Genetic impacts of hatchery stocks on Steelhead in Lower Cowlitz tributaries

1. Genetic impacts of hatchery stocks on Steelhead in Lower Cowlitz tributaries Anne Marshall, Maureen Small, and Julie Henning Washington Department of Fish and Wildlife

2. “The lower Cowlitz winter steelhead historical population may have been one of the largest in the lower Columbia Basin” (Lower Columbia Salmon Recovery and Fish and Wildlife Subbasin Plan, Vol. 1, Chapter 5. 2004) ESA-listed as threatened in 1998 -within the Lower Columbia “Distinct Population Segment” (DPS) Major uncertainty for the DPS: Impact of hatchery-origin steelhead on natural populations

3. Lower Columbia Steelhead DPS – historical populations Lower Cowlitz winter steelhead were designated as a distinct population in recovery planning Cowlitz Basin perimeter Dams prevent access to upper Cowlitz Basin except by trapping and hauling

4. Objectives - • Genetically characterize steelhead in lower Cowlitz tributaries • Determine if natural-origin steelhead are genetically distinct from Cowlitz hatchery stocks • Estimate introgression in natural population from hatchery stocks • Investigate population structure among tributaries • Determine if lower Cowlitz steelhead are distinct from other Lower Columbia populations

5. Sampling design – Sample adults in lower river tributaries over two years Sample size goal of 50 natural-origin adults per tributary system Sample any known hatchery-origin adults encountered Sample 50 fish in each of two years from all three Cowlitz Hatchery stocks

6. Three Steelhead stocks at Cowlitz Trout Hatchery: • Chambers Creek (non-native, Puget Sound) early winter-run • - Cowlitz late winter-run • - Skamania (non-native, lower Columbia) summer-run Hatchery production is mitigation for loss due to hydroelectric dams

7. Smolt releases of Cowlitz Hatchery steelhead stocks, 1995-2008

8. Lower Cowlitz tributaries – adult steelhead sampling sites Cowlitz Trout Hatchery 3 Tributary systems sampled Lower Cowlitz includes Toutle and Coweeman sub-basins, with other hatchery stock releases Columbia River

9. Sampling Methods - Angling and dip netting, March to May - scales & fin tissue taken - careful fish handling & release

10. Tissue sampled from caudal fin for DNA extraction

11. Genetic Methods - Laboratory – Genotypes at 15 microsatellite DNA loci per fish • Statistical Analyses – • Descriptive genetic statistics per sample • Pair-wise differentiation tests among samples • Factorial correspondence analysis of genotypes • Assignment tests for population-origin • Population structure analyses

12. 2008 & 2009 Sampling Results - 77 total natural-origin steelhead 8 marked hatchery fish 100 adults from each hatchery stock Tributary systems totals: Olequa N = 44 Delemeter N = 32 Ostrander N = 1 Cowlitz Trout Hatchery 2008 – 79% males; 2009 – 89% males

13. Genetic differentiation between samples – temporal and population-wide tests Lower matrix: FST values. Upper matrix p-values for genotypic tests. Bold values not significant Temporal samples per population were similar. Lower Cowlitz natural-origin steelhead were differentiated from hatchery stocks. Hatchery stocks differed from each other.

14. Factorial correspondence analysis plot- Individual fish plotted according to genotype Plot of centers - 08 & 09 samples “CowClip” (orange dots) are marked hatchery-origin fish

15. Assignment of individuals to their population of origin GeneClass program Assigned fish are at least 90 times more likely to originate from one sample Unassigned fish have similar likelihoods of originating from two or more samples

16. STRUCTURE analysis – partitions data into genetic clusters using Hardy-Weinberg equilibrium Hatchery and natural-origin steelhead in Cowlitz and Coweeman 1 2 3 4 “K” (number of hypothetical populations) = 4 had highest likelihood

17. STRUCTURE – summary of average percentage of ancestry over all individuals for each sample, 4 genetic clusters Cluster labels based on the dominant population in the cluster

18. Lower Cowlitz natural-origin steelhead – results to this point: • As a group, were genetically distinct from Cowlitz Hatchery stocks • Ancestry estimated from hatchery stocks suggests introgression into wild population • Average ancestry from all hatchery stocks over all natural-origin fish was about 40% • Coweeman steelhead, a nearby population, shared similar ancestry profile How do Lower Cowlitz steelhead compare with other lower Columbia populations?

19. Other Lower Columbia Basin rivers where steelhead population samples were obtained for comparative analyses Natural-origin adults at Cowlitz barrier dam Winter and summer-run populations All samples from natural-origin adult steelhead

20. CowH E W NFLewisCed NFToutle CowH L W NFLewisMer Green SFToutle CowBarrier KalamaW Elochoman EFLewis Cowee CowNat KalamaS Washougal CowHSum 0.01 Neighbor-joining dendrogram of genetic distances among Cowlitz and lower Columbia region steelhead samples Toutle River sub-basin in Cowlitz basin 100 96 79 96 83 96

21. STRUCTURE analysis: Cowlitz steelhead and other Lower Columbia steelhead at K=5 clusters

22. CowH E W NFLewCed NFToutle CowH L W NFLewMer Green SFToutle CowBarrier KalW Elochoman EFLew Cowee CowNat KalS Washougal CowHSum 0.01 Summary of average percentage of ancestry over all individuals for each sample in 5 genetic clusters estimated by STRUCTURE

23. Results summary - Lower Cowlitz tributaries natural-origin steelhead were genetically distinct from all Cowlitz hatchery stocks. The three Cowlitz Hatchery stocks were genetically distinct from each other. Lower Cowlitz steelhead showed introgression from non-native hatchery stocks, especially early winter-run stock. Lower Cowlitz steelhead shared little ancestry with Cowlitz Hatchery native late winter-run stock. Coweeman and Elochoman rivers winter steelhead were most similar to Lower Cowlitz steelhead.

24. Conclusions - Despite large hatchery releases over many years, lower Cowlitz tributaries appear to support a distinct, native population. The non-native, early winter-run hatchery stock appeared to have largest impact on Lower Cowlitz steelhead. Early-winter hatchery males, present on spawning grounds several months later than expected, expanded genetic risks.

25. Management strategies to reduce hatchery impacts Proposal to eliminate non-native, early winter-run stock at Cowlitz Hatchery. Consider use of weirs in summer months to exclude hatchery summer-run stock Revise Hatchery Genetic Management Plans (ESA “permits”)

26. Acknowledgements Chris Gleizes, Mike Blankenship, Bob Gibbons and volunteer anglers conducted field sampling. Jennifer Von Bargen conducted laboratory analyses, John Sneva interpreted scale patterns, and Steve Vanderploeg provided the lower basin map. Genotypic data for other steelhead samples were collected by Todd Kassler and Cheryl Dean, and those samples were collected by WDFW Region 5 staff. This project was funded in part by Tacoma Power and we thank Mark LaRiviere for project support.

27. Questions?