Genetic Risks Associated with Marine Aquaculture - NOAA Fisheries

171 Pages·2012·1.22 MB·English

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 NMFS-
F/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: [email protected]
ii
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
iii
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

iv
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 N
e
are eliminated .............................................................................................................................................. 27
Figure 5. Estimated time to reach 50% of the equilibrium F value, assuming that anthropogenic
ST
activities have completely eliminated population structure and that, at time 0, levels of migration
are restored that will eventually produce the equilibrium F ..................................................................... 31
ST
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
v
vi
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 N T compared to what it would have been without a captive program, provided the N / N ratio is
e e
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

vii
viii