Determining the continent-of-origin and regionof-origin for Atlantic salmon collected at West
Greenland from 1995-2010:
A review of the findings and a look at what the
future holds for molecular genetic methods of
mixed-fishery assessment (in 15 minutes?)
Tim King, US DOI, USGS
Barbara Lubinski, US DOI, USGS
Tim Sheehan, US DOC, NOAA Fisheries
Dave Reddin, CA, DFO
Determining the continent-of-origin and regionof-origin for Atlantic salmon collected at West
Greenland from 1995-2010:
A review of the findings and a look at what the
future holds for molecular genetic methods of
mixed-fishery assessment
Tim King, US DOI, USGS
Barbara Lubinski, US DOI, USGS
Tim Sheehan, US DOC, NOAA Fisheries
Dave Reddin, CA, DFO
Presentation Objectives
Briefly review the phylogeographic patterns observed among
Atlantic salmon populations from mtDNA and nDNA
Discuss the results of west Greenland mixed-fishery analysis at
two scales: continent-of-origin (COO) & region-of-origin
(ROO)
Compare the results of individual assignment (IA) with mixedstock (MSA) analyses
Test the temporal robustness and allele frequency stability of
the Atlantic salmon baseline database at assigning populations
represented in the West Greenland mixed-fishery to COO
Historic Commercial Atlantic Salmon
Fishery at Greenland
(1960-2003)
3,000
Catch
Quota
Metric Tons
2,500
2,000
1,500
1,000
500
0
1960
1963
1966
1969
1972
1975
1978
1981
Year
1984
1987
1990
1993
1996
1999
2002
mtDNA Control Region (CR)
Haplotype Networks
A, G, I,
J, K
CR more variable in western Atlantic
populations
I
ND1 haplotypes also observed in these
populations by Verspoor et al. 1999 and
Nilsson et al. 2001.
I
I
A
B
A, C
B, C, E,
I, J
A, B, C,
D, E, F
G
D
A
F
C
B
E
H
I
J
K
I
Western
Atlantic
NJ Tree - Da Distance
Range-wide Perspective
from 11 microsatellite DNA loci
Eastern
Atlantic/Baltic
Summary of Phylogeographic/Population Studies
 Over 5,000 Atlantic salmon have been genotyped at 12 microsatellite loci
 Western Atlantic populations of salmon are genetically distinct from Eastern
Atlantic populations.
 Microsatellite DNA results confirm findings from mtDNA and other nuclear
markers (e.g., alloyzmes, mini-satellite DNA)
 Wild salmon in Maine are genetically distinct from Canadian salmon
 Genetic divergence exists among populations of wild salmon in Maine rivers
and among Canadian Provinces; similar patterns exist among eastern
Atlantic populations (3 major regions)
 Independent management complicated by the fact that Eastern and Western
Atlantic populations share some foraging range (e.g., West and East
Greenland, Faroe Islands).
GSI of Mixed Fisheries
Microsatellite DNA allows clear delineation of continent-of-origin for
Atlantic salmon harvested in the Greenland mixed-fishery.
What about the mtDNA haplotype variation that suggests incomplete
separation between eastern and western Atlantic salmon?
