Genetics: Science and Implications in Salmon Management
Doug DeMaster
Director, Alaska Fisheries Science Center
NMFS
Jeff Guyon
Genetics Program Manager, Auke Bay Laboratories
NMFS
Bill Templin
Principle Geneticist, Gene Conservation Laboratory
ADF&G
August 25, 2015
Salmon Genetics
Impact?
Caught
Timeline
8-8:10 AM
Doug DeMaster – Director, Alaska Fisheries
Science Center
8:10-8:35 AM Bill Templin – Alaska Department of Fish and
Game Alaska State Fisheries
8:35-9:00 AM Jeff Guyon – National Marine Fisheries Service
Alaska Federal Fisheries (marine)
9-9:30 AM
New technologies and panel discussion
Alaska’s Genetics Program
Genetics applications for fisheries management
Gene Conservation Laboratory
Division of Commercial Fisheries
Alaska Department of Fish and Game
Why does ADF&G have a genetics lab?
Alaska Department of Fish and Game uses genetic information to achieve its mission
to …
protect, maintain, and improve the fish, game, and aquatic plant resources of the
state, and manage their use and development in the best interest of the economy
and the well-being of the people of the state, consistent with the sustained yield
principle.
Why does ADF&G have a genetics lab?
Alaska Department of Fish and Game uses genetic information to achieve its mission
to …
protect, maintain, and improve the fish, game, and aquatic plant resources of the
state, and manage their use and development in the best interest of the economy
and the well-being of the people of the state, consistent with the sustained yield
principle.
The activities of the Gene Conservation Laboratory fall into 4 main categories:
1. Basic research to understand the resource
2. Development of capabilities
3. Inform/Assess management actions
4. Research to inform human activities
Questions that use genetic information
Did exposure to mutagens cause genetic injury?
EVOS oiling experiments
What species of salmon is this?
Atlantic salmon escapees
Is this crab a hybrid?
Snow/tanner crab hybrids
Which broodstock are these unmarked salmon from?
DIPAC broodstock
What is the structure of these populations?
Sockeye salmon in Bristol Bay lakes
Where are these fish going?
Chinook salmon in SE Alaska
Sockeye salmon in the Bering Sea
Who’s fish are being harvested?
Bering Sea salmon bycatch
Applications: Understanding the Resource
Example: Red king crab population structure
Applications: Understanding the Resource
Example: Red king crab population structure
Alaska
Okhotsk Sea
Bering Sea
SE Alaska
Gulf of Alaska
Applications: Understanding the Resource
Example: Red king crab population structure
Seymour Canal
PCO II
Bristol Bay
N Central Gulf of Alaska
Eastern N Pacific
Northern Bering Sea
Aleutian Islands
SE Alaska
PCO I
Applications: Understanding the Resource
Example: Red king crab population structure
Pattern of heterozygosity
Applications: Understanding the Resource
Example: Red king crab population structure
Post-glacial Colonization Routes
Applications: Understanding the Resource
Example: Red king crab population structure
Implications
• Gene flow and ice-age isolations
• Red king crab might be managed on a
small geographic scale in some regions
• Guidance for possible stock enhancement
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
Alaska Department of Fish and Game
NOAA Fisheries
University of Washington
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
VNIRO
ADFG
NOAA ABL
Kamchat NIRO
UW
WDFW
North Pacific Anadromous Fish Commission Partners
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
ADFG
NOAA ABL
UW
DFO
WDFW
NOAA NWC
CRITFC
WSU
USFWS
OSU
Pacific Salmon Commission Partners
IDFG
NOAA SWC
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
172 Populations
42 SNPs
Russia
Coast W AK
Mid Yukon
Up Yukon
Up Kuskokwim
N AK Pen
S AK Pen
Cook Inlet
Up Copper
Low Copper
N SE Alaska
Coast SE AK
Andrew Cr
TBR Taku
BC/WA/OR
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
Russia
Coast W AK
Mid Yukon
Up Yukon
Up Kuskokwim
N AK Pen
S AK Pen
Cook Inlet
Up Copper
Low Copper
N SE Alaska
Coast SE AK
Andrew Cr
TBR Taku
BC/WA/OR
Neighbor Joining based on FST
