle 

closed in captivity in 

the 1990s but still 

limited success with 

egg and start-feeding 

survival; selective 

breeding programs 

planned

No data E Genimpact

FishBase

Ward et al. 

1994

European 

seabass 

(Dicentrarchus 

labrax) 

Atlantic Ocean; 

72°N–11°N, 

19°W–42°E

Brackish and marine; 

demersal, migratory; 

depth 10–100 m; feeds 

on invertebrates and 

fish; sexually mature 

17–46 cm; eggs small 

200,000/kg, batch 

spawner with pelagic 

eggs; max 103 cm, 12 

kg, 15 yr

Atlantic, W. 

Med. and E. 

Med. groups, 

only the latter 

showing subdivided 

populations; 

possible 

selection in some 

allozymes

11,000 t 

(2004), 

slightly 

increasing 

since 1980s

80,000 t (2005), 20-

fold increase since 

1990; eggs throughout 

the year, on-growth in 

sea cages, raceways 

and ponds; hundreds 

of SNP markers

No. of escapes 

unknown; no 

interaction 

studies, but 

genetic studies 

indicate some 

gene flow from 

hatchery stocks 

(W. Med. origin) 

to E. Med. 

natural 

populations

LC Genimpact

FishBase

Lemaire et al. 

2000
15 

Table 2 continued. Comparison of biological and aquaculture-relevant characteristics of Atlantic salmon and marine fish species considered for 

genetic impact studies in Europe by the European Union Genimpact project (Svåsand et al. 2007) and in Asia (i.e., large yellow croaker, 

Liu et al. 2008). FW = freshwater, LC = least concern, LR = low risk, V = vulnerable, E = endangered, and NE = not evaluated. 

Species Range Ecology

Population 

genetics

Wild

harvest Breeding and culture

Interaction

studies

IUCN 

status Reference

Gilthead 

seabream 

(Sparus 

auratus) 

Atlantic Ocean; 

62°N–15°N, 

17°W–43°E

Marine and brackish; 

demersal; 1–30 (150) m 

depth; carnivorous, 

accessorily herbivorous; 

sexual maturity 20–40 

cm; sex reversal at 2 yr 

(male to female); batch 

spawner with up to 1 M 

eggs, 1 mm diameter; 

max 70 cm, 17 kg, 11 yr

Moderate 

genetic structure; 

Atlantic and 

Med. FST = 0.031 

allozymes, 

higher among 

some Tunisian 

samples

9,000 t (2004), 

slightly 

increasing 

since the 

1980s

91,000 t (2004); tank 

and cage rearing, and 

restocking in lagoons; 

family based selection 

program since 2002; 

hundreds of SNP 

markers

Little knowledge 

about 

interactions, 

some Atlantic 

origin among 

Med. 

broodstock; 

possible 

spawning in 

cages

NE Genimpact

FishBase

Alarcón et al. 

2004

de Innocentiis 

et al. 2005

Turbot (Psetta 

maxima) (syn., 

Scophthalmus 

maximus)

Atlantic Ocean; 

30–70°N, 

23°W–42°E

Marine and brackish; 

demersal, 20–70 m, 

migratory; sexual 

maturity 41–54 cm; 

batch spawner with up 

to 5–10 M eggs, max 

100 cm, 25 kg, 25 yr

Little or no 

structure based 

on allozymes 

Atlantic coast of 

Europe; hybrid 

zone between 

North Sea and 

Baltic Sea; two 

Med. lineages

7,000 t, 

fluctuating 

since 1980s

5,000 t (2002); reared 

in concrete tanks; high 

stocking density; 

selection programs 

since mid-1990s; 

chromosome 

manipulation

No data; 

information 

from restocking 

programs 

suggest rapid 

adoption of 

natural diet

NE Genimpact

FishBase

Blanquer et al. 

1992

Nielsen et al. 

2004

Large yellow 

croaker 

(Larimichthys 

crocea) 

Coastal waters

of China and 

SW South 

Korea; 20–

36°N, 110–

127°E

Marine; benthopelagic 

soft bottom; migratory; 

feeds on crustaceans 

and fishes; spring and 

autumn spawning near 

river mouths; sexually 

mature M 17 cm+ and 

2–4 yr; millions of eggs; 

max 80 cm, 29 yr with 

variation between stocks

Three putative 

stocks; loss of 

genetic variation 

in cultured 

stocks

Peak 240,000 

t mid 1970s; 

collapse late 

1980s; 

currently c. 

70,000 t

Hatchery and release 

programs since 1980s; 

released at 6–10 cm 

after 6 months; cage 

rearing 70,000 t 2005; 

2 billion juveniles 

produced 2005

Reduced genetic 

variation in 

captivity; 

suggestion of 

genetic problems 

following 

releases

NE FishBase

Liu et al. 2008

a

Genimpact online at http://genimpact.imr.no b

FishBase online at http://www.fishbase.org c

FishStat Plus (FAO 2010) online at http://www.fao.org/fishery/statistics/software/en
16

Careful application of inbreeding and selection in agricultural settings can dramatically 

improve production gains, but the application of inbreeding and selection requires considerable 

care to minimize genetic problems, not only within the program but also when cultured and wild 

individuals interbreed (Lind et al. 2012). Inbreeding is used in culture programs to reduce 

undesirable variation and improve efficiency of selection and, so long as the rate of inbreeding is 

not too high, most cultured populations can thrive in protective environments. Empirical data 

suggest that cultured populations can withstand sustained inbreeding levels of about 1–2% per 

generation. However, levels of inbreeding that can be tolerated in a benign culture environment 

can be much higher than is typically experienced in the wild. The fitness consequences of 

inbreeding are very context specific and the largest decreases in fitness typically occur in the 

most stressful environments. Indeed, estimates of inbreeding depression in captive populations 

can substantially underestimate the loss of fitness that can occur in natural environments (Wang 

et al. 2002). Inbreeding is a particular risk in culturing species with high fecundity—the case 

with many marine species—because of the ability to found and maintain culture programs from 

only a few individuals (Gjedrem 2005).

Divergence in Captivity

Agricultural strains and varieties often diverge rapidly from wild progenitors. The 

agricultural environment and the improved well-being of cultured organisms typically lead to 

rapid phenotypic divergence of cultured individuals from wild relatives. This can involve 

several factors, including active selection for agriculturally important traits, adaptation to the 

cultured environment, and relaxation of natural selection that occurs in the wild.

Synthesis

The genetic objectives of fish culture and the potential genetic consequences of 

aquaculture for wild populations pose a management and regulatory challenge for resource 

management agencies like NOAA. In general, the factors that are typically associated with 

successful agriculture/aquaculture programs and which lead to what is considered “genetic 

improvement” from an agronomic perspective (rapid divergence from wild populations; strong 

artificial selection for traits that are desirable in the marketplace; heavy reliance on a few, highperforming stocks) are also factors that might pose the greatest potential risks to wild 

populations. Differences between cultured and wild populations arise from selection and 

inbreeding, which tend to reduce variation and lead to divergence between cultured and wild 

individuals.

Widespread monocultures of highly productive stocks can greatly enhance agriculture or 

livestock production, but these practices also leave the system as a whole more vulnerable to 

boom-bust cycles and attack by pests or diseases (Mooney et al. 1995). Agronomists 

increasingly pay careful attention to the rich store of genetic variation contained in native land 

races of species used for food production and ensuring that this diversity is maintained in situ

and in seed banks (e.g., The Millennium Seed-Bank Partnership, http://www.kew.org/scienceconservation/conservation-climate-change/millennium-seed-bank/index.htm). This approach is 

logistically difficult, if not completely infeasible, with most natural populations of marine 

species that might be affected by aquaculture—a reality that argues persuasively for careful 

attention to ensuring persistence of diverse wild populations in situ.
17

Although agriculture and aquaculture share many goals, the capacity to rely on 

genetically improved aquaculture stocks as a foundation for production efficiency is relatively 

undeveloped, especially for marine fishes. Aquaculture has a rich history but not nearly as long 

as agriculture. Carp have been domesticated the longest among fishes, beginning perhaps 4,000-

5,000 years ago in what is now China. Agriculture has relied extensively on development and 

maintenance of domesticated stocks with desirable, marketable qualities. In aquaculture, such 

stocks are now widely used for some species (e.g., salmonids), but for most marine species such 

stocks do not yet exist. Nevertheless, the potential for selective breeding to rapidly change

cultured stocks of marine species is considerable, as selection response is often higher in fish and 

shellfish than in terrestrial farm animals.

The scale of commercial and enhancement aquaculture production underway and under 

contemplation in some parts of the world has potentially large consequences for natural 

population structure and productivity. The actual consequences of conflicts between cultured 

and wild populations depend heavily on best management practices; the effectiveness of efforts 

to reduce risk, size, location, and distribution of production facilities in relation to natural 

populations; and a variety of other factors. The potentially competing goals of aquaculture and 

natural resource conservation are likely to become more problematic as the industry grows and 

strives to be more efficient in response to market forces. This reality emphasizes the need for a 

systematic and comprehensive framework for considering risks and benefits of marine 

aquaculture, which is the topic of the next section.
18

Characterizing Risks and Benefits

Informed decisions about appropriate use of marine aquaculture are best made following 

a comprehensive risk-benefit analysis. Such analyses might be conducted in a number of ways; 

below we modify the framework developed by Waples and Drake (2004) for marine stock 

enhancement, based on experience with Pacific salmon.

Potential benefits are of two kinds: benefits to society and benefits to natural populations. 

This document will not consider economic, social, or political benefits to society in any detail,

because this requires consideration of a wide range of normative issues. Furthermore, benefits to 

society are measured in a fundamentally different currency than are risks to natural populations, 

and this reality greatly complicates the ability to incorporate both into an overall quantitative 

analysis. Nevertheless, it is important to recognize that these normative issues will be implicitly 

(if not explicitly) involved in most decisions about appropriate use of marine aquaculture. 

Potential societal benefits of commercial and stock enhancement aquaculture (e.g., jobs, 

recreational opportunities, species or habitat restoration) are outlined elsewhere in the literature.

Potential Benefits of Artificial Propagation for Natural Populations

Potential benefits include those that directly result from culture activities (1–4), as well as 

those that are indirect consequences of artificial production (5).

1. Reduce short-term extinction risks for endangered populations. Successful hatchery 

programs that provide a benign environment to enhance survival during a life-history 

stage with high natural mortality can help to reduce short-term risks faced by natural 

populations.

2. Help maintain a population at a safe level until factors for decline can be addressed. By 

helping to forestall extinction of a population that is not viable in its current environment, 

this strategy at least allows for the possibility that a self-sustaining natural population 

eventually can be achieved.

3. Speed recovery by providing a demographic boost to an existing population. Rapid 

increases in population size help to minimize the time a population spends at low 

abundance, when it is at highest risk. In theory, a successful short-term supplementation 

program might help speed sustainable natural recovery by temporarily increasing 

abundance of a depressed natural population, which then remains stable at the higher 

population size after the supplementation program terminates. However, few empirical 

examples exist to show that this has actually occurred.

4. Reseed vacant habitat. Translocations have been widely used with terrestrial and 

freshwater species and could potentially have a role for marine species.

5. Reduce harvest pressure on natural populations. Overfishing is a serious problem for

many marine species and existence of a consistent supply of high quality cultured product 
19

at a reasonable price could substantially reduce demand for (and profit from) wild 

harvests.

Artificial propagation has already provided benefit 1 for some critically endangered 

aquatic species, including Redfish Lake sockeye salmon (Oncorhynchus nerka) and white 

abalone (Haliotis sorenseni). Hatchery-based enhancement or replenishment programs

undertaken by public agencies might or might not have tangible benefits for natural populations.

In reality, however, the vast majority of commercial aquaculture operations will neither seek nor 

have any tangible benefits for natural populations. Therefore, most risk-benefit considerations 

for commercial aquaculture will have to focus on evaluating trade-offs between potential benefits 

to society and risks to natural populations.

Genetic Risks to Natural Populations from Aquaculture

Risks to natural populations depend on program goals and the methods used to achieve 

them; as a result, the risks will differ between commercial aquaculture and marine stock 

enhancement (Table 2). In stock enhancement, releasing juveniles (generally in large numbers) 

into the marine environment is integral to the program, and this creates widespread opportunities 

for introgression to occur, even when captive-wild interbreeding is not a specific objective. In 

contrast, aquaculture operations seek closed production systems; any leakage from these systems 

represents a cost that must be minimized to ensure profitability, and this creates an incentive to 

reduce events that could lead to interbreeding of captive and wild individuals. In this case, 

leakage is incidental and unintentional, although it can be nearly impossible to eliminate entirely, 

particularly in the marine environment. Furthermore, although it might be cost-effective to 

reduce escapes to a small fraction of production, the marginal costs for reducing escapes to near 

zero might increase exponentially.

A convenient metric for evaluating genetic risks from aquaculture is the fraction of 

cultured individuals that escape into the wild. However, a more informative measure for 

assessing potential impacts on natural populations is the fraction of natural spawners that 

originated from aquaculture, and assessing this requires more information than can be obtained 

by simply monitoring a culture facility.

Before discussing the risks from escapes, we briefly review circumstances that can create 

opportunities for escape and interbreeding with wild individuals. Escape events can range from 

relatively constant leakage of small numbers of individuals to large catastrophic events involving 

tens of thousands of individuals, millions of gametes or larvae, or more. Escapes from most 

shore-based, closed recirculating culture systems probably pose a negligible risk; in contrast, the 

probability of escapes is highest from ponds and net pen cages in near-shore or open-ocean sites. 

The life stages involved also affect the likely genetic consequences of escapes. A large event 

involving thousands of escaped juveniles would not be expected to lead to the same level of 

introgression as the same number of escaped adults, because many juveniles would be expected 

to die before maturity. Furthermore, the realized level of introgression will depend on the 

relative reproductive success of cultured and wild individuals. A variety of factors, including 

source of broodstock, husbandry practices, duration of the program, and proximity to suitable 

natural spawning habitat, can affect not only the reproductive success in the wild of escaped 

individuals, but also the genetic consequences of interbreeding events that do occur. Finally, 
20

genes from captive individuals are most likely to spread to the wild population when the 

probability of hatchery individuals encountering the natural spawning population is high, which 

generally occurs when culture programs contain reproductively mature individuals and culture 

sites that are close to natural spawning populations.

Strategies to Minimize Genetic Risks

Genetic risks associated with fish culture have been described in several key papers,

including Allendorf and Ryman 1987, Hindar et al. 1991, Waples 1991, Busack and Currens 

1995, Campton 1995, Waples 1999, Brannon et al. 2004, Waples and Drake 2004, Fraser 2008, 

Naish et al. 2008, and Araki and Schmid 2010. Here we briefly consider two general approaches

for minimizing these risks: preventing escapes and reducing the genetic consequences of escapes 

that do occur. In the following subsections, we discuss strategies that can help alleviate specific 

genetic risks.

General approach 1: Reduce opportunities for escapes

The most reliable way to limit genetic interactions between cultured and wild individuals 

is to ensure that few or no captive individuals escape. Closed, land-based systems can be very 

effective in this regard, but such operations are not feasible for many marine species. A variety 

of methods can be used to reduce the number of escapes from marine enclosures. Escapes most 

often result from cage or net pen failures resulting from storm events or damage caused by 

potential predators. Appropriate siting and construction of aquaculture enclosures can limit 

exposure to strong wave or wind action, and the use of guard nets or other devices to discourage 

damage or intrusion by predators can be effective in limiting escapes from marine enclosures. In 

Norway, methods include mandatory reporting of all escape incidents, establishment of a special 

commission to learn from past escape events and disseminate knowledge to both fish farmers and 

equipment suppliers, training of fish farm operators in methods to prevent escapes, and other 

measures. However, as noted above, it is virtually impossible to ensure that no cultured 

individuals will escape from marine enclosures. Therefore, it is important to also consider the 

second general approach.

General approach 2: Reduce opportunities for reproduction

Although ecological consequences (competition, predation, disease transfer) can arise 

from any escape event, direct genetic consequences only occur if the escaped individuals survive 

to maturity and successfully reproduce. For a variety of reasons, the fraction of escapees in the 

spawning population might be smaller than the fraction they comprise of the total population at 

the time of the escape event. Several approaches can potentially be useful here:

1. Recapture escapes before they have an opportunity to reproduce. However, empirical 

data (see Appendix A) suggest that mop-up operations are seldom effective in recapturing 

a significant fraction of escapes.

2. Locate culture operations well away from areas used by natural populations. Knowledge 

about the dispersal capabilities of escaped individuals can be used to suggest a minimum 

distance between culture operations and natural populations.
21

3. Use only sterile fish. Sterility in most fishes can be imposed with high efficiency and 

low cost, and has the potential to significantly reduce risks from escaped individuals. 

Some methods of imposing sterility have been associated with an increase in skeletal 

deformities.

4. Use a highly domesticated population for culture. Escapes from such a population might 

have a greatly reduced probability of surviving to maturity and successfully reproducing 

if they do survive. However, this strategy involves some important trade-offs regarding 

fitness; see discussion under the Managing Risk section below.

Another important general consideration is that, in real-world management applications, 

what are intended as absolute thresholds (e.g., parameter values that should never be exceeded) 

can become viewed as targets to manage for. For example, a program that takes strong steps to 

ensure that a critical metric never drops below 1,000 could have very different consequences for 

natural populations than a program that sets 1,000 as a target, in which case a significant number 

of outcomes with values less than 1,000 could be expected.

Monitoring (see Monitoring subsection in Managing Risk section and see Appendix A) is 

an essential component of any adaptive management strategy to minimize risks. Although 

monitoring by itself does not reduce risks, it can provide information that allows scientists and 

managers to modify biological or physical features of the aquaculture operation to reduce risks. 

The advent of large numbers of highly variable genetic markers in recent years has facilitated 

development of powerful methods for monitoring effects of aquaculture escapes on natural 

populations. For example, Tringali (2006) described a model that uses DNA fingerprints taken 

from aquaculture broodstock to identify cultured progeny after they are released (or escape) into 

the wild. In this two-step process, large samples of wild-caught individuals are screened for a 

small number of gene loci, and this process eliminates most wild-born individuals as potential 

offspring of known captive crosses. The second step screens additional loci on the smaller 

subset of individuals to complete the parentage assignment process. This approach has been 

used for postrelease genetic tracking of cultured red drum (Sciaenops ocellatus) in Texas.

Loss of Diversity within Populations

Genetic variation provides the raw material for evolution. All else being equal, 

populations with low levels of genetic variability have less capacity to respond to stressful 

conditions or environmental changes.

The primary factors affecting the amount of variation in a population are the rate of 

mutation (which creates new genetic variants, or alleles) and the effective population size (Ne), 

which determines the rate at which variation is lost by chance events (genetic drift). Migration 

also plays a role, by spreading new mutations among populations connected through gene flow. 

Managers cannot control the mutation rate, but they can have some control over Ne, which is 

generally smaller than the total number of breeders (N) because of unequal sex ratio or a skewed 

distribution of reproductive success (i.e., some individuals producing a large number of offspring 

and many others producing few or none). The genetic diversity loss rate is inversely 

proportional to Ne and increases rapidly as Ne declines. For example, in each generation the 

expected proportional increase in inbreeding (Δf) and the expected proportional loss of 

heterozygosity at neutral genes are both equal to 1 / (2Ne). In short, mutation creates new genetic 
22

variability, migration spreads the variation among populations, and a large effective size slows 

the rate at which genetic variability is lost by drift.

Ne also plays an important role in facilitating the action of natural selection. Natural 

selection is most effective in large populations, in which slight differences in survival probability 

averaged across many individuals make the outcome of selection highly predictable. In small 

populations, however, genetic changes promoted by natural selection can be overwhelmed by 

those arising from random genetic drift, and favorable alleles can decline and deleterious alleles 

can increase in frequency just by chance. As a consequence, small populations not only lose 

genetic variability at a high rate, they also have a higher probability of drifting away from their 

adaptive peak through random events. Gambling provides an analogous situation. In a large 

casino, even if the house margin is small for every individual bet, steady profits are almost 

inevitable because the ability to average across many, many chance events ensures that the house 

eventually comes out ahead. In a small gambling operation, however, the same small house 

margin will not provide the same buffer against the occasional lucky individual, and as a 

consequence, short-term profits (or losses) will be much more variable. Therefore, smaller 

gambling operations generally must use higher house margins, just as small populations must 

have stronger selection differentials if selection is to predictably overcome random genetic drift.

How large should effective size be for a healthy natural population?

There is no simple answer to this question, but several rules of thumb have been proposed 

in the scientific literature; these collectively have been referred to as the 50/500/5,000 rules.

1. Empirical data from domesticated livestock indicate that inbreeding levels of about 1% 

can be sustained for a number of generations. Ne = 50 produces a 1%/generation increase 

in inbreeding, so this criterion has been proposed as a minimum short-term standard to 

guard against the most serious effects of inbreeding. One caveat is that the response of a 

new population to inbreeding is largely unpredictable, so results for domesticated species 

might not be typical of most natural populations.

2. Theory and some empirical results from Drosophila spp. suggest that if Ne is consistently 

500 or larger, the rate at which the population generates new additive genetic variability 

by mutation should equal or exceed the rate at which variation is lost by genetic drift. A

caveat is that the general applicability of this rule for other species has not been 

rigorously demonstrated.

3. A much larger effective size (≈5,000) might be required to avoid what has been termed 

“mutational meltdown.” A small fraction of mutations are beneficial, and some are lethal 

or nearly so, but the vast majority are slightly deleterious, meaning that they produce a 

slight reduction in fitness. In large populations, natural selection can effectively remove 

these slightly deleterious alleles, or at least keep them at very low frequency, but in small 

populations they can drift to high frequency by chance or even become fixed. Over time 

this creates a considerable fitness drag on the population, which can compromise its 

viability. For selection to be efficient in dealing with slightly deleterious mutations, Ne

has to be much larger than the value required simply to maintain levels of genetic 

variability. It should be noted, however, that this model assumes a completely closed 

population, and rather modest levels of immigration from other natural populations might 

help alleviate some of the fitness decline due to mutational meltdown.
23

Among the most serious threats to within-population genetic diversity that could arise 

from marine aquaculture are those due to what has come to be known as the Ryman-Laikre effect

(see Table 3 for a description of terms). Ryman and Laikre (1991) showed that in assessing the 

effects of fish culture on genetic diversity, it is not sufficient to know only Ne in the cultured or 

wild population; instead, it is necessary to consider the effective size of the cultured-wild system 

as a whole (NeT). NeT is a function of effective size of the captive (NeC) and wild (NeW) 

spawners and the quantity x, which is the fraction of the offspring generation that is progeny of 

individuals that reproduce in captivity (see Appendix A for details). The Ryman-Laikre effect 

refers to a reduction in NeT that occurs when NeC is relatively small and x is relatively large, so 

that offspring of the cultured individuals make up a relatively large fraction of the total 

population (Figure 3). When this happens, many individuals in the population will be closely 

related and this leads to higher levels of inbreeding and reduces Ne. Note that the genetic 

consequences of the Ryman-Laikre effect only occur if progeny of cultured individuals pass their 

genes on to the next generation. Therefore, the relevant definition of the term x should be the 

fraction of the total population of successful spawners that is derived from captively reared

individuals.

The Ryman-Laikre effect raises two general concerns regarding genetic diversity within 

natural populations. First, it can reduce NeT to a low enough absolute level that it raises concerns 

for population viability (see previous section). For marine populations with large effective sizes, 

this is unlikely to occur unless x is large and NeC very small. A much more likely consequence 

for marine species is that NeT, although still relatively large, can be reduced to a small fraction of 

its original value.

Some of the main consequences of the Ryman-Laikre effect can be summarized as 

follows (see Appendix A for more details):

1. NeT is a type of weighted harmonic mean, and as such is most strongly affected by the 

small values (which usually is NeC).

2. If NeC is very small or NeW is very large, NeT generally will be closer to NeC than to 

NeW.

3. If NeW is small (less than 500–1,000), then a variety of scenarios with moderate x and 

NeC values will ensure that NeT / NeW is at least 0.5 (i.e., wild Ne reduced by no more 

than half).

4. If NeW is large (>>104), then the best way to avoid reducing NeT / NeW to less than 0.1 is 

to ensure that x is very low (<<0.1) or NeC is relatively high (>>100).

Table 3. Key terms that quantify the Ryman-Laikre effect.

NeC Effective size of the individuals reproducing in captivity

NeW Effective size of the individuals reproducing in the wild

NeT Effective size of the captive-wild system as a whole

x The fraction of successful spawners that were produced in captivity

1 – x The fraction of successful spawners that were produced in the wild

NeT / NeW The ratio of the overall effective size (after considering the Ryman-Laikre effect) 

to the effective size of the original wild population
24

Figure 3. Schematic diagram of the Ryman-Laikre effect, which can reduce overall effective population 

size in a combined captive/wild system. The effect is strongest when the effective size of the 

captive population in the parental generation (NeC) is relatively small compared to the wild 

population (NeW) and offspring of the captive parents make a relatively large contribution 

(proportion x; lower right) to the overall population in the next generation.

What considerations apply specifically to marine aquaculture?

The Ryman-Laikre method was originally intended to apply to a situation referred to as 

supportive breeding, where a fraction of adults from a natural population are taken into a 

hatchery to increase their productivity (e.g., to provide more harvest opportunities). The original 

concept, then, was of a single population with two phases (captive and wild). This scenario 

might directly apply to some aquaculture operations, if broodstock is sourced from local wild 

populations. In other cases, the cultured stock might be highly domesticated or derived from a 

different population. In these situations, the Ryman-Laikre effect is less relevant, because if 

progeny of cultured fish make a substantial enough contribution to the overall population to 

trigger concerns about inbreeding, the local population would be so swamped with maladapted 

genes that viability would likely be seriously compromised (discussed below under Loss of 

Fitness).

Some marine species are capable of reproduction in net pens or similar containment 

facilities. Although fertilized eggs typically would not be considered “escapes,” they can 

potentially have similar genetic consequences for natural populations. Commercial operations 

will generally try to avoid these situations, as they represent a reduction of marketable product; 

however, there might not be sufficient financial incentives to completely eliminate the problem, 

so the potential consequences for natural populations should be evaluated.

Regarding the 50/500/5,000 rule, an effective size of 50 is clearly too small for long-term 

sustainability of isolated natural populations. For marine species, more reasonable minimum 
25

criteria might be in the 500–5,000 range. However, evaluations that focus on a fixed, critical 

value of Ne do not consider the consequences of proportional reduction in NeW. For example,

many scenarios that satisfy the criterion that NeT ≥ 500 could result in reductions of NeW by 

several orders of magnitude (see Appendix A, Figure A-9). Is it sufficient to ensure that an 

aquaculture program does not result in NeT less than, say, 500 if the effective size of the wild 

population was 1 million before the program began? Even if an effective size of about 500–

1,000 is sufficient to provide for most medium-term evolutionary processes, the total number of 

alleles that can be maintained in a population with effective size of 106 is vastly larger than the 

number that can be maintained in a population with Ne = 103. This rich store of diversity 

provides the raw material for evolution and could be important in dealing with future 

environmental changes. Therefore, proportional reductions in NeW should be considered, along 

with the absolute levels of NeT, in evaluating risks to within-population diversity. From this 

perspective, the wild populations that are at greatest risk from the Ryman-Laikre effect are those 

with very large effective sizes.

Another key factor in determining the magnitude of the Ryman-Laikre effect is the ratio 

Ne / N (effective size to census size). In cultured populations, it is commonly the case that a 

relatively few parents produce most of the offspring, even when efforts are made to equalize 

reproductive success. Therefore, the ratio NeC / N can be substantially less than 1, which means 

that simply using the number of spawners as an estimate of NeC would provide an overly 

optimistic assessment. On the other hand, several studies that have used genetic methods to 

estimate Ne in marine species (fish and invertebrates) suggest that the ratio NeW / N can be very 

low (perhaps 10–3

–10–5) in some species. If this is the case, even very large marine populations 

might have relatively low Ne. If NeW is already several orders of magnitude smaller than the 

census size, then there is less risk that historic NeW will be greatly diminished through the 

Ryman-Laikre effect.

What strategies can help minimize risks to within-population diversity?

In addition to the general strategies discussed above, two specific actions can help reduce 

possibilities for a significant Ryman-Laikre effect.

1. Ensure that escaped cultured individuals do not make up a significant fraction of the 

natural population (i.e., keep x to a small number). The Ryman-Laikre effect disappears 

entirely (aquaculture has no net effect on NeT) if individuals that reproduce in culture 

have the same per-capita production of successful natural spawners as do individuals that 

reproduce in the wild. For large wild populations, NeC / NeW will generally be a small 

number, which puts constraints on how large x can be and still avoid a substantial 

reduction in overall effective population size. In general, substantial reductions in wild 

Ne are possible if x is larger than about 10%.

2. Maintain a large NeC. Because overall NeT converges on NeC as x increases, some 

protection against the most serious losses of diversity also can be achieved by ensuring 

that NeC is as large as possible. A large number of breeding individuals is a necessary but 

not sufficient condition for large NeC; it is also necessary to consider the ratio of effective 

size to census size in captivity (NeC / N). Careful evaluation of the relative contributions 

of different breeders to the surviving progeny can provide important information about 

this critical ratio.
26

If the aquaculture broodstock is developed from local individuals, it is important to 

ensure not only that NeC is large, but also that the breeders are representative of the population as 

a whole with respect to important phenotypic, life history, behavioral, etc. traits, which can be 

associated with local adaptations and are important for long-term population persistence. These 

traits are typically influenced by a combination of genetic and environmental factors. Random 

collection of a sufficient number of individuals across multiple spatial and temporal strata can 

help achieve this objective. However, it should be recognized that sample sizes of broodstock 

that are feasible to consider for most aquaculture operations (perhaps hundreds at most) are too 

small to expect that they can simultaneously be completely representative of the population for a 

large number of traits. Inevitably, not all diversity in the population can be captured in a finite 

collection of captive parents. Furthermore, attempts to broaden the diversity in the broodstock 

collection risk incorporation of multiple populations into a single cultured population, if 

subdivision occurs within the species in the target area. This risk is discussed in the next section.

Of these two strategies, the first (keep reproductively successful escapes to a minimum) 

is by far the most effective way to ensure that aquaculture does not cause major reductions in Ne. 

Increasing NeC serves mainly to minimize the adverse consequences of escapes that cannot be 

avoided.

How long will it take for natural processes to restore lost genetic diversity?

If aquaculture operations lead to loss of genetic diversity within a wild population, but 

the problems that caused the loss are permanently fixed, how long will it take for original levels 

of genetic diversity to be restored by natural processes? In an isolated population, new genetic 

diversity has to be generated entirely by mutation, which is a slow process. For example, if an 

isolated population with Ne = 100 lost all its variation, even for markers with very high mutation 

rates like microsatellites it would take 500 generations or so before most of the diversity was 

restored; for a larger population with Ne = 1,000, the process would take 2,000 or more 

generations (Figure 4). In areas of the genome with lower mutation rates, the process could take 

orders of magnitude longer time. From the shape of the curves in Figure 4, panel A, it is also 

apparent that in general a great deal of time would be required to restore (by mutation alone) 

even a fraction of lost genetic variation.

Most marine populations are not completely isolated, however, and in this case new 

genetic variation can enter populations via migration, which can greatly speed up restoration of 

genetic variability. One scenario is depicted in Figure 4, panel B, which considers a small local 

population size (Ne = 50) that is initially at mutation-drift equilibrium (and hence has low levels 

of genetic variability). This might represent a local population for which genetic diversity has 

been reduced (for example, by overharvest or by the Ryman-Laikre effect). In this example, at 

generation 101 the local population starts to receive 5% immigrants each generation from a 

metapopulation with a total Ne of 1,000. Under these conditions, heterozygosity in the local 

population rises rapidly and approaches the new equilibrium value within about 10 generations—

demonstrating that migration can bring in new genetic variation much faster than it can be 

generated by mutation. The good news about this is that levels of connectivity typical of many 

marine species can greatly speed up the rate at which genetic variation is restored in a local 

population following a bottleneck. On the other hand, high levels of connectivity could also 

facilitate spread of localized genetic effects of fish culture to a wider geographic area.
27

Figure 4. Rate of increase in heterozygosity in natural populations after factors reducing Ne are 

eliminated. Results are based on simulated data for 20 gene loci, each with 20 possible allelic 

states, and assuming a mutation rate of 5 x 10-4

, as is typical for highly variable markers like 

microsatellites. Panel A shows isolated populations with two different effective sizes (Ne = 100 

and Ne = 1,000). Heterozygosity is regenerated entirely by mutation following a complete loss of 

genetic variation. Results are averaged across 100 different replicates for each Ne. Panel B

shows a local population of Ne = 50 in a metapopulation with Ne = 1,000, with initial level of 

heterozygosity reflecting a balance between mutation and genetic drift for Ne = 50. At generation 

101, immigration at 5% per generation starts to bring new alleles into the local subpopulation. 

