R0303 final report v3 - North Pacific Research Board

advertisement
NORTH PACIFIC RESEARCH BOARD PROJECT FINAL REPORT
NPAFC Cooperative Research: The Use of Genetic Stock Identification to Determine the
Distribution, Migration, Early Marine Survival, and Relative Stock Abundance of Sockeye and
Chum Salmon in the Bering Sea
NPRB Project 303 Final Report
J. E. Seeb1, 5, C. Habicht1, R. Wilmot2, C. Guthrie2, S. Urawa3, 6, S. Abe4
1
Alaska Department of Fish & Game
333 Raspberry Road, Anchorage, Alaska 99518
[email protected]
2
National Oceanic & Atmospheric Administration, National Marine Fisheries
Service, Auke Bay Laboratories,
[email protected]
3
National Salmon Resources Center, Fisheries Research Agency
2-2 Nakanoshima, Toyohira-ku, Sapporo 062-0922, Japan
4
Laboratory of Breeding Science, Graduate School of Fisheries Science
3-1-1 Minato, Hakodate 941-8611, Japan
[email protected]
Current Addresses:
5
University of Washington, School of Fisheries and Aquatic Sciences, Box 355020, 1122 NE Boat
Street, Seattle, Washington 98195
[email protected] Phone 206-685-2097
6
North Pacific Anadromous Fish Commission, Suite 502, 889 W. Pender Street, Vancouver, BC,
Canada, V6C 3B2
[email protected]
December, 2007
Abstract
We investigate the stock composition and seasonal distribution Asian and North American sockeye and
chum salmon collected in the Bering Sea during 2002-2004 using genetic markers.
For chum salmon, using allozymes and mtDNA, Japanese investigators identified that Asian and North
American stocks were not randomly distributed. Japanese stocks were distributed in the central Bering
Sea, the distribution of Russian stocks was similar but also spread into the North Pacific Ocean, and
northwestern Alaska stocks including fall chum salmon from the Yukon River were distributed mainly in
eastern North Pacific Ocean. Using supplemental information, Japanese investigators hypothesize a
complete migration model for their hatchery stocks, through the Sea of Okhotsk, seasonally through the
Bering Sea and northwestern Gulf of Alaska, back to Japan.
For sockeye salmon, using single nucleotide polymorphisms, US investigators identified a broader
distribution of North American stocks than suggested by historical tagging studies. Bristol Bay stocks
were the most widely-distributed, accounting for more than half the mixtures in all areas except the
southwestern Bering Sea. Russian stocks were primarily detected in the western Bering Sea, and
differences were detected in the distributions between the eastern- and the western-Kamchatka Peninsula
populations. Stocks from the Gulf of Alaska were also widely distributed throughout much of the Bering
Sea, although at low proportions relative to the Pacific Ocean-wide production estimates.
Data from this project provide the foundation for continuing studies by NPAFC scientists, Pacific Salmon
Commission studies by NOAA and ADFG, and are being used by ADFG to improve harvest management
in Southeast Alaska, Cook Inlet, and Bristol Bay.
Key Words
chum salmon, sockeye salmon, single nucleotide polymorphism (SNP), mitochondrial DNA (mtDNA),
microarray, high seas migration
2
Citation
Seeb, J.E., C. Habicht, R. Wilmot, C. Guthrie, S. Urawa, S. Abe. 2007. NPAFC Cooperative Research:
The Use of Genetic Stock Identification to Determine the Distribution, Migration, Early Marine
Survival, and Relative Stock Abundance of Sockeye and Chum Salmon in the Bering Sea. NPRB
Project 0303 Final Report.
Table of Contents
Chapter
Page
1. Stock-Specific Ocean Distribution of Chum Salmon in the Bering Sea and Its Adjacent Waters
6
2. Genetic Population Structure OF Chum Salmon in the Pacific Rim Inferred from the
Mitochondrial DNA Sequence Analysis
7
3. DNA Microarray for Rapid Detection of Mitochondrial DNA Haplotypes of Chum Salmon
8
4. Genetic Stock Identification of Chum Salmon in the Bering Sea and North Pacific Ocean Using
Mitochondrial DNA Microarray
9
5. Genetic Variation Among Pacific Rim Chum Salmon Populations Inferred from the
Microsatellite DNA Analysis
10
6. Characterization of 13 single nucleotide polymorphism markers for chum salmon
11
7. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific
salmon
12
8. Use of the 5’nuclease reaction for single nucleotide polymorphism genotyping in Chinook
salmon
13
9. Thirty-two single nucleotide polymorphism markers for high-throughput genotyping of sockeye
salmon
14
10. Genetic and Ecological Divergence Defines Population Structure of Sockeye Salmon
Populations Returning to Bristol Bay, Alaska, and Provides a Tool for Admixture Analysis
15
11. Number of alleles as a predictor of the relative assignment accuracy of STR and SNP baselines
for chum salmon
16
12. Single Nucleotide Polymorphism (SNP) Analysis of Southeast Alaska Sockeye Salmon and
Description of BASIS Bering Sea Sampling Cruise Tracks.
