By Lytle P. Denny K.A. Tardy, and C. Lopez Shoshone-Bannock Tribes Fish & Wildlife Department

1. Using Full Parental Genotyping to Determine the Efficacy of Streamside Incubators for Rearing Hatchery-Origin Steelhead Eggs and Increasing Population Abundance in the Yankee Fork Salmon River, Idaho. By Lytle P. Denny K.A. Tardy, and C. Lopez Shoshone-Bannock Tribes Fish & Wildlife Department March 4, 2008

2. SSI Program Background SSI Goal SSI Objectives SSI Methods M & E Goal M & E Objectives M & E Methods Results Discussion

3. Background • Stream-Side Incubator (SSI) Program initiated in 1995 in Upper Salmon River (Figure 1) • Initial Cooperators included • Trout Unlimited • BLM • USFS • Upper Salmon Basin Watershed Project • IDFG • Private landowners • Site are located in five tributaries of the Upper Salmon River (Figure 2) • Incubation methods included using refrigerators, whitlock-vibrant boxes, Jordan-Scotty condominiums,“haddix boxes,” wood incubators, and lastly upwellers.

4. Background • Snake River Steelhead ESU listed October 17, 1997; no distinctions were made between A-run or B-run summer steelhead • SBT envisioned using natural steelhead for broodstock, unfortunately none were available • Early M & E efforts guided by Technical Committee including • IDFG • USFS • USBWP • BLM • SBT • M & E efforts beyond estimating fry production were unsuccessful • SBT completed M & E Plan in 2005 • Focus efforts in Yankee Fork Salmon River • Use DNA Parentage Analysis;

5. SSI Goal • Reintroduce and recover native salmonids to vacant and critically under-seeded habitats until remaining populations can become self-sustaining through natural production

6. SSI Objectives • Incubate approximately 1.0 million eyed-eggs in five Upper Salmon River tributaries • Yankee Fork 375,000 • Panther Creek 250,000 • Basin Creek 125,000 • Morgan Creek 125,000 • Indian Creek 125,000 • Achieve >90% hatch success

7. SSI Methods • Trapping and spawning conducted at Sawtooth Fish Hatchery • Approximately 99 adult pairs needed to achieve 375,000 eyed eggs • 4,200 eggs/female * 90% green egg to eyed egg survival • Adults spawned one-to-one • Estimate fecundity • Eggs checked for BKD; IDFG Fish Health

8. SSI Methods • Egg Incubation (green to eyed) • Following SFH standard protocol • Egg Incubation (eyed to fry) • Stream-side Incubators • Incubated on natural river water • Temperature, DO, and sedimentation are site specific • Flow is adjusted • Hatch success/fry seeded • Count dead eggs and/or fry

9. M & E Goal • Monitor and Evaluate the Tribes’ hatchery steelhead supplementation activities in Yankee Fork so that operations can be adaptively managed to optimize hatchery and natural production, provide dispersal, sustain harvest, and minimize ecological impacts.

10. M & E Objectives • Determine if program objectives for contribution rate of hatchery fish are being achieved and can be improved. • Determine the increases in natural production that results from supplementation of steelhead in Yankee Fork and relate this information to possible limiting factors. • Communicate monitoring and evaluation findings to resource managers.

11. M & E Methods • Spawn adult steelhead – one-to-one matings • Collect genetic samples from all brood fish • Genotype parents at 14 u-sat loci • Outplant known families (eyed eggs) in incubators • Collect genetic sample from age-0+ and age-1+ juvenile steelhead in Yankee Fork in subsequent years • Genotype unknown juveniles at 14 u-sat loci • Perform parentage analysis on parent broodfish and unknown juveniles

12. M & E Approach 2. Collect and Incubate Eggs 3. Incubate Eyed- eggs in incubators F1 generation 1. Spawn Hatchery Adults 4. Release fry volitionally 5. Collect 0+ parr during first fall 6. Collect 1+ parr during second fall

13. M & E Methods • Population size point estimates made for all Yankee Fork age-0+ and age-1+ O. mykiss • Randomly select sampling sites • Perform 3-pass removal electrofishing with block nets • Measure fork length, mass, and collect tissue and scale samples • Analyze condition factor

14. M & E Methods • Perform parental exclusion/pedigree analysis of adult broodstock to Yankee Fork juvenile O. mykiss • Use genetic markers to identify SSI progeny from naturally produced progeny • Determine relative abundance of SSI progeny and natural origin progeny • Estimate SSI survival from egg to fry

