Post on 17-Jun-2022
How can genetic diversity of Chinook salmon populations inhabiting western
Alaska rivers inform management?
University of Washington and Alaska Department of Fish and Game
Pat Clayton photo
1
Pat Clayton
UW:
Jim Seeb andGarrett McKinneyWes LarsonCarita PascalLisa Seeb
ADFG:
Bill Templin andSara Gilk-BaumerTyler DannAndy BarclayNick DeCovich
2
Pat Clayton
UW:
Jim Seeb andGarrett McKinneyWes LarsonCarita PascalLisa Seeb
ADFG:
Bill Templin andSara Gilk-BaumerTyler DannAndy BarclayNick DeCovich
Funded byAlaska Sustainable Salmon Fund
3
We report results that help resolve Western Alaska stocks in mixtures
• Initial screen of 20,000 single nucleotide polymorphisms in Western Alaska populations• New approach to screen paired SNPs
• New approach to screen duplicated SNPs
• Gene map of 20,000 SNPs to aid SNP selection
• Optimization of 857 SNP panel to improve resolution of Kuskokwim/Nushagak stocks• ADFG can analyze ~1000 fish per unit effort
• Cost/fish similar to current screens of a few loci
4
We report results that help resolve Western Alaska stocks in mixtures
• Initial screen of 20,000 SNPs in Western Alaska populations• New approach to screen paired SNPs
• New approach to screen duplicated SNPs
• Gene map of 20,000 SNPs to aid SNP selection
• Optimization of 857 SNP panel to improve resolution of Kuskokwim/Nushagak stocks• ADFG can analyze ~1000 fish per unit effort
• Cost/fish similar to current screens of a few loci
5
We report results that help resolve Western Alaska stocks in mixtures
• Initial screen of 20,000 SNPs in Western Alaska populations• New approach to screen paired SNPs
• New approach to screen duplicated SNPs
• Gene map of 20,000 SNPs to aid SNP selection
• Optimization of 847 SNP panel to improve resolution of Kuskokwim/Nushagak stocks• ADFG can analyze ~1000 fish per unit effort
• Cost/fish similar to current screens of a few loci
6
Extreme examples of genetic diversity . . .
7
. . . that confer adaptive advantage in different ecosystems
HR
Basketball
Shady dealings
8
Between-Population Diversity
• Random drift creates differences
• Natural selection creates differences
• Migration promotes similarities
• Time since divergence magnifies genetic differences—
9
Between-Population Diversity
• Random drift creates differences
• Natural selection creates differences
• Migration promotes similarities
• Time since divergence magnifies genetic differences—
10
Between-Population Diversity
• Random drift creates differences
• Natural selection creates differences
• Gene flow promotes similarities
• Time since divergence magnifies genetic differences—
11
Between-Population Diversity
• Random drift creates differences
• Natural selection creates differences
• Gene flow promotes similarities
• Time since divergence magnifies genetic differences—
12
Time
1
2
43
8 5
67
1
2
3
4
5
8
6
7
Diversity sorted by geography
13
Homing,Drift, and or
Selection
1
2
43
8 5
6
Stream capture confounds geography
7
1
2
3
4
5
6
7
8
14
Homing,Drift, and or
Selection,Gene flow
1
2
43
8 5
67
1
2
3
4
5
6
7
8
Thermal adaptation shapes diversity
15
Homing,Drift, Selection
8
1
2
43
8 5
67
1
2
3
4
5
6
7
Swimming stamina shapes diversity
16
Diversity data is useful to:• Study effective population size
• Identify population relationships
17
Diversity data is useful to:• Population identification
• Resolve composition of bycatch (Watson this symposium)
• Stock identification in near-shore fisheries (i.e., WASSIP)
• Stock assessment using genetic mark recapture (Yukon)
18
Low diversity among W. Alaska stocks 19
Land of a million ponds and one reporting group (Larson PhD)
• Templin (2011) aggregated all WAK stocks for genetic stock identification
• 43 SNPs• Little diversity
• Straying?
• Recent divergence?
Bill Templin
20
Larson et al. (2013) built seasonal migration model for WAK aggregate using 43 SNPs:
Wes Larson
21
Western Alaska
Guthrie et al. (2008-17) reports bycatch of WAK aggregate:
Chuck Guthrie
22
Jim Ianelli
Migration and take of Western Alaska stocks cannot be parsed on a stock-specific basis:
23
-
50,000
100,000
150,000
200,000
250,000
300,000
350,000
400,000
450,000
19
92
19
93
19
94
19
95
19
96
19
97
19
98
19
99
20
00
20
01
20
02
20
03
20
04
20
05
20
06
20
07
20
08
20
09
20
10
20
11
20
12
20
13
20
14
20
15
20
16
20
17
Kuskokwim R.Nushagak R.
Ru
n S
ize
Year
Variable, decreasing, uncertain . . .
24
Can we increase the resolution of DNA datasets to better resolve WAK component stocks?