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
Stock-specific migration in the Bering Sea
Murphy et al. 2009
Stock-Structured Distribution of Western Alaska and Yukon Juvenile Chinook Salmon from United States BASIS surveys, 2002-2007
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
Stock-specific migration in the Bering Sea
Applications: Develop Capabilities
Example: Chinook salmon coastwide baseline
Stock-specific migration in the Bering Sea
Applications: Inform/Assess Management
Example: Stock composition of harvest
Port Moller Test Fishery - Inseason
Applications: Inform/Assess Management
Example:Port Moller Test Fishery - Inseason
http://vimeo.com/110201354
Applications: Inform/Assess Management
0.4
0.6
0.8
1.0
Ugashik 2012
0.2
Togiak
Igushik
Wood
Nushagak
Kvichak
Alagnak
Naknek
Egegik
Ugashik
June 28 – July 6
8 days
0.0
Cumulative abundance
Example:Port Moller Test Fishery - Inseason
6/10
6/20
7/1
7/10
Date
7/20
7/31
Applications: Inform/Assess Management
Example: Stock composition of harvest
Western Alaska Salmon Stock Identification Program – Post season
Applications: Inform/Assess Management
Example: Stock composition of harvest
Western Alaska Salmon Stock Identification Program – Post season
• Political support to fund large scale, collaborative genetic stock
identification study
IF
• Stakeholders agree on necessary information, study design and results
WASSIP Advisory Panel
Alaska Fish and Game
Aleut Corp
Aleutians East Borough
Assoc. Village Council Presidents
Bering Sea Fishermen’s Association
Bristol Bay Native Association
Concerned Area M Fishermen
Kawerak Inc.
Lake and Peninsula Borough
Tanana Chiefs Conference
Yukon River Drainage Fisheries Assoc.
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
Chum salmon
35,921 Individuals
302 Populations
96 SNPs
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
Sockeye salmon
North of Kuskokwim River
Kuskokwim Bay
Bristol Bay
North Peninsula
South Peninsula
Chignik
East of WASSIP
294 Populations
96 SNPs
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
Coast-wide Fisheries
~3,300 km of
coastline
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
Chum salmon:
278 fishery strata sampled
194 fishery strata analyzed
143,258 individuals sampled
74,445 individuals genotyped
Sockeye salmon:
307 fishery strata sampled
216 fishery strata analyzed
182,523 individuals sampled
81,932 individuals genotyped
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
What stocks are caught in my fishery?
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
How may fish of each stock were caught in my fishery?
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
What fishery catches my stock?
Applications: Inform/Assess Management
Example: Western Alaska Salmon Stock Identification Program
What fishery catches my stock?
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Straying Definitions
Adult
Not Home Stream
(uncommitted)
Stray (dies)
Genetic stray
(spawns)
Introgression
(successful hybridization)
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Idealized natural system
Time
No straying
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Reality natural system
Time
Straying/drift equilibrium
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Reality natural system
Time
Equilibrium
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Hatchery straying
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Hatchery straying
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Hatchery straying
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Hatchery straying
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Hatchery straying
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Wells
Map
Siwash
WNH Hatchery
Beartrap
Constantine
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Time
Equilibrium
Hatchery
Hatchery straying
Historical
(pre-hatchery
scales)
Contemporary samples
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Wells River Historical
Wally Noerenberg Hatchery
Wells River Contemporary
Constantine Creek Historical
Constantine Creek Contemporary
