Reintroduction program above Cougar Dam: Assessment of genetic diversity and searching for adfluvial Chinook

Nick Sard, Dave Jacobson, Michael Hogansen, Kathleen O’Malley, Marc Johnson, Michael Banks

Bob Heims, U.S. Army Corps of Engineers

Tissue sampling

Trap and haul facility operational

History of Chinook reintroduction above Cougar Dam

Adult cohorts were assigned to age-3 to -6 NOR adult returns

2007 2008 2009 2010 2011 2012 2013

Offspring – NOR Chinook captured at trap and haul facility

3 4 5 6

3 4 5

Population is not meeting demographic replacement

CRR = Number of offspring / Number of parents

*Females only

Sard et al. In prep.

Most NOR Chinook retuning later in the spawning season were migrants

Migrants

September 1st

Sard et al. In prep.

Genetics: Definitions and examples

5’…gatcggacatacatacatagtatta...3’

A2

Allele 1 – copy from Mom

Allele 2 – copy from Dad

Locus – specific location in the genomeAllele – character state at a locusGenotype – alleles an individual has at a given locus

Locus

Alleles

Fish Locus 1

#1 A1 A2Genotype

A1

Assessment of genetic variation

Heterozygosity Proportion of individuals that have different alleles at a

given locus

Number of alleles Fish Locus 1

#1 A1 A2

#2 A1 A1

#3 A1 A2

#4 A2 A2

Heterozygosity: 2/4 = 0.5Alleles = 2

Our study: 8 loci

Expectation: Reduction in alleles

Variance in fitness, low CRR No change in heterozygosity

Low power

2007 2008 2009 2010 2011 2012 2013

First approach: Parent to offspring

Offspring – NOR Chinook captured at trap and haul facility

3 4 5 6

3 4 5

Alleles were lost

Paired t-test: 95 CIs

No change in heterozygosity

*Low power to detect change Paired t-test: 95 CIs

2007 2008 2009 2010 2011 2012 2013

Second approach: One return cohort

Offspring – NOR Chinook captured at trap and haul facility

Accounts for overlapping generations

X

*

* Assumes no LSDR method

Alleles were lost

Paired t-test: 95 CIs

No change in heterozygosity

Paired t-test: 95 CIs*Low power to detect change

Do NOR migrants restore or contribute new genetic variation?

Migrants

September 1st

Migrants restored lost and contributed new genetic variation

Error bars: SE

*

*No LSDR

*

We found similar results in reintroduction program above Foster Dam

Performed identical analysesReduction in number of allelesNo change in heterozygosityCRR ≈ 1

U.S. Army Corps of Engineers

Conclusions

Genetic variation is being lostDam and river passage, ocean survival, etc.

Migrants may offer a potential solutionMay not be productive in the long runThey may impede adaptationLoss to their own source population(s)

Our ongoing studies provide data Inform managersMonitor strategies to evaluate effectivenessLSDR

Searching for adfluvial Chinook

http://www.nwp.usace.army.mil/Locations/WillametteValley.aspx

?

Is there genetic evidence for adfluvial Chinook above Cougar Dam?

2008 2009 2010 2011 2012

Adults were assigned to juveniles outmigrating the following year

Offspring – juveniles captured in screw trap

Sard et al. Submitted. CJFAS

Juveniles are sampled above the dam

Screw trapGenotyped2,000 / year

Some offspring are missing at least one parent

Three hypotheses to explain missing parents:

1. Genotyping error and assignment criteria

2. Incorrect sex identification of adults

3. Unsampled adfluvial Chinook reside above the dam

Some offspring remain unexplained after testing hypotheses 1 & 2

Mean values for each hypothesis

Known grandparent pairs can be used to identify missing parents

?

Grandparent pair

Parent

Grandoffspring (Juveniles)

Grandparent pair – grandoffspring trio

Our study: 11 loci 35 alleles/locus

We calculated the number of observed trios expected by chance

…

Preliminary evidence suggests adfluvial Chinook may reside above Cougar Dam

Searched for age-1 to -4 missing adults15 comparisons 13 of 15: Observed trios > expected by chance

Two more adult-juvenile pedigrees to assemble Increase age-1 to -4 comparisonsAdd new age-5 and -6 comparisons

Adfluvial parents may account ~7% of offspring missing a parent

Generalized One year - 2011

Anadromous parents Anadromous x Adfluvial? Adfluvial x Adfluvial?

No > Age-4 comparisons

Key points

Part 1: Assessment of genetic variationGenetic variation is being lost

Migrants boost and restore diversity

Part 2: Searching for adfluvial ChinookTwo more adult-juvenile pedigrees to assemble

Test all putative grandparent-grandoffspring trios Genotype at 5 more loci

Acknowledgements

ODFW

Mark Wade

Nik Zymonas

Lisa Borgerson

Kanani Bowden

Ben Clemens

Oregon State University

Carl Schreck

Jen Britt

Sana Banks

Miles Naughton

USACE

Greg Taylor

Doug Garletts

Chad Helms

David Griffith

Some alleles lost are likely due to genetic drift

High Low

Exp. 1 : Genotyping error does not explain all missing parents

Simulated data 800 parents, 2000 offspring, 2% genotyping error rate

Exp. 2: Background on assignments

?Lowest

probability of being false?

0.001

0.01

?Lowest

probability of being false?

0.001

0.01

Exp. 2: Background on assignments

Offspring Mother Father

Kid_001 Mom_001 Dad_001

Kid_002 Unknown Dad_001

Kid_003 Mom_002 Unknown

… … …

Male

Female?

Female

Male?

Locus 1 Locus 1 Locus 2 Locus 2

101 102 201 202

Exp. 2: Background on assignments

Offspring Mother Father

Kid_001 Mom_001 Dad_001

Kid_002 Unknown Dad_001

Kid_003 Mom_002 Unknown

… … …

Male

Female?

Female

Male?

Locus 1 Locus 1 Locus 2 Locus 2

101 102 201 202

101 103 202 204Male?

Exp. 2: Background on assignments

Incorrect sex identification does not explain all missing parents

Grandparentage analysis approachType GP Year

Missing Parent Year

2008 2009 2010 2011 2012 2013

Missing Father

2007 1 2 3 4 5 6 Age

2008 1 2 3 4 5 1

2009 1 2 3 4 2

2010 1 2 3 3

2011 1 2 4

2012 1 5

Missing Mother

2007 3 4 5 6 6

2008 3 4 5

2009 3 5

2010 3

2011

Preliminary evidence suggests adfluvial Chinook reside above Cougar Dam

Type GP YearMissing Parent Year

2008 2009 2010 2011 2012 2013

Missing Father

2007 1 2 3 4 5 6 Age

2008 1 2 3 4 5 1

2009 1 2 3 4 2

2010 1 2 3 3

2011 1 2 4

2012 1 5

Missing Mother

2007 3 4 5 6 6

2008 3 4 5

2009 3 5 Obs. > Exp.

2010 3 Yes

2011 No