25
More DNA markers?Information-rich markers?New analyses protocols?
26
Andy Barclay
More DNA markers?Information-rich markers?New analyses protocols?
27
>20,000 SNPs arranged on 34 chromosomes
Tyler DannGarrett McKinney Meredith Everett
Methods and design:
28
• Single Nucleotide Polymorphism (SNP)Substitution of single DNA base in a gene
29
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
• Single Nucleotide Polymorphism (SNP)Substitution of single DNA base in a gene
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
• Paired SNP (haplotype)Two SNPs in same gene
~24% of loci in Chinook salmon have two or more SNPs
30
• Single Nucleotide Polymorphism (SNP)Substitution of single DNA base in a gene
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
• Paired SNP (haplotype)Two SNPs in same gene
~24% of loci in Chinook salmon have two or more SNPs
(usually thought to be redundant—no additional information)
31
Garrett McKinney
• First SNP arose from historical DNA substitution
C
C
A
T
SNP
32
XX,XXXX years ago
• Haplotypes arise when a more recent substitution occurs
C
G
C
A
T
T
SNP SNP2 haplotypes
TG
TC
AC
33
XX,XXX years ago
XXX years ago
SNP1 Distribution
A
T A
T A
Differentiates Pop. 1 and 2from Pop. 3
Single SNP
34
1
23
SNP2 Distribution
G
C C
Differentiates Pop. 2 and 3from Pop. 1
C
Single SNP2
A
T A
T A
Differentiates Pop. 1 and 2from Pop. 3
SNP1 Distribution
35
1
2 3
Paired SNPs Improve Fine-scale Resolution
SNP1 Distribution SNP2 Distribution Paired SNPs
All populations differentiated
AC
TC
AC
TG
TC
AC
SNP2 Distribution
G
C C
Differentiates Pop. 2 and 3from Pop. 1
C
A
T A
T A
Differentiates Pop. 1 and 2from Pop. 3
SNP1 Distribution
36
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
• Paired SNP (haplotype)Two SNPs in same gene
~24% of loci in Chinook salmon have two or more SNPs
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
• Duplicated SNP (polyploid SNP or paralog)Two copies of same gene with same SNP
~20% SNPs in Chinook salmon occur on duplicated genes
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
T G C A G G A A C T G C A T C C C G G A G T T C C A A T C A G C G G
T G C A G G A A C T G C T T C C C G G A G T T C G A A T C A G C G G
37
1
2
Duplicated genes adaptively important:
38
Data from duplicated SNPs improves resolution of locally adapted stocks:
Morten Limborg
John Gilbey
(duplicates extremely difficult to score until . . .)
39
40
Techniques for this project:• RAD sequencing (RADseq)
• Score thousands of random SNPs on dozens of fish
• Too lab-intense for routine work
• Perfect for genome-wide screen for informative SNPs
• Genotyping by 1000s (Gtseq)• Score hundreds of targeted SNPs on 1000s of fish
• Scores paired and duplicated SNPs
• Perfect for population baselines and mixture analyses
41
Techniques• RAD sequencing (RADseq)
• Score thousands of random SNPs on dozens of fish
• Too lab-intense for routine work
• Perfect for discovering informative SNPs
• Genotyping by 1000s (GTseq)• Score hundreds of targeted SNPs on 1000s of fish
• Scores paired and duplicated SNPs
• Perfect for population baselines and mixture analyses
42
RADseq13 WAK
populations
Higrade,Filter,Test,QC
Singleton genes
Paired genes
Duplicated genes
Gtseq SNP panels
Performance test 17 populations
Carita Pascal
Final QC
43
Results: RADseq alone
44
RADseq alone
• Larson et al. (2014)
• 10,000 loci
• Decompose WAK to three reporting groups
45
RADseq alone
• Larson et al. (2014)
• 10,000 loci
• Decompose WAK to three reporting groups
46
RADseq alone
• McKinney et al. (2018)
• ~20,000 loci
• Further decompose Kuskokwim R. and Nushagak R. into smaller groups
• What can we resolve with Gtseq?
47
RADseq alone
• Mckinney et al. (2018)
• ~20,000 loci
• Further decompose Kuskokwim R. and Nushagak R. into smaller groups
• What can we resolve with GTseq?