Siwash Creek Historical
Siwash Creek Contemporary
Beartrap Creek Historical
Beartrap Creek Contemporary
0.02
0.015
0.01
0.005
0
Pairwise Fst
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
One-way migration model
Contemporary vs. Hatchery
2% stray rate
0.3
6 generations
0.2
0.1
0
-0.1
-0.2
-0.3
-0.3 -0.2 -0.1
0
0.1
0.2
0.3
Historical vs. Hatchery
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Beartrap
Siwash
Constantine
Wells
Applications: Inform Human Activities
Example: Chum salmon hatchery/wild interaction
Implications
• Population structure not visibly eroded
• Introgression rates are highly variable
among locations
• Distance from the hatchery and life history
affect introgression rates
Genetic stock composition analysis of salmon
caught in Alaska federal groundfish trawl fisheries
Jeff Guyon, PhD
Genetics Program
Auke Bay Laboratories
Juneau, AK
August 25, 2015
Chinook Salmon
Chum Salmon
NMFS-AFSC-292
Genetic Stock Composition Analysis of
Chum Salmon Bycatch from the 2013
Bering Sea Walleye Pollock Trawl Fishery
J. A. Whittle, S. C. Vulstek, C. M. Kondzela,
and J. R. Guyon
Genetics Program
Auke Bay Laboratories
Juneau, AK
August 25, 2015
2013 Chum Salmon Bering Sea Bycatch
800
Number of fish X 1,000
700
600
500
400
300
200
100
0
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
Year
1994: Scales (Patton et al., 1998) - 1,204 samples
1994-1995: Allozymes (Wilmot et al., 1998) - 457 (1994) and
1,680 (1995) samples
1996: Allozymes (Seeb et al., 2004) – Eastern shelf
2005–2013: Microsatellites - 1,084 (2005), 1,367 (2006), 1,279 (2007), 629 (2008),
1,437 (2009), 1,048 (2010), 1,472 (2011), 673 (2012), 4,094 (2013) samples
DFO Microsatellite Chum Salmon Baseline
Beacham et al., 2009
Our Stock Groupings
W AK Up/Mid Yukon
NE ASIA
SE ASIA
SW AK
E.GOA/PNW
Principal Coordinate Analysis
11 microsatellites, CSE
Upper/Middle
Yukon
9.92
5.33
Southwest Alaska
Western Alaska
2 0.74
-3.85
-8.44
-8.23
Eastern GOA - PNW
-4.17
Northeast Asia
-0.10
1
Southeast
Asia
3.97
8.04
CIAP-WASC chum salmon collections
Goal II
70°N
Objective 1
– Genotype 144
samples from each of
32 collections at preexisting and new
microsatellite
markers.
Kobuk
Jim
S Koyukuk
Melozitna
Agiapuk
65°N
Eldorado Fish
Ungalik
Chena
Nulato
Kaltag
Unalakleet
Pikmiktalik Anvik
Black
Takotna
Kwethluk
Andreafsky
Tatlawiksuk
Salmon
Kogrukluk
60°N
Kanektok
Objective 2
– Genotype mixture
samples from lower
Yukon and
Kuskokwim rivers.
Kokwok
Stuyahok
Osviak Togiak Iowithla Alagnek
Goodnews Nushagak
Big Cr
Gertrude
Whale Mtn
Chum salmon
baseline collections
Total WASC
First 8 collections
160°W
Meshik
0
75
150
150°W
300 Miles
55°N
2013 Chum Salmon Bering Sea Bycatch
20
600
400
12
A
8
300
B
200
4
100
0
0
0
5
10
15
20
25
30
Statistical week
35
40
45
50
Genetic samples
Bycatch × 1,000
500
Bycatch (125,174)
Genetic samples (4,123)
16
2013 Chum Salmon Bering Sea Bycatch
Correlation coefficient, r > 0.99
Number genetic samples
200
150
100
50
0
0
1,000
2,000
3,000
4,000
5,000
6,000
Number of 'B'season chum salmon bycatch per vessel
2013 Chum Salmon Bering Sea Bycatch
0.5
mean 1994, 1995, 2005-2010
2011
2012
2013
Stock proportion
0.4
0.3
0.2
0.1
0.0
SE Asia
NE Asia
Western AK Upper/Middle SW Alaska
Yukon
Eastern
GOA/PNW
2013 Chum Salmon Bering Sea Bycatch
Area 517
Reporting area
Time period
Number of
samples
517
517
517
Early
Middle
Late
304
1,004
473
Stock proportion
0.8
0.6
0.4
0.2
0.0
Early
Middle
Late
NMFS-AFSC-290
Genetic Stock Composition Analysis of the
Chinook Salmon Bycatch from the 2013
Bering Sea Walleye Pollock (Gadus
chalcogrammus) Trawl Fishery
C.M. Guthrie, H. T. Nguyen, and J.R. Guyon
Genetics Program
Auke Bay Laboratories
Juneau, AK
August 25, 2015
2013 Chinook Salmon Bering Sea Bycatch
140,000
120,000
Bycatch
100,000
Total
"A"
80,000
"B"
60,000
40,000
20,000
0
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013
1979-1982: Scales (Myers and Rogers, 1988)
1997-1999: Scales (Myers et al., 2004)
2005 “B” - 2006: SNPs (ADF&G, Chinook Salmon EIS)
2007 – 2012: SNPs – 867 (2007 “B”), 863 (2008), 386 (2009), 826 (2010),
2,473 (2011), 1,111 (2012), and 1,246 (2013) samples.
