1. Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim Copeland Matthew Campbell, Christine Kozfkay, and Bill Schrader Idaho Department of Fish and Game

2. Viable Salmonid Population Parameters Abundance Abundance How many of them are there? How many of them are there? Productivity Productivity How well do they reproduce & survive? How well do they reproduce & survive? Spatial structure Spatial structure Where are they? Where are they? Diversity Diversity What are they like? What are they like?

3. Abundance is a primary status metric Salmon/steelhead = number of spawning adults Productivity = abundance x age comp. through time Combination measures population resiliency Necessary for sustainable harvest Necessary for conservation of weak stocks & biodiversity Abundance & Productivity Abundance (10 yr geomean) Productivity (geomean R/S) 5% extinction risk 25% extinction risk A B

4. Data collection during spawning is very difficult Status assessments used aggregate data & habitat models from outside DPS Challenges for Snake River Steelhead

5. “A-run” versus “B-run” Stock Ocean Residence Timing over Bonneville Size at returnDistribution A-runUsually 1 yrJune - Aug< 78 cm Tucannon, Grand Ronde, Imnaha, low elevation tribs of Clearwater & Salmon, upper Salmon B-runUsually 2 yrsSept - Oct> 79 cm North & South Fk Clearwater, Lochsa, Selway, SFSR, MFSR “A-run” steelhead Grand Ronde River “B-run” steelhead S.F. Clearwater

6. Characterize allele frequencies from contributing stocks Genotype mixed sample Estimate stock proportions from genetic baseline Genetic Stock Identification

7. Strategy Sample aggregate at Lower Granite Dam (numbers & age composition) Use genetic stock identification Develop data suitable for VSP assessments (abundance & productivity) Address A vs B dichotomy

8. METHODS

9. GENETIC BASELINE 66 sample collections 9 geographic groups 1) Elk Creek (Joseph) 2) Snake/Lower Clearwater 3) South Fk Clearwater 4) Upper Clearwater 5) Imnaha 6) Lower Salmon 7) South Fk Salmon 8) Middle Fk Salmon 9) Upper Salmon

10. Wild steelhead only! Aug 24 – Nov 25 Scales taken, length recorded 13 microsatellite loci from standard set Genetic sex marker 2008 Adult Sampling at Lower Granite Dam

11. Proportion by group estimated with ONCOR For the entire wild run (all samples) By sex (male and female) By size (fork length 78 cm) By run-timing (early, middle, late) By total age (3, 4, and 5 year olds) 95% bootstrap confidence interval Mixture Analyses

12. RESULTS

13. Lower Granite Dam Sampling Sample period missed first 13% of run 46% unclipped fish were hatchery-origin 20,078 wild fish 992 aged, 1,076 genotyped 65.7% genetically female

14. Age composition (n = 992) Ocean Age Freshwater age X12345 1135180204271 2352286168250 35020 10

15. Genetic Stock Composition N = 20,078 A B A A A A B B B

16. By Sex Female Male

17. By Length

18. By Total Age (3 or less)

19. By Total Age (4)

20. By Total Age (5 or greater)

22. By Run-Timing (Early)

23. By Run-Timing (Middle)

24. By Run-Timing (Late)

25. By Run-Timing (Early)

26. By Run-Timing (Middle)

27. By Run-Timing (Late)

28. MAJOR FINDINGS

29. Genetic groups did not conform with TRT population structure Majority from 3 stocks (65%): Snake/Lower Clearwater, Upper Clearwater, Lower Salmon Grand Ronde likely lumped with Snake/Lower Clearwater Two large areas of good habitat have poor representation Middle Fk Salmon & South Fk Salmon Stock Contribution

30. Females comprise 2/3 of adult steelhead Female-biased sex ratios may result from: 1.Males residualize more than females 2.Females may be more iteroparous Dams & long migration reduces successful iteroparity No population effects = widespread male residualization? Sex Composition

31. Length conformed with A/B expectations Salmon River B stocks return over Lower Granite earlier Lower Salmon stock has older age comp than other A-runs All stocks produce smaller/younger & larger/older adults A/B dichotomy masks important diversity for conservation “A-run” versus “B-run”

32. Summary First time Snake River steelhead abundance estimated at the stock/population level This approach provides information relevant to VSP criteria Abundance Age composition Sex ratio Genetic diversity Life history diversity

33. Future Improve baseline Better resolution within some groups (e.g., Lemhi R) Coverage needed in some areas (e.g., Grand Ronde) Resolve differences with TRT population structure? Annual maintenance sampling Sample entire adult run Transition to SNPs Include smolt sampling at Lower Granite Dam