17
13. Distribution of stocks of sockeye salmon in the Bering Sea
18
3
Study Chronology
This project is an outgrowth of NPRB Project 0205 Genetic stock identification of Western Alaska
sockeye salmon (http://doc.nprb.org/web/02_prjs/r0205_final.pdf) that was conducted by ADFG and
NOAA Fisheries. In that project ADFG initiated and applied a baseline data set of microsatellite markers,
and NOAA initiated and applied a set of allozyme markers to begin identifying the stock composition of
juvenile sockeye salmon caught in the NOAA research cruises conducted in the Eastern Bering Sea.
Towards the end of that project ADFG research identified a new class of DNA markers, single nucleotide
polymorphisms (SNPs), which enhanced resolving power and streamlined lab analyses. Some draft work
products from Project 0205 led to publications from Project 0303 (see Smith et al. 2005 a, b).
The objectives of Project 0303 were an expansion of Project 0205 that incorporated NPAFC goals of
Bering/Aleutian Salmon International Survey (BASIS) research (see below). ADFG and NOAA
continued with the microsatellite and allozyme analysis, extending the baselines and including analysis of
samples from BASIS research cruises from the central and western Bering Sea. Chum salmon were
added with the allozyme and microarray research of the Japanese laboratories in Sapporo and Hakodate.
The Japanese laboratories started with a complete allozyme baseline for chum salmon from the Pacific
Rim (Kondzela et al. 2002). They used these markers, along with CPUE data, to map the distribution of
chum salmon stocks throughout the Bering Sea. They conducted additional research to improve
resolution using mtDNA sequence data, microarray analyses of the mtDNA SNPs, and microsatellite
analyses.
ADFG continued the SNP development research; after year one of this project it became clear that the
accuracy available from SNP data obsoleted the value of both the allozyme and microsatellite data for
sockeye salmon. NOAA switched to work on SNP analyses for baseline from Southeast Alaska. ADFG,
with the help of supplemental funds from State of Alaska and Pacific Salmon Commission, reanalyzed all
of the sockeye salmon samples from the Pacific Rim baseline for SNPs and then reanalyzed all of the high
seas samples from BASIS cruises for SNPs.
Introduction
The numbers and biomass of adult salmon returns to many Asian and North American rivers changed
drastically during the 1990s, and there were extreme fluctuations in the abundance and growth of some
stocks (e.g., Beamish et al. 1999, Myers et al. 2007). These dramatic fluctuations in the ocean growth and
4
survival have been attributed to climactic changes impacting the Bering Sea and other marine ecosystems
(Beamish et al. 1999, 2004). The paucity of scientific observations for salmon, ecologically related
species, and environmental conditions in the North Pacific Ocean created a new sense of urgency for
more at-sea research on the biotic effects of anomalous ocean conditions (e.g., Kruse 1998).
The North Pacific Anadromous Fish Commission, a five nation organization established to promote
conservation of Pacific salmon in the North Pacific Ocean and Bering Sea, responded by developing the
Bering-Aleutian Salmon International Survey to address these issues
(http://www.npafc.org/new/science_basis.html). These international research efforts started in 2002 as a
coordinated program of cooperative research to examine the distribution and migration of stocks of
salmon in order to better understand impacts of the variable ocean ecosystem. One important component
of BASIS has been to establish genetic data bases to enable the study of salmon distribution on a truly
stock-specific rather than just a species-specific basis. In this report of BASIS research we use genetic
data to describe the migration and the distribution of both Asian and North American stocks of sockeye
and chum salmon in the Bering Sea.
Genetic markers have proven to be effective tools for many studies of ecology and management of
salmon (e.g., Wood et al. 1989, Habicht et al. 2004, 2007, Beacham et al. 2005). These markers can be
used to discriminate populations in mixed aggregations, and a considerable statistical framework (mixedstock analysis, or MSA) has been developed to estimate composition of mixtures (Debevec et al. 2000,
Pella and Masuda 2001). MSA using gene markers has been especially successful with salmon because
of the discrete populations that result from accurate homing of adults to natal spawning areas (see for
example Wood et al. 1989, Beacham and Wood 1999, Habicht et al. 2007).