Multidimensional Scaling (1-Da)
1
SP-2
SP-4
NB-1
NB-3
NB-4
SP-3
FR-1
SC-1
IR-1
QB-1
NS-1
SC-2
IR-2
EN-1
NF-1
QB-2
0
LA-1
LA-2
ME-6
NF-3
NO-2
NO-1
NF-2
RU-2
Kachkovka
RU-1
Pecha
NF-7
Bristol
Cove
NF-6
IC-1
Ouananiche
Beck
IC-2
NF-5
Trepassey
FI-1
ME-1
ME-2
ME-3
ME-4
ME-5
ME-7
ME-8
ME-9
ME-10
ME-11
ME-12
-1
-2
-1
0
1
2
Population
ME
MEL
NB
NS
QB
NF
LB
IC
NO
FN
SC
IR
SP
Total
Assignment Tests - COO
ME
571
5
36
9
1
12
5
-
-
-
-
-
-
639
MEL
1
90
-
-
-
1
-
-
-
-
-
-
-
92
NB
8
-
76
7
23
5
3
-
-
-
-
-
-
122
NS
5
1
8
88
6
2
-
-
-
-
-
-
-
110
QB
-
-
25
5
89
1
2
-
-
-
-
-
-
122
NF
5
-
7
5
4
71
1
-
-
-
-
-
-
93
LB
-
2
6
1
2
2
32
-
-
-
-
-
-
45
IC
-
-
-
-
-
-
-
95
1
-
-
-
-
96
NO
-
-
-
-
-
-
-
-
99
-
2
-
-
101
FN
-
-
-
-
-
-
-
-
-
61
-
-
-
61
SC
-
-
-
-
-
-
-
-
-
-
38
8
7
53
IR
-
-
-
-
-
-
-
1
-
-
11
48
4
64
SP
-
-
-
-
-
-
-
-
7
-
5
4
68
84
Percent
correctly
assigned to
region
89.4
97.8
62.3
80
73
76.3
71.1
99
98
100
71.7
75
81
91.2
Continent of Origin - Baseline
70.00
60.00
North American
50.00
40.00
30.00
20.00
10.00
00.00
00.00
10.00
20.00
30.00
European
40.00
50.00
60.00
70.00
West Greenland
Fishery
Since 1995, over 12,500
salmon have been sampled
for scale and genetic
analysis during the Fall
fishery.
Qeqertarsuaq
1A
Ilulissat
0A
1B
Sisimiut
Sarfannguaq
Kangaamiut
Collections have ranged
from Sisimiut (NW) to
Qaqortoq (S).
Genetics used to verify
scale results. Thus, the
need for individual-based
assignment.
Maniitsoq
1C
Atammik
Nuuk
0B
1D
Qeqertarsuatsiaat
Paamiut
Salmon were genotyped at
4-11 loci for continent-oforigin (COO) assignment.
1E
2G
Arsuk - Kangilinnguit
Qassimiut
Narsaq
1F
Qaqortoq
Continental Composition
of West Greenland Catch
100%
90%
80%
70%
60%
50%
40%
30%
20%
10%
0%
North American
European
Assignment to COO
100%
90%
80%
70%
60%
50%
European
40%
North American
30%
20%
10%
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
1998
0%
100%
90%
80%
70%
60%
50%
European
40%
North American
30%
20%
10%
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
0%
Individual Assignment and Mixed-Stock Assignment
of West Greenland Atlantic Salmon to Continent-of-Origin
1.00
Individual Assignment (Geneclass)
r = 0.98; t = 6.95; p < 0.0001
0.75
0.50
0.25
0.00
0.02
0.24
0.47
Mixed-Stock Allocation (ONCOR)
0.70
0.93
Individual Assignment Robustness
West Greenland Atlantic Salmon to Continent-of-Origin
Year
Eastern Atlantic
Ratio
Western Atlantic
Ratio
1997
2.3
2.9
2000
2.1
3.0
2001
2.2
3.0
2002
2.3
3.0
2003
2.3
3.0
2004
2.2
2.9
2005
2.3
2.9
2006
2.3
2.9
2007
2.3
3.0
2008
2.3
3.0
2009
2.3
2.9
2010
2.4
2.9
Summary of COO Assignments 1995-2010
 Over 12,500 Atlantic salmon sampled from the West Greenland mixed-fishery
have been genotyped
 Majority of the catch consisted of fish from the western Atlantic although
spatial differences exist in the make-up of the fishery
 IA and MSA results are highly correlated (at COO)
 The proportions of the fishery appear to be temporally stable throughout the
sampled areas
 Baseline is robust a decade after establishment
ROO - Multidimensional Scaling (1 - Da)
Western Atlantic
Eastern Atlantic/Baltic
2
2
NS1
1
QB1
ME 1
4 32
NB1
NB2
QB2
Dim e n s ion 2
Dim e n s ion 2
1
MEL2
MEL1
0
NF2
NS2
NO2
FN1
NO1
SC1
SC2
IR2
0
IR1
SP3
SP4
SP2
LB2
IC1
LB1
-1
-1
IC2
NF1
