improving genetic stock identification of western alaska

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

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Pat Clayton

UW:

Jim Seeb andGarrett McKinneyWes LarsonCarita PascalLisa Seeb

ADFG:

Bill Templin andSara Gilk-BaumerTyler DannAndy BarclayNick DeCovich

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Pat Clayton

UW:

Jim Seeb andGarrett McKinneyWes LarsonCarita PascalLisa Seeb

ADFG:

Bill Templin andSara Gilk-BaumerTyler DannAndy BarclayNick DeCovich

Funded byAlaska Sustainable Salmon Fund

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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

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• Initial screen of 20,000 SNPs in Western Alaska populations• New approach to screen paired SNPs





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• Initial screen of 20,000 SNPs in Western Alaska populations• New approach to screen paired SNPs





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Extreme examples of genetic diversity . . .

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. . . that confer adaptive advantage in different ecosystems

HR

Basketball

Shady dealings

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Between-Population Diversity

• Random drift creates differences

• Natural selection creates differences

• Migration promotes similarities

• Time since divergence magnifies genetic differences—

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• Migration promotes similarities


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• Gene flow promotes similarities


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• Gene flow promotes similarities


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Time

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Diversity sorted by geography

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Homing,Drift, and or

Selection

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8 5

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Stream capture confounds geography

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Homing,Drift, and or

Selection,Gene flow

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Thermal adaptation shapes diversity

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Homing,Drift, Selection

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Swimming stamina shapes diversity

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Diversity data is useful to:• Study effective population size

• Identify population relationships

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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)

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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

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Larson et al. (2013) built seasonal migration model for WAK aggregate using 43 SNPs:

Wes Larson

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Western Alaska

Guthrie et al. (2008-17) reports bycatch of WAK aggregate:

Chuck Guthrie

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Jim Ianelli

Migration and take of Western Alaska stocks cannot be parsed on a stock-specific basis:

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50,000

100,000

150,000

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450,000

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Kuskokwim R.Nushagak R.

Ru

n S

ize

Year

Variable, decreasing, uncertain . . .

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Can we increase the resolution of DNA datasets to better resolve WAK component stocks?

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More DNA markers?Information-rich markers?New analyses protocols?

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Andy Barclay

More DNA markers?Information-rich markers?New analyses protocols?

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>20,000 SNPs arranged on 34 chromosomes

Tyler DannGarrett McKinney Meredith Everett

Methods and design:

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• Single Nucleotide Polymorphism (SNP)Substitution of single DNA base in a gene

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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

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(usually thought to be redundant—no additional information)

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Garrett McKinney

• First SNP arose from historical DNA substitution

C

C

A

T

SNP

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XX,XXXX years ago

• Haplotypes arise when a more recent substitution occurs

C

G

C

A

T

T

SNP SNP2 haplotypes

TG

TC

AC

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XX,XXX years ago

XXX years ago

SNP1 Distribution

A

T A

T A

Differentiates Pop. 1 and 2from Pop. 3

Single SNP

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1

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SNP2 Distribution

G

C C


C

Single SNP2

A

T A

T A


SNP1 Distribution

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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


C

A

T A

T A


SNP1 Distribution

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• Duplicated SNP (polyploid SNP or paralog)Two copies of same gene with same SNP

~20% SNPs in Chinook salmon occur on duplicated genes





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1

2

Duplicated genes adaptively important:

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Data from duplicated SNPs improves resolution of locally adapted stocks:

Morten Limborg

John Gilbey

(duplicates extremely difficult to score until . . .)

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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

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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

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RADseq13 WAK

populations

Higrade,Filter,Test,QC

Singleton genes

Paired genes

Duplicated genes

Gtseq SNP panels

Performance test 17 populations

Carita Pascal

Final QC

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Results: RADseq alone

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RADseq alone

• Larson et al. (2014)

• 10,000 loci

• Decompose WAK to three reporting groups

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RADseq alone

• Larson et al. (2014)

• 10,000 loci

• Decompose WAK to three reporting groups

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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?

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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

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Results: GTSeq, 847 SNPs

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Eek


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.

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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

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• Bay, river mixtures

• >98% accuracy for each reporting group

Eek


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?

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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?

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>20,000 SNPs arranged on 34 chromosomes






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Summary

How will stock-specific data enhance • Evaluation of management strategies?

• Stock assessments?

• Life cycle models?

• Marine survival and migration studies?

• Bycatch evaluations?

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Summary






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Summary






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Summary






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Summary






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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.

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The End

• Paralogs represent a large portion of the salmon genome

• Paralogs are concentrated in the ends of 8 pairs of chromosome arms

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SNP allele frequencies for Chinook salmon from the entire species range:

Pop

Tra

shF

req

[, i]

0 50 100 150

0.0

0.0

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.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

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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

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improving genetic stock identification of western alaska

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