The level of genetic variation quickly rises to approach the level found in the metapopulation as a 

whole.
28

In summary, the following points are the most important considerations for maintaining

diversity within populations:

1. The amount of neutral genetic diversity maintained in a local population is determined by 

a balance between loss of diversity (by genetic drift, and other factors) and generation of 

new variation (by mutation or immigration).

2. Ne determines the rate of genetic drift. Ne is generally less than census size (N) and, in 

many marine species, perhaps orders of magnitude less.

3. Isolated populations probably require Ne of at least 500–5,000 for long-term persistence. 

However, most marine populations are not completely isolated and even low levels of 

migration can bring new variation into a local population.

4. For captive-wild systems, effective size of the cultured-wild system as a whole (NeT) is a 

function of effective size in the captive (NeC) and wild (NeW) phases and the relative 

contribution of cultured individuals to the overall population (x).

5. NeT can be reduced by the Ryman-Laikre effect if a relatively few captive parents (low 

NeC) produce a relatively large fraction of the next generation in the wild (large x).

6. The most reliable strategy to minimize the Ryman-Laikre effect is to ensure that x 

remains relatively low (x << 10%). Maintaining a large NeC helps to place an upper limit 

on how large the reduction in effective size can be for escapes that cannot be avoided.

7. If a nonlocal or highly domesticated source is used for aquaculture broodstock, levels of 

gene flow that might trigger substantial Ryman-Laikre effects would also trigger more 

serious concerns for loss of fitness due to swamping of the wild population with 

maladapted alleles.

Loss of Diversity among Populations

Genetic differences among populations arise from two major processes: genetic drift and 

natural selection. With little or no migration, genetic drift occurs independently within each 

population and they tend to diverge over time. Migration tends to counteract this process of 

divergence by mixing alleles among populations. Most natural populations have achieved some 

sort of balance between migration and drift, whereby the diversifying effects of drift are offset by 

the homogenizing effects of migration. However, current levels of divergence can also reflect 

historical factors, such as recolonization from ice age refugia. Whereas genetic drift is a random 

process, natural selection can consistently favor different genotypes in different localities, which 

over time leads to local adaptation. If selection is strong enough, local adaptations can persist 

even in the face of moderate levels of gene flow.

Genetic diversity among populations confers resilience to natural systems on a variety of 

temporal and spatial scales. In the long term, genetic differences among populations increase the 

chances that at least some will be able to respond and adapt to future changes in the biological 

and physical environments. In the short term, a diverse array of natural populations helps buffer 

the species as a whole from natural fluctuations in environmental conditions. This short-term 

benefit is easily understood as an analog of the portfolio effect. An investment portfolio heavily 

weighted toward a few stocks might occasionally produce outstanding returns but also will be 
29

prone to large negative swings. A more balanced portfolio has less chance of a huge return but 

provides more predictable earnings over time.

Similarly, a species with diverse natural populations that express a range of phenotypic 

and life history traits will generally have some populations that have normal productivity even 

under anomalous environmental conditions. In contrast, a species that has been constrained to 

one or a few widely distributed life history strategies will tend to have boom or bust cycles, 

depending on whether the populations are in or out of synchrony with environmental conditions 

in that year. For example, Schindler et al. (2010) documented portfolio effects in Bristol Bay, 

Alaska, sockeye salmon. The considerable diversity among populations in age structure and run 

timing appears to have reduced temporal variability in total adult returns to Bristol Bay over five 

decades. The authors concluded that if these stocks did not express this life history diversity, the 

variability in adult returns over this period likely would have been more than twice as large. The 

portfolio effect speaks to the importance of conserving populations that are not currently 

particularly distinctive or productive, as they might be important under future environmental 

scenarios.

The major concern regarding loss of among-population diversity is that widespread 

escapes from one or a few aquaculture broodstocks will lead to replacement of numerous, locally 

adapted populations with a smaller number of relatively homogeneous ones. Such replacement 

could erode local adaptations and reduce diversity among populations. A reduction in life history 

diversity—a simplification of the natural populations’ portfolio—could limit the capacity to 

respond to future environmental change. In many marine species, diversity among populations 

has evolved over many hundreds or thousands of years and cannot easily be regenerated once 

lost.

What considerations apply specifically to marine aquaculture?

Conventional wisdom is that because of large population sizes, a general lack of apparent 

barriers to dispersal, and environments that are perceived to be relatively homogenous, most 

marine species are not as strongly structured as are terrestrial, freshwater, or even anadromous 

species. Although each of these points has some empirical support, information is beginning to 

accumulate that challenges the generality of this conclusion. For example, evidence has been 

found for genetically based differences in life history among geographic populations of highly 

mobile species such as Atlantic cod. Absent direct information to the contrary, therefore, it 

would be prudent to assume that local adaptations might exist in the target species.

Many (perhaps most) species that are prospective targets of marine aquaculture can 

disperse widely, either as adults or eggs/larvae or both. As a consequence, escapes from even a 

single locality have the potential to affect many distant populations, with a homogenizing effect 

on diversity. Furthermore, aquaculture escapes might disperse more widely than typical natural 

fish because they don’t have an identifiable home range or territory. This effect is well 

documented in some hatchery and aquaculture programs for Pacific and Atlantic salmon; the 

extent to which it applies to most marine species remains to be determined.

Molecular genetic data are available for natural populations in a wide range of species. 

In the vast majority of cases, these data reflect genetic variation at what are presumed to be 
30

largely neutral gene loci (i.e., genes that are not strongly affected by natural selection). 

Empirical studies show that, although these molecular genetic data provide a great deal of 

information about population connectivity, they generally are not reliable indicators of 

differentiation at genes related to local adaptation. For two reasons related to population size 

(N), this discrepancy between neutral and selected loci could be particularly important for marine 

species.

First, the magnitude of neutral genetic differentiation (for example, as measured by 

genetic distance or the metric FST) is determined by the absolute number of migrants per 

generation (mNe), whereas the ability of migration to counteract local adaptation depends on the 

migration rate (m). If N and Ne are large, then mNe can be large enough to produce low FST

values even if m is very small. For example, a low FST = 0.01 for a species with Ne = 106 implies 

a very small migration rate (m = 0.000025), which would not prevent development of local 

adaptations if selective regimes differed among local habitats.

Second, as previously noted, selection is most efficient in large populations, which 

reinforces the idea that marine species with large populations could be locally adapted, even with 

modest selective differences and even if neutral markers show little evidence of differentiation.

What strategies can help minimize risks to among-population diversity?

As with all genetic risks, the most reliable way to minimize adverse effects on amongpopulation diversity is to ensure that few individuals escape. Other actions that can minimize 

risks include the following:

1. Pay careful attention to locations of broodstock collection. Sourcing broodstock from too 

local a scale risks incorporating related individuals and hence elevating levels of 

inbreeding; collecting too broadly risks mixing individuals from different populations.

2. Keep the geographic scale of areas affected by strays smaller than the area occupied by a 

single population.

3. Obtain as much information as possible about the ecology and life history of the target 

species. In the absence of this information, it will be difficult to quantitatively assess 

risks and develop approaches to minimize them.

4. Regularly monitor for physically marked cultured individuals and genetic markers in 

nearby wild populations. Physical marks or tags on cultured individuals can greatly 

enhance the ability to monitor escapes and molecular markers can help to track genetic 

impact on natural populations. Although these methods by themselves do not reduce 

risks, they can provide vital information that allows better experimental design and 

management of the program.

How long will it take for natural processes to restore lost population structure?

If aquaculture operations lead to loss of genetic diversity between populations, but the 

problems that caused the loss are permanently fixed, how long will it take for original levels of 

population subdivision to be restored by natural processes? Something like the original 

population structure would be restored when the new system reached an equilibrium between 

migration and genetic drift. How long this would take depends primarily on the size of the 
31

populations and the original level of divergence (Figure 5). Many marine species have weak

population differentiation (low FST values) and could reach the new equilibrium relatively 

quickly unless they are very large. For example, a species with original FST = 0.001 that was 

homogenized by human activities could regain half the original value within about 10 

generations, assuming Ne for individual populations was no larger than about 10,000. In 

contrast, for a species with large populations (Ne ≈ 105–106) and original FST = 0.01 (still quite 

low but within the range of many marine species), after normal levels of gene flow were 

restored, it would take thousands of generations to achieve an appreciable fraction of the original 

population differentiation.

Results discussed above apply to genetic diversity that is selectively neutral (but which 

might form the basis for future response to selection). Natural selection could potentially lead to 

faster restoration of diversity among populations, albeit at a demographic cost to the population.

In summary, the following points are the most important considerations for maintenance 

of diversity among populations:

1. Diversity among populations provides a short-term buffer against environmental 

fluctuations and, in the long term, enhances the evolutionary potential of the species.

2. Escapes from aquaculture operations have the potential to erode differences among 

natural populations that have evolved over long time periods.

3. Understanding the ecology and life history of the target species is important to 

developing effective strategies to minimize risks to among-population diversity.

Figure 5. Estimated time (T50, in generations) to reach 50% of the equilibrium FST value, assuming that 

anthropogenic activities have completely eliminated population structure (FST = 0) and that, at 

time 0, levels of migration (m) are restored that will eventually produce the equilibrium FST. For 

a given FST, the equilibrium migration rate depends on Ne in each subpopulation (500, 10,000, 

500,000). Note the log scale on both axes. Data are based on Equation 3 (Appendix A) assuming 

equilibrium FST = 1 / (1 + 4mNe).
32

Loss of Fitness

Aquaculture can lead to loss of fitness in wild populations when captive and wild 

individuals interbreed. The fitness loss can occur through either or both of two mechanisms. 

Domestication leads to genetic changes associated with the culture environment, and these 

changes can be passed on to wild populations by escapes or intentional releases. Domestication 

can occur even when local populations are used to source broodstock. Outbreeding depression

can occur when genetically differentiated populations interbreed—as might happen, for example, 

if nonlocal populations or highly domesticated stocks are used for broodstock and some 

individuals escape into the wild. Outbreeding depression does not directly depend on effects of 

fish culture, but its likelihood of occurrence can be greatly enhanced by stock transfers 

associated with aquaculture operations. These two mechanisms are discussed below.

Domestication

In captive populations, two related processes produce selective regimes that differ 

substantially from those experienced in the wild. First, intentional or inadvertent selection for 

traits that promote survival, reproduction, or both in captivity can increase fitness in the captive 

environment. For example, program operators might intentionally select for traits considered 

desirable, such as size, flesh quality, or feed conversion efficiency. Even without intentional 

selection, captive environments can exert strong inadvertent selective pressures for phenotypes 

that perform well in captivity. Traits that often are influenced by this type of selection include 

behavioral traits that increase feeding rates under captive conditions and earlier spawning time 

(because progeny of these adults grow faster and outcompete others in their cohort).

The second major way that selective regimes differ in captivity is through relaxation of 

selection that occurs in the wild. This does not require positive selection toward adaptations to 

captive life; rather, it arises in a successful captive program because large numbers of individuals 

survive that would not have survived in the wild. Although mortality in the wild might be 

largely random, some fraction is mediated by natural selection, which weeds out individuals with 

maladaptive phenotypes each generation. In a benign captive environment, individuals with 

these maladaptive phenotypes can survive to reproduce, leading to a gradual erosion of fitness of 

captive individuals when they are returned to the wild environment.

These combined effects lead to genetic change in a population that generally makes it 

more fit in the captive environment but less fit in the wild. Note that domestication, which is a 

form of natural selection, does not require (nor generally involve) any genetic change to 

individual fish; rather, it occurs across generations as individuals with certain phenotypes (and 

their associated genotypes) survive and reproduce at different rates than they would in the wild. 

Because of the profound changes in selective regimes and mortality patterns between captive and 

wild environments, some level of domestication is unavoidable. Indeed, genetic adaptation to 

captivity has been documented in a wide range of species, even though the exact mechanisms 

leading to domestication are less well understood.
33

Outbreeding depression

When two individuals mate, the fitness of their offspring can be strongly affected by the 

degree of genetic relatedness of the parents. Animal and plant breeders (including Charles 

Darwin) have long known that matings between close relatives (full or half siblings, or even 

cousins) often produce offspring with reduced fitness; this phenomenon is known as inbreeding 

depression. Conversely, if the parents are too divergent genetically, offspring fitness can also be 

reduced, through a phenomenon known as outbreeding depression. Over time, most natural 

populations have probably achieved a balance between the two forces, resulting in an 

intermediate level of outcrossing that is consistent with viability. Occasionally, natural processes 

create conditions under which strongly diverged populations come into contact, with some level 

of outbreeding depression a likely consequence. Although outbreeding depression has not been 

as well studied as inbreeding depression, numerous empirical examples have been found 

involving natural populations. Furthermore, anthropogenic changes to natural ecosystems, 

including aquaculture, can create conditions in which individuals from genetically differentiated 

populations can interbreed at rates that are orders of magnitude higher than would occur 

naturally.

Two general mechanisms can produce outbreeding depression, either separately or in 

conjunction. First, local adaptations can be diluted when maladapted genes are introduced from 

a genetically divergent population. Second, favorable combinations of genes that have been 

shaped by natural selection to perform well in the local environment can be disrupted by 

recombination (genetic shuffling) that occurs following a hybridization event.

What considerations apply specifically to marine aquaculture?

Most marine aquaculture operations create culture conditions that depart dramatically 

from those experienced in the wild and this should promote rapid domestication. As discussed 

above (Lessons Learned section), some degree of domestication is generally desirable from a 

production standpoint, which creates a tension when evaluating the possible consequences of 

domestication for natural populations. Use of local broodstocks will not avoid domestication, 

but it will avoid additional losses of fitness arising from translocation of genetically divergent 

populations. Some aquaculture operations will involve both factors (broodstock derived from a 

nonnative source and strong domestication for market-related reasons).

As is the case for the other genetic risks, whether aquaculture escapes will actually lead 

to reduced fitness of wild populations (and if so by how much) will depend in a complex way on 

a variety of factors, including the number and life stage of escapes, their probability of surviving 

to maturity, and the probability that mature escapes will successfully reproduce with wild 

individuals.

How long will it take natural processes to restore lost fitness?

If aquaculture leads to loss of fitness in a wild population, but the problems that caused 

the loss are permanently fixed, how long will it take natural processes to restore original levels of 

population fitness? In general, if the forces leading to loss of fitness (domestication, outbreeding 

depression) are eliminated or reversed, natural selection should gradually increase fitness in the 
34

wild population. However, several factors make it difficult to make quantitative predictions 

about the nature and extent of the new levels of fitness.

First, evolution is irreversible, in the sense that it is essentially impossible to recreate the 

exact conditions that led to a prior evolutionary state. Thus although selection might eventually 

produce something like historic levels of fitness of a natural population that had been strongly 

affected by aquaculture, exactly recreating the original population status is generally not an 

achievable objective.

Second, selection can operate in many different ways, both in reducing and restoring 

fitness in the wild. This can be contrasted with evolutionary changes of neutral alleles, which 

can be predicted in a statistical sense based on well-developed population genetics theory. The 

same body of theory can predict responses to selection, but with so many different types of 

selection to consider, the range of possible outcomes is enormous. Furthermore, the strength and 

direction of selection can change on short (ecological) time scales.

Third, basic evolutionary theory tells us that the rate of genetic change depends on the 

amount of genetic variation, the strength of selection, and population size. If strong 

domestication pressures cause rapid change, then the novel selective pressures are relaxed, the 

rate at which fitness increases will not necessarily be as rapid, because the forces acting to

restore fitness might not be as strong.

Finally, by definition natural selection requires that less fit individuals produce relatively 

few or no offspring that survive to reproduce, and this means that selection imposes a 

demographic burden on the population. Thus although natural selection can move a maladapted 

population back toward its adaptive peak, during that process the population could be at 

significant risk and be particularly vulnerable to random demographic and environmental 

variability.

What strategies can help reduce risks to fitness of natural populations?

Assuming that a certain number or fraction of escapes is unavoidable, then two general 

strategies are available to attempt to minimize the fitness consequences of these escapes. In 

Strategy 1, efforts are made to keep the captive population as similar as possible genetically to

the wild population. This necessitates using local fish for broodstock and making efforts to 

reduce the rate of domestication. Under this strategy, it would be difficult to achieve some of the 

benefits to production or cost efficiency that can result from intentional selection for traits that 

are desirable in cultured populations but probably maladaptive in the wild.

Strategy 2 takes the opposite approach: make the cultured population substantially

different genetically from the local wild population, which might be accomplished by using 

nonlocal (and perhaps not locally adapted) sources for broodstock or intentionally selecting for 

traits that are considered beneficial in culture. The logic for this strategy is that if the captive 

population is highly domesticated or otherwise maladapted to local conditions, individuals that 

do escape have a low probability of successfully reproducing.

Strategy 2 thus seeks to minimize the number of genetic interactions between captive and 

wild individuals, but has the unfortunate consequence that interactions that do occur are likely to 
35

produce offspring with greatly reduced fitness in the wild. Conversely, Strategy 1 seeks to 

minimize the adverse effects of interbreeding events that do occur, but has the unfortunate 

consequence that such interactions are likely to be more frequent than those under Strategy 2. 

The overall consequences for natural populations depend in some complex way on the product of 

the number of interbreeding events and the severity of each. Unfortunately, at present we are just 

beginning to understand how to quantitatively evaluate the inherent trade-offs in these two 

strategies, which is necessary before on can determine which strategy will be less detrimental to 

wild populations. Figure 6 is a conceptualization of how such an evaluation might be carried 

out. In this figure, the curves show possible relationships between a measurable outcome (e.g., 

fitness of the wild population) and the degree of genetic differentiation between cultured and 

wild individuals.

Captive / Wild Similarity

Fitness

low

low

high

high

Fitness

low

high

High escapes

High survival

Low escapes

Low survival A

B

Figure 6. Hypothetical relationship between fitness of a wild population and the degree of genetic 

similarity between the wild population and a captive population from which some individuals

routinely escape. The solid and dashed curves illustrate some of the possible shapes of this 

relationship; the vertical lines represent practical limits to how different or how similar the 

hatchery population can be made compared to the wild. All else being equal, higher rates of 

escapes or higher survival of escapes will lead to greater reductions in fitness (panel B) than will 

lower rates of escapes or survival (panel A).
36

In theory, under ideal conditions there should be no fitness loss if captive and wild fish 

are genetically identical, or if they are so divergent that no interbreeding is possible. Values of 

hatchery-wild differentiation between these extremes should show some level of reduction in 

fitness, but the shape of this relationship is unknown. The two vertical lines illustrate the 

practical limits to what can be achieved. The vertical lines on the right indicate that it is 

impossible, in the benign selective regimes in culture, to produce fish with identical adaptations 

to wild fish. The vertical lines on the left indicate how different any given cultured and wild 

populations might be under realistic conditions.

Under this framework, the following approach could be used to reach a decision about 

whether to pursue Strategy 1 or Strategy 2:

1. Determine the shape of the curve (probably through modeling, informed by some 

empirical data) and how it changes with various parameters considered;

2. Determine where the vertical lines fall with respect to inflection points on the curve 

(probably based on existing information); and

3. Determine which strategy leads to higher fitness.

For example, in Figure 6, panel A, if the “similar” strategy can achieve a level of 

captive/wild similarity indicated by the vertical line on the right and the “different” strategy can 

achieve a captive/wild difference as indicated by the vertical line on the left, then the “similar” 

strategy leads to higher fitness if the dashed curve describes the true relationship, while the 

“different” strategy leads to higher fitness if the solid curve describes the true relationship. If 

constraints for both strategies are shifted to the left (Figure 6, panel B), then the “different” 

strategy is preferable regardless of the shape of the relationship. Alternatively, one could assume 

a fixed value for one strategy and ask how extreme the other must be to become better. The key 

question would then become whether it is feasible to achieve the required level of captive/wild 

similarity or difference. If this type of analysis were conducted over a wide range of conditions, 

it might emerge that, given the practical situations likely to be faced by marine aquaculture, one 

strategy is consistently preferable to the other.

The height of the curves in Figure 6 will depend on the level of escapes and how 

successful they are in reproducing (compare Panels A and B). The extreme case of Strategy 2 is 

to ensure that the broodstock is sterile or otherwise incapable of reproducing in the wild. This is 

discussed in the Sterilization subsection below.

In summary, the following points are the most important considerations for maintenance 

of fitness:

1. Domesticated aquaculture populations typically have low fitness in the wild and the 

fitness reductions can be even greater if the cultured population is not derived from local 

sources.

2. Low fitness of cultured individuals in the wild has two contrasting consequences for 

natural populations:

• Domesticated escapes are less likely to survive to maturity, and if they do are less 

likely to successfully reproduce; but,
37

• Domesticated escapes that do manage to reproduce in the wild can have particularly 

deleterious consequences for fitness of natural populations.

3. Research currently underway should provide some insights into whether strong 

domestication of aquaculture broodstocks is likely to reduce or increase risks to fitness of 

natural populations.

Other Risk Factors

This document focuses on genetic risks. However, a comprehensive risk-benefit analysis 

should also consider a number of related risks and benefits. For completeness we briefly list 

some important risks below (see Waples and Drake 2004 for a more thorough discussion).

Competition and Predation

Aquaculture escapes can prey on wild populations and also compete with natural 

individuals for food or territory. Escapes that mature can compete with natural adults for 

spawning sites and access to mates. If the number of escapes is sufficiently large, their presence 

might impose other forms of selection that alter characteristics of wild populations important to 

survival and reproductive success. Effects on wild populations can occur even if the escaped 

individuals do not complete a life cycle in the wild—for example, if they destroy spawning nests 

of wild individuals or divert mating efforts by wild individuals into unproductive spawnings.

Disease and other Mortality Factors

Diseases and parasites are pervasive in the marine environment and are part of the 

ecological and evolutionary histories of all marine species. However, because of high rearing 

density, aquaculture operations can greatly magnify the incidence of naturally occurring diseases 

and parasites, and movements of eggs, fish, or fish products into new geographic areas can 

expose natural populations to new pathogens for which they have little or no natural resistance. 

Risks from introduced pathogens and parasites include temporary epidemics, long-lasting 

population reductions, and even extinction of wild populations. For example, Burreson et al. 

(2000) used molecular methods to show that the parasite Haplosporidium nelsoni (popularly 

known as MSX), which has decimated populations of the eastern oyster (Crassostrea virginica) 

along the Atlantic coast of the United States, most likely originated from translocations of Pacific 

oyster, C. gigas, from Japan. Risks posed by disease agents are harder to quantify than those 

posed by competition or predation, as a single individual transferred to a recipient population can 

have dramatic consequences. Disease agents also can be spread by water, independent of any 

releases of cultured individuals.

Low Power to Detect Adverse Effects

Because natural variability in most natural populations is relatively high, the ability to 

detect deleterious fitness effects of aquaculture escapes can be low, even in the most ambitious, 

well-designed program. This means that by the time adverse effects are detected, they might 

have already occurred for many years and might have long-lasting consequences for natural 

populations.
38

Programmatic Inertia

Experience with fish hatchery programs indicates that, once begun, hatchery programs 

can be difficult to stop for political or social reasons, even if there is compelling biological 

evidence regarding their ineffectiveness or their adverse impacts on natural populations. 

Therefore, a key question in considering whether to initiate a new commercial aquaculture 

operation is: Can the operation be terminated or modified if a biological evaluation indicates its 

costs or detrimental effects are greater than its benefits?

Risks to Natural Populations from other Anthropogenic Activities

Although this technical memorandum focuses on effects of marine aquaculture, it is 

important to remember that natural populations of marine species are also affected by a variety of 

other anthropogenic activities, including fishing, pollution, and habitat loss and degradation. A 

brief summary of some other anthropogenic factors follows.

Humans harvest a wide variety of marine species for food, and for some of these species 

(e.g., Atlantic cod), significant exploitation has occurred for a millennium or more. Concerns are 

growing not only for depletion of individual species, but also for major changes to marine 

ecosystems. A recent review of the status of global fisheries (Worm et al. 2009) found that in 

half of the well-studied ecosystems, the mean exploitation rate had declined to a level that should 

allow reaching maximum sustainable yield; however, nearly two-thirds of the world’s fish stocks 

still need rebuilding. Furthermore, the last decade has seen increasing recognition that sizeselective fisheries might be causing evolutionary changes in life histories of some heavily 

exploited fish populations (e.g., Kuparinen and Merilä 2007).

For terrestrial species around the world, loss and degradation of habitat is perhaps the 

most pervasive threat to biodiversity. In contrast, the role that offshore marine habitats play in 

population dynamics of marine species is poorly understood. The best studied component is 

benthic habitats that can be damaged by bottom trawls, which are widely used in many U.S. 

fisheries. Anthropogenic changes to nearshore habitats, which are vital to juvenile rearing for 

many species, are better studied, and anthropogenic changes here (such as dredging, draining and 

filling wetlands, and armoring shorelines) can profoundly affect demographic and ecological 

processes in marine ecosystems (Levin and Stunz 2005). In tropical areas, rising water 

temperatures and declining pH due to increased CO2 concentrations are putting increasing 

pressure on reef-building corals and other marine organisms with carbonate skeletons.

Relatively little attention has been given to pollution as a major risk factor for 

commercially and ecologically important marine fish species. Some exceptions include 

nutrients, sediments (Fabricius 2005), and trash (plastics and other marine debris, Gregory 2009). 

Little is known about the impacts of toxic chemical contaminants, which are complex and 

expensive to study. Effects of pollution are likely to become increasingly important in the future, 

given that 1) society is releasing chemicals into the ocean at a rate that exceeds the capacity of 

scientific institutions to study and understand their ecological impacts, 2) many toxics are 

pervasive and persistent in the marine environment and can be difficult or impossible to mitigate 

once released, and 3) the extent to which toxics will interact with other large-scale ecological 

forcing pressures (e.g., climate change and ocean acidification) is largely unknown.
39

Managing Risk

An important management consideration is to identify characteristics of marine 

aquaculture programs that help to ensure sustainability not only for these programs but also for 

wild populations. In this section we discuss a number of different tools that might be used to 

help manage genetic risks associated with marine aquaculture. This is not intended to be a 

comprehensive list; rather, the objective is to provide potentially useful examples, some of which 

are still under development and need further evaluation for practical usefulness.

Fault Tree and Risk Assessment Pathway

Kapuscinski et al. (2007) and Senanan et al. (2007) developed a fault tree and risk 

assessment pathway to assist in identifying and evaluating genetic risks associated with releases 

or escapes of transgenic individuals into the wild. We have modified these tools to assist in 

evaluating and monitoring genetic risks associated with escapes of aquaculture individuals into 

marine environments. The fault tree (Figure 2) describes the sequence of events leading to 

introgression of genes from escaping cultured individuals into the gene pool of wild relatives. 

The corresponding risk assessment pathway (Figure 7) guides the conduct of a systematic 

assessment of risk of gene flow from these cultured individuals into the wild population.

Aquaculture Genetics Management Plan

In the Pacific Northwest, the Hatchery Science Review Group has undertaken a 

comprehensive review of salmon hatchery operations in western Washington state (Mobrand et 

al. 2005), and efforts are currently underway to expand the evaluations to the entire Columbia 

River basin. An important outgrowth of the Hatchery Science Review Group effort has been 

development by NMFS of the framework for the Hatchery Genetics Management Plan, which 

provides a standardized format for describing the operation of each hatchery program for salmon 

and steelhead (Oncorhynchus mykiss) and the potential effects of each program on ESA-listed 

species. We have adapted the Hatchery Genetics Management Plan format to better reflect 

particular issues associated with marine aquaculture programs or operations in the Aquaculture 

Genetics Management Plan (AGMP, see Appendix B). Careful preparation of this document for 

each program will greatly facilitate application of the Kapuschinski et al. (2007) and Senanan et 

al. (2007) fault trees and risk assessment pathways, with emphasis on the genetic risks identified 

at the beginning of this section.

State and Federal Guidelines

Although the U.S. Fish and Wildlife Service frequently must deal with genetic issues 

associated with artificial propagation of fish species, and various guideline documents have
40

Figure 7. Pathway for conducting an assessment of gene flow. Asterisk (*) denotes an assessment step 

that requires empirical information on traits of the cultured organism. BCn refers to the nth 

generation backcrosses between F1 hybrids and wild relatives. (Adapted with permission from 

Kapuscinski et al. 2007, copyright Centre for Agricultural Bioscience International.)
41

circulated in draft form over the years, the agency has no formal policy guidelines on this issue.2 

Hard et al. (1992) produced a technical memorandum for NMFS that discusses in detail genetic 

and other considerations associated with artificial propagation of Pacific salmon. However, that

document focused primarily on identifying situations under which artificial propagation might 

provide at least a temporary benefit to populations listed under the ESA. Thus although the 

general issues are similar to those considered here, the goals of using artificial propagation under 

the ESA differ substantially from those associated with most commercial marine aquaculture 

operations and stock release for enhancing commercial or recreational fisheries.

The published guidelines that are perhaps most directly relevant to the issues considered 

here are the Genetic Policy for the Release of Finfishes in Florida, produced by the Florida Fish 

and Wildlife Conservation Commission (FFAWCC 2007), which state (p. 4) that:

It is the policy of the [commission] that all activities involving the release of fin

fish shall be undertaken with full consideration of their impacts on natural 

biological diversity and in ways that do not threaten the state’s natural biological 

heritage.

These guidelines cover intentional and unintentional releases and include considerable 

emphasis on aquaculture and marine stock enhancement. Genetic risks identified in the 

guidelines (loss of diversity within and between populations and loss of fitness and adaptive 

potential) closely parallel those considered here. The guidelines indicate that preliminary 

analyses should be conducted to determine whether it is necessary to complete a genetic 

management plan for the proposed program; the guidelines also provide a template for such a 

plan, which shares many similarities with the AGMP proposed here. The guidelines advocate an 

adaptive management approach to consideration of artificial propagation. Actions that might be 

called for depending on the circumstances include:

1. Developing a plan for genetic management of the aquaculture activity,

2. Identifying geographic boundaries of relevant natural stocks,

3. Preventing the translocation of nonindigenous genomes,

4. Minimizing potential impacts from propagation-related genetic changes (domestication) 

in cultured individuals,

5. Managing the proportion of cultured individuals in admixtures of cultured and wild 

individuals,

6. Monitoring recipient populations when genetic risks are deemed moderate to high, and

7. Undertaking action to eliminate detected genetic hazards.

The State of Alaska has also had genetic guidelines regarding aquaculture operations for 

more than three decades. The current genetic guidelines, which have been in place since the 

mid-1980s (ADFG 1985), were developed primarily to protect the state’s abundant wild salmon 

populations, but have been applied more broadly. Specific policy provisions include the 

following:

 2 D. Campton and S. Chambers, U.S. Fish and Wildlife Service, Portland, OR. Pers. commun., December 2009.
42

1. Live salmonids, including gametes, cannot be imported from other states.

2. Transport of stocks among major geographic areas within the state is prohibited.

3. Transport within regions can be considered after reviewing phenotypic characteristics and 

distance of transport.

4. Significant or sensitive wild stocks should be identified, and stocks cannot be introduced 

into areas where they might significantly affect these wild populations.

5. In watersheds with significant wild stocks, only broodstock derived from local 

populations can be used for stocking.

6. Establishment of drainages that serve as wild stock sanctuaries is encouraged.

7. A single donor stock cannot be used to found more than three hatchery stocks.

8. Broodstock collection should be representative with respect to run timing.

9. Cultured populations should strive to maintain effective population size of at least 400.

10. Cooperative research among university, state, federal, and private sector scientists to 

address key uncertainties is encouraged.

Atlantic Salmon in Maine

Following many decades of decline of Atlantic salmon in North America, the species has 

received federal protection in the United States and Canada. In the United States, all remaining 

natural populations (from Androscoggin River northward along the Maine coast to the Dennys 

River) are listed under the ESA as a distinct population segment (DPS). The DPS includes 

conservation hatchery populations, but not populations cultured in commercial aquaculture 

operations.

North America also hosts aquaculture operations for Atlantic salmon, with annual 

production in New England ranging to 16,000 metric tons over the last decade (Figure 8). 

Substantial production also occurs in British Columbia and the maritime provinces of Canada. 

