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Challenges and opportunities for genetics-based
fisheries management of recently diverged stocks
STUDENTS/POSTDOCS:
• Andrew Veale (Postdoc, 2014-16)
• Matt Lemay (PhD, 2014)
• Karen Frazer (MSc, 2013)
• Stephanie Kirk (MSc, 2010)
• Bryson Sjodin (MSc, 2018)
• Lucas Elliott (MSc, 2019)
FUNDING:
PARTNERS:
• Hillary Ward, Matt Neufeld (MFLNRO)
• Sue Pollard, Paul Askey (FFSBC)
• Rich Bussanich (ONA)
• Will Warnock (CCRIFC)
§ Predicted that by 2048 the ocean would be empty of fish
§ Reported fishing stocks had collapsed in 29 percent of the world’s fisheries
FISH SPECIES COMPLETED/IN PROGESS:
• Inshore hagfish
• Sea lamprey
• Japanese lamprey
• Elephant shark
• Little skate
• Spotted gar
• Japanese medaka
• Zebrafish
• Southern platyfish
• Atlantic cod
• Three-spined stickleback
• Zebra mbuna
• Tigerfish
• Golden mbuna
• Happy cichlid
• Blue mbuna
• Pacific bluefin tuna
• Atlantic salmon
• Rainbow trout
• Channel catfish
• Fugu
• Freshwater pufferfish
• Indonesian coelocanth
• South African coelocanth
• Nile tilapia
• Pacific bluefin tuna
• Atlantic salmon
• Rainbow trout
• Channel catfish
• Fugu
• Freshwater pufferfish
• Indonesian coelocanth
• South African coelocanth
• Nile tilapia
• Great white shark
• Chinese sturgeon
• Bowfin
• Bichir
• European freshwater eel
• Orange roughy
• Blind cave fish
• Atlantic herring
• Bighead carp
• Wuchang bream
• Silver carp
• Rare gudgeon
• Tiger tail seahorse
• Lanternfish
• Golden arowana
• Japanese seabass
• Large yellow croaker
• Tongue sole
§ Distribution of neutral genetic variation
§ Applications:
− defining stocks
− analyzing mixtures
− identifying specimens
− monitoring restocking initiatives
− guiding aquaculture operations
§ Recently isolated stocks may not exhibit divergence at neutral loci
§ Low levels of gene flow may persist
Nm is > 1 the allele frequencies in the subpopulations will remain homogenised (Wright 1931)
§ Recently isolated stocks may not exhibit divergence at neutral loci
§ Low levels of gene flow may persist
§ Recently isolated stocks may not exhibit divergence at neutral loci
§ Low levels of gene flow may persist
Both cases limit the effectiveness of neutral
genetic markers for informing fisheries management
§ Recently isolated stocks may not exhibit divergence at neutral loci
§ Low levels of gene flow may persist
Loci influenced by selection may offer valuable population
markers on more recent (ecological) time scales
§ Extension of population genetics
§ Transition from analyzing genotypic data at a handful of molecular markers to 1,000’s to >100,000’s across genome
§ Discrimination between locus-specific & genome-wide effects
Photo: P. Henry
Photo: P. Henry
§ Migratory ecotypes
§ Anadromous
§ Resident (kokanee)
Photo: P. Henry
§ Migratory ecotypes
§ Anadromous
§ Resident (kokanee)
§ Reproductive ecotypes
§ River/stream-spawning
§ Beach/shore-spawning
Photo: P. Henry
During the glacial retreat 12,000 ybp:
§ Temporary corridors to proglacial lakes
§ Anadromous sockeye migrated into refugia and became trapped ~10,000 ybp
Ecotype divergence likely occurred since isolation <10,000 years before present
1. Is divergent selection driving differentiation between sockeye salmon migratory and reproductive ecotypes?
2. Does the use of outlier loci improve accuracy and cost-
effectiveness relative to conventional approaches to genetics-based fisheries management?
§ Okanagan Lake located between the Monashee & Cascade mountain ranges
- spans 351 km2, average depth 76 m
§ Kokanee in Okanagan Lake exhibit two sympatric ecotypes
STREAM SPAWNERS
SHORE SPAWNERS
§ Larger body size§ Bright red/green colouration
§ More pronounced sexual characteristics§ Peak spawning time early October
§ Spawn in pairs, male mate defense
§ Smaller body size§ Darker, more uniform colouration
§ Less pronounced sexual characteristics§ Peak spawning time late October
§ Spawn in schools
STREAM SPAWNERS
SHORE SPAWNERS
§ Low levels of neutral genetic differentiation detected between ecotypes (Taylor et al. 1997, 2000)
§ Low individual assignment probabilities to ecotype (71% and 76% accurate, Taylor et al. 2000)
§ Unacceptable error rates in mixed composition analyses using microsatellites (Withler 2000)
Russello et al. (2012) Evol. Appl.
