Estimating the Age and Origin of Spring/Summer Chinook Salmon at Lower Granite Dam

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

5. Lower Granite Dam Fish LadderChinook 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

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

9. Genetics overview • Asses the power of standardized genetic baseline to infer origin of Chinook salmon in the Snake River • 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 • 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 • 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. Collection Sample size 1 Tucannon 161 2 Imnaha 137 3 Minam 138 4 Lostine 101 5 CatherineCr 124 6 LyonsFerryH(Fall) 137 7 ClearwaterR(Fall) 110 8 NezPerceTribalH(Fall) 134 9 LoloCr 109 10 NewsomeCr 109 11 DworshakH. 92 12 RedRiver 86 13 Powell(Lochsa) 138 14 S.ForkClearwater 187 15 RapidRiverH 141 16 BigCr(upper'01) 156 17 BigCr(upper'02'03) 69 18 JohnsonCr 143 19 Secesh 137 20 JohnsonCr(suppl.) 105 21 SawtoothH 181 22 W.ForkYankeeFork 59 23 E.ForkSalmonR 141 24 Pahsimeroi 105 25 Marsh 141 26 BearValley('98'01) 99 27 BigCr(lower'98'02) 77 28 DeckerFlats 82 29 ElkCr 36 30 KnoxBridge 92 31 PovertyFlats 91 32 StolleMeadows 91 33 ValleyCr(lower) 94 34 ValleyCr(upper) 95 35 CrookedF 100 36 Lemhi 47 37 CamasCreek 46 38 Wenaha 46 4137 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. Neighbor-joining dendrogram of 38 baseline collections Lostine 4 Tucannon 35 1 68 7 Fall Chinook 65 6 65 8 2 22 23 30 21 21 96 Upper Salmon 28 51 17 33 83 34 24 32 36 Imnaha 2 3 Grande Ronde 52 5 31 5 38 53 10 Rapid River Hat. 100 7 RapidRHat/CW/GR 2 15 12 9 11 4 35 Clearwater 13 9 30 13 61 14 16 100 17 45 27 51 MiddleForkSalmon 37 74 25 90 26 98 29 20 18 100 20 SouthForkSalmon 46 19 40 31 14 30 44 32 0.1

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) 1.0% 0.8% 2x 3x 0.6% Percent of Individuals sampled multiple times 0.4% 0.2% 0.0% 2005 2006 (N=934) (n=1522) Year

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

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

23. 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. 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 • Age composition estimates were very precise and accurate using scales from live fish at Lower Granite Dam • 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. • ~<1% of fish sampled at LGD are duplicates • Proportional assignment of hatchery and wild fish was consistent over the two years for which samples were examined. • 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 • What is the required resolution for managers in the Snake River Basin? • Can we achieve that resolution in Snake River baseline? • We need to develop variance estimators..? • Using scales patterns can we further refine the Hatchery/Wild estimation at LGR (work is in progress at IDFG Nampa Research? • We are close to completing the Steelhead baseline… do we want to continue this work on Steelhead?