Eek
GoodnewsArolikKanektok
Kwethluk
Kisaralik
KogruklukAniak
Necons
George
Togiak
KoktuliStuyahok
Iowithla
48
Results: GTSeq, 847 SNPs
49
Eek
GoodnewsArolikKanektok
Kwethluk
Kisaralik
KogruklukAniak
Necons
George
Takotna
Pitka Fork
Tatlawiksuk
Population
Reporting Groups
Upper
Kuskokwim
Kuskokwim
River
Kuskokwim
Bay
PitkaFork 1.00 0.00 0.00
Takotna 0.86 0.12 0.02
Tatlawiksuk 1.00 0.00 0.00
Necons 0.99 0.01 0.00
George 0.00 1.00 0.00
Kogrukluk 0.01 0.91 0.09
Aniak 0.04 0.89 0.07
Kisaralik 0.01 0.94 0.05
Kwethluk 0.03 0.92 0.05
Eek 0.04 0.86 0.10
Kanektok 0.03 0.29 0.69
Arolik 0.00 0.09 0.90
Goodnews 0.00 0.00 1.00
Reporting Group
Upper
Kuskokwim
Kuskokwim
River
Kuskokwim
Bay
Upper Kuskokwim 0.96 0.04 0.01
Kuskokwim River 0.02 0.92 0.06
Kuskokwim Bay 0.01 0.12 0.87
Kuskokwim River• Bay, river mixtures
• >90% accuracy except for Kuskokwim Bay
• Kanektok has misassignment to Kuskokwim R.
50
Togiak
KoktuliStuyahok
Iowithla
Population
Reporting Group
Togiak
Lower
Nushagak
Upper
Nushagak
Togiak 1.00 0.00 0.00
Iowithla 0.00 1.00 0.00
Stuyahok 0.00 0.98 0.02
Koktuli 0.00 0.01 0.99
Nushagak River
51
• Bay, river mixtures
• >98% accuracy for each reporting group
Eek
GoodnewsArolikKanektok
Kwethluk
Kisaralik
KogruklukAniak
Necons
George
Togiak
KoktuliStuyahok
Iowithla
Takotna
Pitka Fork
Tatlawiksuk
Kusko/Nush• Near shore or bycatch mixtures
• Three solid reporting groups
• Nushagak underperforms• Balance baseline?
• Adjust SNPs?
52
Summary• Even-though there is comparatively low diversity
among Western Alaska stocks
• There are now methods to subdivide biologically, ecologically, and socially important subgroups
• Fine tuning SNP panels and expanded baseline should rescue Nushagak assignments
• How will stock-specific data enhance• Evaluation of management strategies?• Stock assessments?• Life cycle models• Marine survival and migration?• Bycatch studies?
53
Summary• Even-though there is comparatively low diversity
among Western Alaska stocks
• There are now methods to subdivide biologically, ecologically, and socially important subgroups
• Fine tuning SNP panels and expanded baseline should rescue Nushagak assignments
• How will stock-specific data enhance• Evaluation of management strategies?• Stock assessments?• Life cycle models• Marine survival and migration?• Bycatch studies?
54
>20,000 SNPs arranged on 34 chromosomes
Summary• Even-though there is comparatively low diversity
among Western Alaska stocks
• There are now methods to subdivide biologically, ecologically, and socially important subgroups
• Fine tuning SNP panels and expanded baseline should rescue Nushagak assignments
• How will stock-specific data enhance• Evaluation of management strategies?• Stock assessments?• Life cycle models• Marine survival and migration?• Bycatch studies?
55
Summary
How will stock-specific data enhance • Evaluation of management strategies?
• Stock assessments?
• Life cycle models?
• Marine survival and migration studies?
• Bycatch evaluations?
56
Summary
How will stock-specific data enhance • Evaluation of management strategies?
• Stock assessments?
• Life cycle models?
• Marine survival and migration studies?
• Bycatch evaluations?
57
Summary
How will stock-specific data enhance • Evaluation of management strategies?
• Stock assessments?
• Life cycle models?
• Marine survival and migration studies?
• Bycatch evaluations?
58
Summary
How will stock-specific data enhance • Evaluation of management strategies?
• Stock assessments?
• Life cycle models?
• Marine survival and migration studies?
• Bycatch evaluations?
59
Summary
How will stock-specific data enhance • Evaluation of management strategies?
• Stock assessments?
• Life cycle models?
• Marine survival and migration studies?
• Bycatch evaluations?
60
Acknowledgements (in addition to AKSSF)
Seed funding to move into map-based genomics: can we find the genes that matter?
Core funding for 25 years to discover gene markers useful for management and conservation of salmonids.
61
The End
63
64
• Paralogs represent a large portion of the salmon genome
• Paralogs are concentrated in the ends of 8 pairs of chromosome arms
65
SNP allele frequencies for Chinook salmon from the entire species range:
Pop
Tra
shF
req
[, i]
0 50 100 150
0.0
0.0
50
.15
ARF
Pop
Tra
shF
req
[, i]
0 50 100 150
0.4
0.8
AsnRS72
Pop
Tra
shF
req
[, i]
0 50 100 150
0.0
0.4
0.8
C3N3
Russia Pacific Rim N. America
66
Panel SNPs available
HigradeSNPs
Pass QC Final
IDFG (PNW-AK) 299 299 293 157
ADFG1 (Misc) 20000 338 274 232
ADFG2 (Kusko) 20000 350 254 219
ADFG3 (Nush) 20000 356 271 239
Total 1343 1092 847
67