shore spawning sites n = 138
stream spawning sites year = 2007
a) 8 outlier loci b) 44 neutral loci
Shore Stream
Ln P
(D|K
)
Ln P
(D|K
)
K K
Shore Stream
1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10
-13850.0
-13900.0
-13950.0
-14000.0
-14050.0
-14100.0
1.00
0.80
0.60
0.40
0.20
0.00
1.00
0.80
0.60
0.40
0.20
0.00
-2270.0
-2290.0
-2310.0
-2330.0
-2350.0
-2370.0
Russello et al. (2012) Evol. Appl.
Genotyped at 52 expressed sequence tag-linked microsatellites
a) 8 outlier loci b) 44 neutral loci
Shore Stream
Ln P
(D|K
)
Ln P
(D|K
)
K K
Shore Stream
1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10
-13850.0
-13900.0
-13950.0
-14000.0
-14050.0
-14100.0
1.00
0.80
0.60
0.40
0.20
0.00
1.00
0.80
0.60
0.40
0.20
0.00
-2270.0
-2290.0
-2310.0
-2330.0
-2350.0
-2370.0
Russello et al. (2012) Evol. Appl.
Genotyped at 52 expressed sequence tag-linked microsatellites
Frazer & Russello (2013) J. Evol. Biol.
No parallel patterns of divergence in a BC-wide sampling
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RADseq genotyped 5,996 SNPs
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Neutral (n = 5,976) Outlier (n = 20)
Lemay & Russello (2015) Mol. Ecol.
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Data Ecotype Accuracy (± SD) 20 outlier loci Stream 0.9999 (± 0.0007)
Shore 0.9999 (± 0.0006)
20 neutral loci Stream 0.8277 (± 0.0517) Shore 0.8400 (± 0.0592)
500 neutral loci Stream 0.9413 (± 0.0168) Shore 0.9598 (± 0.0158)
!
Lemay & Russello (2015) Mol. Ecol.
RADseq genotyped 7,347 SNPs
126 outlier SNPs
shore-spawning kokanee x
stream-spawning kokanee
R68810 independently detected in
4 systems across 2 drainages
R68810 maps to leucine-rich
repeat-containing protein-9 gene
(LRRC9)
Veale & Russello (2017) GBE
Veale & Russello (2017) Sci. Rep.
Developed a TaqMan® assay and genotyped 1519 sockeye/kokanee from
47 sites across pan-Pacific distribution
Evidence for directional
divergence across the
natural range of O. nerka in
Russia, Alaska and Canada
>99% correct assignment to
reproductive ecotype
• GG = shore
• GT/TT = stream
G (shore) allele could be
associated with loss of
function, leading to a lack of
spawning habitat preference
Veale & Russello (2017) Sci. Rep.
RADseq genotyped 7,347 SNPs
219 outlier SNPs
anadromous x resident
75 of which independently
detected in ≥ 2 comparisons
7 of which independently detected
in ≥ 4 comparisons
Annotations identifying genes
associated with development,
environmental tolerance &
immune response
Veale & Russello (2017) GBE
Hatchery conservation programs
are increasingly being employed
to reintroduce or maintain local
populations
Sockeye salmon hatchery
restocking in Skaha Lake began in
2004
Need for monitoring sockeye
population establishment and
introgression trends with the
resident kokanee population
Okanagan Lake
Skaha Lake
Vaseux Lake
Osoyoos Lake
Penticton
Oliver
Okanagan Falls (Skaha dam)
McIntyre Dam
Zosel Dam
0 10 km
USA
CANADA
Oka
naga
n R
iver
Oka
noga
n R
iver
N
BRITISH COLUMBIA
WASHINGTON
OREGON
Columbia River
Vancouver
Seattle
Portland
Skaha Lake
Sockeye Kokanee20cm 20cm
Veale & Russello (2016) Evol. App.
Genotyped samples from reference populations, annual trawl surveys and
angler surveys collected over 8-year period at previously published and
newly developed TaqMan assays based on our RADseq data (n = 35)
Sample Year Sampling Period Type Age Sample size 2003 September - October Kokanee Reference 3+ 130 2012 September - October Sockeye Reference 3+ 148 2008 September - October Annual Trawl Survey 0 96 2010 September - October Annual Trawl Survey 0 96 2012 September - October Annual Trawl Survey 0 96 2014 September - October Annual Trawl Survey 0 96 2013 September - October Annual Trawl Survey 1 - 2 136 2015 September - October Angler Survey 2 - 5 45
Veale & Russello (2016) Evol. App.