Substantial effort in this project focused upon marker development to generate Pacific Rim data bases.
Here we report the results from marker discovery and the three year investigation into the distribution and
migration of chum and sockeye salmon in the Bering Sea.
Overall Objectives
The proposed research was originally designed to investigate:
1) the stock composition and abundance of Asian and North American sockeye and chum salmon in
the Bering Sea,
2) their seasonal migration routes and timing, and
3) factors affecting the oceanic distribution and abundance of each regional stock.
5
For objectives 1 and 2, samples collected by research vessels in the Bering Sea and adjacent Pacific
waters in 2002-2004 were to be examined by using allozyme, microsatellite DNA, single nucleotide
polymorphism (SNP) DNA, or rapid DNA sequencing (microarray) techniques depending upon baselines
and techniques supported by the host laboratories. However, substantial breakthroughs in DNA
chemistry and instrumentation occurred during implementation of the project. Population data for
sockeye salmon using newly developed SNPs obsoleted the other approaches; therefore, all of the
samples for sockeye salmon were reanalyzed for SNPs.
A major accomplishment of this project was to be the international exchange of genetics samples and
ecological data from nationally-funded cruises. Often in the past these have been considered by
governments to be proprietary information. NPAFC nations working in the Bering Sea (USA, Japan, and
Russia) agreed to share access to a common, comprehensive database on salmon distribution and
environmental conditions in the Bering Sea and participate in cooperative analyses of these data.
Substantial work went into staging and completing objectives 1 and 2 above. However, because of the
huge number of collaborators from three different nations, the coordination and exchange of ecological
data proceeded slowly. Although substantial progress is being made, this project proceeded without the
ability to address objective 3.
Manuscripts (.pdf files; please double click on the first page to open)
6
Chapter 1. Stock-Specific Ocean Distribution of Chum Salmon in the Bering Sea
7
Chapter 2. Genetic Population Structure of Chum Salmon in the Pacific Rim Inferred from the
Mitochondrial DNA Sequence Analysis.
8
Chapter 3. DNA Microarray for Rapid Detection of Mitochondrial DNA Haplotypes of Chum Salmon.
9
Chapter 4. Genetic Stock Identification of Chum Salmon in the Bering Sea and North Pacific Ocean
Using Mitochondrial DNA Microarray.
10
Chapter 5. Genetic Variation Among Pacific Rim Chum Salmon Populations Inferred from the
Microsatellite DNA Analysis.
11
Chapter 6. Characterization of 13 single nucleotide polymorphism markers for chum salmon.
12
Chapter 7. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific
salmon.
13
Chapter 8. Use of the 5’nuclease reaction for single nucleotide polymorphism genotyping in Chinook
salmon.
14
Chapter 9. Thirty-two single nucleotide polymorphism markers for high-throughput genotyping of
sockeye salmon.
15
Chapter 10. Genetic and Ecological Divergence Defines Population Structure of Sockeye Salmon
Populations Returning to Bristol Bay, Alaska, and Provides a Tool for Admixture Analysis.
16
Chapter 11. Number of alleles as a predictor of the relative assignment accuracy of STR and SNP
baselines for chum salmon (revisions accepted and in press Trans Am. Fish Soc.).
17
Chapter 12. Single Nucleotide Polymorphism (SNP) Analysis of Southeast Alaska Sockeye Salmon and
Description of BASIS Bering Sea Sampling Cruise Tracks.
18
Chapter 13. Distribution of sockeye salmon in the Bering Sea based upon SNP analyses.
19
Conclusions
There are several very constructive outcomes from this project.
First, at the start of this project, coastwide and shared data bases for allozymes were the primary source
for stock identification studies by many US agency and NPAFC scientists (see Habicht et al. 2001 for
sockeye salmon and Kondzela et al. 2002 for chum salmon). Scientists also were applying new DNA
markers, in these species primarily microsatellites and mtDNA haplotypes, and finding increased
resolution of stock differences. However no shared coastwide data bases were available. This project
enabled NPAFC scientists to test and validate new markers for the shared data bases. Additionally, a new
class of markers emerged in Project R0205, SNPs, and substantial additional effort went into SNP
discovery and data base development in this project (Chapters 6-9, 11).