In general, the industry rears juveniles in private freshwater facilities before transferring them to 

anchored net pens or sea cages for feeding in the marine environment until they reach market 

size. Unintentional escapes from the net pens and cages and amplification and release of 

pathogens and parasites are the primary risk factors for natural populations.

In recognition of these conservation concerns, the North Atlantic Salmon Conservation 

Organization passed the Williamsburg Resolution to “minimize impacts from aquaculture, 

introductions and transfers, and transgenics on the wild salmon stocks” (NASCO 2003). 

Because the U.S. populations are ESA listed, it was necessary for the U.S. agency permitting 

commercial aquaculture operators (U.S. Army Corps of Engineers) to consult with the U.S. Fish 

and Wildlife Service and NMFS to determine whether proposed actions were likely to adversely 

affect listed salmon. That formal consultation resulted in issuance of a Biological Opinion 

(NMFS 2003), which determined that the proposed aquaculture activities might adversely affect 

but were not likely to jeopardize the existence of the listed DPS.
43

Figure 8. Recent aquaculture production of Atlantic salmon in New England. Data from Table 1.6.1 in 

USASAC 2011.

Issues associated with escaped farmed salmon that were considered in the Biological 

Opinion included redd superimposition, competition for food or space, and genetic introgression. 

Protective measures that were recommended to help ensure that the adverse effects do not rise to 

a level that would constitute legal jeopardy include: 1) use of only North American stocks for 

production, 2) implementation of containment measures to reduce escapes, 3) prohibitions on 

stocking transgenic salmon, and 4) 100% marking of all salmon placed in marine pens within the

United States. Each of these requirements has been incorporated into permit requirements and is 

verified through annual third party audits.

The National Research Council conducted a review of the status of Atlantic salmon in 

Maine, and the resulting report (CASM 2004) contains a detailed discussion of genetic issues, 

including the Ryman-Laikre effect.

Genimpact

The European Union supported a multiyear project (Genimpact, online at http://

genimpact.imr.no/) to evaluate the genetic impact of aquaculture activities on native populations. 

The overall objective was to bring together scientists and stakeholders to develop information 

that would be useful for policy makers. Specific goals were to 1) develop consensus statements 

on the genetic impact of farming activities and its implications for aquaculture management, 

stock conservation, and environmental safety and 2) integrate the scientific basis for the 

establishment of preventive measures for important aquaculture species. The final report 

(Svåsand et al. 2007) summarizes results of four workshops that covered topics such as genetics 

of domestication, monitoring, modeling, and management options to reduce impacts. Results of 

this work have been incorporated at various places in this document (e.g., Table 2).
44

Examples of Risk Assessment Tools

The All H Analyzer

Another outgrowth of the Hatchery Science Review Group effort was development of the 

All H Analyzer, or AHA model, which was designed to integrate consideration of effects of 

habitat, harvest, hatcheries, and hydropower development in a single model. The model deals 

with individual hatchery-wild population systems that experience harvest and various types of 

habitat conditions. The module that assesses evolutionary effects of hatcheries draws heavily on 

the work of Ford (2002) to assess the reduction in fitness of natural populations caused by 

domestication. The AHA model has seen widespread use throughout western Washington and 

the Columbia River basin and has some potential application to marine aquaculture. The AHA 

model was recently reviewed critically by the Recovery Implementation Science Team (RIST 

2009), which concluded that the model can be useful in developing guidelines and evaluating 

relative impacts; however, the members cautioned that they “do not think that the AHA model 

can accurately predict the outcomes of specific hatchery or habitat actions in a quantitative way” 

(RIST 2009, p. 4).

The Offshore Mariculture Escapes Genetic/Ecological Assessment (OMEGA) Model

The OMEGA model (ICF 2012) was developed by NMFS and ICF International as a tool 

for use by scientists and resource managers to better understand potential negative impacts of 

farmed escapes on wild populations. The goals of OMEGA are to: 1) provide insights into risks 

associated with escapes from marine aquaculture, 2) identify research priorities, 3) explore 

options for design of sustainable aquaculture programs, and 4) inform policy and management 

decisions regarding genetic and ecological risks of aquaculture.

The OMEGA model includes three major components: biology of the cultured 

population, aquaculture facilities and operations, and biology of the wild population. Each 

component includes modules that describe specific assumptions used to model interactions of 

escapes and their effects on natural populations. The “wild” component describes recruitment, 

survival, growth, and age structure of the wild population. The model allows for the possibility 

that escapes might not survive, if they do they might not encounter a wild population, and if they 

encounter a wild population they might not reproduce successfully.

By evaluating different aquaculture operation scenarios, OMEGA allows the user to 

compare trends in total abundance of escapes and wild fish, as well as effects of the aquaculture 

program on survival of wild fish. OMEGA simulates a user-defined scenario of aquaculture 

escapes over a period of 100 years. Abundance, frequency, and size of escapes is defined by 

model inputs that specify the number, length of time, and size of fish held in offshore pens, and 

the likely magnitude and frequency of escape events.

OMEGA defines density-dependent life stages that mimic ecological interactions through 

competition for food and space. Effects of genetic and ecological interactions are calculated 

under a user-specified set of assumptions. These assumptions define the survival of escapes in 

nature, their likelihood of encountering conspecifics, the breeding success of escapes, and the 
45

consequence of interbreeding on the long-term survival of wild conspecifics. Calculation of loss 

of fitness in the wild population is based on the phenotypic fitness model described by Ford 

(2002).

Based on a demonstration of an earlier version of the model, we believe that OMEGA has 

the potential to provide useful information for managers dealing with marine aquaculture issues. 

Before widespread application, it will be important to evaluate performance under realistic 

scenarios, and caveats noted in the Lessons Learned section above about predictive capabilities 

for individual programs would also apply here.

Risk Trade-offs

Some risks are correlated in such a way that strategies to reduce one exacerbate another. 

In these cases, it is generally impossible to simultaneously reduce both types of risk, which sets 

up some inevitable trade-offs with respect to management options. Waples and Drake (2004) 

discuss a number of these trade-offs for programs that are designed to enhance natural 

populations. For aquaculture programs or operations, a major trade-off involves the choice of 

broodstock source. Using locally derived broodstock will tend to reduce genetic and ecological 

differences between cultured and wild individuals, but at the same time increase the likelihood 

that individuals that escape will survive to reproduce; using nonlocal or highly domesticated 

broodstock reduces the changes that escapes will reproduce successfully, but those that do would 

pass on very maladaptive genes to the wild population. Another trade-off arises if the decision is 

made to develop a local broodstock. Collection from too small an area helps minimize the risk 

of obtaining a population mixture, but increases the risk of founding the program on a narrow 

and perhaps nonrepresentative genetic base. This latter risk can be reduced by collection from 

diverse and widely separated geographic locations, but this increases the risk of mixing more 

than one gene pool in the program.

Monitoring

Monitoring genetic as well as ecological effects of aquaculture should be an integral 

component of any production program. A well-designed, integral monitoring program with 

participation by the aquaculture operation (or agency conducting stock enhancement) and the 

appropriate regulatory agencies is the most effective means of detecting escaped individuals in 

the wild and their effects on natural populations; such a program can also provide information 

about effectiveness of measures to reduce this risk, such as changes in confinement technology, 

and can permit rapid implementation of remedial responses (Kapuscinski et al. 2007, Senanan et 

al. 2007). Furthermore, a well-designed monitoring program can help maximize efficiency by 

reducing unnecessary or excessively expensive sampling efforts. Senanan et al. (2007) 

developed a monitoring and assessment pathway for releases of transgenic individuals into the 

wild that we have modified to help guide monitoring efforts associated with escapes of 

aquaculture individuals into the marine environment (Figure 9).

Considering the global scale at which marine stock enhancement and aquaculture 

programs are conducted (Leber et al. 2004), monitoring any sort of effects on natural populations

currently plays only a very minor role. Nevertheless, there are some exceptions, and excellent 
46 

Detect change in the number of fish species 

Detect change in the relative abundance

Points of entry

Pattern and frequency of 

escapes

Detect escaped 

individuals

Presence of conspecifics or closely 

related species in the wild

No Yes

Successful mating

Detect escaped 

fish at all life stages

Yes

Detect F1 hybrid 

offspring

No, but sufficiently large numbers

to have nongenetic effects

No, but sufficiently large numbers Yes

to have nongenetic effects

Population establishment Detect population 

change of both escaped 

and wild individuals

Detect 

backcross

offspring (BCn

)

Escape genes spread Trojan gene effect

Successful reproduction

Level of genetic harms

Individual level

Immediate

population level

Long-term

population level

Generation time

First generation

> First generation

Several generations

Community level

Figure 9. Monitoring should focus on specific measurable end points (illustrated by trapezoids) in the 

cascade of potential changes that might result from escape and spread of cultured individuals. 

Types of impacts are organized into individual, population, and community levels. Generation 

time refers to the number of generations after the escapes. BCn refers to the nth generation 

backcrosses between F1 hybrids and wild relatives. (Adapted with permission from Senanan et al.

2007, copyright Centre for Agricultural Bioscience International.) 

examples of programs to monitor genetic effects on natural populations can be found for Atlantic 

cod in Norway (Svåsand et al. 2004), red sea bream (Pagrus major) and other marine species in 

Japan (Kitada et al. 2009), and red drum in the southeastern United States (several references 

cited in the Example section below). In the following, we highlight some features of an effective 

monitoring program.
47

Robust Monitoring is an Integral Part of Production

A robust monitoring program, integral to an aquaculture program, is characterized by 

clear, achievable, and measurable objectives. Such objectives inform a logically consistent risk 

assessment process to identify, prioritize, and select measurable end points that can help trigger 

appropriate remedial responses. Senanan et al. (2007) outlined an iterative approach for 

planning, conducting, and evaluating a monitoring program:

1. Define the monitoring end points;

2. Define parameters and measurable variables;

3. Design sampling schemes and test for adequate statistical power of sampling;

4. Choose and employ appropriate sampling methods;

5. Analyze, interpret, and store data;

6. Refine the monitoring design based on lessons learned from data collection and analysis;

and

7. Inform risk management decisions.

Resulting data can help guide future risk assessments.

Identifying Remedial Responses

A robust monitoring program clearly identifies the remedial responses that would ensue 

when particular end points are reached based on monitoring. Unless actions to be taken as a 

result of particular outcomes are discussed and agreed to ahead of time, an effective and timely 

response to information gained through monitoring is unlikely. A full range of remedial actions 

should be clearly defined and associated with particular monitoring end points (Hard 1995b). 

These actions include, at a minimum:

1. Take steps to minimize escapes,

2. Expand spatial scope or temporal frequency of monitoring,

3. Consider transfer of production to an alternative facility with greater containment 

success,

4. Consider reproductive containment measures, and

5. Cease production.

Identifying Measurable End points

A robust monitoring program includes measurable end points that are tailored to the life 

history of the species under culture. Here we adapt six measurable end points identified by 

Senanan et al. (2007) for monitoring releases of transgenic organisms to the goal of monitoring 

the effects of escaped aquaculture individuals:

1. Presence of escapes,

2. Presence of F1 hybrid offspring,
48

3. Presence of backcross hybrid offspring,

4. Presence of escaped individuals at all life stages,

5. Population change of wild individuals, and

6. Changes in the numbers of local fish species and their relative abundance.

The ability to detect escapes and their descendants can be enhanced considerably by 

marking all cultured individuals, either through physical tags or by using genetic marks. 

Modeling the consequences of escapes through genetic simulations is also likely to be useful in 

helping to refine monitoring methods, including the spatial scope and temporal frequency of 

monitoring.

Statistical Power

A robust monitoring program includes a realistic assessment of statistical power to detect 

undesirable effects. Hard (1995b) pointed out that genetic monitoring for changes in traits 

important to fitness and performance (e.g., life history characters) often will be complicated by 

the difficulty of 1) determining the source of changes in phenotypic variation (i.e., genetic versus

environmental) and 2) low statistical power to detect such changes. One particularly pernicious, 

incorrect inference can occur when a failure to detect genetic differences arising between 

cultured and natural individuals leads to the conclusion that no such differences exist. This 

problem is likely to arise when monitoring is not systematic or during the initial phases of an 

aquaculture program with limited ability to contain escapement from the facility. Hard (1995b) 

recommended including an integral research component to production systems that can provide 

valuable information on the ways in which genetics versus environment contribute to key 

differences between cultured and wild individuals (i.e., the traits most sensitive to domestication 

in protective culture). Senanan et al. (2007) provided guidance on estimating power, sampling

design, and sampling requirements to detect effects at various levels, including changes in wild 

population size or species composition.

Opportunities for Research

Coordinated production and research, along with rigorous monitoring, is essential to 

providing baseline information to detect changes resulting from aquaculture and identifying 

opportunities to evaluate sampling efficiency. For most cultured marine species, information on 

life history, genetics, and population structure is limited. Aquaculture programs provide an 

opportunity to improve this information through associated research. Studies in the following 

areas would be especially valuable in improving monitoring and reducing risks of aquaculture to 

wild populations (Senanan et al. 2007):

1. Patterns of escapes and efficacy of confinement measures;

2. Movement of the target species within local habitats;

3. Survival rate and reproductive success of escaped cultured individuals in the wild;

4. How fish density affects the above characteristics;

5. Genetic diversity of cultured stocks and potentially impacted populations;
49

6. Abundance of potential receiving populations and their temporal and spatial variation;

7. Fish community composition and natural variation;

8. Sampling efficiency for different locations, gear types, and environmental conditions; and

9. Modeling studies that can make use of data acquired by experiments, field studies, and 

monitoring and make predictions from a larger parameter space than established by data.
50

Frequently Asked Questions

What level of interbreeding with cultured individuals is completely safe for wild 

populations?

A value of 5% has often been proposed as an upper limit to the fraction of cultured 

individuals breeding in wild populations (e.g., as adopted by the State of Florida in its genetics 

policy, FFAWCC 2007). In fact, however, no level of interbreeding can be regarded as 

completely safe for natural populations if it continues indefinitely. That was the conclusion of a 

scientific panel (reported in Grant 1997) convened to consider this question with respect to 

straying of hatchery salmon. Even a very low level of interbreeding can be harmful if it 

continues long enough. This conclusion is based on two well-established facts from evolutionary 

biology: 1) most selective differentials (s) measured in the wild are relatively small (typically a 

few percent, and mostly less than 5%), and 2) migration of nonnative genes into a population can 

swamp local adaptations if the migration fraction (m) is larger than s. The Florida Genetics 

Policy acknowledged these points, but concluded from this that limiting migration rate to 5% 

would provide sufficient protection for adaptively maintained alleles. In practice, an upper limit 

often becomes a target that is actively managed for. If most realized rates of interbreeding of 

cultured and wild individuals are around 5% and continue for more than a few generations, the 

expectation is that large numbers of alleles that are currently selectively maintained will be lost 

or will drift to very different frequencies.

It is important to remember that the rate of migration does not necessarily equal the rate 

of genetically effective migration (gene flow). The genetic risks discussed here and in the 

previous section apply to situations in which the escaped aquaculture individuals survive to 

reproduce and successfully transmit their genes to subsequent generations. In some cases, the 

rate of gene flow can be much lower than m, but the degree to which this is true is likely to vary 

considerably among species, populations, geographic areas, and particular features of the 

aquaculture program.

Is it better to use a highly domesticated stock for aquaculture (because escapes are likely to 

have low fitness in the wild), or is it better to keep the aquaculture stock as similar as 

possible to local wild populations? Or would an intermediate strategy be best?

Unfortunately, there is no simple answer to this question. The net effects on natural 

populations will depend in a complex way on the number of interbreeding events, how 

detrimental each event is, and the time period over which they occur. Strongly diverged 

aquaculture populations might have fewer per capita interactions with wild populations (e.g., 

because they differ markedly in behavior, life history, or other phenotypic traits), but each 

interbreeding event that does occur is likely to be more detrimental to the wild population. If the 

cultured population is kept more similar to local natural populations, each interbreeding event is 

likely to be less harmful, but there could be many more such events. The net effects in each case 

must be some function of the number of interbreeding events and how bad each one is. It seems 
51

likely that either strategy might be better under particular circumstances. In theory, either 

extreme strategy could be less detrimental than an intermediate one that involved a moderately 

domesticated population with strong captive wild interactions (Figure 6, see also Lorenzen 2005, 

Baskett and Waples in press, and discussion in Appendix A).

Is it necessary to derive local broodstocks in each location, or can proven and successful 

broodstocks be imported from other areas?

This is another question for which there is no simple answer. With regard to genetic 

effects on natural populations, the trade-offs between using local broodstocks that are similar to 

local natural populations and divergent broodstocks that are strongly domesticated or derived 

from different areas are discussed in response to the question above. A variety of additional 

factors, such as potential for disease transfer, should also be considered if importing broodstocks 

is under consideration. If the target species is not native to the local area, then there are few 

concerns regarding interbreeding with local populations, unless interspecific hybridization is a 

possibility (which often is the case among fishes). However, importing nonnative species has 

caused ecological problems in many of the world’s ecosystems, so proposals of this type should 

receive special scrutiny.

Our knowledge about fish culture and its effects on natural populations has improved 

considerably in recent years. If aquaculture programs follow new and improved 

guidelines, can’t they avoid the problems of the past?

It is true that our understanding of how to run effective and efficient fish culture 

operations has grown considerably, as has understanding about how to reduce some of the most 

serious threats these programs pose to natural populations. However, it is a mistake to think that 

these advances are capable of removing all risks to natural populations. The environments 

experienced by cultured and natural individuals differ so dramatically in so many ways that some 

level of domestication in individuals used in commercial culture or in stock enhancement is 

inevitable. In fact, substantial domestication is likely a prerequisite for profitable commercial 

aquaculture production of many marine species. Unless containment is 100% effective, the 

results of domestication can affect natural populations. Therefore, the key question is not 

whether improved methods can eliminate all risks, but whether aquaculture operations can be 

managed in such a way that the resulting risks to natural populations do not rise above a level 

deemed to be acceptable. Scientists can help evaluate the levels of risk associated with different 

types of programs and their likely consequences for natural populations, but policy makers must 

determine whether the resulting risks are acceptable from a societal standpoint.

How many breeding individuals must be maintained in a cultured population?

In aquaculture, individuals that mature and spawn are generally not marketable and so 

represent a cost of production, which efficient operations will try to minimize. From the 

aquaculture standpoint, the minimum number of broodstock to maintain is probably determined 

largely by concerns for minimizing effects of inbreeding. Assuming cultured populations can 

withstand sustained inbreeding levels of 1–2% per generation, this would require a minimum of 

about 25–50 individuals per generation, based on the relationship Δf = 1/2Ne. Because effective 

population size can be much smaller than census size due to uneven sex ratio and highly skewed 
52

reproductive success, the number of breeders required to keep inbreeding levels below 1–2% 

could be much higher than 25–50. For example, Gold et al. (2008) used genetic parentage 

analysis to evaluate 13 spawning events involving 27 female and 18 male red drum in a Texas 

marine enhancement program. The mean effective number of parents contributing to a single 

spawn was only 2.6 and the estimated effective number of parents for the 2003 cohort as a whole 

was 29 to 47, depending on the release site. An important factor reducing effective size 

compared to the theoretical maximum was failure of many females to spawn.

Whether the aquaculture breeding population size is large enough to adequately account 

for potential effects on natural populations depends on a variety of factors discussed under the 

Genetic Risks to Natural Populations from Aquaculture subsection of the Characterizing Risks 

and Benefits section above.

If diversity is important, what is wrong with breeding between aquaculture and wild 

individuals—doesn't that create more diversity?

Breeding between cultured and wild individuals can affect both types of diversity: 

diversity within populations and diversity between populations. The consequences of these 

effects will vary depending on several factors.

Diversity among most natural marine populations has developed over hundreds or 

thousands of years. Interbreeding with cultured individuals cannot easily increase this diversity, 

but it can reduce it rapidly. For example, if escaped individuals survive and widely disperse, 

they could interbreed with a number of historically distinct wild populations. This can introduce 

nonnative genes into wild populations at rates much higher than would occur naturally, which in 

turn can reduce historic differences in genetic and life history traits between populations and 

make them all more similar to a single, cultured population.

The effects of interbreeding with cultured individuals on diversity within a single 

population are more complicated to analyze. Depending on the circumstances, interbreeding 

with cultured individuals can increase, decrease, or have no net effect on genetic and life history 

diversity within a wild population. Interbreeding with cultured individuals is most likely to 

increase diversity in a wild population that has undergone an extreme bottleneck. In this 

situation, cultured supplementation can increase the overall population size and minimize further 

losses of diversity. If the cultured population is closely related to the wild population, it also 

could help restore some variability that had been lost from the wild component. However, as 

discussed above regarding the Ryman-Laikre effect, it is more likely that interbreeding with 

aquaculture individuals will reduce genetic diversity in the local population, perhaps by a 

substantial amount.

If the cultured population is genetically different from the wild population, breeding 

between the two populations can indeed increase diversity within the combined population, at 

least temporarily. However, this increased diversity can come at the cost of reduced fitness. For 

example, a domesticated cultured population can diverge genetically from a wild population in 

many ways that will make it less able to survive in the wild. Interbreeding with such a cultured 

population could initially increase genetic diversity of a wild population, but the added diversity 

would include much genetic variation that reduces fitness in the wild. Therefore, the net effect 
53

could be a substantial genetic load to the wild population. Similar considerations apply to 

cultured populations that are derived from local wild populations from a different geographic 

area.

Even if aquaculture programs reduce diversity within and among populations and natural 

fitness, won’t natural selection restore these qualities over time?

This is probably true in at least some cases, given evolutionary time scales (hundreds to 

thousands to millions of years). However, aquaculture has the ability to dramatically change, in 

relatively short time periods, population characteristics that have evolved over many generations. 

Restoration of a dynamic equilibrium between mutation, migration, genetic drift, and selection 

can take a very long time, even if the risk factors are eliminated (see examples in Characterizing 

Risks and Benefits section above). Furthermore, the outcome is far from certain. Populations 

that are substantially affected by these factors might find themselves in a race to re-evolve 

something like their original genetic characteristics before they go extinct due to loss of genetic 

variability and reduction in fitness.
54

Example

Here we use a proposed marine aquaculture program for a hypothetical species (Species 

X) to illustrate how some of the risk assessment and risk management tools discussed above can 

be implemented in a programmatic evaluation. Species X’s biology is loosely based on that of 

the red drum, which has been the subject of aquaculture and marine stock enhancement efforts 

for more than 20 years in the Gulf of Mexico and the Atlantic Ocean. Extensive evaluations 

have been conducted for some of these programs and this provides an opportunity to tune the 

example to realistic biological scenarios. Information presented below uses a simplified format 

based on the AGMP (Appendix B). For simplicity, we focus here on genetic issues rather than 

the full complement of topics that would be covered by an AGMP. The following information is 

based on material provided by the applicant seeking the permit.

Information from the AGMP

Section 1. Background Information

• The proposed site is in U.S. continental shelf waters of the Gulf of Mexico.

• Objective is commercial production in cage culture.

• Species X is large (can exceed 20 kg) and long-lived, with indeterminate growth. Based 

on information available for red drum, we assume a generation time of approximately 12 

years, a maximum life span of 30–50 years or more, and maturity at 35–80 cm (age 3–6). 

We also assume that female batch fecundity increases exponentially with weight and can 

exceed 106 for large individuals.

• The expected production level is 1,500 tons per year, assuming 40 net pens, each holding 

about 50,000 fish that are marketed at 1–2 kg.

• Expected escapes are 1% of production, or 20,000 fish/year.

• The application is for a renewable permit for 10 years. The intent is to continue 

operations indefinitely as long as they are profitable and meet management and 

conservation guidelines.

• This is a commercial operation and has no plausible benefits to the natural populations, 

except perhaps indirectly via reducing harvest pressure. Performance standards and 

performance indicators for genetic risks are discussed in Section 8 below.

Section 2. Relationship of Program to other Management Objectives

The aquaculture program for Species X will be operated consistent with NOAA 

Aquaculture Program guidelines for marine finfish aquaculture. The AGMP for this program has 

been developed with attention to these guidelines and state regulations permitting aquaculture 

operations.
55

Section 3. Facilities

Broodstock are spawned in closed freshwater systems. Techniques for year-round 

spawning are well established using manipulation of temperature and photoperiod. After 

hatching, larvae are shipped in plastic bags to 1-acre receiving ponds. Fingerlings are moved 

within 30 days (at ≈3 cm) to larger ponds for growout to stocking size (about 20–25 cm).

Transfer to marine net pens occurs twice a year, being adjusted to production, harvest,

and fallowing cycles in the marine net pens. Net pens are larger than commonly used in 

nearshore aquaculture, and approximate 2,500 m3 with a maximum density of 7.5 kg/m3

. Care is 

taken that net structures are flexible, attached to a rigid frame, and anchored in ways that meet 

the technical standards demanded by open water operations. Oxygen levels are monitored to 

avoid hypoxia, which is related to the oxygen consumption of the fish and the water flow in the 

cages. Feed is delivered through automatic, submerged feeding channels. Feces and waste feed 

are monitored to optimize production and minimize impact on marine benthos and food webs. 

The net pen operations are marked such that ship traffic and the general public are diverted from 

the site.

Sections 4-6. Broodstock

For purposes of comparison, this proposal includes two different broodstock scenarios.

• Option 1: Mature adults are collected from natural habitats within 20 km of the culture 

site. At least 50 adults with approximately 1:1 sex ratio are maintained at all times. Each 

year, about one-fourth of the spawners are returned to the wild and replaced with new 

individuals. During the spawning season (late summer/fall), group spawning occurs in 

tanks and resulting eggs are collected and cultured as described above.

• Option 2: Fingerlings are obtained from a commercial provider and reared as described 

above. The commercial provider uses approximately 200 adults per year but replaces 

only about 10–25% per year. The commercial broodstock was developed two decades 

ago and originated from several localities on the east and west sides of Florida.

Section 7. Incubation and Rearing

Content for this section is to be provided by the applicant in the associated AGMP.

Section 8. Effects on Natural Populations

Relatively little detailed information is available on the biology of natural populations of 

this species. Based on data for red drum and other marine finfish, it is assumed that local 

populations are only weakly differentiated, perhaps following an isolation-by-distance pattern. 

Spawning areas have not been identified but are likely inshore, as eggs and larvae are rarely 

found in offshore waters. Sport and commercial fisheries are managed on the basis of regional 

stocks that bear an uncertain relationship to natural populations. The species is not considered 

overfished according to Magnuson-Stevens Act guidelines. Natural population sizes in the Gulf 

of Mexico are thought to be in the range 105

–107 mature individuals.
56

Performance standards (and associated performance indicators) designed to address 

genetic risks include:

• Performance standard 1: Maintain adequate genetic diversity in broodstock. Performance 

indicator 1: Effective population size of at least 50 per generation.

• Performance standard 2: Mark all fish to facilitate identification and recovery of escaped 

fish. Performance indicator 2: Fraction of farmed fish without visible marks in a random 

sample.

• Performance standard 3: Keep fraction of escapes below 1% of total annual production. 

Performance indicators 3: Fraction of losses by life stage that are unaccounted for, and 

size and longevity of damaged sections of net pens that can allow escapes.

• Performance standard 4: Limit fraction of natural spawners that are aquaculture escapes 

to less than 1% in any local area. Performance indicator 4: Fraction of escaped fish 

found with natural spawners.

Section 9. Monitoring

Routine monitoring includes the following:

• Performance standard 1: Regular observations of the numbers of fish participating in 

spawning activity.

• Performance standard 2: Regular random samples of farmed fish to determine fraction 

with illegible marks.

• Performance standards 3: Regular inventories of stock to quantify unexplained losses and 

regular underwater inspections of net pen integrity.

• Performance standard 4: No monitoring planned. We expect that any farmed fish that do 

escape will have only a small chance of successful reproduction.

Section 10. Research

In the aquaculture program, routine data collection (for estimation of survival and growth 

rates to each life stage in culture) would provide opportunities for research into performance and 

possible adaptation in captivity. Research on genetic risks would likely differ between option 1 

and option 2 for broodstock scenarios (see Sections 4–6 above), as one would expect no (or very 

limited) genetic difference between local wild and captive fish in option 1, whereas genetic 

differences from historical sources as well as from local wild populations would be expected 

under option 2. In the first scenario, the main research question would be to test the null 

hypothesis of no genetic difference between wild and captive fish, whereas in the second

scenario, the magnitude and nature of genetic changes occurring during broodstock development, 

as well as the level of gene flow from farm escapes to wild populations, could be starting points 

for research.
57

Analysis

The general lack of specific biological information for the target species complicates the 

analyses. In this example, information is used for red drum and other marine finfishes, but it 

should be recognized that this additional source of uncertainty heightens the risks associated with 

the proposed program. The facilities appear to generally meet industry standards. The 

freshwater operations function under a separate permit and are not considered in detail here, 

except the spawning protocols.

Monitoring Performance Indicators

The proposed action (regular observations of the numbers of fish participating in 

spawning activity) is unlikely to be adequate to meet performance indicator 1 (maintain Ne ≥ 50). 

Genetic analyses (e.g., Gold et al. 2008) have shown that, on any given day, only a small fraction 

of adults contribute gametes in group spawnings, but over the course of the season, a larger 

fraction of the population contributes to the offspring. This information is difficult or impossible 

to obtain by simple observation of spawning activity (which, in any case, is likely to occur at 

night). A reasonable assumption is that Ne of the hatchery component is unlikely to be more than 

about 50% of the number of spawners and could be considerably less.

Periodic random samples should suffice to determine whether a significant fraction of the 

population has lost its distinguishing marks (performance indicator 2). However, more 

information is needed on exactly how the marks will be applied, as well as evidence from tag

retention studies. Performance standard 3 is more challenging to evaluate. Although the 

proposed monitoring measures should provide some useful information to determine whether the 

less than 1% escapes goal has been met, the proposal does not contain enough information to 

assess the likelihood that containment measures are sufficient to keep escapes below this level. 

This would be easier to evaluate if the applicant had provided data for previous years 

demonstrating that comparable operations have resulted in sufficiently low levels of escapes.

Regarding performance standard 4, since no monitoring is planned, it seems the 

applicants are assuming that the level of natural spawning will be sufficiently low if performance 

standard 3 is met. However, the two standards measure different things: Standard 3 refers to the 

fraction of the cultured population that escapes, whereas standard 4 refers to the fraction of 

natural spawners that are escaped fish. So even if escapes are limited to 1% of the farmed fish, 

the effects on natural populations could be large or small, depending on the size of the natural 

population. If 1% of the farmed fish escape and spawn naturally, that would be approximately 

104 farmed fish interacting with an estimated 105

–107 natural fish, or about 0.1% to 10% of the 

wild population. If natural abundance is at the low end of the estimated range and the expected 

number of fish escape and breed, the result could be significant introgression of farmed genes 

into the natural population. If natural abundance is near the top end of the estimated range, then 

1% escapes would not represent a sizeable fraction of all spawners, unless all the escapes 

spawned in a limited geographic area where they could represent a larger fraction of a local 

spawning population. As the proposal did not include any discussion of the probability that 

escaped fish would survive to reproduce, we consider a range of scenarios below.
58

Loss of Diversity within Populations

Here we review information necessary to evaluate the effective size of the combined 

wild-farmed system, assuming some farmed fish escape and spawn. Under broodstock option 1, 

50 spawners are used per year. Assuming a ratio of about 0.1–0.5 for effective size:census size, 

this means that the offspring in a yearly cohort would be produced by about Nb = 5–25 effective 

parents. Under option 2, a total of 200 spawners are used per year, resulting in an estimated Nb = 

20–100 effective parents. These are yearly estimates of effective size. In broodstock option 1, 

25% of the spawners (12–13 fish) are replaced each year, and over a 12-year generation, this 

means that about 200 total individuals are used. Therefore, we also considered a scenario with 

NeC = 100 (assuming NeC / NC = the upper limit of 0.5). For option 2, if we assume that 10–15% 

of the broodstock are replaced each year, the program would use about 500 different spawners 

over a generation, suggesting a maximum NeC of 250. The wild population is thought to number 

105

–107 mature individuals. For natural populations of marine fish, estimated Ne / N ratios are 

generally no higher than 0.1 and can be orders of magnitude lower. This suggests that Ne in the 

wild component could be in the range 103–106, which is consistent with estimates for red drum 

(Turner et al. 2002).

We use equation 1 to evaluate the expected effective size of the total system (NeT) and 

compare it to the control situation (NeW = effective size of the unsupplemented wild population).