Low proportions of sockeye and hybrids detected in 2008 & 2010 age-
0 samples; by 2012, 28% were sockeye, rising to 41% in 2014
2008 2009 2010 2011 2012 2013 2014
0.0
0.2
0.4
0.6
0.8
1.0
Year
Prop
ortio
n of
pop
ulat
ion
Kokanee
SockeyeHybrid
Veale & Russello (2016) Evol. App.
2008 2009 2010 2011 2012 2013 2014
0.0
0.2
0.4
0.6
0.8
1.0
Year
Prop
ortio
n of
pop
ulat
ion
Kokanee
SockeyeHybrid
The number of hybrids detected rose proportionally with the increase
in sockeye, and exhibited an intermediate phenotype.
Veale & Russello (2016) Evol. App.
Okanagan Lake
Skaha Lake
Vaseux Lake
Osoyoos Lake
Penticton
Oliver
Okanagan Falls (Skaha dam)
McIntyre Dam
Zosel Dam
0 10 km
USA
CANADA
Oka
naga
n R
iver
Oka
noga
n R
iver
N
BRITISH COLUMBIA
WASHINGTON
OREGON
Columbia River
Vancouver
Seattle
Portland
Skaha Lake
Sockeye Kokanee20cm 20cm
Lemay & Russello (2015) Mol. Ecol.
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Veale & Russello (2017) GBE
Final Report for Contract/File #: 1070-20/GS16NLE107
6
Figure 2. STRUCTURE bar plot for K = 5. Each vertical line is an individual; each color
represents an inferred genetic cluster.
period of 500,000 using correlated allele frequencies under a straight admixture model.
The most likely number of clusters was determined by varying the number of clusters (K)
from 1 to 20 with ten iterations per value of K and calculating ΔK (Evanno et al., 2005)
as implemented in STRUCTURE HARVESTER (Earl & Vonholdt, 2011). Results for the
identified optimal values of K were summarized using CLUMPP (Jakobsson &
Rosenberg, 2007) and plotted using DISTRUCT (Rosenberg, 2004).
Results
Consistent levels of within-site genetic variation were detected across all sampled sites.
Allelic richness varied from 1.77 to 2.00 alleles per locus, with levels of expected
heterozygosity ranging from 0.210 to 0.376 (Table 1). A minimum of 80% of genotyped
loci were polymorphic per site, averaging 90% across sites (Table 1).
Koot
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Lak
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Mead
ow C
reek
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enay
Lak
e
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r Dun
can
Rive
r
Koot
enay
Lak
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Lard
eau
Rive
r
Koot
enay
Lak
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t Arm
Fish
eries
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enay
Lak
e
Wes
t Arm
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ek
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enay
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t Arm
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sevo
ir
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reek
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askit
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evoi
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tsha
n Re
sevo
ir
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ater
shed
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r
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inka
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r
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ake
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ek
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rior P
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askit
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r
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wl
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askit
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r
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mbi
a Rive
r
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askit
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evoi
r
Main T
rawl
Kinb
askit
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evoi
r
Woo
d Tr
awl
Kook
anus
a Res
evoi
r
Luss
ier R
iver
Kook
anus
a Res
evoi
r
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ury C
reek
Sloc
an L
ake
Bona
nza C
reek
Sloc
an L
ake
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on C
reek
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us L
ake
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rior P
latea
u
Wha
tsha
n Re
sevo
ir
Arro
w W
ater
shed
Willi
stin
Res
evoi
r
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inka
Rive
r
Chris
tina L
ake
Sand
ers C
reek
Chris
tina L
ake
Shor
e
D
Koot
enay
Lak
e
Mead
ow C
reek
Koot
enay
Lak
e
Lowe
r Dun
can
Rive
r
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enay
Lak
e
Lard
eau
Rive
r
Koot
enay
Lak
e
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t Arm
Fis
herie
s
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enay
Lak
e
Wes
t Arm
Kok
anee
Cre
ek
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enay
Lak
e
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t Arm
Sho
re
Arro
w Re
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ir
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Cree
k
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mbi
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ver
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ke
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e
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rior P
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aski
t Res
evoi
r
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Tra
wl
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aski
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evoi
r
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ver
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aski
t Res
evoi
r
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Tra
wlKi
nbas
kit R
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oir
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d Tr
awl
Kook
anus
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sevo
ir
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ier R
iver
Kook
anus
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ir
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ury
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an L
ake
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nza
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an L
ake
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on C
reek
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horo
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ake
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rior P
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ir
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ater
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