SNP discovery primarily targeted sockeye salmon but was also done on Chinook and chum salmon. The
original project concept submitted to NPRB included similar objectives for Chinook salmon; however,
those components were not funded. It turned out that SNP discovery, with leverage monies from ADFG,
could be done on all three species with some extra coordination.
During year two of this project it became clear that shared microsatellite data bases were going to be
extremely difficult to implement (see review of Pacific Salmon Commission efforts in Seeb et al. 2007).
The chum salmon portion of this project was successfully completed by Japanese laboratories with the
use of allozymes and mtDNA haplotypes (Chapters 1-4). However, the US laboratories retooled with the
help of Pacific Salmon Commission infrastructure grants, and they reanalyzed the samples from the entire
Pacific Rim using the 45 newly developed SNP markers (Chapter 12-13). In addition to Project 0303
funding, substantial support for this reanalysis came from State of Alaska general funds and the Pacific
Salmon Commission Northern Fund. Finally, NPAFC funded labs from Russia and Korea to participate
in SNP training for future collaborations at the US laboratories.
Results from Project 0303 led to many continuation projects. For chum salmon, Japan is continuing its
research on the migration patterns using the mtDNA baselines developed in this project. Additionally,
NPAFC requested that the NPRB principal investigators draft an NPAFC paper that builds upon the SNP
20
baseline started for chum salmon in this project to encourage the use of this baseline by labs in member
nations. This paper will be presented at the NPAFC annual meeting in 2008. ADFG has continued to
develop new SNPs to enhance the baseline to resolve stakeholder conflicts in the very contentious near
shore fisheries in the eastern Bering Sea and North Gulf of Alaska that either target chum salmon or take
chum salmon as bycatch.
For sockeye salmon, both ADFG and NOAA are using the SNP baseline developed in Project 0303 for
stock identification projects funded by the Pacific Salmon Commission. ADFG is also using the baseline
to resolve stock mixtures in fisheries in Southeast Alaska and Cook Inlet. The most high visibility use of
these data might be the in-season analyses that report the relative strength of stocks in the Port Moller test
fishery, giving ADFG advance knowledge of relative abundance to help plan the district openings in
Bristol Bay (e.g., see Chapter 10). ADFG made numerous reports to the Alaska Board of Fisheries based
upon these NPRB results.
For Chinook salmon, the SNPs developed in this project led to a funded AYKSSI project to complete a
baseline and identify the components of the BSAI bycatch in 2005-2006.
Finally, because of the outreach in this project (see below), the Gordon and Betty Moore Foundation has
partnered with the University of Washington to build the infrastructure to continue cooperative SNP
research to study the migration and distribution of Pacific salmon started in Project 0303. The new
University of Washington laboratory will discover more high resolution SNPs; train graduate students and
post docs from US, Japan, and Russia; conduct BASIS research as well as study the stock composition of
BSAI bycatch of Chinook salmon; and provide open access SNP data bases for other researchers.
Publications
Refereed publications
Elfstrom, C.M., C.T. Smith, and J. E. Seeb. 2006. Thirty-two single nucleotide polymorphism markers for
high-throughput genotyping of sockeye salmon. Molecular Ecology Notes 6:1255–1259.
Habicht, C., L.W. Seeb, and J.E. Seeb. 2007. Genetic and Ecological Divergence Defines Population
Structure of Sockeye Salmon Populations Returning to Bristol Bay, Alaska, and Provides a Tool
for Admixture Analysis. Transactions of the American Fisheries Society 136:82–94.
Moriya, S., S. Sato, S. Urawa, A. Urano, and S. Abe. 2004. Development of DNA microarray for rapid
identification of mitochondrial DNA haplotypes in chum salmon. Fish Genetics and Breeding
Science, 33: 115-121. (In Japanese with English summary.)
21
Moriya, S., S. Urawa, O. Suzuki, A. Urano, and S. Abe. 2005. DNA microarray for rapid detection of
mitochondrial DNA haplotypes of chum salmon. Marine Biotechnology 6: 430-434.
Myers, K.W., N.V. Klovach, O.F. Gritsenko, S. Urawa, and T.C. Royer. 2007. Stock-specific
distributions of Asian and North American salmon in the open ocean, interannual changes, and
oceanographic conditions. North Pacific Anadromous Fish Commission Bulletin 4:159–177.
Sato, S., H. Kojima, J. Ando, H. Ando, R. L. Wilmot, L. W. Seeb, V. Efremov, L. LeClair, W. Buchholz,
D.-H. Jin, S. Urawa, M. Kaeriyama, A. Urano, and S. Abe. 2004. Genetic population structure of
chum salmon in the Pacific Rim inferred from mitochondrial DNA sequence variation.