N W

x

N C

x

N T

e e

e 2 2 (1 )

1

− +

=

 (1)

The above analysis suggests that yearly values of NeC = 5–25 (for option 1) and 20–100 (for 

option 2), NeW = 103–106, and x = 0.001–0.1, while generational values of captive effective size 

might be as high as NeC = 100 (option 1) or 250 (option 2). Note that under option 1, broodstock 

are removed from the wild population, so NeW is adjusted to account for this. Inserting these 

values into the above equation produces the results shown in Table 4.

One point to note is that under almost all of the scenarios shown in Table 4, the overall 

effective size would satisfy the criterion of Tringali and Bert (1998), who proposed that NeT not 

be allowed to drop below 500. The only scenario that fails to meet this standard is scenario A for 

option 1 (NeT = 351). Note also that if x is as small as 0.001, any changes to overall Ne from the 

Ryman-Laikre effect are expected to be very small, even for the low range of NeC values 

(scenario H). However, under several of the possible scenarios, although NeT remains relatively 

large, it is reduced to only a fraction of its original value. This result occurs, for example, when 

escaped farmed fish comprise 1% of successful spawners (x = 0.01) and NeW is large initially 

(106) and NeC is small (5–20): NeT would then be about 5% of its original value for option 1 and 

17% for option 2 (scenario F). Assuming x = 0.1 (upper end of the estimated range), NeT will not 

be more than about 3% of its original value when wild population size is large (scenario C and 

scenario D).

These results illustrate the point that large wild populations are at the greatest risk from 

proportional reductions in Ne due to the Ryman-Laikre effect, even when the resulting NeT is still 

moderately large. These reductions might have no immediate fitness consequences; however, a 
59

Table 4. Results of applying equation 1 to various combinations of parameter values for the proposed 

aquaculture program for Species X, under two different options for sourcing broodstock.

A B C D E F G H

Option 1

X 0.1 0.1 0.1 0.1 0.01 0.01 0.01 0.001

N 1,000 1,000 106 106 1,000 106 106 106

NeW 950 800 ≈106 ≈106 950 ≈106 ≈106 ≈106

NeC 5 100 5 100 5 5 100 5

NeT 351 899 500 9,920 951 47,664 5.0 × 105 8.3 × 105

NeW / NeT 0.351 0.899 <0.001 0.010 0.951 0.048 0.505 0.835

Option 2

X 0.1 0.1 0.1 0.1 0.01 0.01 0.01 0.001

NeW 1,000 1,000 106 106 1,000 106 106 106

NeC 20 250 20 250 20 20 250 20

NeT 763 1,176 1,997 24,504 1,015 1.7 × 105 7.2 × 105 9.5 × 105

NeW / NeT 0.763 1.176 0.002 0.025 1.015 0.167 0.725 0.954

population with Ne = 106 can maintain many more rare alleles than one with Ne = 500, and this 

might be important for long-term viability and evolvability of the population. Would such a 

reduction be acceptable? Science alone can’t answer this question; it also requires consideration 

of societal values and tolerances to different kinds of risk.

Loss of Diversity among Populations

This risk is hard to quantify, given the lack of information specific to the target species. 

In general, concerns increase when there is disparity between the geographic scale of population 

genetic structure and either a) the geographic scale over which broodstock are collected, b) the 

geographic scale over which escaped fish stray, or both. The application does not provide 

sufficient information on any of these parameters for a rigorous evaluation of risk.

In general, marine fish species with similar life histories show relatively weak population 

genetic structure, a result also reported for red drum by Gold et al. (2002). However, as noted 

above, large populations can have very low migration rates (e.g., m < 0.001) and still exchange 

enough migrants to maintain similar allele frequencies. Furthermore, several empirical examples 

now call into question the conventional assumption that most marine species with high dispersal 

capability are not likely to exhibit strong local adaptations.

Loss of Fitness

Commercial aquaculture involves rearing to market size under artificial conditions in 

captivity, so substantial fitness differences (compared to wild fish) can be expected to develop 

over time even in a population derived from local fish (as in option 1). For example, Saillant et 

al. (2007) found that juvenile growth rate is heritable in red drum and this trait likely would be 

under strong selection in aquaculture. If the broodstock source is not local or has been 

assembled from multiple different sources (as in option 2), then any fish that escape would be 

expected to perform even less well in the wild. This loss of fitness (of farmed fish in the wild) is 

something of a two-edged sword for evaluating risk. If the fitness loss is substantial, few 
60

escaped fish would survive to reproduce, but the few that did could pass on very maladapted 

genes to the natural population. With a more modest fitness loss, more escaped fish would 

survive to spawn naturally, but each interbreeding event with wild fish would probably not be as 

detrimental. The net fitness effects of these two scenarios are difficult to predict, which also 

makes it difficult to determine which option is less likely to cause major reductions in wild 

population fitness. However, this ambiguity applies to the genetic consequences of option 1 and 

option 2; there might be sound ecological reasons (e.g., concerns for spread of disease) for 

deciding whether importation of nonlocal broodstock is appropriate.

Comments

This hypothetical example includes a considerable amount of information on some 

aspects of the program but little information about other key features. This makes it difficult to 

make quantitative predictions of risks, but it also is probably typical of many types of situations 

that managers would confront in making decisions about appropriate uses of marine aquaculture.

Given the available information, a quantitative analysis was possible only for changes in 

effective population size, and this only by considering a wide range of possible values for some 

key parameters. The very qualitative analyses of risks of fitness and diversity among populations 

identified causes for concern that suggest a careful consideration of risks by the public regulatory 

agency might be warranted. All of the genetic consequences of escapes scale with their 

fractional representation in the natural spawning population, which depends not only on the 

number of escapes but also on their probability of surviving to reproduce. Therefore, efforts 

should focus on preventing the former and gathering information about the latter. Here are 

several specific steps that could be taken to help resolve some key uncertainties regarding the 

proposed project.

1. Characterize the genetic structure of the natural populations. Given the typically low 

genetic signal and various sources of random noise, it is important to include a temporal 

dimension to the sampling design (Waples 1998). Patterns that are consistent across two 

or more time periods are more likely to be robust indicators of population genetic 

structure.

2. Identify time(s) and place(s) of natural spawning by local populations.

3. Conduct surveys in the wild to map distribution of escaped fish. How does the 

distribution of escapes match the geographic scale from which broodstock are collected? 

How does it match the population genetic structure? Are escaped fish (especially mature 

individuals) found in natural spawning areas?

4. Determine (or clarify, if known) whether all farmed fish are marketed before they reach 

maturity, or whether at least some can mature in marine net pens. This will determine 

whether genetic leakage from spawning in net pens is an issue that needs to be 

considered.

5. Periodically inspect and certify containment systems, as well as fish handling procedures.

6. Develop a contingency plan to deal with significant escape events. Perhaps this could 

include an outreach/education program to ask commercial and recreational fishers to 

report frequency of marked farmed fish in catches.
61

Discussion

The major objective of this technical memorandum is to provide information to assist 

NOAA in fulfilling its marine aquaculture regulatory and policy mandates under existing laws. 

We emphasize that, although we focus here on genetic issues, this is intended to complement 

(and not substitute for) consideration of the numerous ecological issues associated with 

aquaculture operations, which are discussed elsewhere. Furthermore, although this document 

focuses on marine finfish, most of the issues discussed here apply more broadly to aquaculture 

operations for shellfish and other invertebrates, as well as freshwater finfish.

Like many federal agencies, NOAA has several and potentially competing 

responsibilities and legislative mandates for marine aquaculture, including enabling development 

of sustainable aquaculture and stewardship responsibility for living marine resources. Although 

the profitability of commercial marine aquaculture operations might be enhanced by the use of 

highly domesticated strains that grow fast, have high fillet yield, tolerate crowding, and resist 

disease under cultured conditions, in general this type of operation produces individuals that are 

maladapted to natural conditions, and if they interbreed with wild fish they can reduce viability 

of natural populations.

All the genetic consequences of marine aquaculture are proportional to the fraction of 

successful natural spawners that are escaped fish. Therefore, by far the best strategy to minimize 

opportunities for adverse genetic interactions is to ensure that farmed fish do not escape in the 

first place. Once fish escape, experience suggests that even concerted efforts to recapture them 

will be only marginally successful at best. Because no aquaculture system in the marine 

environment can ensure 100% containment through either physical or reproductive containment 

measures, it is important to consider the scale of operations permitted to provide adequate 

safeguards for natural populations, given some inevitable level of escapes.

Although escaped farmed fish can have ecological consequences for marine ecosystems 

as soon as they escape, they have direct genetic effects only if they survive to successfully 

reproduce and contribute genes to natural populations. Therefore, this report is concerned with 

situations in which natural populations of the targeted aquaculture species occur in or near the 

geographic vicinity of the aquaculture operation. For example, most of the genetic issues 

discussed here do not apply to Atlantic salmon aquaculture operations in western North America, 

as there are no native Atlantic salmon with which the escaped fish can interbreed. In these 

situations, genetic concerns are restricted to indirect effects, such as potential disruption of 

spawning activities, introduction of disease agents, or changes to selective regimes experienced 

by native populations of other species.

The factors that determine how likely escaped fish are to spawn with local natural 

populations are diverse and almost certainly vary widely across species and geographic areas 

(and perhaps over time as well). Because these factors have a strong influence on actual genetic 
62

risks posed by marine aquaculture, achieving a better understanding of how they function should 

be an important research priority.

In evaluating evolutionary consequences of marine aquaculture, it is important to 

consider their proposed duration. Effects that might be inconsequential if only a single pulse 

event is involved can become substantial if they continue repeatedly across years and 

generations. For example, an extreme, single-generation bottleneck of Ne = 4 and a less severe 

but more prolonged bottleneck of Ne = 50 for 13 generations both result in about the same total 

loss of genetic variability. This argues for careful consideration of proposed programs that are 

expected to operate indefinitely, with opportunities for continual genetic inputs to wild 

populations over considerable periods of time.

A key decision in any aquaculture operation is choosing the broodstock source and this 

issue is also of keen interest to regulators. It is useful to briefly contrast two extreme scenarios 

regarding the broodstock source: Strategy 1 uses a recently developed stock based on individuals 

collected from the local area, while Strategy 2 uses a productive but highly domesticated stock 

derived from nonlocal populations. With respect to ecological issues, there are reasons for 

concern about use of nonlocal broodstock (e.g., introduction of novel diseases or parasites). Use 

of a local broodstock is also indicated if the intention is to use the survival advantage provided 

by fish culture to help boost abundance in a local natural population (by direct supplementation). 

However, for commercial aquaculture operations that are intended to be closed systems, the 

relative genetic consequences of these two scenarios for natural populations are more 

complicated to assess (see Frequently Asked Questions).

This key topic also merits more detailed research and evaluation. One point that should 

be emphasized, however, is that use of a locally derived broodstock is not a panacea that 

eliminates genetic concerns for marine aquaculture. Results that have accumulated over the last 

decade show that even in conservation salmon hatcheries that use locally derived broodstock, 

hatchery fish typically show lower fitness in the natural environment than do wild fish. 

Furthermore, salmon programs release juveniles into the wild where they spend a good part of 

their life cycle, so even larger fitness decreases likely would be associated with marine 

aquaculture programs that propagate the entire life cycle in captivity.

All of the major genetic concerns associated with marine aquaculture have been 

recognized for at least 2–3 decades, especially with respect to artificial propagation of salmon, 

and a considerable body of empirical evidence has accumulated to demonstrate that each concern 

can and has been realized for natural populations. However, it is also the case that for any given 

type of program, observed effects on natural populations typically cover a wide range from no 

detectable effect to substantial changes. This means that, although genetic risks of artificial 

propagation can be characterized and assessed as described in this document, it typically will be 

the case that considerable uncertainty is associated with predicting the exact consequences of any 

particular program.

Therefore, it is important for scientists, managers, and policy makers to discuss how to 

deal with uncertainty and what is an appropriate way to assign burden of proof. Should proposed 

programs or operations be allowed to go forward unless it can be convincingly demonstrated that 

they will cause serious harm? Or should proposed programs not be allowed to proceed unless it 
63

can be demonstrated with a high degree of certainty that adverse effects will not occur? These 

questions will repeatedly arise in considering the most appropriate ways to implement marine 

aquaculture. They cannot be answered by science alone, but how they are answered can have a 

profound effect on the nature and magnitude of aquaculture programs that are considered 

permissible. The same general questions, it should be noted, are relevant to assessing the 

consequences of other anthropogenic actions that affect marine populations (such as fishing or 

habitat modification), as well as the consequences of propagation programs that release large 

numbers of individuals of other taxa into the wild (e.g., birds, insects, or trees).

To provide a context for evaluating effects of aquaculture, we also briefly considered 

some other anthropogenic activities that can have substantial effects on marine species. On a 

global scale, fishing probably has the largest effect, as harvest managers typically aim to reduce 

targeted species to half or less of their pristine biomass. Furthermore, substantial ecosystem 

effects of harvest can occur at removal levels well below those thought to lead to maximum 

sustainable yield. And bycatch of nontarget species and long-lasting, physical changes to marine 

environments caused by some harvest methods have substantial effects around the world. 

Anthropogenic changes to nearshore marine habitats are also pervasive, and these areas are 

important for early life stages of a wide range of marine species.

Human impacts to offshore habitats are not as obvious, and at present, we have only 

limited understanding of the consequences of those changes for natural populations. However, 

there are many reasons to expect that these pressures will increase in coming decades. First, the 

global human population continues to grow, particularly in vulnerable coastal areas. Second, 

marine pollution is an escalating problem, and new, potentially toxic, compounds are developed 

and placed into use faster than their biogenic effects (and interactions) can be adequately studied. 

Finally, global climate change brings the likelihood of warmer water, altered current patterns, 

and increasing acidification that could dramatically alter marine habitats and ecosystems in the 

twenty-first century.

Considering only aquaculture of marine finfish (the focus of this paper), global effects on 

natural populations probably are much smaller than for harvest or habitat modification. 

However, the footprint is much larger if one takes a broader view of artificial propagation in the 

marine environment to include marine net pens for salmonids (with large operations on several 

continents) and marine stock enhancement programs that involve juvenile releases (sea 

ranching), which are conducted on huge scales for hundreds of species worldwide. Furthermore, 

marine aquaculture programs have grown rapidly in some areas outside the United States and 

might do so within U.S. waters in the near future. In any given area and for any given 

ecosystem, therefore, marine aquaculture programs might have biological consequences that 

equal or exceed those of other anthropogenic activities. Finally, because marine aquaculture 

involves direct intervention in reproduction, growth, and survival of the target species, it has the 

potential to cause evolutionary changes that have long-lasting or permanent consequences for 

natural populations. For all these reasons, marine aquaculture programs merit careful evaluation 

on a case-by-case basis to determine the most appropriate regulatory response.
64
65

Glossary

[Editor’s note: For cross-reference in the explanation of evolutionary terms, those also listed in 

the glossary appear in boldface.]

Allele. An alternative form of a gene. Each diploid individual has two alleles (one from each 

parent) for each gene locus.

Artificial selection. Differential survival or reproduction of individuals with different 

phenotypes in an artificial system (e.g., one controlled by humans). Artificial selection can 

be intentional or can arise indirectly from selective regimes in cultured environments that 

differ from those in the wild.

Assortative mating. A departure from random mating in which similar individuals mate among 

themselves either more often than would occur by chance (positive assortative mating) or 

less often (negative assortative mating). Positive assortative mating can lead to inbreeding.

Diploid. Having two copies of each type of chromosome; generally, one copy is derived from 

each parent. In contrast, haploid individuals have one set of chromosomes.

Domestication. Genetic changes associated with artificial propagation that affect fitness in 

captive and wild environments. Domestication results from a combination of two forces: 

selection for traits that are adaptive in the captive environment and relaxation of selection 

against traits that are maladaptive in the wild.

Effective population size (Ne). An index that determines the rates of many evolutionary 

processes in populations. The rate of genetic drift is proportional to 1/Ne, which means that 

it is higher in small populations.

Escape. In the context of this document, an individual that has escaped from captivity and may 

or may not survive to reproduce in the wild (often also called an escapee).

Fitness. The capability of an individual to pass its genes on to the next generation. Relative 

fitness determines how successful a given individual will be compared to other individuals 

within the same population at the same time. Mean absolute fitness of a population is a 

reflection of its ability to consistently replace itself over time. Fitness of individuals and 

populations can depend strongly on the environment in which it is measured.

F1, F2. Used to denote the number of generations following an episode of interbreeding. The F1

generation is progeny of the interbreeding event; the F2 generation is progeny of F1

individuals.
66

FST. A measure of the level of genetic differentiation among populations. FST values can range 

from 0 (no genetic differences among populations) to 1 (different populations fixed for 

different alleles), although for highly polymorphic markers (like microsatellites) the 

maximum FST can be considerably less than 1. Generally, marine fishes have lower FST

values than do anadromous or freshwater species.

Gene. The basic unit of heredity in living organisms. A gene is a section of DNA that has 

predictable functions, such as coding for a specific protein or regulating cellular processes.

Genotype. The genetic makeup of an individual. The genotype at a single gene locus is 

specified by the two alleles an individual carries; a multi-locus genotype is specified by 

alleles at multiple gene loci.

Genetic drift. Random changes in allele frequency between generations. Genetic drift occurs in 

all finite populations but can be quite strong in small populations.

Genetic diversity. The range of genes and genotypes found in an individual, population, or 

species. Heterozygosity is a common measure of genetic diversity within individuals or 

populations; genetic distance and related measures quantify genetic diversity among 

populations.

Heterozygosity. A measure of genetic diversity within individuals or populations. An 

individual with two different alleles at a gene locus is a heterozygote (a homozygote has two 

copies of the same allele). The average fraction of individuals that are heterozygotes is a 

measure of heterozygosity.

Inbreeding. Mating between close relatives. Inbreeding is rare in large, randomly mating 

populations but is inevitable in small populations because everyone rapidly becomes related. 

Assortative mating that causes relatives to mate with each other more often than would 

occur by chance can also lead to high levels of inbreeding. Inbreeding can lead to 

inbreeding depression.

Inbreeding depression. A reduction in fitness caused by mating between close relatives, leading 

to reduced heterozygosity and expression of deleterious recessive alleles.

Introgression. Movement of genetic material from one species or population into another, as a 

result of interbreeding.

Natural selection. The process by which different traits become more or less frequent in a 

population, due to consistent effects on survival or reproduction of individuals that express 

those traits.

Outbreeding depression. Loss of fitness that results from matings between genetically 

divergent individuals. Outbreeding depression can occur through two different mechanisms: 

dilution of local adaptation (extrinsic outbreeding depression) or breakdown of coadapted 

gene complexes (intrinsic outbreeding depression). In the former, fitness loss typically 

occurs in the F1 generation; in the latter, it often will not occur until the F2 or later 

generations.
67

Phenotype. The observed state of an individual, as measured at one or more traits (e.g., age, 

size, number of fin rays, parasite load). The phenotype is the result of environmental 

variation combining with the genotype to affect phenotypic expression at one or more 

observable traits.

SNP. For single nucleotide polymorphism. A type of DNA variation in which, for a specific 

location in the genome, individuals differ by a single base pair in their DNA sequence. Most 

SNPs involve just two different base pairs, each representing a different allele. More than 1 

million SNPs have been identified in the human genome.
68
69

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Appendix A: In-depth Material

Appendix A provides a more in-depth treatment of material discussed in the body of this 

report regarding the genetic effects of fish culture on wild fish populations. To aid the reader, to 

the extent feasible, this appendix uses the same headings found in the body, although not all 

sections there have corresponding entries here. We draw on several sources of information, 

mainly collected from experiences of 1) contained rearing of salmonid fishes to market size (fish 

farming); 2) rearing and intentional releases of salmonid fishes for stock augmentation, 

supplementation, or sea ranching; 3) captive breeding programs for endangered or at risk 

salmonid fishes; and 4) farming and sea ranching of marine fish species. All of these areas have 

been subject to recent reviews.

Sources of Information

Genetic Impacts of Escaped Farmed Atlantic Salmon (Salmo salar) on 

Wild Salmonid Populations

Ferguson, A., I. A. Fleming, K. Hindar, Ø. Skaala, P. McGinnity, T. Cross, and P. Prodöhl. 

2007. Farm escapes. In E. Verspoor, L. Stradmeyer and J. L. Nielsen (eds.), The 

Atlantic salmon: Genetics, conservation, and management, p. 357–398. Blackwell

Scientific Publishing, Oxford, UK.

Glover, K. A., M. Quintela, V. Wennevik, F. Besnier, A. G. E. Sørvik, and Ø. Skaala. 2012. 

Three decades of farmed escapees in the wild: A spatio-temporal analysis of Atlantic 

salmon population genetic structure throughout Norway. PLoS ONE 7(8):e43129. 

Online at http://dx.doi.org [DOI name 10.1371/journal.pone.0043129, accessed 27 

August 2012].

Hansen, L. P., and M. L. Windsor. 2006. Interactions between aquaculture and wild stocks of 

Atlantic salmon and other diadromous fish species: Science and management, challenges 

and solutions. ICES J. Mar. Sci. 63(7):1159–1161 (and several papers, p 1163–1371).

Thorstad, E. B., I. A. Fleming, P. McGinnity, D. Soto, V. Wennevik, and F. Whoriskey. 2008.

Incidence and impacts of escaped farmed Atlantic salmon Salmo salar in nature. NINA 

Special Rep. 36. Commissioned by the Salmon Aquaculture Dialogue. Online at 

http://www.worldwildlife.org/what/globalmarkets/aquaculture/dialogues-salmon.html

[accessed 6 December 2011].

Genetic Impacts of Stock Enhancement and Sea Ranching

Waples, R. S., and J. Drake. 2004. Risk-benefit considerations for marine stock enhancement: 

A Pacific salmon perspective. In K. M. Leber, S. Kitada, H. L. Blankenship, and T. 

Svåsand (eds.), Stock enhancement and sea ranching: Developments, pitfalls, and 

opportunities, 2nd edition, p. 260–306. Blackwell Scientific Publishing, Oxford, UK.
90

Waples, R. S., M. J. Ford, and D. Schmitt. 2007. Empirical results of salmon supplementation 

in the northeast Pacific: A preliminary assessment. In T. M. Bert (ed.), Ecological and 

genetic implications of aquaculture activities, p. 383–403. Kluwer Academic Publishers, 

Dordrecht, the Netherlands.

Genetic Effects Occurring during Captive Breeding and Rearing

Araki, H., B. A. Berejikian, M. J. Ford, and M. S. Blouin. 2008. Fitness of hatchery-reared 

salmonids in the wild. Evol. Appl. 1:342–355.

Araki, H., B. Cooper, and M. S. Blouin. 2007. Genetic effects of captive breeding cause a rapid, 

cumulative fitness decline in the wild. Science 318:100–103.

Fraser, D. J. 2008. How well can captive breeding programs conserve biodiversity? A review 

of salmonids. Evol. Appl. 1:535–586.

Genetic Impacts of Aquaculture of Marine Species of Shellfish and Finfish

Bert, T. M. (ed.). 2007. Ecological and genetic implications of aquaculture activities. Kluwer 

Academic Publishers, Dordrecht, the Netherlands.

Svåsand, T., D. Crosetti, E. García-Vázquez, and E. Verspoor (eds.). 2007. Genetic impact of 

aquaculture activities on native populations. Genimpact final scientific report. EU 

contract RICA-CT-2005-022802. Online at http://genimpact.imr.no/ [accessed 6 

December 2011].

Lessons Learned

General Lessons

Here we review the relevant information accumulated by the above references by 

formulating some general lessons learned from these activities. These might serve as starting 

points for discussion leading to the formulation of a regulatory policy for development of marine 

aquaculture.

Expect the unexpected

Virtually every new culture program presents a number of surprises and these unexpected 

events often can increase risks to natural populations. For example:

1. Diseases that are rare (and often undetected) in wild populations can become greatly 

magnified in fish farms or other dense concentrations of fish. This can happen in wild 

fish as well (VHS in the Great Lakes, for example).

2. Attempts to establish a broodstock based on a single target population can unintentionally 

incorporate individuals from other populations (Hedgecock et al. 2001).

3. Cultured populations can mature at unexpected times and seasons (Johnson and Pravecek 

1996), as can wild populations.
91

4. Escaped farmed fish can lead to an increased rate of interspecific hybridization, through 

mechanisms that are poorly understood.

5. It is conceivable that escaped rainbow trout (Oncorhynchus mykiss) could help spread 

Gyrodactylus salaris, a freshwater parasite deadly to Atlantic salmon, to nearby rivers by 

moving between rivers through brackish water.

Program goals

Risks and benefits are best evaluated in the context of program goals. Points to consider 

are:

1. Risks to wild populations can be difficult to identify, detect, and measure. These 

assessments are more difficult in the absence of clear goal statements.

2. Similarly, potential benefits can only be evaluated in reference to stated goals.

3. If a program has multiple goals, it might not be possible to simultaneously achieve all of 

them.

4. Clearly articulated goals are also essential for program evaluation and adaptive 

management.

Adaptive management

Lessons about effects on natural populations are often slowly learned from experience.

1. The major risks of salmon enhancement programs were identified 2–3 decades ago 

(STOCS 1981, Ryman 1981 [fish gene pools], Hindar et al. 1991, Waples 1991). 

However, for many years these concerns had little effect on management, in part because 

of difficulties in making quantitative predictions about consequences of a specific 

program or activity. Recent studies (Berejikian and Ford 2004, Araki et al. 2008) provide 

an increasingly robust body of empirical evidence to demonstrate adverse effects on 

natural populations.

2. Additional issues are related to higher individual growth rate and other changes caused 

by the selective breeding programs and domestication during whole-life captivity.

3. Many of the effects of cultured fish on wild fish were not fully appreciated in salmon 

aquaculture despite demonstrated evidence for these effects.

4. Marking cultured fish often can be insufficient to detect effects when they are released or 

escape. Initiatives to mark farmed fish (and livestock) have been resisted because of 

expense, health and welfare issues to the animals, and uncertain benefits of marking.

Evidence for effects of farm fish on wild fish is important to obtain

The types of evidence most important to document include:

1. Baseline genetic and ecological characterization.

2. Genetic marks or physical tags on farm fish or other ways of accounting for escapes of 

farmed fish.
92

3. In the absence of this information, effects might not always be easily attributable to a

particular factor.

Diversity of natural populations

The most reliable way to ensure long-term sustainability is to conserve a diverse array of 

natural populations or native races.

1. Ultimately, adaptation of natural populations to environmental variation is constrained by 

genetic variability in traits that affect fitness in the wild.

2. Most genes that influence fitness phenotypes have not been identified, and most such 

phenotypes are thought to be affected by several to many genes with small effect.

3. It is therefore crucial to conserve phenotypic diversity within and among natural 

populations.

4. One coarse but risk-averse approach is to conserve natural habitat quality (including 

minimizing opportunities for invasions by genetically modified organisms) so that natural 

populations can maintain sufficiently robust populations with adequate diversity to 

respond to future challenges.

Monitoring

An effective monitoring component is important but cannot compensate for the failure to 

implement risk-averse strategies.

1. Monitoring is designed to detect responses or effects but not necessarily to provide 

guidance on how to intervene.

2. The consequences of failure to implement risk-averse strategies cannot be overcome with 

monitoring alone, no matter how well designed.

3. A monitoring program will be most effective if designed and implemented at the outset of 

a production program and can be tailored to specific program requirements.

Lessons from Salmon Aquaculture

Escapes

In the marine environment, the most common rearing technologies consist of large nets or 

ponds capable of holding large numbers of fish above a certain body size. This technology is 

“open” in the sense that it allows communication with the outside world with respect to escaped 

fish, fish disease agents, and organic matter (fish feed and feces). Escaped farm fish is the 

primary concern when considering genetic impacts on wild populations, but fish disease agents 

can also be important, as they can cause changes in population size or selection regimes of wild 

populations.

Fish can escape from the net pens for various reasons (Jensen et al. 2010). They can be 

lost during routine handling operations such as net changing or harvest. They can escape 

through holes in the nets or containment devices made by human error (boats, propellers, etc.) or 
93

by predators attacking the nets. They can escape in big accidents where the nets themselves or 

the structures holding the nets are broken down by ice, severe storms, or during towing 

operations. Onshore ponds can be flooded during storms. Several fish-farming countries keep 

records of the number of fish escaping from containment and some records also keep track of 

causes of escape (Thorstad et al. 2008). Finally, fish can escape that are too small for the mesh 

sizes in the net pens; their number is poorly known.

Better control of fish and water is offered by tank rearing in freshwater hatcheries and 

production facilities. Both inflowing and outflowing water can be controlled, and total control of 

fish is achievable, although not necessarily achieved in practice. Escapes have occurred from 

hatcheries and tank rearing facilities, but are often easier to detect and can be more localized. In 

sum, escapes into the environment of farm fish can occur at all life stages and times of the year.

Recapture of escaped fish

Efforts to recapture escaped farm fish have had limited success. Points to consider are:

1. Large-scale escapes occur during bad weather conditions when recapture might be 

impossible.

2. Farmed fish can spread rapidly after they escape (Skilbrei et al. 2010), so an immediate 

response can be essential to the success of recapture efforts. This can be particularly 

important if (as has occurred in Norway) escaped fish have recently been medicated and 

are thus not suitable for human consumption.

3. Some escapes can go undetected by inadequate technology.

4. Recapture techniques are not often scaled to the necessary capacity and immediacy (e.g., 

how to catch the biggest escape events with up to 500,000 1–3 kg salmon on short 

notice).

5. In small populations having a high incidence of farm escapes, recapture can be affected 

by weirs at the river mouth or by selective fishing (for farm escapes) in the river, with 

obligatory release of accidentally caught wild fish.

Postescape survival

Captively bred fish can disperse over large areas. The intentional transfer of fish and fish 

eggs over distances that are well beyond the species’ dispersal capability is leading toward 

homogenization of fish communities (Rahel 2000, Naylor et al. 2005) and potentially also 

affecting the genetic structure of species (Ryman 1981, STOCS 1981, Hindar et al. 1991). Apart 

from this, aquaculture programs can increase the dispersal rates and dispersal distances of fish 

populations. Hatchery-produced fish can (but not always) stray more than wild fish (Quinn 

1993, Jonsson and Jonsson 2006), depending on the life stage and location of release. An 

experiment comparing farm smolts and local wild smolts released into a river mouth showed a 

higher straying rate in the farm fish (Jonsson and Jonsson 2006).

Fish escaping from fish farms can show very high straying rates. When farm salmon 

escape during the time of the year when natural smolts and adults migrate (late spring and 

summer), these escapes tend to migrate into rivers in the vicinity of the escape site (Hansen et al.
94

1987, Youngson et al. 1997, Whoriskey and Carr 2001). Autumn and winter escapes of farm 

salmon show a much wider dispersal (Hansen et al. 1987, Hansen 2006), being found in rivers 

located several hundred miles away. Fish escaping upon attainment of sexual maturity show a 

more limited dispersal and can be easier to recapture (Chittenden et al. 2011).

Marking

Adequate marking and monitoring are necessary to detect fish that do escape.

1. Many aquaculture operations operate on thin economic margins, which can limit their 

ability to devote resources to monitoring and detection of escaped fish.

2. Activities to help reduce risk of aquaculture production to wild fish should become an 

integral part of an aquaculture program or operation during initial planning and inception 

to provide a clear and consistent framework for assessing benefit and risk.

3. Early freshwater escapes often show wild-type morphology upon recapture.

4. Early seawater escapes (at smolt stage) show sea-ranched-type morphology.

5. Eggs and alevins of farm female origin could be identified by color pigment differences 

when farm fish were fed canthaxanthin as a colorant, but are harder to distinguish when 

farm fish are fed synthetic astaxanthin, which is the natural pigment (Lura and Sægrov 

1991a, 1991b).

6. DNA microsatellite markers might not be reliable in distinguishing wild from farm 

salmon, as the variability among farm strains and wild populations make detection of 

origin (among potentially many different ones) difficult.

7. Microsatellite markers can be effective following large-scale escapes from a single 

farm/cohort (Glover et al. 2008), and in experimental setups where parents (escaped or 

wild) and their offspring are sampled.

8. By searching among 4,500 single nucleotide polymorphisms (SNPs) in wild populations 

and farmed strains of Atlantic salmon, Karlsson et al. (2011) were able to find a 

diagnostic set of 60 SNPs for identifying group membership (wild or farmed) in spite of 

considerable genetic variation among wild populations and among farmed strains.

