1. Estimating the Age and Origin of Spring/Summer Chinook Salmon at Lower Granite Dam Christian Smith USFWS Abernathy Lab, Longview, WA Jody White Quantitative Consultants, Inc. Boise, ID Cooperators: Matt Campbell and Tim Copeland, IDFG Shawn Narum, CRITFC Paul Moran, NOAA-Fisheries Scott Marshall, LSRCP

2. Objectives Estimate the age composition of Snake River Spring/Summer Chinook Salmon migrating upstream of Lower Granite Dam Determine the power and sensitivity of the Snake River Chinook baseline to allocate unknown individuals to reporting groups Estimate the stock composition using genetic mixture analysis of the Snake River Spring/Summer Chinook Salmon migrating upstream of Lower Granite Dam

3. General Methods 2005 (8%) and 2006 (10%) Chinook migrating upstream from April 1 – August 15 were sampled systematic/random) at LGR fish ladder (Jerry Harmon, NOAA fisheries) All fish were measured, scales sampled, external tags and marks noted, and scanned for PIT and CWT. All wild fish scales were read by IDFG technicians at Nampa Research, Nampa Idaho. All wild fish and a subsample of hatchery fish were genotyped at the USFWS Abernathy and IDFG Eagle Genetics Labs.

4. Genetic Stock Identification/Stock Composition Estimation Schematic Systematic Random Sample of Chinook/Steelhead Adults (Run Year) Lower Granite Dam Ladder Trap Wild/Hatchery Tags/Scale Patterns/Marks Take Scales from each fish Age Genotype Sample All Watersheds Baseline Development Hatchery Populations Population Identification Natural Populations Temporal/Spatial Stability (Periodic Sampling) Estimate where they are from

5. Lower Granite Dam Fish Ladder Chinook Samples 2005 (8% sample) –1,573 (74%) hatchery adipose clip, CWT or known PIT tag present –544 (26%) wild/natural adipose fin present, no associated marks or tags 2006 (10% sample) –1,821 (71%) hatchery –739 (29%) wild/natural

6. Lower Granite Spring/Summer Chinook Aggregate Age Composition (error bars = 1 SD)

7. Lower Granite Wild Chinook Age Composition 2007 Early vs. Late Run Timing

9. Genetics overview 1.Asses the power of standardized genetic baseline to infer origin of Chinook salmon in the Snake River 2.Use the baseline to allocate Chinook salmon sampled at LGD to Snake River reporting groups based on origin (hatchery vs wild) and age.

10. Genetic Mixture Analysis 1)proportional assignment (mixture analysis):  Stock proportions of a mixture are estimated.  E.g., 15% belong to pop 1 30% belong to pop 2 55% belong to pop 3 2) individual assignment (assignment tests):  Stock assignments of individual fish are estimated.  E.g., fish 1 is from pop 2 fish 2 is from pop 3 etc.

11. Genetic Mixture Analysis 1)Assignment / allocation to populations:  Fish are assigned or proportions are allocated to baseline populations. 2) Assignment / allocation to reporting groups:  Genetically similar populations are pooled into aggregates called “reporting groups”  Fish are assigned or proportions are allocated to these reporting groups.

12. Used updated version of the published Snake River microsatellite baseline: Narum SR, Stephenson JJ, Campbell MR. 2007. Genetic variation and structure of Chinook salmon life history types in the Snake River. Transactions of the American Fisheries Society 136:1252-1262. 13 microsatellite markers in 38 collections

13. RapidRHat/CW/GR 0.1 4 1 7 6 8 65 68 35 22 23 21 28 96 33 34 83 51 21 30 24 36 32 17 2 2 3 5 52 38 10 15 100 53 5 12 11 35 9 13 14 61 30 13 4 9 7 31 16 17 100 27 37 51 45 25 26 29 98 90 74 18 20 100 19 31 40 30 32 44 14 46 20 2 Lostine Tucannon Fall Chinook Imnaha MiddleForkSalmon SouthForkSalmon Upper Salmon Grande Ronde Rapid River Hat. Clearwater Neighbor-joining dendrogram of 38 baseline collections

14. MPGs vs genetic reporting groups MPGs combine spring and summer Chinook salmon, genetics separates all spring from summer, but is not able to distinguish among summer stocks. Grand Ronde / Clearwater / Imnaha / Rapid River grouping. –GR+Imn, Clear, Rapid or GR+Clear+Rapid, Imn Insufficient sampling of some MPGs?

15. Individual assignment of baseline fish

16. Proportional assignment of simulated fish

17. Proportional assignment of tagged fish

18. Genetic samples Rapid / Clearwater Salmon Fall Chinook

19. Genetic samples Rapid / Clearwater Salmon Fall Chinook

20. Proportion of fish sampled more than once (samples exhibiting identical genotypes) 2005 2006 1.0% 0.8% 0.6% 0.4% 0.2% 0.0% Year Percent of Individuals sampled multiple times 2x 3x (N=934) (n=1522)

21. Hatchery and wild returns to reporting group in 2005 and 2006 2005: 2006: wild hatchery

22. Wild returns to LGD assigned by scale age and return year

23. Reporting GroupGSI Estimate 95% CI (very preliminary) ODFW Estimate Tucannon River10811 - 2245 Imnaha River451203 – 704311 Rapid River/Clearwater/Grande Ronde 34773067 – 4121993* Lostine River140 – 76219 Middle Fk Salmon894491-1140 South Fk Salmon17941315 – 2192 Upper Salmon17781403 – 2192 Snake Falls254140 – 438 2005 reporting group escapement estimates Lower Granite Dam. Confidence intervals are ?. ODFW Estimates are from a mix of weir mark-recaptures and redd expansions. * = only for Grande Ronde not Rapid River or Clearwater River tributaries (see next slide).

24. Reporting GroupGSI Estimate 95% CI (very preliminary) ODFW Grande Ronde Estimate Rapid River/Clearwater/Grande Ronde. 34773067 – 4121993* Example: How do we break down a large reporting unit into management areas? Use the known escapement (esc.) estimates: Clearwater Esc. = Reporting Group - Grande Ronde Esc. – Rapid River Esc. - Additional data from weirs in the Clearwater R.can be used to further partition the estimate.

25. Conclusions 1.Age composition estimates were very precise and accurate using scales from live fish at Lower Granite Dam 2.Baseline used here allows allocation to genetic reporting groups with ~90% accuracy. Allocation to MPGs and populations is generally less accurate. Baseline provides resolution for individual assignment for stream-type vs ocean-type Chinook. 3.~<1% of fish sampled at LGD are duplicates 4.Proportional assignment of hatchery and wild fish was consistent over the two years for which samples were examined. 5.Qualitative differences in age structure of fish assigned to different reporting groups were noted, but none were statistically significant.

26. Further Questions and Discussion Topics 1.What is the required resolution for managers in the Snake River Basin? 2.Can we achieve that resolution in Snake River baseline? 3.We need to develop variance estimators..? 4.Using scales patterns can we further refine the Hatchery/Wild estimation at LGR (work is in progress at IDFG Nampa Research? 5.We are close to completing the Steelhead baseline… do we want to continue this work on Steelhead?