Environmental Biology of Fishes 69: 37-50.
Smith, C.T., J. Baker, L. Park, L.W. Seeb, C. Elfstrom, S. Abe, J.E. Seeb. 2005. Characterization of 13
single nucleotide polymorphism markers for chum salmon. Molecular Ecology Notes 5:259-262.
Smith, C.T., C.M. Elfstrom, L.W. Seeb, and J.E. Seeb. 2005. Use of sequence data from rainbow trout
and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology 205(14):41934203.
Smith, C.T, J.E. Seeb, P. Schwenke, and L.W. Seeb. 2005. Use of the 5’nuclease reaction for single
nucleotide polymorphism genotyping in Chinook salmon. Transactions of the American Fisheries
Society 134:207-217.
Smith, C.T. and L.W. Seeb. 2007. Number of alleles as a predictor of the relative assignment accuracy
of STR and SNP baselines for chum salmon. Transactions of the American Fisheries Society
(revision accepted and in press).
Urawa, S., J. Seki, M. Kawana, T. Saito, P. A. Crane, L. W. Seeb, M. Fukuwaka, and E. Akinicheva.
2006. Origins of juvenile chum salmon caught in the southwestern Okhotsk Sea during the fall of
2000. Bull. National Salmon Resources Center, 8: 9-16.
North Pacific Anadromous Fish Commission papers
Abe, S., S. Sato, R. R. Edparina, H. Ando, M. Kaeriyama, S. Urawa, and A. Urano. 2004. Stock
identification of chum salmon by mitochondrial DNA sequence analysis. NPAFC Tech. Rep. 5:
82-83.
Habicht, C., N. V. Varnavskaya, T. Azumaya, S. Urawa, R. L. Wilmot, C. M. Guthrie III, and J. E. Seeb.
2005. Migration patterns of sockeye salmon in the Bering Sea discerned from stock composition
estimates of fish captured during BASIS studies. NPAFC Tech. Rep. 6: 41-43.
Moriya, S., A. Urano, S. Urawa, O. Suzuki, and S. Abe. 2004. Development of DNA microarray for rapid
detection of mitochondrial DNA haplotypes of chum salmon. NPAFC Tech. Rep. 5: 28-30.
Sato, S., M. Yoon, S. Abe, and S. Urawa. 2007. Update of mitochondrial DNA baseline for stock
identification of chum salmon. (NPAFC Doc. 1019) 26 p. National Salmon Resources Center,
Fisheries Research Agency, 2-2 Nakanoshima, Toyohira-ku, Sapporo 062-0922, Japan.
22
Sato, S., S. Moriya, T. Azumaya, O. Suzuki, S. Urawa, S. Abe, and A. Urano. 2004. Genetic stock
identification of chum salmon in the central Bering Sea and adjacent North Pacific Ocean by
DNA microarray during the early falls of 2002 and 2003. (NPAFC Doc. 793) 21 p. National
Salmon Resources Center, Toyohira-ku, Sapporo 062-0922, Japan.
Sato, S., S. Takahashi, L.W. Seeb, J.E. Seeb, F. Fukuwaka, and S. Urawa. 2006. Stock identification of
winter chum salmon by mitochondrial DNA and SNP analyses. (NPAFC Doc. 963). 8 p.
National Salmon Resources Center, Fisheries Research Agency, Toyohira-ku, Sapporo 0620922, Japan.
Seeb, L. W., C. T. Smith, W. D. Templin, R. L. Wilmot, and, J. E. Seeb. 2004. Development of a Pacific
Rim baseline for chum salmon based on single nucleotide polymorphism markers (SNPs).
(NPAFC Doc. 824) 10 p. Alaska Department of Fish and Game, 333 Raspberry Road,
Anchorage, AK, USA 99518.
Seeb, L. W, W. D. Templin, C. T. Smith, C. Elfstrom, S. Urawa, R. L. Wilmot, S. Abe, and, J. E. Seeb.
2005. SNPs provide an Easily-Standardized Baseline for NPAFC Studies of Chum Salmon
(NPAFC Doc. 907) 12 p. Alaska Department of Fish and Game, 333 Raspberry Road,
Anchorage, AK, USA 99518.
Templin, W. D., C. T. Smith, J. E. Seeb, and L. W. Seeb. 2005. SNPs provide high throughput resolution
for migratory studies of Chinook salmon. (NPAFC Doc. 908) 10 p. Alaska Department of Fish
and Game, 333 Raspberry Road, Anchorage, AK, USA 99518.