Reproduction of escaped individuals

Reproductive capabilities of captively bred fish in the wild can vary widely. Experiments 

with releases of captively bred and reared salmonids at various life stages from eggs, parr, and 

smolt into the river to post-smolts and subadults released from oceanic sites show that the earlier 

life stages have better reproductive performance in the wild (Fleming et al. 1996, Einum and 

Fleming 1997). This suggests a within-generation, environmental effect of captive rearing.

Number of fish escaping and the proportion they make up in wild spawning populations do 

not necessarily decrease over time.

Official records of the number of farm fish escaping from Norwegian aquaculture suggest 

a decline in the relative number of farm fish escaping during 1993–2007 (Directorate of Fisheries 

2012). This statement holds for either of the two species which have been farmed on a large 
95

scale during this period, Atlantic salmon (Figure A-1) and rainbow trout (Figure A-2). For 

Atlantic salmon, the trend is even stronger if unofficial escape records for the years 1988–1992 

are included.

In comparison, a relatively new species in fish farming, Atlantic cod (Gadus morhua), 

suggests a similar decreasing temporal trend in number of fish escaping per ton produced. 

However, this species currently has a much higher number of fish escaping per ton produced 

(Figure A-3). For Atlantic cod, it is suggested that the higher rate of escape from net pens is 

caused by two behaviors not seen in salmonids; active biting at meshes in the nets, and active

Figure A-1. Farm Atlantic salmon escapes, official Norwegian records.

Figure A-2. Farm rainbow trout escapes, official Norwegian records.

0

0.5

1

1.5

2

2.5

3

3.5

1990 1995 2000 2005 2010 2015

No. escapees per ton

Year

0

1

2

3

4

5

6

7

8

9

10

1990 1995 2000 2005 2010 2015

No. escapees per ton

Year
96

Figure A-3. Farm Atlantic cod escapes, official Norwegian records.

searching for holes by individual fish (Hansen et al. 2009). Moreover, being pelagic spawners, 

cod can spawn in net pens and thereby produce unknown numbers of escaped individuals that are

not recorded in program statistics. These observations suggest that new species in aquaculture 

will pose novel challenges for containment.

Even though fish farmers have improved their ability to contain fish in net pens,

especially following new technical standards from 2004 (Jensen et al. 2010), the total number 

escaping does not necessarily decrease. The main reason for this is the rapid increase in 

production itself. Norwegian official records indicate little change in the number of escaped 

Atlantic salmon from fish farms during 1993–2007, being 250,000 to 900,000 fish annually 

(Figure A-4). Unofficial records indicated that even higher numbers of fish escaped annually 

from farms during 1988–1992; an interdepartmental group estimated 1.6 million fish escaped 

annually. After a record low number in 2008 (111,000), the numbers of farmed salmon escaping 

have increased again with 225,000, 291,000, and 365,000, respectively, for 2009–2011. High 

numbers of escaped farm salmon have also been recorded elsewhere, including Scotland, Ireland, 

western United States, and Canada. It has been estimated that more than 396,000 Atlantic 

salmon escaped into the Pacific Ocean from farms in British Columbia, Canada, from 1991 to 

2001 (Gaudet 2002). More than 595,000 fish were accidentally released from fish farms in 

Washington State from 1996 to 1998 (Noakes et al. 2000). Escaped farm Atlantic salmon have 

been found as far north as the Bering Sea (Brodeur and Busby 1998).

Recent developments in fish farming technology have led to increased use of very large 

cages in salmon farms, with one cage (net pen) holding 700 tons of fish and one farm holding

3,500 tons of fish (e.g., 2 million fish at 1.75 kg) or more. For comparison, the 2008 estimate of 

prefishery abundance of all wild Atlantic salmon in the North Atlantic was 3.5 million fish (ICES 

2009). This suggests that a single catastrophic event, where all of the fish from a big cage 

escape, can have a large effect on natural populations.

0

10

20

30

40

50

60

70

80

2002 2004 2006 2008 2010 2012

No. escapees per ton

Year
97

Figure A-4. Reported number (in 1,000s) of escaped farm Atlantic salmon by year from hatcheries and 

grow-out farms in Norway. (Adapted from Directorate of Fisheries 2012.)

Estimates of escaped farm fish in the catches of wild fish have been made from 

classification of farm and wild fish based on external morphology and scale characters (Fiske et 

al. 2006). The proportions of escaped farm Atlantic salmon in wild Norwegian spawning 

populations were highest around 1990 (>30% on average, among fish caught near spawning) and 

somewhat lower during recent years (Fiske et al. 2006 and Figure A-5). Estimates of the 

proportions of escaped farm salmon vary over space and time, being higher on the outer coast 

than in the rivers and in autumn catches than in summer catches within rivers (Figure A-5). 

Proportions can be particularly high in rivers near strong concentrations of fish farms (Fiske et 

al. 2006), and especially so in populations that have declined for reasons that might or might not 

have to do with fish farming activities.

On the east coast of North America, escaped salmon outnumbered wild fish by as much 

as 10 to 1 in some rivers. For example, after massive escapes in southwest New Brunswick, 

Canada in 1994, 1,200 farm salmon were counted entering the province’s Magaguadavic River 

compared to 137 wild fish (Atlantic Salmon Federation 2004). Escaped farm salmon of at least 

partial European origin (as determined by DNA analyses) have also been found in the 

Magaguadavic River even though only farm salmon of local origin are licensed for use in

Canada (Atlantic Salmon Federation 2005). A recent overview for eastern North America stated

that escaped farmed salmon had been found in 54 of 62 rivers investigated within a 300 km 

radius of the aquaculture industry since 1984, including 11 rivers that contain endangered salmon 

populations (Morris et al. 2008). On average, escaped farmed salmon made up 9.2% of adult 

salmon entering rivers in this area. In Norway, there is some evidence that the actual number of 

escaped farm salmon can exceed the reported number considerably, at least in some years, but 

the extent of this disparity is uncertain in most cases because of the low numbers of marked farm 

fish. New technical standards for sea cages and initiatives to produce larger smolts for release in 

sea cages have likely improved this situation in recent years.

0

100

200

300

400

500

600

700

800

900

1000

1992 1996 2000 2004 2008 2012

Reported no. escapes

Year
98

Figure A-5. Percent farm escaped Atlantic salmon (unweighted averages) by year in river fishing during 

summer (Δ) and in experimental catches during autumn shortly before spawning (●) in 

Norwegian rivers. (Adapted from Hansen et al. 2007 and SACASM 2009.)

Joint Lessons from Salmon Aquaculture and Hatcheries

Long-term sustainability

Little evidence exists to show that artificial propagation can improve the long-term 

sustainability of natural populations. Artificial propagation can alleviate short-term risk of 

extinction, and there are several examples involving long-term captive culture of fish which 

demonstrate that artificial propagation can maintain broodstocks for several generations in 

protective culture. This proven track record indicates that artificial propagation can help to 

preserve valuable natural genetic resources of a population at risk of extinction for short periods 

while causes for decline are being addressed. However, how long such programs can perpetuate 

these populations is not known for certain and, even if very long-term propagation were feasible, 

it is not known how long a population can be propagated in protective culture and retain the 

ability to be viable in the wild environment (Waples and Drake 2004). Furthermore, even if 

artificial propagation could produce more naturally reproducing adults than those produced 

naturally, it is not yet known whether artificial propagation would result in a net benefit to a 

natural population. As stated elsewhere, unless supplementation of wild production is a direct 

goal of aquaculture production, benefits to wild populations from aquaculture programs can 

often be limited to relaxed harvest pressure on wild fish due to affordable aquaculture products 

on the market.

Genetic changes associated with artificial propagation are inevitable (Table A-1). 

Artificial selection programs intentionally select for genetic changes in traits that are of 

economic importance. Some of these traits are likely also important performance traits in the 

wild. Other captive breeding programs do not intentionally select for altered performance in the 
99

Table A-1. Compilation of genetic changes between cultured and wild salmonid populations in 

phenotypic traits. Sources: Hindar et al. 1991 and references therein, their Table 1; Ferguson et 

al. 2007; Fraser 2008 and references therein, his Table 5.

Trait Change in cultured populations

Egg size Lower in cultured populations (opposite seen)

Egg survival Equal or lower in cultured populations

Juvenile survival Lower in cultured populations (opposite seen)

Juvenile physical fitness Lower in cultured populations

Body morphology Variable results

Territorial behavior Weaker in cultured populations

Aggression Variable results between studies and species

Dominance Higher in cultured populations

Concealment behavior Lower in cultured populations

Wariness Lower in cultured populations

Predator response/avoidance Lower in cultured populations

Juvenile growth rate Higher in cultured populations

Precocious male maturity Lower in cultured populations

Age (and size) at smoltification Lower to equal in cultured populations

Ocean survival Lower in cultured populations

Ocean and river recapture rate Lower in cultured populations

Seawater growth rate Higher in cultured populations

Adult body size Variable results

Adult run timing Variable results

Age at sexual maturity Higher in selected cultured populations

River recapture rate Lower in cultured populations

Straying rate Higher in cultured populations

Return rate Lower in cultured populations

Male spawning performance Lower in cultured populations (opposite seen)

Female spawning performance Lower in cultured populations

Disease resistance Variable results (dependent on origin)

Interspecific hybridization Increases among offspring of cultured fish

wild but can inadvertently do so by the fish being adapted by natural selection to the captive 

environment, by sampling only a limited genetic variation when creating and maintaining the 

captive broodstock, by excluding natural selection to a natural environment, and by excluding 

sexual selection during spawning. Moreover, some of these programs introduce genetic 

differences in performance traits between captively bred and local wild fish by basing the captive 

stock or stocks on fish of nonlocal origin.

Farm salmon differ genetically from wild salmon in morphological, behavioral, and 

ecological traits that are affected by domestication, even where the origin is local. Fleming and 

Einum (1997) compared a seventh generation strain of farm salmon in Norway with its principal 

founder population from the wild—the River Namsen population. The fish were reared in a 

common environment and compared for several fitness-related traits. Farm salmon showed more 

robust bodies and smaller fins. Farm juveniles were more aggressive in a tank environment, but 

wild juveniles dominated in a stream-like environment. Farm juveniles were also more riskprone, reappearing from cover soon after a simulated predator attack (see also Johnsson et al.
100

2001). Growth performance in farm juveniles was higher than in wild juveniles (see also 

Thodesen et al. 1999).

Similar results were obtained in comparisons between another strain of farm salmon and 

two wild populations (Einum and Fleming 1997). These results suggest that farming generates 

rapid genetic change due to genetic drift and intentional and unintentional selection in culture, 

and that some changes involve important fitness-related traits. The higher growth rate of farm 

salmon also carries over in the wild where farm and farm-by-wild offspring have shown higher 

growth rates than offspring resulting from wild-by-wild crosses (Einum and Fleming 1997,

McGinnity et al. 1997, 2003, Fleming et al. 2000) (Figure A-6).

Figure A-6. Changes in the proportional constitution of the Atlantic salmon population in the River Imsa 

following the release of native wild and farm spawners. The number above each bar represents 

either the total population size (spawners and adult offspring) or the sample size examined at each 

life stage (age 0 and outmigration). Two age groups of outmigrants existed, age-1 and age-2, and 

are stacked on top of each other for each offspring type. In asterisk (*) bar, potential egg 

deposition was 19,443 for native females and 29,388 for farm females. Black bars = farm 

offspring, white bars = native offspring, and gray bars = hybrid offspring. (Adapted with 

permission from Fleming et al. 2000, copyright The Royal Society.)
101

Fitness

Fitness in the wild of captively bred fish declines with number of generations in captivity. 

In steelhead (Oncorhynchus mykiss), Araki et al. (2007) measured lifetime reproductive success 

of the first two generations that were reared in captivity and bred in the wild after they were 

released. By reconstructing a pedigree with DNA-microsatellite markers, they showed that 

genetic effects of domestication reduced subsequent reproductive capabilities by approximately 

40% per captive-reared generation when fish are moved to natural environments.

Araki and coworkers also conducted a meta-analysis to compare their data with those 

from other hatchery stocks with known number of generations in hatcheries. This analysis 

suggested an exponentially declining curve at a 37.5% fitness decline per generation of captive 

rearing. Araki et al. (2007) argued that this continuing decline with generations in captivity 

supports genetic effects as the primary cause, as purely environmental effects should not 

accumulate over generations. There is also a tendency for nonlocal hatchery broodstocks to have 

lower relative fitness than locally derived stocks (Araki et al. 2008).

Genetic risks

Genetic risks associated with fish culture can be reduced but not eliminated entirely. The 

primary reason that genetic risks of cultured fish on wild fish cannot be completely avoided is 

because the risk of escape in open systems and even some closed recirculating systems is always 

present, if even at low levels. Reproductive containment is not 100% effective. Because 

broodstock selection and collection cannot retrieve the entire genetic and phenotypic repertoire 

of a wild population, even if sampling is random and reasonably representative, genetic 

divergence is assured. Furthermore, the characteristics of the culture environment intended to 

maximize in-culture survival to market size or reproduction impose distinctly different selective 

pressures on cultured fish than on wild fish. The opportunity for genetic change from 

domestication can be rapid in such situations (Waples and Drake 2004). Finally, not all risks can 

be minimized simultaneously. For example, efforts to minimize phenotypic divergence from 

wild fish (e.g., in body conformation or reproductive timing) can increase the likelihood of 

ecological interactions, including interbreeding, when escapes do occur.

Direct effects

The consequences for natural populations of interbreeding with cultured fish depend on a 

variety of factors. Escapes of cultured fish into the wild are best approached as an experimental 

perturbation with the potential for adverse genetic as well as ecological effects on wild 

populations. For most species, the life history consequences of interbreeding between divergent 

cultured and wild populations are poorly known. Life history characters in most species studied 

to date indicate that many of these characters affect reproductive fitness in the wild, are 

influenced by environmental as well as genetic factors, are often correlated with other characters 

in complex ways that reflect trade-offs in performance at different life stages or in different 

ecological activities, and often have “plastic” expression (i.e., the phenotype produced by a given 

genotype depends on the environmental context, so that often no single genotype is superior in 

all environmental settings).
102

Given these uncertainties, with potentially severe consequences for natural populations, a 

risk-averse approach might have the following elements: 1) potential for escapes and their longterm genetic consequences are considered during the early stages of program planning; 2) if 

concerns for these consequences are substantial, a number of remedial actions can be considered;

3) production could be initiated at a reasonably small scale and conducted in areas that permit 

rigorous monitoring of potential recipient wild populations; and 4) regular evaluation and 

monitoring can facilitate prompt remedial action (Hard 1995b).

Indirect effects

Reduced population size and other indirect genetic effects have been associated with fish 

culture. Indirect genetic effects do not require interbreeding or exchange of genes; rather, they 

occur because of altered selective regimes (which can affect local adaptations) or reductions in 

population size (which also reduces the effective population size [Ne] and can erode genetic 

variability). These indirect genetic effects can occur between species that usually do not meet, 

such as between Atlantic salmon and native species in the Pacific Ocean and between rainbow 

trout and native species in the Atlantic Ocean, as well as between farmed and wild populations of 

the same or closely related species.

In a meta-analysis, contrasting the marine survival and abundance of wild salmonids in 

areas of salmon farming with nearby wild populations in areas without salmon farming, Ford and 

Myers (2008) demonstrated a significantly lower marine survival or abundance in wild 

populations near fish farms. Their analyses included effects of Atlantic salmon farming on wild 

Atlantic salmon in Scotland, Ireland, and Canada; on wild sea-run brown trout (Salmo trutta) in 

Ireland; and on wild coho salmon (Oncorhynchus kisutch), pink salmon (O. gorbuscha), and 

chum (O. keta) salmon in Canada. In many cases, the reductions in survival or abundance of 

wild fish were greater than 50%. The estimates of the mean effect in the meta-analysis were 

significant and negative, suggesting that salmon farming has reduced the survival of wild salmon 

and trout in many populations and countries. In another analysis, Vøllestad et al. (2009) found 

stronger reductions in the catches of wild Atlantic salmon in western Scottish and western 

Norwegian rivers than in other regions of Scotland and Norway, and implicated intense fish 

farming as one possible cause. A more detailed analysis of one-sea-winter Atlantic salmon in 

Norway suggested that the negative temporal trend of returns was stronger in the presence of 

salmon farms on the migration route of the smolts in coastal/fjord areas (Otero et al. 2011).

Ford and Myers (2008) did not explicitly study the mechanisms by which salmon farming 

affects wild populations, but noted that stronger effects on wild populations were found in the 

Atlantic than in the Pacific (British Columbia, Canada) and that one possible cause could be 

interbreeding with escaped farm salmon, in addition to other impacts. Either of the whole-river 

experiments described below suggests that interbreeding between escaped farm salmon and wild 

salmon can reduce population size of the wild population (Fleming et al. 2000, McGinnity et al.

2003). A reduction in population size of the wild population can also be caused by pathogens 

and parasites, competition and displacement, predation, interspecific hybridization, or by any 

combination of these.

Long-term studies of stock and recruitment in steelhead populations suggest how 

different levels of hatchery-produced individuals in the population affect spawner-recruit 
103

relationships and population sizes (Chilcote 2003). Based on studies in 12 steelhead populations 

in Oregon, he found a negative effect on recruitment of increasing proportions of hatcheryproduced individuals in the spawning population. At 50% hatchery steelhead among the 

spawners, the mean productivity of the population (measured as the number of recruits per 

spawner) was reduced by 63% relative to the same number of wild spawners (Chilcote 2003).

Effects caused by introduced pathogens and parasites can be temporary epidemics or 

long-lasting population reductions and even extinction of local wild populations. Effects on wild 

populations can be severe even for endemic parasites, such as salmon lice (Lepeophtheirus 

salmonis). Outbreaks of salmon lice on wild fish are connected with louse density in fish farms 

and sometimes with lice on escaped farmed fish (Bjørn et al. 2009, Revie et al. 2009). 

Consequences for wild fish include curtailed life history of anadromous brown (sea) trout, 

reduced individual growth rate, reduced individual and population fecundity, and increased 

seawater mortality. Atlantic salmon farming in the Pacific Ocean has been implicated in 

increased mortality of endemic pink salmon. Comparison of populations exposed to fish farms 

with populations not exposed to them in British Columbia have shown that population growth 

rate was lower for the exposed populations during sea lice infestations than for exposed 

populations before the infestations or for the unexposed populations (Krkosek et al. 2007).

Salmon lice have also been shown to transfer virus (infectious salmon anemia, ISA) 

between fish and have recently been shown to exhibit multiple resistance to therapeutics used in 

European fish farms. In some fish farming areas, the number of farm salmon and trout is now so 

great that even strong and efficient control of sea lice in the farms cannot prevent lethal 

infections of wild smolts by sea lice when migrating through the area. This has been indicated in 

modeling studies (Heuch and Mo 2001, Figure A-7 and Figure A-8) and more recently 

demonstrated by empirical and experimental studies in intense fish farming areas (Bjørn et al.

2009). Direct experimental evidence that sea lice–induced mortality can be substantial comes 

from releases of hatchery-reared smolts in Ireland, where emamectin-treated (providing lice 

protection) smolts showed increased survival and were 1.8 times as likely to return as adults 

compared to control fish (Gargan et al. 2012)

Two barriers limit natural spread of pathogens in anadromous species in the wild: 1) the 

change of habitat and associated osmotic and physiological transitions from freshwater to salt

water and back again, and 2) homing behavior of anadromous salmonids. Both of these barriers 

can be broken down by translocation, genetic modification during domestication, and the 

deliberate and unintentional releases of salmonids by humans (Bakke and Harris 1998).

One example related to salmon translocations is introduction of the parasite Gyrodactylus 

salaris to Atlantic salmon populations in 40 Norwegian rivers. This parasite does not appear to 

be native to Norway, and was probably first imported to a central hatchery with salmonid eggs or 

juveniles from the Baltic in the 1970s (Johnsen and Jensen 1991). From the central hatchery, the 

parasite spread to other hatcheries and rivers with intentional transport and releases for stock

enhancement and with aquaculture escapes. Long-term reductions in population size of affected 

Atlantic salmon populations average 85% (Johnsen et al. 1999). Support for the hypothesis that 

G. salaris is an introduced species has come from experiments showing higher resistance to the 

parasite in Baltic than in Norwegian Atlantic salmon (Bakke 1991) and molecular genetic studies 

(Bakke et al. 2007). Such long-distance translocations of cultured fish can result in 
104 

Figure A-7. Simulation of the number of sea lice produced in Norwegian waters as a consequence of 

growth in the salmon farming industry. Arrows indicate target levels of the number of sea lice 

per fish in fish farms. (Reprinted with permission from Heuch and Mo 2001, copyright InterResearch.)

Mean louse burden

Billions of louse eggs produced

Figure A-8. Simulation of the infection pressure of sea lice at different target levels of the number of sea 

lice per fish in fish farms. Black indicates wild salmonids, white indicates salmonids escaped 

from farms, and diagonally lined indicates farmed salmonids. (Reprinted with permission from 

Heuch and Mo 2001, copyright Inter-Research.)

0

50

100

150

200

250

300

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004

Year

Millions of lice / Billions of eggs 

Millions of lice

Billions of eggs Two lice/fish

Four lice/fish

Ten lice/fish

0.5 lice/fish
105

translocations of pathogens that might reduce wild population sizes and thus have indirect 

genetic effects on wild fitness.

Dispersal of cultured salmonids and products are also heavily implicated in the spread of 

whirling disease Myxosoma cerebralis (Modin 1998, Bartholomew and Reno 2002), a sporozoan 

disease that can affect many anadromous salmonid species, and furunculosis, caused by the 

bacterium Aeromonas salmonicida salmonicida. Furunculosis was introduced to Norwegian fish 

farms in 1985 with smolts from Scotland, and spread rapidly from the first few infected farms to 

reach 550 fish farms (70% of the total) by the end of 1992 (Johnsen and Jensen 1994). More 

than 250,000 salmon escaping during 1988–1989 were from farms infected with furunculosis. 

The disease was found among spawning salmon the following autumn, first among farm escapes 

and later also among wild fish. By 1992 furunculosis had been registered in 74 Norwegian 

rivers. In four rivers, the disease reached epidemic proportions (Johnsen and Jensen 1994). 

Long-term effects of furunculosis do not seem to be as strong as for some parasitic diseases.

Some viral diseases such as ISA often lead to high mortality and were previously not 

considered to spread easily between populations. ISA was detected in Norwegian fish farms in 

1984, and subsequently in Canada (1996), Scotland (1999), and the United States (2001). In 

1999 clinical ISA was detected for the first time in wild Atlantic salmon and in escaped farmed 

Atlantic salmon entering the same river (Lovely et al. 1999, Bouchard et al. 1999). Three wild

broodstock fish in the Magaguadavic River died from the disease. They were found after 

cohabiting a trap in the river with escaped farm salmon, some of which were infected with ISA. 

This suggests 1) that wild salmon are susceptible to ISA and 2) if it was transmitted to the wild 

fish from infected farmed fish, then infected farmed fish do pose a risk to wild salmon (Carr and 

Whoriskey 2002).

Spawning interactions potentially affecting population size include destruction of nests of 

early spawning wild females by later spawning farm females (Lura and Sægrov 1991b). In New 

Zealand, spring-spawning rainbow trout have been found to destroy the nests of autumnspawning brown trout (both species are introduced). Another type of spawning interaction is 

interspecific hybridization. Hybridization rates are often elevated where species meet after 

human translocation and also increase following escapes of farmed fish (Youngson et al. 1993,

Hindar and Balstad 1994). When interspecific hybrids survive but are infertile, the effect is an 

increase in competition for food and space by intermediate phenotypes and a likely reduction of 

population size of the species providing eggs and potentially both parental species.

All of the above-mentioned factors that reduce population sizes also have the potential to 

alter selective regimes, for example, by favoring more disease-resistant individuals when new 

infectious agents are introduced, by favoring resident fish in the presence of increased mortality 

for migrants, or by favoring individuals that compete effectively in the presence of fastergrowing, aggressive offspring of escaped farmed fish. Moreover, high numbers of escaped 

farmed fish at certain life stages can lead to altered selection from density itself, for example,

during juvenile stages where fish escape directly into juvenile rearing habitats. To our 

knowledge, little research has been done in this field, the most relevant being empirical and 

experimental studies of character displacement and character release in fishes (Robinson and 

Wilson 1994, Schluter 1994), and the concept of limiting similarity of coexisting species 

(MacArthur and Levins 1967). At the molecular level, changes in MHC I genetic variation have 
106

been implicated in Irish brown trout following the buildup of salmon aquaculture (Coughlan et 

al. 2006).

Genetic effects

Genetic effects have occurred in native populations following invasion of intentionally or 

accidentally released cultured fish. In an earlier review, Waples (1991) grouped genetic effects 

of fish releases into two classes: direct and indirect. Direct genetic effects are those caused by 

interbreeding and include changes in allele frequencies, in genetic diversity within and between 

populations, and in adaptive traits. Indirect genetic effects can be caused by any factor that 

causes a reduction in population size of the wild population (thereby increasing genetic drift) or 

alters the selective regime experienced by the wild population. They were dealt with in the 

previous subsection.

At the same time, a review of the literature on the genetic effects following releases of 

nonnative salmonid populations (Hindar et al. 1991) provided two broad conclusions:

1. The genetic effects of (intentionally or accidentally) released salmonids on natural 

populations are typically unpredictable; they vary from no detectable effect (on genetic 

constitution) to complete introgression or displacement.

2. Where genetic effects on performance traits have been detected, they appear always to be 

negative in comparison with the unaffected native populations. For example, reduced 

total population size has been observed following introductions of exogenous 

populations, and also reduced performance in a number of traits, which can explain such 

population declines (e.g., lower survival in fresh and sea water).

More recent experience from salmon farming has indicated genetic effects of escaped 

farm fish in empirical and experimental studies. Molecular genetic changes were demonstrated 

in the wild salmon population in the Glenarm River, Northern Ireland, resulting from the 

spawning of escaped farmed salmon (Crozier 1993). A follow-up sample was taken from the 

river 7 years later (Crozier 2000). Overall genetic variation across eight allozyme loci indicated 

that the wild population remained significantly different from the preescape population and from 

the immediate postescape population. The presence of an allele not having been previously 

detected in this population suggested that further incursion(s) of farmed salmon might have taken 

place. Molecular genetic changes to native populations, following escapes of farm salmon at the 

juvenile and adult stages, were also shown in three rivers in Ireland by using mitochondrial DNA 

and nuclear DNA markers (Clifford et al. 1998a, 1998b).

Analyses of historical and contemporary scale samples in Norwegian rivers using DNA 

microsatellites demonstrated that genetic changes had occurred in three rivers (the Opo, Vosso,

and Eio, Skaala et al. 2006). These changes could be tied to intrusion of escaped farm salmon in 

the Vosso (Sægrov et al. 1997) and likely also in the other two rivers. No changes in the genetic 

profiles were found in four other rivers (the Namsen, Etne, Granvin, and Hå), even if expected in 

two of them. Small reductions in genetic distances among populations were observed in the 

contemporary samples compared with the historical samples, indicating a reduction in population 

differentiation over time, likely due to immigration of escaped farmed salmon. A recent, 

enlarged study of microsatellite diversity over 3 decades in Atlantic salmon populations in 21 
107

Norwegian rivers corroborated these findings by showing highly significant genetic changes over 

time in 4 of the populations and a significant reduction in spatial genetic structure over time 

(Glover et al. 2012).

Experimental demonstration that escaped farm Atlantic salmon affect wild populations 

comes from controlled, whole-river experiments in Norway and Ireland. In the River Imsa, 

Norway, a lifetime, natural experiment was carried out using fifth generation farm salmon 

spawners released together with local wild fish in the river (Fleming et al. 2000). In the 

Burrishoole River system in Ireland, eggs of artificially made crosses of first and second

generation offspring of farm salmon, wild salmon, first and second generation hybrids, and first

generation backcrosses were planted in the river (McGinnity et al. 1997, 2003). In both the Imsa 

and the Burrishoole experiments, lifetime reproductive success (spawning to adult return, or eggs 

to adult returns) was considerably lower in farm fish than in wild fish, and changes in the wild 

population were found that are likely deleterious to the population. Details of the Imsa 

experiment (Fleming et al. 2000) and the Burrishoole experiment (McGinnity et al. 1997, 2003), 

both here following the summary of Ferguson et al. (2007), are given in the two subheadings 

below.

The Imsa experiment—In the River Imsa in Norway, farm and native adult Atlantic 

salmon had similar prespawning migration patterns and nesting locations, though farm females 

spawned before native females. Both types of males began courting females shortly after 

release; however, native males were more active doing so and retained less of their testes 

unspawned. The findings from supplementary experiments in a controlled, artificial spawning 

arena paralleled those from the river, indicating that farm males were competitively and 

reproductively inferior, obtaining fewer spawnings and having 24% of the breeding success (i.e., 

number of live embryos parented) of native males. Farm females also showed a reproductive 

inferiority (e.g., fewer nests, lower egg survival), achieving just 32% of the breeding success of 

native females.

During September-October the following year, offspring from spawnings in the river 

were sampled by electrofishing the River Imsa. The proportion of farm to native genotypes had 

shifted dramatically from that at release (56% farm) to this stage, with farm genotypes now 

composing slightly less than 20% of the population (Figure A-6). Moreover, most of the farm 

genetic representation was in the form of hybrid offspring between farm females and wild males. 

Pure farm offspring comprised less than 8% of the 0+ parr.

Based on the breeding success in the arena experiment, the early survival of farm 

genotypes was estimated to be 70% that of native genotypes. Thereafter, there was no significant 

evidence of differential freshwater survival, as farm genotypes composed 18% of the smolt 

population. There were, however, indications of resource competition in freshwater, as there was 

considerable diet overlap among native, farm, and hybrid offspring. Moreover, the total 

production of smolts was 28% below that expected based on the potential egg deposition and the 

16-year stock-recruitment relationship for the Imsa (Jonsson et al. 1998). For native females, 

smolt production was 31–32% below that expected in the absence of farm females. This effect 

can reflect competitive asymmetries, as native parr were smaller than farm and hybrid parr due to 

differences in growth rate and parental spawning dates. There were also indications of 

displacement of native parr further upstream. The approximate 30% depression in smolt 
108

production observed was the second largest in 16 years of records (Jonsson et al. 1998). 

Moreover, it occurred despite the absence of competition from older salmon cohorts and during a 

period that was favorable for smolt production, at least at a broad geographic scale.

As smolts, the offspring types showed distinct behavioral and life history differences. 

Farm smolts descended earlier and at a younger age than native smolts, with hybrids being 

intermediate. Hybrid smolts were also longer and heavier than native smolts, while farm smolts 

weighed less for a given length than their counterparts. Despite these differences, there were no 

significant differences in marine survival to maturity, the overall lifetime success of farm fish 

relative to wild fish being 16%. All adult recaptures were made in the coastal fishery or the 

River Imsa, and no fish were reported straying into other rivers. The mean age at maturity of 

hybrid salmon (3.4 years) was significantly less than that of native salmon (4.2 years) because of 

differences in their age at smolting and poor survival of native age-1 smolts.

The Burrishoole experiment—This experiment, comprising three cohorts (1993, 1994, 

1998) of Atlantic salmon, was undertaken in the Burrishoole River system in western Ireland. 

This involved multiple families of the following seven groups: native wild (all cohorts), farm (all 

cohorts), F1 hybrid wild × farm (male and female reciprocal groups, 1993 and 1994 cohorts), F2

hybrid wild × farm (1998 cohort), BC1 backcrosses to wild (1998 cohort), and BC1 backcross to 

farm (1998 cohort) (Table A-2). As the aim of the experiment was to look at genetic differences 

without the confusion of behavioral differences, eggs and milt were stripped from mature adults 

and artificially fertilized (see McGinnity et al. 2003 for further details). Fertilized eggs were 

incubated to the eyed stage in the hatchery with cumulative mortalities being recorded. The 

highest egg mortality occurred in the F2 hybrid group (median 68%), which was significantly 

higher than all other groups (e.g., wild 3%).

Table A-2. Lifetime successes of wild, farm, and hybrid groups of Atlantic salmon in the Burrishoole 

system, Ireland, averaged over several cohorts where available. Survival of the wild group is 

taken as 1.0. Where another group is not significantly different from the wild group, it is also 

given a value of 1.0. When significantly different, then the actual survival relative to the wild 

group is used. Data for marine survival of F2 hybrids are not available and were set at 1.0. Data 

from McGinnity et al. 2003.