Templin et al., 2011
Templin et al., 2011
2013 Chinook Salmon Bering Sea Bycatch
1400
140
2013 BSAI Bycatch/Sample Distribution
1200
120
Total Bycatch
Genotyped Samples
100
800
80
600
60
400
40
200
20
0
0
3
5
7
9 11 13 15 17 24 26 28 30 32 34 36 38 40 42 44
Statistical Week
Samples
Bycatch
1000
2013 Chinook Salmon Bering Sea Bycatch
80%
70%
60%
2008
2009
2010
2011
2012
2013
50%
40%
30%
20%
10%
0%
Russia
Coast W Mid-Yukon Up Yukon N AK Pen
AK
GOA
Coast SE
AK
BC
West Coast
US
NMFS-AFSC-291
Extension of Genetic Stock Composition Analysis
to the Chinook Salmon Bycatch in the Gulf of
Alaska Walleye Pollock (Gadus chalcogrammus)
Trawl Fisheries, 2013
Jeff Guyon
Charles Guthrie, III
Andrew Munro
William Templin
Jim Jasper
Genetics Program
Auke Bay Laboratories
Juneau, AK
Gene Conservation Laboratory
Alaska Dept of Fish and Game
Anchorage, AK
August 25, 2015
2005 – 2006: SNPs – 219 (Winter 2006), 62 (Summer 2005-6), 127 (Fall
2005-6) samples
2010 – 2013: SNPs – 161 (2010), 240 (2011), 948 (2012), and 693 (2013)
samples.
2013
2012
2011
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
1998
1997
1996
1995
1994
1993
1992
50,000
45,000
40,000
35,000
30,000
25,000
20,000
15,000
10,000
5,000
0
1991
Number of Chinook salmon
2013 Chinook Salmon GOA Bycatch
2013 Chinook Salmon GOA Bycatch - Pollock
80%
70%
2010GOA-Samples
2011GOA-Samples
60%
2012GOA-Bycatch
2013GOA-Bycatch
50%
40%
30%
20%
10%
0%
Acknowledgements
NMFS
Chris Kondzela
Chuck Guthrie
Sharon Wildes
Hanhvan Nguyen
Jackie Whittle
Scott Vulstek
North Pacific Observer Program
ADF&G
Bill Templin
Andrew Munro
Jim Jasper
Alaska Groundfish Data Bank
Julie Bonney
Katy McGauley
Ken Hansen
Alaska Seafood Cooperative
John Gauvin
Funding
NMFS AKSSF NPFRF
New Genetic Technologies
Genetic tools and their uses for management are increasing
RAD Sequencing
…ACTAGCTGACTGTACGTAC…
…ACTAGCTGGCTGTACGTAC…
RAD Sequencing/Genomics – Example from UW and ADFG
Larson et al., 2014
Fragment
Size
F1 (sample)
F0(male2)
Locus 1
F0 (male1)
F0 (female)
F1 (sample)
F0(male2)
F0 (male1)
F0 (female)
Parentage Analysis
Locus 2
Parentage Analysis (SWFSC) - Slide from Carlos Garza
Forensic Analysis (NWFSC) – Slide from Linda Park and Jeff Hard
A National Forensics Program for NOAA
Provide genetic and
morphological analyses
Serve all regions of the Office
of Law Enforcement (OLE)
eDNA (metagenomics)
Collect water sample
Isolate residual DNA
from sloughed cells
Sequence DNA for species ID