Urawa, S., M. Kawana, T. Azumaya, P. A. Crane, and L. W. Seeb. 2005. Stock-specific ocean
distribution of immature chum salmon in the summer and early fall of 2003: estimates by
allozyme analysis. (NPAFC Doc. 896) 14 p. National Salmon Resources Center, Toyohira-ku,
Sapporo 062-0922, Japan.
Urawa, S., S. Sato, N. Varnavskaya, P. A. Crane, and T. D. Beacham. 2007. Genetic stock identification
of juvenile chum salmon caught in the Okhotsk Sea during the Fall of 2003. NPAFC Tech. Rep.
7: 72-74.
Urawa, S., T. Azumaya, P. A. Crane, and L. W. Seeb. 2005. Origins and distribution of chum salmon in
the central Bering Sea. NPAFC Tech. Rep. 6: 67-70.
Urawa, S., J. Seki, M. Kawana, T. Saito, P. A. Crane, L. Seeb, K. Gorbatenko, and M. Fukuwaka. 2004.
Juvenile chum salmon in the Okhotsk Sea: their origins estimated by genetic and otolith marks.
NPAFC Tech. Rep. 5: 87-88.
Urawa, S., T. Azumaya, P. A. Crane, and L. W. Seeb. 2004. Origin and distribution of chum salmon in
the Bering Sea during the early fall of 2002: estimates by allozyme analysis. (NPAFC Doc. 794)
11 p. National Salmon Resources Center, Toyohira-ku, Sapporo 062-0922, Japan.
Yoon, M., V. Brykov, N. Varnavskaya, L. W. Seeb, S. Urawa, and S. Abe. 2004. Mitochondrial DNA
analysis of genetic variation in the Pacific Rim populations of chum salmon. (NPAFC Doc. 792)
25 p. Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate 0418611, Japan.
23
Yoon, M., S. Sato, J.E. Seeb, R.L. Wilmot, S. Urawa, A. Urano and S. Abe. 2005. Genetic variation
among chum salmon populations in the Pacific Rim inferred from the mitochondrial and
microsatellite DNA analyses. (NPAFC Doc. 898) 20p. Graduate School of Fisheries Sciences,
Hokkaido University, 3-1-1 Minato, Hakodate 041-8611, Japan.
Yoon, M., S. Sato, J.E. Seeb, R.L. Wilmot, S. Urawa, A. Urano, and S. Abe. 2006. Genetic variation
among Pacific Rim chum salmon populations inferred from the microsatellite DNA analysis
(NPAFC Doc. 964). 20p. Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1
Minato, Hakodate 041-8611, Japan.
Zelenina, D., A. Khrustaleva, A. Volkov, C. Habicht, C. Smith, J. Seeb. 2005. A Case Study of Two
Genetic Markers for Inter-Laboratory Collaboration: SNPs Provide Transportability without
Standardization. (NPAFC Doc. 913) 14 p. Russian Federal Research Institute of Fisheries &
Oceanography, Federal Fisheries Agency of Russia, VNIRO, 17 V. Krasnoselskaya, Moscow,
Russia.
Outreach
Oral Presentations
ADFG, oral reports to State of Alaska Board of Fisheries, 2004-2007.
Guthrie, C., R. Wilmot, C. Habicht, and J.E. Seeb. SNP variation in sockeye salmon from Southeast
Alaska and Northern British Columbia, Science Bridging Five Nations: The Bering-Aleutian
Salmon International Survey, American Fisheries Society annual meeting, Anchorage, 2005.
Habicht, C., C. Guthrie, R. Wilmot, and J.E. Seeb. DNA markers identify distribution of stocks of
sockeye salmon in the Bering Sea.
1. BASIS 2004: Salmon and Marine Ecosystems in the Bering Sea and Adjacent Waters,
Sapporo, 2004.
2. Science Bridging Five Nations: The Bering-Aleutian Salmon International Survey, American
Fisheries Society annual meeting, Anchorage, 2005.
Kondzela, C. Origin of immature and juvenile chum salmon collected on U.S. BASIS surveys, Science
Bridging Five Nations: The Bering-Aleutian Salmon International Survey, American Fisheries
Society annual meeting, Anchorage, 2005.
Sato, S., L.W. Seeb, J.E. Seeb, M. Fukuwaka, S. Takahashi, and S. Urawa. Origins of juvenile chum
salmon inhabiting the North Pacific Ocean during the winter: rapid estimates by SNP markers.