Group

Fertilization 

to eyed egg

Eyed egg to 

smolta

Eyed egg to 

smoltb

Smolt to 

adult

Lifetime 

successa

Lifetime 

successb

Wild 1.00 1.00 1.00 1.00 1.00 1.00

BC1W 1.00 0.89 1.00 1.00 0.89 1.00

F1HyW 1.00 0.73 1.00 0.58 0.42 0.58

F1HyF 0.87 0.50 0.63 0.61 0.27 0.33

F2Hy 0.34 1.00 1.84 n.a. (0.34) (0.63)

BC1F 1.00 0.79 1.59 0.39 0.31 0.62

Farm 0.79 0.41 0.76 0.07 0.02 0.04 a

This assumes that displaced parr have the same survival as parr of the same group remaining in the experiment 

river, that is, that the river is not at its parr carrying capacity and spare habitat is available for displaced parr. b

This assumes that displaced parr emigrating from the experimental river do not survive, that is, that the river is at its 

parr carrying capacity.
109

Aliquots of each family were maintained in a hatchery tank until 11 months as a control 

on the field experiments. No significant differences in survival among groups were found to this 

age. However, given that total mortality was less than 10% under “protected” hatchery 

conditions, there was little opportunity for detectable differential survival. These hatchery 

controls serve to demonstrate that all groups were potentially equally viable and that the 

differential survival apparent in the wild was the result of genetic or maternal differences.

Farm salmon showed significantly lower representation than wild in the samples of 0+ 

parr of all three cohorts from the experiment river at the end of the first summer (Table A-2); 

“hybrids” (i.e., F1 and F2 hybrids and BC1 backcrosses) were intermediate or not significantly 

different from wild fish. During the period from May 0+ to September 1+ (i.e., second year), the 

highest proportion of emigrant parr, taken in the experiment trap, was from the wild group and 

the lowest from the farm group, with “hybrids” intermediate in representation (in all three 

cohorts). In the river 0+ parr, it was found that farm parr were largest in size, wild parr smallest, 

and “hybrids” intermediate, as expected from the selection of farm strains for increased growth 

rate. Thus downstream migration was inversely proportional to parr size and proportional to 

cohort density over the three cohorts, indicating competitive displacement of wild parr by the 

larger farm and “hybrid” fish. Although displaced wild parr were found to survive downstream 

under the experimental conditions used, such survival would not occur if suitable unoccupied 

habitat were not available. This would be the case, for example, when a river is at parr carrying 

capacity or where the spawning area debouches directly to sea, as might be typical for escaped 

farm salmon spawning in some circumstances.

Smolt output was assessed in two ways. First, as the actual numbers of migrants taken in 

the experiment trap, which assumes that emigrant parr do not survive, that is, the river is at its 

parr habitat carrying capacity. In spite of displacement of the wild parr, the farm group produced 

significantly fewer smolts for the 1993 and 1994 cohorts, but was not significantly different for

the 1998 cohort. The “hybrids” had variable representation among cohorts due to differential 

emigration as a result of different planting densities. The second estimate of smolt output 

assumed that emigrant parr have the same survival downstream as parr of the equivalent group 

remaining in the experimental river. This scenario is equivalent to the intrusion of farm salmon 

into a river with parr habitat in excess of that required by the wild population. With the 

exception of the F1 wild mother hybrid group of the 1993 cohort and the F2 hybrid group, all 

groups had significantly lower smolt production relative to wild. Again farm salmon 

consistently had the lowest smolt production relative to wild in all three cohorts (34%, 34%, 

55%).

Adult salmon returned from sea after one and two sea winters (1SW and 2SW). In the 

1SW returns, all groups, except the BC1 backcross to wild, showed a significantly lower return 

relative to wild. In the 2SW returns, all groups, except farm of the 98 cohort, showed a 

proportionately greater return. However, the Burrishoole population is primarily a 1SW stock 

and the wild 2SW return was only 2.5% of the total return. Farm salmon have been bred for late 

maturity, a trait with high heritability under such conditions (Jónasson et al. 1997). Overall the 

farm group showed a 0.3% return compared with 8% for wild smolts. Egg deposition is likely to 

be the limiting factor in salmon recruitment, and taking account of the differential egg production 

of 1SW and 2SW females (Mangel 1996) shows that total potential egg deposition was 
110

significantly lower than wild for all groups except BC1 backcross to wild. Overall the 

concordance of the results in the three cohorts considerably increases confidence in the findings.

Lifetime success in the Burrishoole experiment—estimated as egg-to-adult survival and 

taking that of wild fish as 100%—varied from 2% in farm-by-farm offspring to 27–89% in 

various hybrid- and backcross groups, with backcrosses to wild fish being the highest among 

these (Table A-2). One conclusion of the study was that repeated interbreeding of escaped farm 

salmon with wild salmon had a cumulative negative effect on the wild population and could in 

the long run lead numerically weak populations into an extinction vortex.

A recent experiment in Canada, designed to study potential local adaptation to acidified 

rivers in Atlantic salmon populations and whether or not repeated interbreeding with farm 

salmon influenced this adaptation, found mixed evidence for reduced local adaptations by 

interbreeding (Fraser et al. 2008). Wild juveniles had higher survival in acidic water than farm 

salmon or wild-by-farm hybrids. In contrast, the backcrosses and second generation wild-byfarm hybrids performed equally well if not better than wild salmon in acidic water for the life 

stages studied. Follow-up studies on farm-wild hybridization across divergent wild populations 

and multiple traits found evidence that hybrid fitness decreased with increasing divergence 

between the hybridizing populations, but these studies also had limited ability to predict changes 

in specific traits (Fraser et al. 2010).

When interbreeding between genetically different populations results in a reduction in 

fitness relative to both parental genotypes, it is often referred to as outbreeding depression. The 

mechanisms responsible for outbreeding depression fall into two different categories: 1) local 

adaptation, where the hybrid population lacks adaptations to its environment; and 2) 

coadaptation, where the hybrid population contains combinations of alleles at different loci that 

are not adapted to each other (Templeton 1986). Outbreeding depression can occur in the first 

hybrid generation, among their offspring, or even in later descendants (Lynch 1991). The degree 

of fitness loss seems to depend on how distant a cross is (extent of genetic differentiation 

between the parents).

In the Burrishoole experiment (McGinnity et al. 2003), significantly higher egg mortality 

occurred in the F2 hybrid group (median 68%) than all other groups (e.g., wild 3%). Since the 

first generation backcrosses, which used aliquots of the same eggs as F2 hybrids, showed 

significantly lower mortality (8%), this high F2 hybrid mortality is not due to maternal or egg 

quality effects and most likely reflects outbreeding depression (McGinnity et al. 2003). Another 

case of outbreeding depression in Atlantic salmon is provided by the crossing of anadromous and 

landlocked Atlantic salmon (Sutterlin et al. 1987), where lower early survival rates and 

morphological abnormalities were found in hybrid (landlocked by anadromous) offspring.

One experiment with temporally isolated populations of pink salmon from the same 

stream provides an instructive case of outbreeding depression. Across its endemic range, this 

species has a rigid 2-year life cycle and breeds only once, followed by death. Thus two 

populations exist in the same river, one spawning in odd-numbered years and the other in evennumbered years. Gharrett and Smoker (1991) produced hybrids between two such temporally 

isolated populations by fertilizing eggs of one population with cryopreserved sperm from the 

other. They observed good return rates and increased variances in body size among first-
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generation hybrids, suggesting that hybrids were more genetically variable than purebred groups. 

Second-generation hybrids, however, produced very low return rates, suggesting that outbreeding 

depression had occurred.

This outbreeding depression was not likely caused by the two populations being adapted 

to different environments; in the long run, the environments in odd- and even-numbered years in 

the same river should be alike. Rather, the outbreeding depression seems to have been caused by 

disrupting coadapted gene complexes that evolved independently in the two populations.

Genetic technologies

Breeding programs and applications of genetic technologies are poorly developed for 

most aquaculture species, and the potential consequences for wild populations have not yet been 

carefully evaluated. How fish respond to intensive culture in protective environments remains 

unclear for most species. This is treated in some detail in the next subsection.

Lessons from Marine Stock Enhancement

The lessons learned from detailed studies of salmonid fishes can have relevance for a 

number of other species that are used in aquaculture or intended for such use. However, the 

salmonid fishes constitute a small number of species among the roughly 20,000 fish species and 

a limited palette of life histories, particularly compared to marine fishes. Also, increased focus 

on marine aquaculture and the long-term studies of some marine species in particular invite a 

comparison between salmonids and marine fishes.

A recent report of the genetic impact of aquaculture on native populations in the 

European Union (Svåsand et al. 2007, http://www.genimpact.imr.no) gives summary information 

on economically important finfish and shellfish in European aquaculture. In Table 3 (body of 

this report), we compared information on Atlantic salmon with information on the marine fish 

species treated by Svåsand et al. (2007). To supplement and compare the information about each 

species, we also extracted data from FishBase (http://www.fishbase.org) and the primary 

literature.

Key life history characteristics of marine fishes

Much less is known about the basic biology of most marine species compared to salmon. 

Although culture of marine finfish offshore is now technically feasible, few marine fishes have 

been successfully cultured to maturity and many of the basic environmental requirements of 

marine fishes for successful growth, development, and reproduction are not well understood. In 

Europe, the development of aquaculture production seems successful for European seabass 

(Dicentrarchus labrax) and gilthead seabream (Sparus auratus), while there are still challenges 

to culturing well-known species such as Atlantic cod and Atlantic halibut (Hippoglossus 

hippoglossus).

Marine fishes are very numerous and exhibit a wide diversity of life histories; 

furthermore, in general, there is considerably less knowledge about the basic biology of these 

species (genetics, ecology, abundance) than for salmonids. Marine fishes typically:
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1. Can have very small eggs to large eggs,

2. Exhibit reproductive behaviors from broadcast spawning to mouth brooding,

3. Are pelagic to benthic spawning,

4. Exhibit internal or external fertilization,

5. Display no parental care to extensive parental care,

6. Range from young to old age at sexual maturity,

7. Express variable interspawn interval and senescent periods,

8. Can be r- or K-selected,

9. Show considerable variation in body size, and

10. Show considerable variation in population size.

Despite the great diversity in these life history traits, it seems that those species that are relevant 

marine culture species look remarkably similar to salmon: the marine species treated in Table 3

are migratory, large-sized, show high age at sexual maturity, and are often piscivorous. In many 

cases, these species are also increasingly produced in intensive culture before the impacts of 

cultured fish on wild populations are understood.

In general, on an equivalent spatial scale, marine species show lower levels of molecular 

genetic differentiation among populations than do anadromous or freshwater species. 

Comparisons of a number of fish species using enzyme electrophoresis show that genetic 

structure (i.e., amount and distribution of genetic variation) differs between marine, anadromous,

and freshwater species. Gyllensten (1985), in a comparison of 19 fish species, found that the 

average fraction of the total gene diversity allocated between localities (called GST or FST) 

increases in the order marine (0.016), anadromous (0.037), and freshwater (0.294) species, 

whereas the total gene diversity (average heterozygosity, called HT) is higher in marine (0.063) 

than in freshwater (0.043) and anadromous (0.041) species.

Ward et al. (1994), in a study of 113 species, obtained the same qualitative but slightly 

different quantitative results, some of which are referred to in Table 3. They suggested that the 

average degree of genetic differentiation between subpopulations within species in the various 

environments could be interpreted as marine subpopulations exchanging between 10 and 100 

times more migrants per generation than freshwater species, using Wright’s (1943) relationship 

between FST and the number of migrants Nem, FST = 1 / (1 + 4Nem), where Ne is effective 

population size and m is migration rate in an island model of migration.

Evidence for local adaptations of marine species

Local adaptations have for a long time been recognized in freshwater and anadromous 

fishes, for example in salmonid fishes by Ricker (1972), Taylor (1991), and Garcia de Leaniz et 

al. (2007). Given the homing tendency of migrating salmonids and the estimates of high genetic 

differentiation between subpopulations in molecular genetic markers, this comes as no surprise.

In marine fishes, on the other hand, pelagic egg or larval stages coupled with low 

differentiation between subpopulations in molecular genetic markers suggest that the gene flow 
113

between localities is too high for strong local adaptations to develop. Recent research employing 

a broader panel of genetic markers, however, suggests that marine fishes might be more 

genetically structured than previously thought, and that accompanying ecological differences 

provide strong evidence for local adaptations in a number of species (Hauser and Carvalho 

2008).

Opportunities for natural reproduction of farmed fishes

Many marine fishes have been shown to spawn successfully in captivity, including net 

cages. Successful spawning in cages where eggs, larvae, or juveniles are capable of escaping to 

the surrounding water column poses the opportunity of genetic interactions between cultured and 

wild fish if those escaped individuals survive to reproductive maturity (Jørstad et al. 2008). If 

spawning in culture is frequent—and especially if it is undetected—it is feasible for propagule 

pressure from the program to pose an unacceptable risk to wild populations in the area, 

particularly if these populations are depressed in abundance or genetic diversity.

The very high fecundity of many marine species means that a small number of 

broodstock can potentially have a large genetic impact on natural populations. Females of many 

marine fish species are capable of producing a large number of small eggs or larvae, which in the 

wild are often broadcast into the water column with no maternal care. If survival of eggs or 

larvae in culture to market size or to maturity is sufficiently high, relatively few adults can be 

considered or sampled for aquacultural broodstock. In haddock (Melanogrammus aeglefinus), it 

was recently shown that the potential for inbreeding was high during communal breeding of this 

gadoid fish (Trippel et al. 2009). Such practice substantially increases the probability of genetic 

differentiation between cultured and wild fish, thereby increasing adverse genetic consequences 

of interbreeding whenever it does occur.

Detecting the genetic effects of cultured marine fishes on natural populations

Steps to detect these effects include:

1. Document presence and if possible estimate abundance of escaped fish,

2. Document presence of F1 hybrid offspring,

3. Document presence of backcross hybrid offspring,

4. Document presence of escaped fish at all life stages (larval, juvenile, preadult, adult),

5. Determine whether there has been a population-level change of wild individuals, and

6. Determine numbers of local fish species and their relative abundance.

To our knowledge, interaction studies of marine cultured fish species with wild conspecifics are 

still limited. In European aquaculture, Atlantic cod are probably among the best studied species, 

primarily because of studies of genetically marked cod juveniles released to the wild (Bekkevold 

et al. 2006, Jørstad et al. 2008).
114

Effects of escaped fish

A good deal of evidence suggests that significant numbers of fish have escaped from 

marine net pens in the Mediterranean, but few studies have rigorously or quantitatively addressed 

this issue, and in general program operators are not required to document escapes (Hansen and 

Windsor 2006, Dempster et al. 2007). One study (Bahri-Sfar et al. 2005) found that European 

seabass of western Mediterranean origin that were farmed in the eastern Mediterranean and 

subsequently escaped had established naturally reproducing populations, but these appeared to be 

distinct from the local eastern seabass populations.

Freshwater environments are generally regarded as being more prone to invasions than 

marine environments. This is likely connected to the fragmented and inaccessible (island) nature 

of many freshwater environments, where many fish communities are far from being ecologically 

saturated. Another category of environments prone to invasions are those that are disturbed by 

humans. Among the marine environments, those occurring along the coast and in estuaries are 

most likely to fall into this category.

Studies of biological invasions have been more common in the freshwater environment 

than in the marine environment. Lessons from freshwater fishes suggest that invasive species 

have some ecological characteristics in common. This has been used to perform risk assessment 

for alien fishes in the North American Great Lakes (Kolar and Lodge 2002). Whether this is 

useful for genetic risk assessment of species taken into fish culture is so far unknown.

Ecological roles and mechanisms of impact

Marine species offer a greater diversity of ecosystem roles and functions than salmonid 

fishes, which are all high in the food web, many of them being top fish predators. Incidentally, 

this is also the case for most of the marine fishes being developed for aquaculture, but not for the 

common carp (Cyprinus carpio), one of the major products of freshwater fish culture.

Mechanisms of impact that have been empirically verified by studies of salmonids 

include interbreeding between cultured and wild populations of the same or a related species, 

competition with and potential displacement of wild fish, reciprocal disease transmission 

between wild and cultured populations, and altered selective regimes for the wild population 

following contact with cultured fish. Other mechanisms that should be considered when 

developing guidelines for marine aquaculture include but are not limited to:

1. Predation,

2. Herbivory and detritivory,

3. Broadcast spawning,

4. Disease agents that are shared between species, and

5. Ecosystem modifiers.

Predation of escaped farmed fish on wild fish has not been described as a result of salmon 

aquaculture (other than anecdotally, to our knowledge), but is described from escapes of tilapia 

(Oreochromis spp.). Increased aquaculture production and escapes of marine piscivorous fish 

like cod likely will increase predation pressure on migrating smolts of salmonids.
115

Case studies of marine species for which captive breeding and culture programs have been 

developed

Table 3 (body of this report) provides a list of selected marine species for which genetic 

impacts of ranching and farming have been treated in the literature. Common to these species is 

that interaction studies are in their infancy, and predictions of impacts by marine finfish culture 

programs such as cod farming are largely based on the salmonid literature (Bekkevold et al.

2006).

Lessons from Agriculture

The long history of agriculture has provided a number of insights into how human 

production systems and natural populations differ and can lead to conflicts when cultured and 

natural organisms interact in the wild. The environmental impacts of agriculture are generally 

well-known, but they are often highly location specific and some agricultural effects on the 

environment can take a long time to appear. Agricultural impacts include the use of fertilizers 

and pesticides, irrigation and drainage, and intensive harvest, which contribute to increased 

pollutant loads, mechanical disturbance, and offsite effects through manipulation of soil and 

surface water; however, these impacts vary with the type of habitat converted to agricultural use. 

Consequently, understanding the myriad of environmental impacts of agriculture on the natural 

environment and the populations it supports is an exceedingly complex task.

Nevertheless, many of the risks posed by human production systems to natural systems 

have long been recognized and several lessons about the effects of agriculture on wild 

populations are clear (Tilman et al. 2001, Green et al. 2005, Millennium Ecosystem Assessment 

2005). First, agricultural operations can reduce biodiversity through ecosystem simplification, 

loss of ecosystem services, and direct extirpation and displacement of wild populations. Second, 

risk to the genetic diversity within and among natural populations can occur through habitat loss 

or degradation or through genetic interactions between cultured and wild organisms. Third, 

because cultured organisms are typically adapted to the agricultural environment, interactions 

between them and natural organisms in the wild can lead to substantial losses of fitness in natural 

populations through the direct genetic effects of interbreeding and introgression, or through 

indirect genetic effects that result from changes in the regime of natural selection. Such fitness 

losses have long been predicted from evolutionary and life history theory and have now been 

documented repeatedly in a variety of taxa. Finally, the risks posed by cultured organisms to 

wild organisms can be reduced through careful siting and monitoring of agricultural operations,

but they can seldom be avoided entirely. Moreover, reducing some risks can escalate others; for 

example, increasing the genetic divergence between cultured and wild organisms to facilitate 

agriculture can reduce the opportunity for interactions between them, but when interactions do 

occur the consequences could be much larger. Such interactions threaten the diversity of natural 

populations that are critical for long-term viability in the face of unpredictable environmental 

change.

Theoretical and empirical developments in the last few decades provide increasingly 

strong evidence that such effects on natural populations are real. However, a considerable 

amount of uncertainty remains, particularly when trying to anticipate the effects of specific 

aquaculture programs on particular populations in particular areas.
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Aquaculture has focused on improving growth rate, feed conversion efficiency, early 

maturation, high larval quality, disease resistance, and product quality. A primary goal of the 

aquaculturist, like other plant and animal breeders, is to produce fish efficiently with desirable 

phenotypes, or more precisely, to increase the frequency of desirable phenotypes in the cultured 

population. The primary aims of a breeding program are to increase the survival and production 

of farmed animals and improve product quality, as determined by market forces (Gjedrem 2005).

Initially, desirable phenotypes are likely to be characterized by rapid growth, high flesh 

quality, ease of culture, controlled maturity, and high disease resistance. Experiments to improve 

growth and disease resistance in fish began by the 1920s (Embody and Hayford 1925). Thus 

selection in aquaculture tends to focus on growth rate, feed conversion efficiency, early 

maturation, high larval quality, disease resistance, product (flesh) quality, and domesticability 

(e.g., tameness, adaptation to captivity, reduced stress in confinement). Some of these traits also 

have large environmental components and their expression can vary considerably in different 

culture environments due to phenotypic plasticity (Gjedrem 2005).

Sterilization

Sterilization of salmon can be achieved through induction of triploidy (production of 

three sets of chromosomes). This has two potential benefits: 1) prevention of gene flow from 

cultured to wild fish, and 2) diverting energy that would have gone into sexual maturation into 

production of body mass (O’Flynn et al. 1997). Triploidy is achieved by preventing the 

disjunction of the second polar body from the newly fertilized egg, which can be done by giving 

a temperature or pressure shock after fertilization (Benfey et al. 1988, Quillet and Gaigon 1990). 

The result is a fish with two copies of the maternal chromosome, instead of one from each sex as 

in normal diploid individuals. Triploidy generally results in complete sterility in females, but not 

in males. If the sperm are irradiated before fertilization, followed by administration of heat or 

pressure shocking, only the two maternal chromosome copies will be functional, resulting in 

gynogenetic diploid (all-female) offspring (Kirpichnikov 1981, Quillet and Gaigon 1990). In the 

common carp, partial sterility has been achieved by genetic modification controlling the 

gonadotropin-releasing hormone (and thereby gonad development) by so-called antisense 

sequence (Hu et al. 2006).

All-female embryos can be produced for triploidization by using sex-reversed females as 

the functional “male” parent in the previous generation. The latter is achieved by first feeding 

female fry with a diet containing a particular concentration of male hormone, resulting in 

functional sperm-producing testes. Therefore a two-generation process is involved, where the 

second generation triploid fish are not hormonally treated. Molecular identification of the sexdetermining locus of Atlantic salmon can facilitate production of all-female lines (e.g., Artieri et 

al. 2006).

In salmon farming conditions, the overall yield of triploids has been shown to be lower 

than diploids due to poorer marine survival (O’Flynn et al. 1997). In ranching experiments, 

Cotter et al. (2000) have shown substantially reduced river returns of triploid salmon when 

compared with diploids.
117

Although sterilization is rarely 100% successful, this approach has the potential to 

significantly reduce risks from escaped salmon (Cotter et al. 2000), common carp (Hu et al.

2006), and other aquatic species. The most common method of inducing sterility is to make 

individuals triploid by giving a heat or pressure shock to the eggs shortly after fertilization. 

Triploid fish grow and survive well (Burke et al. 2010, Benfey 2011), but show an increase in 

skeletal deformities. This has been used as an argument to discourage production of triploid fish 

with reference to animal welfare considerations. Recent results suggest that skeletal deformities 

can be reduced by adding more phosphorous to the diet of sterile farmed fish (http://www.imr.no

/nyhetsarkiv/2011/mai/gode_resultat_med_steril_oppdrettslaks/en).

Trade-offs among Competing Risks

A trade-off in the consequences of encounter can arise from the relationship between the 

degree of divergence and the encounter rate. Fish that are more similar are likely to encounter 

each other at higher rates, with more opportunity for genetic interaction (especially 

interbreeding) but perhaps milder consequences of each interaction. By contrast, fish that are 

more divergent can encounter each other at lower rates but the consequences of encounter for 

fitness loss can be more serious. Consequently, encounters between cultured and wild fish are 

never risk free but the risk depends on the rate of encounter and the degree of divergence 

(Kapuscinski et al. 2007). The aquaculturist must recognize this relationship and the potential 

for consequences of encounter to grow if aquaculture goals lead to greater divergence between 

cultured and wild fish. This recognition is integral to the paramount consideration of developing 

sustainable marine aquaculture alongside healthy, viable natural populations in their marine 

habitats.

Characterizing Risks and Benefits

Potential Benefits of Artificial Propagation for Natural Populations

A. Reduce short-term extinction risks for endangered populations and

B. Help maintain a population at a safe level until factors for decline can be addressed

Bringing a population at risk of extinction into protective culture can reduce immediate 

risk of extinction by improving stage-specific survival generally or minimizing risk of mortality 

of reproductive adults or their embryos (Hard et al. 1992). In this way, captive propagation can 

significantly increase the number of individuals to be returned to the wild. Maintaining a 

population in the short term (at least several decades or generations of the species) through 

artificial propagation and helping to reduce short-term extinction risk are the potential benefits to 

natural populations that are best-documented in the empirical record. Zoos around the world 

maintain species and populations of a wide range of taxa that might be extinct in the wild 

without such programs. Frankham et al. (2002) contains a good discussion of genetic issues 

associated with such programs.

A number of examples can be cited from aquatic species. For example, by 1990 the last 

remaining sockeye salmon (Oncorhynchus nerka) from the Snake River were nearly extinct. 

This population, from Redfish Lake in Idaho, is particularly distinctive, as it spawns at a higher 

elevation (2,000 m) and has a longer freshwater migration (1,500 km) than any other sockeye 
118

salmon population in the world (Waples et al. 1991). The few (16) adults that returned in 1991–

1996 were spawned and their progeny, together with some smolts collected when they were 

outmigrating from the lake, were reared to adulthood in captivity (Flagg et al. 2004). The major 

goal of this captive broodstock program was to perpetuate the gene pool for a short period of 

time to give managers a chance to identify and address the most pressing threats to the 

population. Considerable efforts have been made to conserve as much as possible of the genetic 

diversity that survived the bottleneck (Kozfkay et al. 2008), and a recent analysis (Kalinowski et 

al. 2012) estimated that the captive program had managed to retain approximately 95% of the 

original genetic variation over about five salmon generations. In 2010 well over 1,000 adult 

sockeye salmon returned to Redfish Lake—more than at any time in more than 50 years. Most 

of these were hatchery produced; it remains to be seen how the population will fare if and when

the hatchery program is terminated. Nevertheless, captive propagation has helped to rescue a 

unique gene pool that was on the brink of extinction and give it a chance for survival.

The white abalone (Haliotis sorenseni) was listed throughout its range (southern 

California and northern Mexico) as endangered under the U.S. Endangered Species Act (NOAA 

2001; 66 FR 29054, May 29, 2001). The species had declined to such a low density in the wild 

that natural reproduction was unlikely and extinction was predicted by 2010 (White Abalone 

Recovery Team 2008). Although recovery goals included eventual establishment of numerous 

self-sustaining populations in the wild, given the critical and immediate nature of the risks, 

captive propagation is viewed as a crucial component of near-term efforts. Molecular methods 

have shown that adults removed from the wild retain high levels of genetic diversity (Gruenthal 

and Burton 2005), and captive breeding will be conducted at multiple sites to help reduce risks of 

catastrophic failure (White Abalone Recovery Team 2008). Molecular techniques are being used 

to ensure broodstock integrity and in the future can facilitate assessment of outplanting efforts.

How long can populations be propagated artificially and still retain viability in the wild? 

This is a difficult question to answer. Some aquatic species have been intensively cultured for 

more than a century, and some facilities are perhaps that old. However, few populations or 

stocks have been continuously cultured for very long periods of time. For the past several 

decades in Japan, returns of approximately 50 million chum salmon per year have been 

maintained almost entirely by hatchery propagation, while natural habitats have been blocked or 

degraded and natural production has dwindled (Masuda and Tsukamoto 1998). These fish are 

spawned and their progeny reared for a short time in hatcheries, but they spend the majority of 

their life in the Pacific Ocean, so they are exposed to natural selection for part of their life cycle. 

Kaeriyama and Edpalina (2004) have recently raised concerns about long-term effects of these 

hatchery programs on fitness and sustainability of the natural populations.

C. Speed recovery by providing a demographic boost to an existing population

For populations that are depressed but not at high short-term risk, an increasingly popular 

strategy is to use artificial propagation to boost abundance and perhaps speed recovery. Is this 

strategy successful? The answer depends on what is used as a measure of success. Many of 

these supplementation programs can produce more adults than would result from wild 

reproduction by the same number of spawners. However, virtually no empirical data exist 

regarding the effects of artificial propagation on long-term viability of natural populations. For 
119

an empirical review of various ways to measure the success of supplementation efforts for 

Pacific salmon and steelhead, see Waples et al. (2007).

D. Reseed vacant habitat

Reintroductions to formerly occupied habitats have been attempted for a wide variety of 

plant and animal species. In general, probability of success is enhanced when the source 

population is wild, large numbers of individuals are released, the causes for the original decline 

have been addressed (Fischer and Lindenmayer 2000), and appropriate models have been used to 

assess the species’ habitat requirements (Cook et al. 2010). Tettlebach and Smith (2009) describe 

efforts that have met with at least short-term success in using hatchery outplanting to restore a 

New York population of the bay scallop (Argopecten irradians) after it was nearly eradicated in 

the wild by a series of brown tide algal blooms.

E. Reduce harvest pressure on natural populations

Overfishing is a serious problem for many marine species, and existence of a consistent 

supply of high quality cultured product at a reasonable price could substantially reduce demand 

for (and profit from) wild harvests (Engelsen et al. 2004).

Genetic Risks to Natural Populations from Aquaculture

Unmonitored, large-scale releases of cultured individuals into the wild is a global issue 

that affects a wide range of plant and animal species in addition to fish (see Laikre et al. 2010 for 

a review). Bartley et al. (2004) list nearly 100 marine stock enhancement programs in 

developing countries, in addition to numerous programs in countries such as Japan and Norway 

that have a long history of sea ranching and fish farming, respectively. General discussions of 

genetic risks associated with fish culture can be found in Allendorf and Ryman 1987, Hindar et 

al. 1991, Waples 1991, Busack and Currens 1995, Campton 1995, Waples 1999, Brannon et al.

2004, Waples and Drake 2004, Fraser 2008, Naish et al. 2008, and Araki and Schmid 2010.

Escapes of cultured animals to the wild are the primary means by which aquaculture and 

production of domesticated individuals pose a threat to natural populations. Escape events can 

range from relatively constant leakage of small numbers of individuals to large catastrophic 

events involving tens of thousands of individuals, millions of gametes or larvae, or more (e.g., 

Jensen et al. 2010). Escapes from most shore-based, recirculating culture systems, such as those 

that have been used for salmonid culture in Iceland (Thorarensen and Farrell 2011), probably 

pose a negligible risk. The probability of escapes is highest for net pen cages in nearshore or 

open ocean sites exposed to storm events or without adequate safeguards against escapes in 

effluent.

Loss of diversity within populations

Crow and Kimura (1970) is a good general reference for standard population genetic 

principles, including the rates of genetic drift and increase in inbreeding. Detailed accounts of 

many of the issues discussed here in a conservation context can be found in Frankham et al.

(2002) and Allendorf and Luikart (2007). Franklin (1980) proposed what became known as the 

50–500 rule, based on empirical data that suggested the following: 1) Ne of 50 produces 
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inbreeding at about 1% per generation [1% = 1 / (2Ne) = 1 / (2 × 50)], and this level of 

inbreeding can be tolerated in short-term captive breeding populations (e.g., cattle or sheep), but 

2) a larger effective size (Ne ≈ 500) is required to provide a balance between mutation and drift 

for quantitative genetic traits. Subsequently, others (e.g., Lynch and Gabriel 1990, Lande 1994, 

Lynch and Lande 1998) developed an idea first proposed by Wright (1931) and showed that an 

effective size much larger than 500 (perhaps 5,000) might be required to prevent a “mutational 

meltdown” through accumulation of slightly deleterious alleles.

Unless Ne is large, selection cannot operate effectively to eliminate slightly deleterious 

alleles, and they accumulate over time and can drift to high frequency just by chance. 

Furthermore, even if an effective size of about 500–1,000 is sufficient to provide for most 

medium-term evolutionary processes, the total number of alleles that can be maintained in a 

population with effective size of 106 is vastly larger than the number that can be maintained in a 

population with Ne = 103 (Ryman et al. 1995b). Ryman et al. (1995b) were probably the first to 

point out that orders of magnitude reductions in huge fish populations could have a substantial 

effect on allelic diversity, even if effective population size and heterozyosity remained very 

large. Waples and Naish (2009) discussed this issue and provided a hypothetical numerical 

example.

Most marine species have overlapping generations, which complicates calculation of Ne. 

Felsenstein (1971) and Hill (1972, 1979) developed methods to calculate Ne per generation in 

species with overlapping generations. Waples et al. (2011) developed a hybrid Felsenstein-Hill 

method that combines the best features of both approaches; the hybrid method uses age-specific 

survival and fecundity data (as are found in a standard Leslie matrix) and can accommodate 

overdispersed variance in reproductive success (as occurs in many marine species).