-2
-2
-2
-1
0
Dimension 1
1
2
-2
-1
0
Dimension 1
1
2
Population
ME
MEL
NB
NS
QB
NF
LB
IC
NO
FN
SC
IR
SP
Total
Assignment Tests - ROO
ME
571
5
36
9
1
12
5
-
-
-
-
-
-
639
MEL
1
90
-
-
-
1
-
-
-
-
-
-
-
92
NB
8
-
76
7
23
5
3
-
-
-
-
-
-
122
NS
5
1
8
88
6
2
-
-
-
-
-
-
-
110
QB
-
-
25
5
89
1
2
-
-
-
-
-
-
122
NF
5
-
7
5
4
71
1
-
-
-
-
-
-
93
LB
-
2
6
1
2
2
32
-
-
-
-
-
-
45
IC
-
-
-
-
-
-
-
95
1
-
-
-
-
96
NO
-
-
-
-
-
-
-
-
99
-
2
-
-
101
FN
-
-
-
-
-
-
-
-
-
61
-
-
-
61
SC
-
-
-
-
-
-
-
-
-
-
38
8
7
53
IR
-
-
-
-
-
-
-
1
-
-
11
48
4
64
SP
-
-
-
-
-
-
-
-
7
-
5
4
68
84
Percent
correctly
assigned
to region
89.4
97.8
62.3
80
73
76.3
71.1
99
98
100
71.7
75
81
91.2
Summary of ROO Assignments
Mixed-Stock Analysis
Gauthier-Ouellet, M, M Dionne, F Caron, TL King, and L. Bernatchez. 2009.
Spatiotemporal dynamics of the Atlantic salmon (Salmo salar) Greenland
Fishery inferred from mixed-stock analysis. Canadian Journal of Fisheries and
Aquatic Sciences 66:2040-2051.
Individual Assignment
Sheehan, TF, CM Legault, TL King, and AP Spidle. 2010. Probabilistic-based
genetic assignment model: assignments to subcontinent of origin of the
West Greenland Atlantic salmon harvest. ICES Journal of Marine Science
67:537-550.
Other Molecular Approaches for COO
Several loci have been shown to exhibit high resolution
of COO:
SS1
SSOSL438*
SsaD486
Ssa202*
SsaA86
Ssa289*
SsaA119
SSOSL311*
SsaA124
Combination - microsatellite locus (SS1) & mtDNA RFLP (ND 1)
See Gilbey J. et al. 2005. Novel DNA markers for rapid, accurate and costeffective discrimination of continental origin of Atlantic salmon
(Salmo salar L.). ICES.
Emerging molecular techniques Single Nucleotide Polymorphisms (SNPs)
Massively parallel (or next generation) sequencing
Acknowledgements
NOAA Fisheries and USGS
provided funding for the research
The following provide tissue or DNA
Tom Cross
Albert Pendas
Eric Verspoor
John Taggart
Andrew Ferguson
Jose Sanchez Prado
Fiona O’Flynn
John Bailey
KNAPK
Staff from the Greenland Nature Institute
G.W. Friars
T. Rex Porter
Gil Farmer
Terry Goff
Trevor Goff
Doug Aitkin
Tony Mills
Spurgeon Lloy
Participants in the West Greenland Program
Aquatic Ecology Branch
Leetown Science Center
Biological Resources Division
PGA Methods
Continent of
Origin
EUR
US Partitioning
Sub-continent of Origin
NA
CAN
US
PN
CT
MK
DPS
OTH
1.
COO assignment
3.
6.
2.
Binomial assignment
for unsampled
individuals
Binomial assignment via
standardized probabilities
Multinomial assignment
via adult returns
4.
Misclassification
adjustment
7.
Adjust migration M (10
months)
5.
Binomial assignment for
unsampled individuals
ROO Summary
PGA Model
• We have developed and applied a method to estimate sub-COO partitioning
of catch
• Probabilistic approach incorporates the uncertainty of fine-scale genetic
assignments and sampling
• Provides estimated US take at West Greenland
Results
• Among fish identified as being of western Atlantic origin, the majority of the
catch originates from Canada
• Within the US, the majority of the catch comes from the Penobscot
• The effect of the West Greenland harvest on individual US stocks varies
annually
– Even a relatively small harvest could have significant impacts on stocks
experiencing periods of low abundance