1. Second NPAFC International Workshop on Factors Affecting Production of Juvenile Salmon,
Sapporo, 2006.
2. SNP Workshop II, Applications of SNP Genotyping in Fisheries Management. Girdwood,
2006.
Seeb, J. Ecological genetics: recent advances in gene detection provide high-throughput analyses. North
Pacific Anadromous Fish Commission/Pukyong National University, Pusan, Korea, 2004.
24
Seeb, J. Innovative markers provide high-throughput, high-resolution DNA data for resolving chum and
Chinook salmon bycatch in the Bering Sea pollock fishery.
1. Annual meeting of American Fisheries Society, Anchorage, Alaska, 2005.
2. University of Washington School of Aquatic and Fisheries Science, Seattle, 2005.
3. Fourth Annual Center of Excellence Symposium, Sapporo, Japan, 2005.
4. North Pacific Fishery Management Council workshop, Anchorage, Alaska, 2006.
Seeb, J. Importance of genetic stock identification to BASIS research, Special Symposium Science
Bridging Five Nations: The Bering-Aleutian Salmon International Survey, American Fisheries
Society annual meeting, Anchorage, 2005.
Seeb, L. SNP and microsatellite DNA describe chum and Chinook salmon origins, Science Bridging Five
Nations: The Bering-Aleutian Salmon International Survey, American Fisheries Society annual
meeting, Anchorage, 2005.
Seeb, J.E., R.L. Wilmot, N. Varnavskaya , C. Guthrie, and C. Habicht, DNA markers track the
distribution and migration of sockeye salmon in the Bering Sea, NPAFC-PICES Joint
Symposium on the status of Pacific salmon and their role in North Pacific marine ecosystems,
Jeju, Korea, 2005.
Smith, C. Single nucleotide polymorphisms (SNPs) provide standardized genetic data for inter-laboratory
and inter-jurisdictional studies, Science Bridging Five Nations: The Bering-Aleutian Salmon
International Survey, American Fisheries Society annual meeting, Anchorage, 2005.
Poster presentations at scientific meetings
Habicht, C., J. Miller, L. Fair, C.A. Woody, K.M. Ramstad, M. Link, G.R. Johnston, K.L. Pronzati, E.S.
Lardizabal, R. Wilmot, J.H. Clark, J.E. Seeb. 2005. Applying genetic data to management
needs: sockeye salmon returning to Bristol Bay drainages.
1. 2005 Annual Meeting of the American Fisheries Society, Anchorage, AK.
2. SNP Workshop II, Applications of SNP Genotyping in Fisheries Management. Girdwood,
2006.
Seeb, J.E., R.L. Wilmot, S. Urawa, S. Abe, L.W. Seeb, and C.T. Smith. Single Nucleotide
Polymorphisms (SNPs) Provide Standard DNA Data for Bering-Aleutian Salmon International
Survey (BASIS) Studies.
1. BASIS 2004: Salmon and Marine Ecosystems in the Bering Sea and Adjacent Waters,
Sapporo, 2004.
2. SNP Workshop II, Applications of SNP Genotyping in Fisheries Management. Girdwood,
2006.
Seeb, J., A. Antonovich, W. Templin, L. Seeb, C. Habicht, G. Johnston, K. Pronzati, E. Lardizabal, C.
Elfstrom and C. Smith. 2005. Single Nucleotide Polymorphisms (SNPs) provide high
throughput and high resolution DNA data for sockeye salmon.
1. 2005 Annual Meeting of the American Fisheries Society, Anchorage, AK.
2. SNP Workshop II, Applications of SNP Genotyping in Fisheries Management. Girdwood,
2006.
25
Acknowledgements
The host agencies provided substantial match towards completion of this project. The study could not
have been done without access to the research cruises of the R/V Kaiyo maru (funded by Japan), the R/V
TINRO (funded by Russia), and the F/V Great Pacific and F/V Sea Storm (funded by the United States).
Chapters 1-5 were variously supported, in part, by Grants-in-aid from the Fisheries Agency of Japan,
Northern Advancement Center for Science and technology, Hokkaido, and the Ministry of Education,
Culture, Sports, Science and Technology, Japan. The North Pacific Anadromous Fish Commission
provided special project funds for Russian and Korean collaborators to run BASIS samples at the Alaska
Department of Fish and Game laboratory in Anchorage. Additional support for the reanalysis of the DNA
(SNP) baseline for sockeye salmon came from both the Pacific Salmon Commission and the State of
Alaska general funds; ADFG is currently using these data to improve management of stocks in Southeast
Alaska, Cook Inlet, and Bristol Bay.