Ryman and Laikre (1991) provided the following expression for effective population size 

in a captive-wild system:

N W

x

N C

x

N T

e e

e 2 2 (1 )

1

− +

= (2)

where NeT = effective size of the cultured-wild system as a whole, NeC = effective size of the 

individuals reproducing in captivity, NeW = effective size of the individuals reproducing in the 

wild, x = the fraction of spawners in the offspring generation that were produced in captivity,

1 – x = the fraction of spawners in the offspring generation that were produced in the wild, and 

the Ryman-Laikre effect disappears entirely (i.e., there is no net change in overall effective size) 

under two special cases. In case 1, x / (1 – x) = NeC / NeW. In case 2, x = 0.

In Case 1, the ratio of captive to wild contributions is the same as the ratio of the effective 

sizes of the two phases. In this situation, the captive individuals do not contribute 

disproportionately to the overall population and NeT is the sum of NeC + NeW. In stock 

enhancement, Case 1 would generally be considered an unsuccessful program because the 

hatchery has not enhanced population size; for marine aquaculture, where stock enhancement is 

not a goal, Case 1 still might be considered financially successful, as long as the numerical losses 

due to escapes were not large enough to compromise program goals. Case 2 implies that either 
121

a) there is no aquaculture program, b) there is a program but there are no escapes, or c) some 

individuals escape but do not contribute any genes to subsequent generations. In these cases, 

NeT is simply NeW, less any reduction to NeW that results from taking individuals from the wild 

into captivity.

The Ryman-Laikre effect (reduction in overall Ne) is largest when x / (1 – x) is large 

compared to NeC / NeW, in which case NeT is reduced compared to the sum of the wild and 

captive components (NeC + NeW). Marine species are potentially susceptible to large RymanLaikre effects because NeW is typically much larger than NeC (perhaps orders of magnitude 

larger), and high fecundity creates the possibility that x can be large even if only a relatively few 

spawners are used for broodstock (Tringali and Bert 1998, Hedgecock and Coykendall 2007). 

Tringali and Bert (1998) showed that if the objective is to ensure that NeT ≥ 500, the goal can be 

achieved with NeC ≥ 50 and x ≤ 17%; if NeC is at least 100, the culture fraction can be as high as 

30% without driving NeT below 500. These results are not very sensitive to the initial value of 

NeW provided that it is at least 500. However, even if NeT remains above some absolute target, it 

still might be reduced to a fraction of the original value, as discussed below.

Figure A-9 quantitatively illustrates the Ryman-Laikre effect for scenarios that should be 

plausible for at least some marine species. In panel A, NeC was assumed to be 100, which is 

about the upper limit for effective sizes associated with the best-studied marine stock 

enhancement programs. For any given value of x, NeT quickly asymptotes at a rather modest 

value, regardless how large NeW is. Panel B shows that, even with the aquaculture fraction as 

small as 0.1 (10%), effective size of the cultured-wild system as a whole can be a tiny fraction of 

NeW. If NeW is on the order of 106 or 107 (perhaps realistic for some of the species subject to 

aquaculture), an aquaculture operation with escapes that comprise 10% of the breeding 

population would probably reduce Ne of the wild population by 3 or 4 orders of magnitude.

Table A-3 shows how overall NeT and NeT / NeW vary with different parameters that 

might be applicable to marine aquaculture programs. These examples assume that 200 captive 

individuals are used for broodstock, and that the ratio NeC / N is either high (0.5) or low (0.05), 

leading to NeC = 100 or 10, respectively. In this example, NeW is assumed to be either 103 or 106

and the fraction of successful spawners that are of captive origin is assumed to be either 1% or 

10%. If NeW is relatively low (103), these parameters lead to little or no reduction in overall Ne, 

except for NeC = 10 and x = 0.1, in which case wild Ne is reduced by nearly 50%. Results are 

considerably different for large wild populations (NeW = 106

), in which case the best case 

scenario (NeC = 100; x = 1%) leads to a 50% reduction in Ne and the other scenarios all lead to 

90% or greater reductions in effective size. Of course, a captive contribution of 1 or 10% to 

successful natural spawners represents a lot more total escapes for NeW = 106 compared to NeW = 

103.

The captive effective size used in Figure A-9, panel A (NeC = 100) is as large or larger 

than values that have been reported for marine stock enhancement programs (Tringali 2006,

Gold et al. 2008, Kitada et al. 2009, Gruenthal and Drawbridge 2012). However, if the species is 

long-lived and different individuals are spawned every year, it should be possible to increase NeC

to at least 500 or so over the course of a generation.
122

NeW

102 103 104 105 106 107

NeT / NeW

0.0

0.5

1.0

 10

 70

500

NeC

Captive fraction = 0.1

102 103 104 105 106 107

NeT

102

103

104

105

106

0.01

0.1

0.3

0.5

Captive fraction (x)

NeC = 100

NeC

A

B

Figure A-9. Illustration of the Ryman-Laikre effect and its consequences for effective population size 

(Ne). In panel A, unless x is small, NeT will not be much larger than NeC, regardless how large 

NeW is. In this example, it is assumed that NeC is 100. In panel B, unless NeW is relatively small 

and NeC is unusually large or x is very small, NeT generally will be a small fraction of NeW. This 

example assumes that the captive fraction (x) is 0.1; that is, progeny of captive individuals make 

up 10% of the overall natural spawners.

The magnitude of the Ne / N ratio in marine species remains controversial. Hedgecock 

(1994) proposed that the ratio could be very low in marine species because of highly variable, 

“sweepstakes” recruitment. According to this hypothesis, most females produce no surviving 

offspring at all, while progeny of a rare few individuals happen to end up in the right place at the 

right time to find sufficient food and escape predators. This scenario predicts family correlated 

survival and could lead to very low Ne / N ratios. Hauser and Carvalho (2008) reviewed 

empirical estimates for marine species (which include several in the range 10-3

–10-5) and 
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Table A-3. Examples of the Ryman-Laikre effect for some scenarios that involve relatively small 

fractional contributions from escapes (x ≤ 0.1). N is the initial wild population size. It is assumed 

that captive individuals are removed from the wild population and this reduces effective 

population size in the wild (NeW) by the quantity NeC.

Aquaculture fraction (x)

0.001 0.001 0.001 0.01 0.01 0.01 0.01 0.1 0.1 0.1

N = 1,000

NeW 500 930 990 500 930 990 500 930 990 —

NeC 500 70 10 500 70 10 500 70 10 —

NeT 501 932 992 510 948 1,000 610 986 550 —

NeT /NeW — 0.50 0.93 0.99 0.51 0.95 1.00 0.61 0.99 0.55

N = 106

NeW ≈106 ≈106 ≈106 ≈106 ≈106 ≈106 ≈106 ≈106 ≈106 —

NeC 500 70 10 500 70 10 500 70 10 —

NeT ≈106 9.9×105 9.1×105 8.5×105 4.2×105 91,074 48,053 6,961 999 —

NeT /NeW — 1.00 0.99 0.91 0.85 0.42 0.09 0.05 0.007 0.001

suggested more detailed mechanisms that could explain such tiny ratios. However, all of the tiny 

estimates are from indirect genetic methods, which can be subject to various biases. Additional 

discussion of these issues can be found in Hedrick (2005), Palstra and Ruzzante (2011), and Hare 

et al. (2011).

Under some circumstances, it is possible for the Ryman-Laikre effect to increase overall 

effective size. This can only happen if the ratio of effective size to census size is higher in 

captivity than it is in the wild, that is, when NeC / NC > NeW / NW. Empirical data show that in 

captive populations, a relatively few individuals generally contribute disproportionally to 

offspring production and this reduces NeC / NC. However, NeW / NW can also be quite low in 

natural marine populations, and if the difference between NeC / NC and NeW / NW is large enough,

it can more than compensate for differential productivity between captive and natural spawners. 

Table A-4 provides an example.

Table A-4. Hypothetical examples showing how the Ryman-Laikre effect can result in an increase in NeT

compared to what it would have been without a captive program (NeW*), provided the Ne / N ratio 

is substantially higher in captivity than in the wild.

Scenario A Scenario B

x 0.50 0.50

Nw 500.00 500.00

Nc 50.00 50.00

NeW / Nw 0.10 0.10

NeC / Nc 0.20 0.50

NeW* 50.00 50.00

NeW 45.00 45.00

NeC 10.00 25.00

NeT 33.00 64.00

NeT / NeW* 0.66 1.29
124

In this hypothetical example, the census size in the wild is Nw = 500 and NeW / Nw is 0.1, 

so in the absence of a captive program, wild effective size is NeW* = 50, and this is useful as a 

point of reference. NC = 50 adults are collected from the wild for broodstock, leaving 450 in the 

wild with effective size NeW = 45. If we assume that NeC / NC = 0.2 (scenario A), then NeC = 10, 

and NeT = 33, assuming the captive fish produce half of the offspring the next generation (x = 

0.5). The overall effective size (33) is only 2/3 of the NeW* = 50 that would have occurred 

without a captive program, so overall Ne declined in spite of a higher effective size:census size in 

captivity. However, if this differential is stronger (NeC / NC = 0.5, Scenario B), the result can be 

an increase in overall Ne (to 64 in this case). Hedrick et al. (1995; 2000) showed that, in a 

captive propagation program for the endangered Sacramento River winter-run Chinook salmon 

(Oncorhynchus tshawytscha), the relatively modest contribution of program fish (small x), 

combined with relatively high Nb / N ratio in the hatchery, meant that the juvenile release 

program did not appreciably reduce NeW compared to NW and might have increased it slightly.

Figure 3 and Table 4 (body of this report) assume a single generation of cultured-wild 

genetic interactions. Several authors (Waples and Do 1994, Wang and Ryman 2001, Duchesne 

and Bernatchez 2002) have considered the more realistic scenario that involves multiple 

generations of genetic interactions. In such analyses, an important factor is whether the natural 

population increases in abundance as a result of supplementation with cultured individuals; if so, 

the reduced levels of genetic drift in the larger overall population can help compensate for 

increased levels of inbreeding attributable to using a relatively few breeders in captivity. As 

increasing natural population abundance is not a likely consequence (nor a general objective) of 

commercial aquaculture, the relevant scenarios involve populations that do not increase in size 

but might, over time, receive continual inputs of genes from cultured individuals derived from 

relatively few parents. Under these conditions, the Ryman-Laikre effects are cumulative across 

generations, in which case regularly incorporating fresh spawners into the broodstock is 

important to help reduce long-term erosion of diversity.

The above material and that in the main text also assumes a single closed population. An 

alternative way to think about the problem involves a system of subpopulations connected by 

migration. Under these conditions, the global (metapopulation) effective size can be either larger 

or smaller than the sum of the subpopulation Nes, depending on various factors related to patterns 

of migration, local extinction, and spatial and temporal variation in productivity (see Whitlock 

and Barton 1997 and Wang and Caballero 1999 for discussion). Tufto and Hindar (2003) 

considered a variation of this type of model that allowed consideration of source-sink dynamics 

(e.g., unidirectional migration from one population into another, as might occur with 

unintentional escapes from an aquaculture program). Results of this model showed that the total 

effective size can be reduced by several orders of magnitude if the captive component of a 

population is much smaller than the wild component—a result similar to the conclusions reached 

using the Ryman-Laikre model. Migration can greatly speed up restoration of genetic variation 

in depleted populations, as demonstrated by Duchesne and Bernatchez (2002).

Loss of diversity among populations

A pervasive theme in ecology is that biological diversity contributes to the stability of 

ecosystem processes and the services they provide, a concept that has become a major argument 

for conservation of biodiversity. In ecology, conservation of biological diversity has focused 
125

primarily on the effects of species diversity on ecosystem stability, but evidence is growing that 

diversity among populations within species may also be important to ecosystem dynamics. The 

population-level diversity of some species may act like a diversified portfolio of investments, 

buffering fisheries and incomes from the ups and downs of particular populations. For general 

reading about the statistical and ecological basis of this portfolio effect, see Markowitz (1952), 

May (1974), Tilman and Downing (1994), and Doak et al. (1998).

Perhaps the best empirical example of the benefits of the portfolio effect is the fishery for 

sockeye salmon in Bristol Bay, Alaska (Hilborn et al. 2003, Schindler et al. 2010). Harvest has 

been maintained at roughly 10 million fish annually for a century, in spite of large annual 

fluctuations in abundance of individual stocks and stock complexes. Notably, the stock complex 

that currently produces more than half of the total harvest was a minor contributor (<10%) to the 

fishery a half-century ago. Other examples involving aquatic species include Worm et al. (2006), 

Lindley et al. (2007), Levin and Lubchenco (2008), and Greene et al. (2010).

Genetic diversity is an important component of the diversity among populations. The F

statistics developed by Wright have been enormously useful for characterizing genetic variation 

among natural populations. Wright (1931) showed that, under an island model at equilibrium, 

the expected value of FST, which measures genetic divergence among populations, is given 

approximately by

FST = 1 / (1 + 4mNe) (3)

Although the numerous assumptions underlying this simplistic model are rarely if ever 

completely satisfied in nature (Waples 1998, Whitlock and McCauly 1999), this basic 

relationship has been widely used to provide insights into levels of migration consistent with 

molecular genetic data.

In recent years, a great deal of attention has focused on trying to understand the 

relationship between the parameters m and mNe and what they mean for marine species. The 

migration rate, m (the fraction of individuals exchanged each generation), is key to estimating 

demographic connectivity and independence among local populations, and this has sparked 

considerable interest in estimating marine dispersal, especially at planktonic larval stages 

(Cowen et al. 2000, Shanks et al. 2003, Levin 2006, Bradbury et al. 2008). In contrast, 

molecular genetic data primarily provide information about mNe (the product of migration rate 

and effective size; see above equation), the units of which are individuals per generation. This 

produces a disconnect between the saturation points for genetic versus demographic dispersal. In 

large marine populations, tiny migration rates (m) that have little influence on demographic 

connectivity could produce a large enough number of migrants (mNe) to essentially homogenize 

indices of neutral genetic diversity. A number of authors have discussed the challenges this 

poses to drawing inferences about demographic processes in marine species from genetic data 

(Hauser and Carvalho 1994, Waples 1998, Palsboll et al. 2007, Waples et al. 2008, Lowe and 

Allendorf 2010).

Patterns of genetic variation in aquatic species have been reviewed by Gyllensten (1985), 

Ward (1994), and Hauser and Carvalho (2008). Ward et al. (1994) reviewed molecular genetic 

data (primarily allozymes) for fishes and found that mean values for FST were highest for 
126

freshwater species, moderate for anadromous species, and lowest for marine species. 

Conversely, Dewoody and Avise (2000) found that levels of microsatellite diversity within 

populations (average numbers of alleles per locus and average heterozygosity) showed the 

opposite trend: marine fishes had the highest levels of within-population diversity and freshwater 

fishes had the lowest (comparable to values found in nonpiscine animals). Because FST is 

inversely related to the combined parameter mNe, a low FST can be due to a high migration rate 

(m), a large effective size (Ne), or both. Thus large marine populations with low FST still might 

experience low migration rates, which facilitate local adaptation.

The relationship between FST and mNe can take a long time to reach equilibrium. If a 

population system is distorted from historical migration-drift equilibrium, then original migration 

patterns (at rate m per generation) are restored, the number of generations required for FST to 

move half the distance toward the new equilibrium (T50) is given by (Whitlock 1992):

ln[(1 ) (1 1/(2 )]

ln(0.5)

50 2

m Ne

T − − = (4)

Equation 4 can be informative for evaluating anthropogenic and “natural” disturbances. 

For example, to consider the example shown in Figure 5 (body of this report), where human 

activities have completely homogenized diversity among populations (FST = 0), assuming local 

Ne = 1,000 and m = 0.004 (so that mNe = 4), this equation predicts about 81 generations are 

required to move halfway toward the new equilibrium, in good agreement with simulation results 

(e.g., after 81 generations following complete homogenization, FST had risen to a bit over 0.02, 

about halfway to the new equilibrium of about 0.045). Alternatively, consider a scenario where a 

marine population restricted to a glacial refugium during the Pleistocene epoch subsequently 

dispersed into different areas, where it maintained moderately large population sizes (Ne = 104) 

connected by weak gene flow (mNe = 1, so m = 10-4

).

Equation 4 indicates that under these conditions, it would take more than 2,700 

generations for FST to reach even half its new equilibrium value of 0.2. It is thus clear that many 

large marine populations whose distribution was affected by Pleistocene or more recent events 

could have FST values that are well below equilibrium for current levels of gene flow. In these 

cases, use of equilibrium models based on empirical FST values would overestimate current 

levels of gene flow, which would tend to underestimate potential for local adaptation. This 

would be particularly true for species with long generation times.

Figure A-10 illustrates these points by contrasting time to reach equilibrium for two 

groups of 10 populations: one with Ne = 100 in each subpopulation and one with Ne = 1,000. In 

this example, both groups had the same level of original population subdivision (FST ≈ 0.04) and 

both were completely homogenized (FST = 0) by anthropogenic activities. If quasi-natural 

conditions and original levels of connectivity are restored, the system with relatively small (Ne = 

100) subpopulations will approach its original FST level within about 10 generations—a time that 

is very rapid on evolutionary time scales but still could represent a considerable number of years 

for long-lived species. In contrast, in the system of larger subpopulations, restoration of the 

original level of population subdivision would require 200–300 generations.
127

Figure A-10. Time to reach migration-drift equilibrium (indicated by stable FST over time) in two groups 

of 10 subpopulations with different effective sizes (Ne = 100 and Ne = 1,000). It is assumed that 

both metapopulations originally were characterized by a level of migration such that mNe = 4, 

which produces an equilibrium FST of about 0.045, and that these natural migration rates were 

restored after an event that completely homogenized population subdivision. Results are based 

on simulated data using 20 microsatellite loci, each with a maximum of 10 alleles. The arrow 

indicates 81 generations, the theoretical time to move 50% of the way to a new equilibrium based 

on Equation 4 and assuming Ne = 1,000, m = 0.004.

Ryman et al. (1995b) proposed that FST might be used as a metric to gauge the effects of 

loss of diversity among populations. One possible criterion might be that anthropogenic 

activities should not be allowed to reduce FST appreciably from the value that occurs under 

“natural” conditions.

This example of inherent risk trade-offs emphasizes the point that once humans intervene 

directly in survival and reproduction of natural populations, we become managers of these 

processes. Over evolutionary time scales, natural populations sort out among themselves the

levels of connectivity that are adaptive. When humans intervene and decide what levels of

connectivity to manage for, errors are possible in both directions. Many (perhaps most) species

that are prospective targets of marine aquaculture can disperse widely, either as adults,

eggs/larvae, or both. Furthermore, aquaculture escapes might disperse more widely than typical

natural fish because they don’t have an identifiable home range or territory. This effect is well 

documented in some hatchery and aquaculture programs for Pacific and Atlantic salmon; the 

extent to which it applies to typical marine species largely remains to be determined.

Loss of fitness

Frankham (2008) reviewed empirical evidence for genetic adaptation to captivity in 

species conservation programs. He found predictable correlations between degree of 

domestication and selection strength, Ne, and number of generations in captivity and discussed
128

some factors that could help alleviate deleterious effects on wild populations when captive

populations were reintroduced to the wild. Christie et al. (2012) showed that adaptation of wild

steelhead to a hatchery environment can be detected within a single generation, with potentially 

serious consequences for fitness in the wild. An analysis by Doyle (1983) of domestication in 

aquaculture settings suggested that inadvertent domestication selection can be as strong as

deliberate artificial selection. Hauser and Carvalho (2008) reviewed evidence that is beginning 

to accumulate to suggest that even marine species with high dispersal capability can exhibit local 

adaptations.

Inbreeding depression and outbreeding depression can be thought of as phenomena that 

occur at either extreme of a continuum that measures genetic differences among individuals that 

interbreed (Waples 1995). Reduced fitness can occur if the individuals are either too similar 

genetically (as in close relatives) or too genetically divergent. Lynch (1991) presented a uniform 

framework for considering inbreeding depression and outbreeding depression and showed that it 

is possible for both phenomena to occur at the same time.

Outbreeding depression can occur through two related mechanisms: a) loss of local 

adaptation (simple dilution of locally adapted alleles by nonlocal alleles) or b) breakdown of 

coadapted gene complexes (groups of genes that function effectively as a unit). If individuals 

from two divergent populations interbreed, loss of local adaptation is generally found in the F1

generation, but breakdown of coadapted gene complexes typically is seen only in the F2 or later 

generations (unless the fitness consequences resulting from this breakdown are very strong). 

This is because F1 hybrids contain one complete chromosomal complement from each 

population, and it is not until they interbreed to produce the F2 generation that genetic shuffling 

occurs among the parental sets of chromosomes (Tallmon et al. 2004). Recently, Edmands 

(2007) and Frankham et al. (2011) reviewed evidence for both inbreeding depression and 

outbreeding depression and reached somewhat different conclusions about their relative 

importance: Edmands (2007) concluded that the risks were more or less comparable and 

Frankham et al. (2011) concluded that the risks of outbreeding depression were generally rather 

small. They agreed, however, that empirical studies of inbreeding depression are much more 

common than those of outbreeding depression. Nevertheless, the direct consequences of 

inbreeding have seldom been examined in fish in the wild (Wang et al. 2002). Thrower and Hard 

(2009) showed that these consequences can be serious for survival of steelhead released to the 

wild, even if inbreeding depression is weak or undetectable in captivity.

Tufto (2001) used a simple quantitative genetic model to evaluate the demographic 

consequences of releasing individuals that are maladapted to local conditions (as might occur 

unintentionally with aquaculture escapes). He found that reductions in local abundance can 

occur if the fraction of released individuals is sufficiently large and they are sufficiently 

maladapted to local conditions.

Lorenzen (2005) presented a detailed theoretical analysis of the potential for marine stock 

enhancement to provide societal benefits over and above those that can be obtained from optimal 

exploitation of wild stocks alone. His analysis focused on population dynamics, recruitment, and 

density dependence and accounted for biological differences between hatchery and wild fish. 

Although the latter did not involve an explicit genetic model, some of his results are relevant to 

the question of whether it is better to pursue strategy 1, keep the cultured population as similar as 
129

possible to the wild population, or strategy 2, maximize divergence between cultured and wild 

population.

Lorenzen concluded that, assuming gene flow from the cultured population into the wild 

continues indefinitely at a constant rate, the worst-case scenario is when the hatchery population 

is only moderately maladapted compared to the wild population. This implies that either extreme 

strategy (if attainable) might be preferable to an intermediate one. If this is the case, then the 

optimal strategy will depend on a) the shape of the relationship between the degree of hatcherywild difference and wild population fitness and b) the practical limits to how “similar” and 

“different” the hatchery and wild populations can be (Figure 6, body of this report; see also 

Lorenzen et al. 2012, Huisman and Tufto 2012).

This conclusion is supported by a more recent study by Baskett and Waples (in press), 

who used a model that includes quantitative genetics and population dynamics to tackle the key 

question regarding the merits of strategy 1 versus strategy 2. Important results include the 

following:

• Although the quantitative genetic model developed by Lande (1976) and adopted by Ford 

(2002) has been shown to be relatively robust to simplifying assumptions, extreme forms 

of the “different” strategy strongly violate two key assumptions: selection is weak and 

phenotypic distributions are normal and unimodal. As a consequence, it is necessary to 

consider the full phenotypic distributions to properly evaluate the “different” strategy.

• In their extreme forms, either strategy could potentially be consistent with high wild 

population fitness. Whether the necessary extremes can be achieved is an open question. 

For either strategy, it will be important to evaluate the consequences for wild populations 

if things do not go as planned.

• The “different” strategy is only viable if there are opportunities for strong purifying 

selection to eliminate maladapted genotypes after escape but before reproduction.

• Effects on fitness can be sensitive to the relative life cycle timing of escape/release, 

density dependence, and natural selection.

In its most common formulation, Dollo’s Law, named after the late nineteenth and early

twentieth century Belgian paleontologist Louis Dollo, states that complex characters that have 

been lost during the course of evolution cannot be regained (Simpson 1953). It is something less 

than a law, as some exceptions have been noted. A broader view of the underlying principle is 

that evolution is generally irreversible for either of two reasons: 1) evolution of even simple 

structures is exceedingly complex and it is statistically improbable that the exact same course of 

evolution would be followed more than once, forwards or backwards; 2) the process of evolution 

is constrained in many ways, and many transitions might only be permissible in one direction. If 

novel selective pressures are relaxed, the rate at which fitness increases will not necessarily be as 

rapid, because the forces acting to increase fitness might not be as strong (Allendorf and Hard 

2009). For a recent review of ideas related to Dollo’s Law, see Collin and Miglietta (2008).

In a recent summary of 266 peer-reviewed papers, Araki and Schmid (2010) asked 

whether hatchery stocks and wild stocks differed in fitness and in genetic variation, and whether 

stocking affected population abundance. A variety of species were included in their review—
130

salmonid and flatfish species were most studied (17.3% and 15.1%, respectively), followed by 

bream, drum, and cod species with 8.1%, 4.4%, and 4.0%. Seventy studies compared hatchery 

and wild stocks, of which 23 showed significantly negative effects of hatchery rearing on the 

fitness of stocked fish and 28 showed reduced genetic variation in hatchery populations. None of 

these studies showed a positive effect of hatchery rearing on the fitness of released fish.

Araki and Schmid (2010) found a few cases where no obvious effect of hatchery rearing 

was observed and a positive contribution to population abundance was indicated. Studies on 

black sea bream (Acanthopagrus schlegelii) in Hiroshima Bay, Japan, did not reveal a fitness 

effect of hatchery rearing and also provided the only example of a potentially positive 

contribution of hatchery stocking on population abundance (Jeong et al. 2007, Blanco Gonzalez 

et al. 2008a, 2008b). Araki and Schmid (2010) noted that this case study also provided an 

example of reduced size-at-age over time, potentially due to the intensive stocking and the likely 

increased competition for natural resources (Blanco Gonzalez et al. 2009). A recent study from 

Korea suggested loss of alleles in farmed black sea bream relative to wild populations, but no 

significant reduction in heterozygosity (An et al. 2010).

The last decade has seen increasing recognition that most problems in conservation are 

not strictly ecological or evolutionary, but eco-evolutionary in the sense that they involve the 

interaction of ecological and evolutionary processes (Stockwell et al. 2003, Kinnison and 

Hairston 2007, Ezard et al. 2009, Carlson et al. 2011). This perspective is particularly important 

in evaluating the consequences of fitness reductions in wild populations caused by genetic 

interactions with cultured individuals. Although natural selection can help restore fitness if the 

flow of maladapted genes stops, this comes at a demographic cost to the population.

Risks to Natural Populations from other Anthropogenic Activities

This is a very large topic and we make no attempt to be comprehensive. To provide some 

context for evaluating effects of marine aquaculture, we briefly discuss three anthropogenic 

factors that have potentially large effects on natural populations of marine species.

Fishing

In the United States, the Magnuson-Stevens Fishery Conservation and Management Act 

(MSA, Public Law 94-265, revised 1996 and 2006) directs conservation and management actions 

for marine species under federal jurisdiction. National Standard One of the revised statute 

stipulates that, “Conservation and management measures shall prevent overfishing while 

achieving, on a continuing basis, the optimum yield from each fishery for the United States 

fishing industry.”

The term overfishing has been defined as a level of fishing mortality that jeopardizes the 

capacity of a fishery to produce the maximum sustainable yield on a continuing basis, while 

overfished describes a stock whose size is sufficiently small that a management change is 

required to achieve rebuilding. Fixed biological references points are used to determine whether 

stocks are overfished; if so, the MSA automatically triggers aggressive management actions that 

are projected to rebuild the stock within a short time period (10 years or less in most cases).
131

These provisions make MSA one of the strongest conservation laws in the world. By 

way of comparison, for example, Canada has no federal fishery management system with fixed 

biological reference points comparable to MSA, and COSEWIC (Committee on the Status of 

Endangered Wildlife in Canada, the scientific body charged with assessing status under Canada’s 

Species at Risk Act) has concluded that a number of marine fish populations in Canada are at 

significant extinction risk (a list of marine species that have been evaluated is at http://www

.cosewic.gc.ca/eng/sct5/index_e.cfm).

However, in spite of some successful rebuilding efforts, the latest assessment shows that 

at least 46 U.S. stocks remain overfished, according to MSA guidelines (NMFS 2009). Even 

though overfished stocks might still have relatively large numbers of adults, reductions in allelic 

diversity can be substantial (Ryman et al. 1995b). Furthermore, MSA does little to address 

increasing concerns by some that fishery selectivity (in particular, preferential harvest of older 

and larger individuals) exerts strong evolutionary pressure that can change genetically based life 

history traits of natural populations, potentially compromising their long-term viability (Walsh et 

al. 2006, Law 2007). Under many plausible scenarios, harvest rates that are consistent with 

long-term sustainability could be much lower than those that would be predicted to produce 

maximum sustainable yield using current models.

Unfortunately, our understanding of the genetic underpinnings of life history traits 

susceptible to fishery selectivity is too limited to permit robust predictions about long-term 

consequences of selective harvest. In some respects, therefore, uncertainties about the 

evolutionary consequences of selective harvest parallel uncertainties associated with long-term 

fitness consequences of interbreeding between captive and wild fish. Although Hard et al.

(2008) concluded that no single study has irrefutably demonstrated fishery-induced evolution in 

a wild population, considerable circumstantial evidence for its occurrence exists. In addition, 

empirical evidence is accumulating that evolutionary changes in life histories of some heavily 

exploited fish populations might already be widespread (Swain et al. 2007). High and selective 

exploitation has the potential to substantially decrease genetic diversity and reduce the capacity 

of a population to respond to natural evolutionary forces, even if exploitation and the intensity of 

selection are subsequently reduced (Allendorf and Hard 2009). Indeed, the failure of many 

collapsed populations to recover following substantial reductions in exploitation (Hutchings 

2000) provided early indications that fishery-induced evolution might result from 

overexploitation.

Figure A-11 illustrates some of the tradeoffs inherent in implementation of harvest 

management. Low harvest rates (0 ≈ 0.2) promote diversity and ecosystem functions (high 

biomass, large individuals, few collapsed species); moderate harvest rates (0.4 ≈ 0.6) can 

maximize catch but have noticeable ecosystem effects; higher harvest rates generally produce 

greater employment opportunities but at substantial biodiversity costs (see also Botsford et al.

1997).

Loss and degradation of habitat

For terrestrial species around the world, loss and degradation of habitat is perhaps the 

most pervasive threat to biodiversity. In contrast, the role that offshore marine habitats play in 

population dynamics of marine species is poorly understood, in part because studies are difficult 
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Figure A-11. Schematic representation of expected effects of increasing exploitation rate on several 

biological indicators of population and ecosystem health. (Adapted from an analysis by Worm et 

al. 2009 of the Georges Bank marine fish community.)

to conduct. Bottom trawls can dramatically affect the sea floor as well as structure-forming 

invertebrates that play primary roles in supporting marine ecosystems (de Marignac et al. 2008). 

Until the 1980s, these activities were largely restricted to soft bottom habitats, but in recent years 

technological advances have allowed trawlers to fish nearly all benthic habitats on the 

continental shelves and deeper slopes (CEEF 2002).

Effects of anthropogenic changes to nearshore habitats are better documented than their 

offshore counterparts. A large number of marine fish species with offshore distributions as adults 

use nearshore and estuarine habitats for juvenile rearing (Beck et al. 2001). This is typically the 

most sensitive life stage for marine species. Nearshore habitats are also indirectly affected by 

land-based activities that alter patterns of biogenic and inorganic material delivery to the ocean. 

For example, a series of large, mainstem dams and reservoirs in the Columbia River basin has 

dramatically altered physical and biological characteristics of the river’s plume (Bottom et al. 

2005), which can play an important ecological and energetic role for planktivores such as larval 

and juvenile fish (Peterson and Peterson 2008).

Global climate change poses many complex challenges for fishery management 

(Hollowed and Bailey 2009), but two in particular are directly relevant to habitats provided by 

reef-building corals. On the one hand, warmer sea temperatures can exceed the thermal 

tolerance for corals and their photosynthetic symbionts, leading to mass bleaching events. On 
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the other hand, higher atmospheric CO2 levels reduce pH in the ocean, making it more difficult 

for calcifying organisms to build their skeletons. In the decades to come, these two factors are 

expected to create extremely stressful conditions for corals and the organisms that depend on 

them for food and habitat (Hoegh-Guldberg et al. 2007).

