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 Offspring – NOR Chinook captured at trap and haul facility

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 1 st 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 genome  Allele – character state at a locus  Genotype – alleles an individual has at a given locus Locus Alleles FishLocus 1 #1A1A2 Genotype A1

Assessment of genetic variation  Heterozygosity  Proportion of individuals that have different alleles at a given locus  Number of alleles FishLocus 1 #1A1A2 #2A1 #3A1A2 #4A2 Heterozygosity: 2/4 = 0.5 Alleles = 2  Our study:  8 loci  Expectation:  Reduction in alleles  Variance in fitness, low CRR  No change in heterozygosity  Low power

First approach: Parent to offspring Offspring – NOR Chinook captured at trap and haul facility

Alleles were lost Paired t-test: 95 CIs

No change in heterozygosity *Low power to detect changePaired t-test: 95 CIs

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 1 st

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 analyses  Reduction in number of alleles  No change in heterozygosity  CRR ≈ 1 U.S. Army Corps of Engineers

Conclusions  Genetic variation is being lost  Dam and river passage, ocean survival, etc.  Migrants may offer a potential solution  May not be productive in the long run  They may impede adaptation  Loss to their own source population(s)  Our ongoing studies provide data  Inform managers  Monitor strategies to evaluate effectiveness  LSDR

Searching for adfluvial Chinook

? Is there genetic evidence for adfluvial Chinook above Cougar Dam?

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 trap  Genotyped  2,000 / 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 adults  15 comparisons  13 of 15: Observed trios > expected by chance  Two more adult-juvenile pedigrees to assemble  Increase age-1 to -4 comparisons  Add new age-5 and -6 comparisons

Adfluvial parents may account ~7% of offspring missing a parent  Generalized  One year  Anadromous parents  Anadromous x Adfluvial?  Adfluvial x Adfluvial?  No > Age-4 comparisons

Key points Part 1: Assessment of genetic variation  Genetic variation is being lost  Migrants boost and restore diversity Part 2: Searching for adfluvial Chinook  Two 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 HighLow

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?

? Lowest probability of being false? Exp. 2: Background on assignments

OffspringMotherFather Kid_001Mom_001Dad_001 Kid_002UnknownDad_001 Kid_003Mom_002Unknown ……… Male Female? Female Male? Locus 1 Locus Exp. 2: Background on assignments

OffspringMotherFather Kid_001Mom_001Dad_001 Kid_002UnknownDad_001 Kid_003Mom_002Unknown ……… Male Female? Female Male? Locus 1 Locus Male? Exp. 2: Background on assignments

Incorrect sex identification does not explain all missing parents

Grandparentage analysis approach TypeGP Year Missing Parent Year Missing Father Age Missing Mother

Preliminary evidence suggests adfluvial Chinook reside above Cougar Dam TypeGP Year Missing Parent Year Missing Father Age Missing Mother Obs. > Exp Yes 2011No