26
References Cited
Beacham, T. D. and C.C. Wood. 1999. Application of microsatellite DNA variation to estimation of
stock composition and escapement of Nass River sockeye salmon (Oncorhynchus nerka ). Canadian
Journal of Fisheries & Aquatic Sciences 56(2):297-310.
Beacham, T.D., J.R. Candy, B. McIntosh, C. MacDonnachie, A. Tabata, K. Kaukinen, L. Deng, K.M.
Miller, and R.E. Withler. 2005. Estimation of stock composition and individual identification of
sockeye salmon on a Pacific Rim basis using microsatellite an major histocompatibility complex
variation. Transactions of the American Fisheries Society 134:1124-1146.
Beamish, R.J., D.J. Noakes, G.A. McFarlane, L. Klyashtorin, V.V. Ivanov, and V. Kurashov. 1999. The
regime concept and natural trends in the production of Pacific salmon. Canadian Journal of
Fisheries and Aquatic Sciences 56:516-526.
Beamish R.J., R.M. Sweeting, and C.M. Neville. 2004. Improvement of juvenile Pacific salmon
production in a regional ecosystem after the 1998 climatic regime shift. Transactions of the
American Fisheries Society 133:1163-1175.
Debevec, E. M., R. B. Gates, M. Masuda, J. Pella, J. Reynolds, and L. W. Seeb. 2000. SPAM (Version
3.2): Statistics program for analyzing mixtures. Journal of Heredity 91: 509-511.
Habicht, C, W.D Templin, C. M Guthrie III, R. L. Wilmot, G.A. Winans, E. Iwamoto, J.E. Seeb and L.W.
Seeb. 2001. Status report for genetic stock identification studies of Pacific Rim sockeye salmon.
(NPAFC Doc. 562). Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage,
Alaska 99802. (http://www.npafc.org/restricted_doc/2001%20Documents_PDF/562(usa).pdf)
Habicht, C., J.B. Olsen, L. Fair, and J.E. Seeb. 2004. Smaller effective population sizes evidenced by
loss of microsatellite alleles in tributary-spawning populations of sockeye salmon from the
Kvichak River drainage. Environmental Biology of Fish 69:51-62.
Habicht, C., L.W. Seeb, and J.E. Seeb. 2007. Genetic and ecological divergence defines population
structure of sockeye salmon populations returning to Bristol Bay, Alaska, and provides a tool for
admixture analysis. Transactions of the American Fisheries Society 136:82-94.
Kondzela, C.M., P.A. Crane, S. Urawa, J.B. Burger, N.V. Varnavskaya, V.V. Efremov, X. Luan, W.B.
Templin, K. Hayashizaki, R.L. Wilmot, and L.W. Seeb. 2002. Development of a comprehensive
allozyme baseline for Pacific-rim chum salmon. (NPAFC Doc 629) 23 pages. Alaska Department
of Fish and Game, 333 Raspberry Road, Anchorage, AK USA 99518.
Kruse, G.H. 1998. Salmon run failures in 1997-1998: a link to anomalous ocean conditions? Alaska
Fisheries Research Bulletin 5:55-63.
Myers, K.W., N.V. Klovach, O.F. Gritsenko, S. Urawa, and T.C. Royer. 2007. Stock-specific
distributions of Asian and North American salmon in the open ocean, interannual changes, and
oceanographic conditions. NPAFC Bulletin 4: 159–177.
Pella, J. and M. Masuda. 2001. Bayesian methods for analysis of stock mixtures from genetic characters.
Fishery Bulletin 99: 151-167.
27
Seeb, L.W, A. Antonovich, M.A. Banks, and 17 others. 2007. Development of a standardized DNA
database for Chinook salmon. Fisheries 32(11):540-549.
Smith, C.T., J. Baker, L. Park, L.W. Seeb, C. Elfstrom, S. Abe, J.E. Seeb. 2005a. Characterization of 13
single nucleotide polymorphism markers for chum salmon. Molecular Ecology Notes 5:259-262.
Smith, C.T., C.M. Elfstrom, L.W. Seeb, and J.E. Seeb. 2005b. Use of sequence data from rainbow trout
and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology 205(14):41934203.
Wood, C.C., D.T. Rutherford, and S. McKinnell. 1989. Identification of sockeye salmon (Oncorhynchus
nerka) stocks in mixed-stock fisheries in British Columbia and Southeast Alaska using biological
markers. Canadian Journal of Fisheries and Aquatic Sciences 46:2108-2120.
28
Download