Pollution

To date, efforts to assess pollution effects have primarily focused on pollution that is both 

inexpensive to monitor and overtly harmful to coastal and blue-water ecosystems. Much less is 

known about the impacts of toxic chemical contaminants that require expensive analytical 

methodologies to track in the marine environment. Toxics also pose a complex research 

challenge because they have nuanced (and often nonlethal) but important effects on physiology 

and performance of individual fish. Understanding linkages between toxic compounds in the 

marine environment and the fitness of marine organisms requires research expertise in 

immunology, reproductive biology, endocrinology, neurobiology, developmental biology, and 

other specialized physiological disciplines. Moreover, evaluating the significance of pollution 

relative to other human-induced impacts requires quantitative extrapolation of biological 

responses for specific organ systems in individual fish up to the scale of populations and 

communities. This is thus a very challenging area of research, but work by NOAA scientists and 

others is beginning to connect the dots between toxic chemicals and the health, viability, and 

sustainable management of wild fish stocks. Key factors to consider in assessing overall risks 

from pollution include the following:

1. Marine fish are still at risk from pollution discharges that took place in the twentieth

century (Peterson et al. 2003). Many toxics are pervasive and persistent in the marine 

environment, and they can be difficult or impossible to mitigate once released.

2. Society is manufacturing and releasing chemicals into the ocean at a rate that exceeds the 

capacity of scientific institutions to study and understand their ecological impacts. More 

than 75,000 potentially toxic substances are currently manufactured in the United States. 

Of these, the chemicals that pose a substantive risk to marine fish populations probably 

number in the thousands. Classes of chemicals of emerging concern include 

nanomaterials, pharmaceuticals, and plasticizers.

3. Pollution inputs to the ocean are highly heterogeneous in space and time. Although 

persistent and bioaccumulative chemicals can now be found in every corner of the globe, 

the geographical severity of the pollution problem tends to scale with human population 

density. All socioeconomic indicators point to an expanding pollution problem in the 

decades ahead, in tandem with human population growth and development along the 

coastal margins of the United States. For example, the future risk of oil spills will likely 

increase in proportion to increasing maritime commerce and transport.

4. Diffuse sources of pollution (e.g., atmospheric deposition and terrestrial stormwater 

runoff) have overtaken conventional end-of-pipe discharges in terms of total loadings to 

the ocean. These nonpoint sources are much more difficult to control.

5. The extent to which toxics will interact with other large-scale ecological forcing 

pressures (e.g., climate change and ocean acidification) is largely unknown.
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6. Existing coastal monitoring programs throughout the United States are inadequate to 

accurately profile pollution exposure for many marine fish stocks.

Discussion

Although these three risks from other anthropogenic activities were considered above 

under separate subheadings, they often have overlapping and synergistic effects on natural 

populations. For example, in the broad sense pollution can be considered a component of 

habitat, and many physical effects on marine habitats would co-occur with pollution, especially 

in coastal areas. Furthermore, pollution is one of the ecological impacts of marine aquaculture 

that has caused the greatest concern and the motives for initiating artificial propagation programs 

can be tied to habitat loss. Finally, an unfortunate and long-lasting habitat consequence of some 

fishing activities is the persistence of derelict fishing nets that pose ongoing risks to marine 

species (Good et al. 2010). Therefore, these anthropogenic impacts are not independent and their 

cumulative impacts can be synergistic (Crain et al. 2008, Hutchings and Fraser 2008).

Managing Risk

Monitoring

The primary events that aquaculturists, public regulatory agencies, or both should 

monitor and quantify where feasible include: the magnitude and frequency of escapes, the 

frequency of reproductive encounters, occurrence of F1 hybrid offspring between cultured and 

wild fish, and the occurrence of backcross descendants in the wild, indicative of genetic 

introgression (Kapuscinski et al. 2007). These events can help in estimating the likelihood of 

adverse genetic effects. This likelihood is a function of a number of probabilities, acting in 

sequence, including the probability of escape, survival of escaped fish to maturity, probability of 

encounter, probability of mating, probability of successful reproduction, and the probability of 

postreproduction survival of hybrid offspring in the wild.

Key considerations

The consequences of genetic interactions between cultured and wild marine fish for 

natural population structure and viability depend on a number of key factors. The parameters 

that tend to determine the consequences of genetic interactions between these groups, once they 

occur, depend primarily on the genetic divergence between the groups, particularly for traits 

important to survival and fitness in the wild. These parameters include the difference in genetic 

background between the cultured and wild individuals, and the degree to which plasticity 

influences the expression of the phenotype in the wild versus the protective culture environment.

Careful monitoring must be a priority

Determining whether such consequences have occurred requires constant vigilance and 

consistent, careful monitoring. Aquaculture monitoring programs should be designed and 

implemented before the initiation of a culture program or commercial operation. Monitoring 

design is critical; it must identify specific, measurable end points that are closely linked to the 

presence and impact of escaped cultured fish (Senanan et al. 2007). These end points include 
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(Figure 9, body of this report): the pattern and frequency of escaped cultured fish at all life stages 

(their presence, abundance, and distribution), detecting F1 progeny (their presence, abundance, 

and distribution), detecting backcross progeny (their presence, abundance, and distribution), 

detecting changes in both cultured and wild populations (their abundances and phenotypic 

differences), and detecting changes in local fish species and their relative abundance. Some 

important issues to keep in mind are the power to detect such effects—which depends on the size 

of the program, the differences between the groups, and the efficacy of monitoring—and 

identifying clear remedial responses when effects are detected. The use of genetic markers, 

external marks, and other tools can greatly facilitate detection.

Use of Models in Research

Reliable predictions of the fate of a wild population receiving immigration of cultured 

fish would require that all of the population parameters were known; this is hardly true of any 

population and particularly not for wild fish populations (Ryman et al. 1995a). Ecologically and 

genetically realistic experiments, such as lifetime fitness studies (and lifetime effects studies), are 

time consuming and costly to undertake and nonetheless only describe a particular combination 

of wild and cultured fish for a particular set of environmental conditions. The only available 

solution to this problem is to use the results of empirical and experimental studies to develop 

computer-based simulation models. A handful of such models are presented below.

Modeling how interbreeding can change the composition of wild populations

Hutchings (1991) modeled the threat to wild salmon populations experiencing various 

intrusion rates of escaped farmed salmon and small or large fitness differences among the 

offspring. Based on data from common garden experiments of wild and farm Atlantic salmon, 

Hindar et al. (2006) developed a more detailed model to predict the future of wild salmon 

populations experiencing invasions of escaped farm salmon. Simulations with a fixed intrusion 

rate of 20% escaped farm salmon at spawning (a long-term average for Norwegian populations) 

suggest that substantial changes take place in wild salmon populations within 10 salmon 

generations (≈40 years). Low-invasion scenarios suggest that farm offspring are unlikely to 

establish in the population, whereas high-invasion scenarios suggest that populations are 

eventually composed of hybrid and farm descendants. Recovery of the wild population was not 

likely under all circumstances, even after many decades of no further intrusions. The model also 

suggested that managers of wild salmon will have difficulty finding broodstock of the original 

wild population after a few generations of high intrusion rates.

Quantitative genetic model for immigration of maladapted individuals

A model incorporating density-dependent effects of escaped farmed fish on wild 

populations was developed by Tufto (2001). He used a quantitative genetic model that included 

immigration of maladapted individuals into wild populations where the outcome was determined 

by density-dependent regulation and local stabilizing selection. One result was a reduction in 

total equilibrium size (carrying capacity) when immigrants deviated more than 2.8 genetic SDs

from the local optimum and immigration was high relative to the strength of stabilizing selection. 

Comparison of the selected strains of farmed Atlantic salmon and wild populations (e.g., in 
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growth rate) suggests that the above conditions are typical of those that occur presently in many 

rivers (Tufto 2001).

Modeling changes in effective population size (Ne) caused by interbreeding

Any reduction in absolute population size is expected to lead to a reduction in Ne, unless 

the species has some behavioral pattern that equalizes reproductive success or family size when 

numbers decline. Changes in migration patterns between local populations also have the 

potential to change the Ne of the total population. Whereas low, symmetric gene flow between 

populations increases the total Ne, asymmetric gene flow will decrease it (Tufto and Hindar 

2003). In the extreme case of one-way gene flow, the total Ne will eventually approximate that 

of the donors. As an example, it has been estimated that the major strains of farm Atlantic 

salmon in Norway have an average Ne of about 80 individuals. If we ignore genetic differences 

between each of the four major strains, the total Ne of farm salmon is roughly 320 individuals. 

The total Ne of the wild Atlantic salmon is not known, but it is probably on the order of 104

or 

105 per generation. The total Ne of the farm plus wild salmon, assuming one-way gene flow 

from escaped farmed to wild populations, is then Ne = 320 individuals (Tufto and Hindar 2003).

The Trojan Gene hypothesis for genetically modified fish

Muir and Howard (1999) developed the Trojan Gene hypothesis to study a situation 

where genetically modified fish are developed that attain a large size at sexual maturity and 

thereby totally dominate spawning, should they escape to the wild. The Trojan Gene hypothesis 

has been used to model introduction(s) of cultured fish (genotypes) that have superior fitness at 

breeding but leave offspring with very poor survival capabilities, potentially leading to a 

population extinction vortex. A net fitness model to help quantify trade-offs between mating 

advantages of genetically modified organisms in the wild and reduced offspring viability was 

subsequently developed by Muir and Howard (2001, 2002). This model can be useful in 

evaluating relative invasion and extinction risks (Kapuscinski et al. 2007).
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Appendix B: Aquaculture Genetic Management 

Plan (AGMP)

Note: This is a draft attempt to adapt the Hatchery Genetic Management Plan template 

that is used in the Pacific Northwest for salmon hatcheries to finfish aquaculture programs.

1. General Program Description

1.1. Name of aquaculture program.

1.2. Species and population (or stock) under culture.

Give common and scientific names.

1.3. Responsible organization and individuals.

Indicate lead contact and on-site operations staff lead.

Name (and title):

Institution or Company:

Address:

Telephone:

Fax:

Email:

Other institutions, companies, co-operators, or organizations involved, including 

contractors and extent of involvement in the program:

1.4. Location(s) of culture program and associated facilities.

Include location and state.

1.5. Type of program.

The default assumption is “closed culture” (natural populations not regularly incorporated 

into broodstock); explain if different.

1.6. Purpose (goal) of program.

The default assumption is commercial production; explain if different. Example: “The 

goal of this program is the production of red drum for commercial food use.”
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1.7. List of program Performance Standards.

Performance standards are designed to achieve the program goal or purpose, and are 

generally measurable, realistic, and time specific. Examples of these standards, their 

corresponding indicators, and how they are incorporated into a monitoring and evaluation plan 

are shown in Table B-1.

Table B-1. Example of performance standards.

Performance standards Performance indicators Monitoring and evaluation plan

Meet program production goals Number of adults collected and 

individuals reared by life stage

Monthly program production 

records

Minimize opportunities for 

interaction with wild fish 

through proper broodstock 

management and marking

Numbers (type) of marked fish Monthly program production 

records

Maintain stock integrity and 

genetic diversity

Number of broodstock 

collected, phenotypic 

characteristics (sex, age, size, 

etc.), Ne

Spawning guidelines, monthly 

program production records

Minimize interactions with wild 

fish through effective 

containment methods

Records of documented 

escapes and losses 

unaccounted for

Monthly program production 

records, marking data

Maximize in-culture survival of 

broodstock and their progeny

Fish culturists and pathologists 

will monitor the health of 

cultured stocks on a monthly 

basis and recommend 

preventative actions to 

maintain fish health

Monthly program production 

records

Fish health monitoring records

Limit the impact of pathogens 

associated with culture program 

on wild fish

Fish pathologists will diagnose 

fish health problems and 

minimize their impact

Vaccines will be administered 

when appropriate to protect 

fish health

A fish health database will be 

maintained to identify trends in 

fish health and disease and 

implement fish health 

management plans based on 

findings

Fish health monitoring records

Ensure culture operations

comply with state and federal 

water quality standards through 

proper environmental 

monitoring

National Pollutant Discharge 

Elimination System (NPDES)

compliance requirements

Monthly NPDES report records
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1.8. List of program performance indicators, designated by benefits and risks.

Performance indicators provide information about the degree to which program standards 

have been achieved. Monitoring and evaluation of performance indicators is important to 

determine the success of efforts to maximize benefits and minimize risks. The list of 

performance indicators should be separated into two categories: benefits that the aquaculture 

program will provide to the industry, or in meeting culture objectives while minimizing adverse 

impacts on natural species and the environment; and risks to natural fish that can be posed by the 

aquaculture program, including indicators that respond to uncertainties regarding program effects 

associated with a lack of data.

1.8.1. Performance indicators addressing benefits.

Example: “Quantify survival and production rates for aquaculture program fish to 

market.”

1.8.2. Performance indicators addressing risks.

Example: “Quantify escapes of aquaculture fish and their genetic impacts on natural fish 

populations.”

1.9. Expected size of operation or program.

In responding to the two elements below, take into account the potential for effects on 

natural populations from escapes of cultured fish or from collection of natural fish for 

broodstock.

1.9.1. Proposed annual broodstock collection level, if any (maximum number of adult fish).

1.9.2. Expected annual level of escapes (maximum number) by life stage and location.

Use standardized life stage definitions by species: embryo, larva, juvenile, subadult, 

mature adult, spawning adult.

1.10. Current program performance, including estimated survival rates, production levels, 

and escape levels. Indicate the source of the data.

Provide estimated survival rate, total production number, and escape number data 

available for the most recent 12 years, or for the number of years of available and dependable 

information. Indicate program goals for these parameters.

1.11. Date program started (years in operation), or is expected to start.

1.12. Expected program duration.
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2. Relationship of Program to other Management Objectives

2.1. Describe alignment of the aquaculture program with any regional or national 

aquaculture plan or policy or other regionally accepted policies. Explain any proposed 

deviations from the plan or policies.

Example: “The aquaculture program will be operated consistent with the____________,

with the exception of ____________.”

2.2. List all existing cooperative agreements, memoranda of understanding, memoranda of 

agreement, or other management plans or court orders under which program operates.

Indicate whether this AGMP is consistent with these plans and commitments, and explain 

any discrepancies.

3. Facilities

Provide descriptions of the aquaculture facilities that are to be included in this plan, 

including dimensions of collection, holding, incubation, and rearing facilities. Indicate the fish 

life stage held or reared in each. Also describe any instance where operation of the culture 

facilities, or new construction, results in destruction or adverse modification of critical habitat 

designated for natural populations.

3.1. Broodstock collection facilities (or methods).

3.2. Fish transportation equipment (description of pen, tank truck, or container used).

3.3. Broodstock holding and spawning facilities.

3.4. Incubation facilities.

3.5. Rearing facilities.

3.6. Describe operational difficulties or disasters that have led to significant fish mortality.

3.7. Indicate available backup systems, and risk aversion measures that will be applied, 

that minimize the likelihood for the take of natural fish that can result from equipment 

failure, water loss, flooding, disease transmission, or other events that could lead to injury 

or mortality.

Example: “The facility will be staffed full-time, and equipped with a low-water alarm 

system to help prevent catastrophic fish loss resulting from system failure” or “The program will 

use only commercially available broodstock and will not involve direct take of wild fish.”

4. Broodstock Origin and Identity

Describe the origin and identity of broodstock used in the program, its status, annual 

collection goals, and relationship to wild fish of the same species and population.
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4.1. Source.

List all historical sources of broodstock for the program. Be specific (e.g., natural 

spawners from location X; commercial broodstock from Corporation Y).

4.2. Supporting information.

4.2.1. History.

Provide a brief narrative history of the broodstock sources. For natural populations, 

specify their status relative to critical and viable population thresholds. For existing aquaculture 

stocks, include information on how and when they were founded, sources of broodstock since 

founding, and any purposeful or inadvertent selection applied that changed characteristics of the 

founding broodstock.

4.2.2. Program size.

Specify number of breeders of each sex to be used each year or the total number and sex 

ratio. Specify plans for rotating or replacing broodstock and how long (number of years) 

individual breeders will be used. For broodstocks originating from natural populations, provide 

estimates of the proportion of the natural population that will be collected for broodstock and 

explain how broodstock collection will affect the natural population status relative to critical and 

viable thresholds.

4.2.3. Past and proposed level of natural fish in broodstock.

If using an existing broodstock, include information on how many natural fish were 

incorporated annually into the broodstock.

4.2.4. Genetic or ecological differences.

Describe any known genotypic, phenotypic, or behavioral differences between current or 

proposed aquaculture stocks and natural stocks in the target area. What is the source of this 

information?

4.2.5. Reasons for choosing.

Describe any special traits or characteristics for which broodstock was selected.

4.3. Indicate risk aversion measures that will be applied to minimize the likelihood for 

adverse genetic or ecological effects to listed natural fish.

5. Broodstock Collection

Include information on the location, time, and method of capture (e.g., net, trap, beach 

seine, etc.) Describe capture efficiency and measures to reduce sources of bias that could lead to 

a nonrepresentative sample of the desired broodstock source.
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5.1. Source.

Indicate whether commercial broodstock will be used or wild fish will be collected. If 

the latter, describe the method for a) identifying the target population, if more than one 

population might be present, and b) distinguishing aquaculture-origin fish from natural fish.

5.2. Sampling design.

Identify the target number and life stage to be collected. Provide data for previous years 

if applicable.

5.3. Disposition of aquaculture-origin fish collected in surplus of broodstock needs.

Describe procedures for remaining within programmed broodstock collection or 

allowable cultured fish levels, including culling.

5.4. Fish transportation and holding methods.

Describe procedures for the transportation (if necessary) and holding of fish, especially if 

captured unripe or as juveniles. Include length of time in transit and care before and during 

transit and holding, including application of anesthetics, salves, and antibiotics.

5.5. Describe fish health maintenance and sanitation procedures applied.

5.6. Disposition of carcasses.

Include information for spawned and unspawned carcasses, sale or other disposal 

methods, and use.

5.7. Indicate risk aversion measures that will be applied to minimize the likelihood for 

adverse genetic or ecological effects to listed natural fish resulting from the broodstock 

collection program.

Example: “This program will use commercial broodstock and will not involve direct take 

of wild fish” or “The risk of fish disease amplification will be minimized by following Fish 

Health Policy sanitation and fish health maintenance and monitoring guidelines.”

6. Mating

Describe fish mating procedures that will be used, including those applied to meet 

performance indicators identified previously.

6.1. Selection method.

Specify how spawners are chosen (e.g., randomly over natural breeding season, randomly 

from mature fish on a certain day, selectively chosen, or prioritized based on aquaculture or 

natural origin).
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6.2. Males.

Specify expected use of backup males, and repeat spawners.

6.3. Fertilization.

Describe spawning protocols applied, including the fertilization scheme used (such as 

equal sex ratios and 1:1 individual matings, equal sex ratios and pooled gametes, or factorial 

matings). Explain any fish health and sanitation procedures used for disease prevention.

6.4. Cryopreserved gametes.

If used, describe number of donors, year of collection, number of times donors were used 

in the past, and expected and observed viability.

6.5. Indicate risk aversion measures that will be applied to minimize the likelihood for 

adverse genetic or ecological effects to listed natural fish resulting from the mating scheme.

7. Incubation and Rearing

Specify any management goals (e.g., increase juvenile survival) under which the 

aquaculture program is currently operating for the stock in the appropriate sections below. 

Provide data on the success of meeting the desired hatchery goals. 

7.1. Incubation.

7.1.1. Number of eggs taken and survival rates to hatching.

Provide data for the most recent 12 years (1998–2009) or for years dependable data are 

available.

7.1.2. Cause for, and disposition of, surplus egg takes.

Describe circumstances where extra eggs can be taken (e.g., as a safeguard against 

potential incubation losses), and the disposition of surplus fish safely carried through to the egg 

or larval stage to prevent exceeding programmed levels.

7.1.3. Loading densities applied during incubation.

Provide egg size data, standard incubator flows, standard loading, and other physical 

conditions (or other incubation density parameters).

7.1.4. Incubation conditions.

Describe monitoring methods, temperature regimes, minimum dissolved oxygen criteria 

(influent/effluent), silt management procedures (if applicable), and any other parameters 

monitored.
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7.1.5. Fish health maintenance and monitoring.

Describe fungus control methods, disease monitoring and treatment procedures, 

incidence of yolk-sac malformation, and egg mortality removal methods.

7.1.6. Indicate risk aversion measures that will be applied to minimize the likelihood for 

adverse genetic and ecological effects to fish during incubation.

Example: “Eggs will be incubated using __________ to minimize risk of catastrophic 

loss due to __________.”

7.2. Rearing.

7.2.1. Provide survival rate data (average program performance) by life stage for the most 

recent 12 years (1998–2009) or for years dependable data are available.

7.2.2. Density and loading criteria (goals and actual levels).

Include density targets (lbs fish/gpm flow, lbs fish/ft3 rearing volume, etc.).

7.2.3. Fish rearing conditions.

Describe monitoring methods, temperature regimes, minimum dissolved oxygen, CO2, 

total gas pressure criteria (influent/effluent if available), and standard management procedures 

applied to rear fish.

7.2.4. Indicate biweekly or monthly fish growth information (average program 

performance), including length, weight, and condition factor data collected during rearing, 

if available.

7.2.5. Indicate monthly fish growth rate and energy reserve data (average program 

performance), if available.

7.2.6. Indicate food type used, daily application schedule, feeding rate range (e.g., % body 

weight/day and lb/gpm inflow).

7.2.7. Fish health monitoring, disease treatment, and sanitation procedures.

7.2.8. Indicate the use of “natural” rearing methods as applied in the program.

7.2.9. Indicate risk aversion measures that will be applied to minimize the likelihood for

adverse genetic and ecological effects to fish under propagation.

8. Program Effects on Natural Populations

8.1. List all permits or authorizations in hand for the aquaculture operation or program.
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8.2. Provide descriptions, status, and projected actions that could affect natural 

populations in the target area.

Note: This is a feature of the Hatchery Genetics Management Plan process for salmon in 

the Pacific Northwest. In other applications, it will be important to determine whether it is more 

appropriate for this section to be completed by the applicant or the regulatory agency.

8.2.1. Description of natural population(s) potentially affected by the program.

Include information describing: adult age class structure, sex ratio, size range, migration 

timing, spawning range, spawn timing, and juvenile life history. Emphasize spatial and temporal 

distribution relative to cultured fish release locations.

8.2.2. Status of natural population(s) potentially affected by the program.

Describe the status of the natural population(s) relative to “critical” and “viable” 

population thresholds (see definitions in Attachment 1).

Provide the most recent 12-year (e.g., 2000-present) abundance data, survival data by 

life-stage, or other measures of productivity for the natural population, if available. Indicate the 

source of these data.

8.2.3. Describe aquaculture activities, including associated monitoring and evaluation and 

research programs that can lead to genetic effects on natural fish in the target area, and 

provide estimated annual levels of take (see Attachment 1 for definition of take).

Describe aquaculture activities that can lead to the take of natural populations in the 

target area, including how, where, and when the takes might occur; the risk potential for their 

occurrence; and the likely effects of the take. Example: “Broodstock collection directed at red 

drum has a “high” potential to take natural red drum adults, through capture, and handling at 

_______ between _______ (date) and _______ (date). Trapping and handling devices and 

methods can lead to injury to natural fish through descaling, delayed migration and spawning, or 

delayed mortality as a result of injury or increased susceptibility to predation.”

Provide information regarding past takes associated with the program (if known),

including numbers taken and observed injury or mortality levels for natural fish.

Provide projected annual take levels for natural fish by life stage (juvenile and adult) 

quantified (to the extent feasible) by the type of take resulting from the aquaculture program 

(e.g., capture, handling, tagging, injury, or lethal take). Provide projected annual take levels for 

natural fish.

Indicate contingency plans for addressing situations where take levels within a given year 

have exceeded, or are projected to exceed, take levels described in this plan for the program. 

Example: “The number of days that red drum are collected at _______ will be reduced if the 

total mortality of handled fish is projected in-season to exceed the 1998–2009 maximum 

observed level of _______ fish.”
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8.2.4. Ecological interactions.

Describe fishes or other species that could 1) be negatively impacted by the program, 2) 

be positively impacted by program. Give most attention to interactions between natural and 

program fish.

9. Monitoring and Evaluation of Performance Indicators

This section describes how performance indicators listed in Section 1.10 will be 

monitored. Results of performance indicator monitoring will be evaluated annually and used to 

adaptively manage the aquaculture program, as needed, to meet performance standards.

9.1. Monitoring and evaluation of performance indicators presented in Section 1.10.

9.1.1. Describe plans and methods proposed to collect data necessary to respond to each 

performance indicator identified for the program.

9.1.2. Indicate whether funding, staffing, and other support logistics are available or 

committed to allow implementation of the monitoring and evaluation program.

9.2. Indicate risk aversion measures that will be applied to minimize the likelihood for 

adverse genetic and ecological effects to natural fish resulting from monitoring and 

evaluation activities.

10. Research

Provide the following information for any research programs conducted in direct 

association with the aquaculture operation or program described in this AGMP. Provide 

sufficient detail to allow for the independent assessment of the effects of the research program on 

natural fish. If applicable, correlate with research indicated as needed in any propagation plan 

approved by NOAA. Attach a copy of any formal research proposal addressing activities 

covered in this section. Include estimated take levels for the research program with take levels 

provided for the associated aquaculture program in Table B-2.

10.1. Objective or purpose.

Indicate why the research is needed, its benefit or effect on natural fish populations, and 

broad significance of the proposed project.

10.2. Cooperating and funding agencies.

10.3. Principal investigator or project supervisor and staff.

10.4. Status of stock, particularly the group affected by project, if different than the 

stock(s) described in Section 2.

10.5. Techniques: include capture methods, drugs, samples collected, tags applied.
147

Table B-2. Estimated natural fish take levels by aquaculture activity. Instructions: 1) an entry for a fish 

to be taken should be in the take category that describes the greatest impact; 2) each take entered 

in the table should be in one take category only (there should not be more than one entry for the 

same sampling event); and 3) if an individual fish is taken more than once on separate occasions, 

each take must be entered in this take table.

Species affected:___________________ Population:_________________ Activity:________________

Location:___________________ Dates:_________________ Program operator:__________________

Type of take

Annual take of natural fish by life stage 

(number of fish)

Eggs Larvae Juveniles Adults

Observe or harassa

Collect for transportb

Capture, handle, and releasec

Capture, handle, tag/mark/tissue sample, released

Removal (e.g., broodstock)e

Intentional lethal takef

Unintentional lethal takeg

Other take (specify)h

a

Contact with natural fish through surveys, collection, or other effects.

b

Take associated with fishing or trapping operations where natural fish are captured and transported. c

Take associated with fishing or trapping operations where natural fish are captured or handled.

d

Take occurring due to tagging or biosampling of fish collected through fishing or trapping operations. e

Natural fish removed from the wild and collected for use as broodstock.

f

Intentional mortality of natural fish, usually as a result of spawning as broodstock.

g

Unintentional mortality of natural fish, including loss of fish during transport or holding prior to spawning or prior 

to transfer.

h

Other takes not identified above as a category.

10.6. Dates or time period in which research activity occurs.

10.7. Care and maintenance of live fish or eggs, holding duration, transport methods.

10.8. Expected type and effects of take and potential for injury or mortality.

10.9. Level of take of natural fish: number or range of fish handled, injured, or killed by 

sex, age, or size, if not already indicated in Section 2 and the attached “take table” (Table 

B-2).

10.10. Alternative methods to achieve project objectives.

10.11. List species similar or related to the cultured species; provide number and causes of 

mortality related to this research project.
148

10.12. Indicate risk aversion measures that will be applied to minimize the likelihood for 

adverse ecological effects, injury, or mortality to natural fish as a result of the proposed 

research activities.

11. Attachments and Citations

Include all references cited in the AGMP. In particular, indicate databases used to 

provide data for each section. Include electronic links to the databases used (if feasible) or to the 

staff person responsible for maintaining the database referenced (indicate e-mail address). 

Attach or cite (where commonly available) relevant reports that describe the facility operation 

and impacts on natural species or their critical habitat. Include any Environmental Impact 

Statements, Environmental Assessments, Biological Assessments, benefit/risk assessments, or 

other analysis or plans that provide pertinent background information to facilitate evaluation of 

the AGMP.

12. Certification Language and Signature of Responsible Party

“I hereby certify that the information provided is complete, true, and correct to the best of my 

knowledge and belief. I understand that the information provided in this AGMP is submitted for 

the purpose of _________________________, and that any false statement may subject me to 

the criminal penalties of _________________________.

Name, title, and signature of applicant:

Certified by _____________________________ Date: _____________
149

Attachment 1: Definition of Terms Referenced in the

AGMP Template

Cultured fish: A fish that has spent some part of its life cycle in an artificial environment and 

whose parents were spawned in an artificial environment.

Cultured population: A population that depends on spawning, incubation, hatching, or rearing 

in a hatchery or other artificial propagation facility.

Hazard: Undesirable events that an aquaculture program is attempting to avoid.

Natural fish: A fish that has spent essentially all of its life cycle in the wild and whose parents 

spawned in the wild. Synonymous with natural origin recruit (NOR).

Natural origin recruit (NOR): See natural fish.

Natural population: A population that is sustained by natural spawning and rearing in the 

natural habitat.

Population: A group of historically interbreeding fish of the same species of hatchery, natural, 

or unknown parentage that have developed a unique gene pool, that breed in approximately the 

same place and time, and whose progeny tend to return and breed in approximately the same 

place and time. They often, but not always, can be separated from another population by 

genotypic or demographic characteristics. This term is synonymous with stock.

Preservation (conservation): The use of artificial propagation to conserve genetic resources of 

a fish population at extremely low population abundance and high potential for extinction, using 

methods such as captive propagation and cryopreservation.

Research: The study of critical uncertainties regarding the application and effectiveness of 

artificial propagation for augmentation, mitigation, conservation, and restoration purposes, and 

identification of how to effectively use artificial propagation to address those purposes.

Stock: See population.

Take: As defined under the U.S. Endangered Species Act, Section 3(19), to take is to “harass, 

harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any 

such conduct.”

Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center

NOAA Technical Memorandum NMFS-NWFSC118 Stout, H.A., P.W. Lawson, D.L. Bottom, T.D. Cooney, M.J. Ford, C.E. Jordan, R.G. Kope, 

L.M. Kruzic, G.R. Pess, G.H. Reeves, M.D. Scheuerell, T.C. Wainwright, R.S. Waples, E. Ward, 

L.A. Weitkamp, J.G. Williams, and T.H. Williams. 2012. Scientific conclusions of the status review 

for Oregon coast coho salmon (Oncorhynchus kisutch). U.S. Dept. Commer., NOAA Tech. Memo. 

NMFS-NWFSC-118, 242 p. NTIS number PB2012-113458.

117 Maynard, D.J., T.A. Flagg, W.C. McAuley, D.A. Frost, B. Kluver, M.R. Wastel, J.E. Colt, and 

W.W. Dickhoff. 2012. Fish culture technology and practices for captive broodstock rearing of ESAlisted salmon stocks. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-117, 65 p. NTIS 

number PB2012-110667.

116 Lian, C.E. 2012. West Coast open access groundfish and salmon troller survey: Protocol and results 

for 2005 and 2006. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-116, 52 p. NTIS 

number PB2012-107486.

115 Plummer, M.L., W. Morrison, and E. Steiner. 2012. Allocation of fishery harvests under the 

Magnuson-Stevens Fishery Conservation and Management Act: Principles and practice. U.S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-115, 84 p. NTIS number PB2012-107485.

114 Bradburn, M.J., A.A. Keller, and B.H. Horness. 2011. The 2003 to 2008 U.S. West Coast bottom 

trawl surveys of groundfish resources off Washington, Oregon, and California: Estimates of distribution, 

abundance, length, and age composition. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC114, 323 p. NTIS number PB2012-105507.

113 Ford, M.J. (ed.). 2011. Status review update for Pacific salmon and steelhead listed under the 

Endangered Species Act: Pacific Northwest. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC113, 281 p. NTIS number PB2012-104687.

112 Skidmore, P.B., C.R. Thorne, B.L. Cluer, G.R. Pess, J.M. Castro, T.J. Beechie, and C.C. Shea. 

2011. Science base and tools for evaluating stream engineering, management, and restoration proposals. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-112, 255 p. NTIS number PB2012-104660.

111 Leonard, J., and P. Watson. 2011. Description of the input-output model for Pacific Coast fisheries. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-111, 64 p. NTIS number PB2011-113405.

Most NOAA Technical Memorandums NMFS-NWFSC are available at the

Northwest Fisheries Science Center Web site, http://www.nwfsc.noaa.gov