16. Field Identification Step 1. Field ID Step 2. Genetic ID Hatchery smolt Rainbow Trout Outplant Y Do not sample Physical tag/mark? Parented by hatchery broodstock or Natural-origin? SAMPLE COLLECTED Hatchery-origin N Natural-origin

17. Juvenile (unknown origin) Sawtooth Parent (M) Sawtooth Parent (F) Sawtooth Parent (M) SSI Outplant

18. Results In 2006, 52 parent pairs were spawned Outplanted approximately 214,750 eyed-eggs in four incubators Lost one incubator because of an elk Average hatch success was 98.6% without Jordan Creek incubator 155,908 fry successfully emigrated

19. Results In 2006, we sampled 18 randomly stratified reaches and collected approximately 349 age-0+ O. mykiss. In 2007, we sampled 21 randomly statified reaches and collected approximately 123 age-1+ O. mykiss. All adult and juvenile tissue samples sent to Abernathy Fish Technology Center for DNA parentage analysis

22. Total estimated age-0+ O. mykiss abundance and estimated streamside progeny abundance. Stratum four shows the highest abundance of incubator progeny at 50% of the population. Overall estimated age-0+O. mykiss equaled 17,850 (± 2207) juveniles in 2006 with 4,268 (± 1244) individuals being from stream-side incubator origin. We estimate that 23.9% (95% C.I. = 19.3 – 27.5%) of the Yankee Fork steelhead population in 2006 originated from supplementation program.

23. Average condition and length of natural (unidentified) versus streamside incubator progeny (identified). There is no difference in mean condition factor or mean length between identified streamside incubator progeny and natural spawning steelhead in YF.

24. Relative abundance of salmonid species in Yankee Fork during 2006. Steelhead is the most ubiquitous species throughout Yankee Fork equaling >50% richness in five of the six strata sampled. Bull trout were the most dominant species in stratum five while chinook and cutthroat abundances were highest in stratum four and seven, respectively.

25. Relative abundance of salmonid species in Yankee Fork during 2007. Steelhead is the most ubiquitous species throughout Yankee Fork equaling >60% richness in six of the seven strata sampled. Bull trout were again the most dominant species in stratum five while chinook and cutthroat abundances were highest in stratum four and seven, respectively.

26. Neighbor-Joining phylogram topology and genetic distance relationship between 8 analysis groups. Values at nodes indicate bootstrap support among 1000 replicate data sets.

27. The neighbor-Joining phylogram topology and genetic distance relationship between 8 analysis groups, and age class differences within groups.

28. Discussion Parentage analysis indicates that SSI juveniles successfully emerge and survive in-stream through their first year of life. It is very difficult to speculate the fate of juvenile steelhead after their first year of life under current program operations. Parentage analysis provides a foundation for understanding movement of juvenile steelhead. Movement of age-0+ fish is relatively small and downstream from incubators. Interestingly, 100% of all juveniles sampled in Upper Yankee Fork were SSI origin and this area is likely an excellent area to bolster supplementation

29. Discussion • SSI produce parr (23.9% age-0+) • No statistical difference in condition or length of SSI progeny and natural-origin progeny • Achieve outplanting objective of 375,000 eyed eggs • Increase sampling for better resolution between sites • Habitat is relatively vacant and can support increases in supplementation • 2006 density 0.027 fish/m2

30. Discussion Predominate age class is 50-80mm Migration time and age at migration is unknown, however, we sample few fish above 80mm indicating 1+ juveniles may be migrating from the Yankee Fork before their second fall

31. Recommendations Increase supplementation Increase sampling efforts Operate rotary screw trap and enumerate migrating juveniles Need adult enumeration (i.e. weir)

32. ACKNOWLEDGEMENTS • Sawtooth Fish Hatchery • Brent Snider • Roger Elmore • Jocelyn Hatch • Phil Stone • Danielle Corfch • Caleb Price • Lars Alsager • Mel Hughes • Abernathy Fish Technology Center- • Conservation Genetics Laboratory • William Ardren • Andrew Matala • LSRCP • Scott Marshall • Chris Starr • Joe Krakker • US Forest Service • Volunteers • Jared Moss • Garret “Dr. Death” Galloway • Ty Broncho • SBT • Andy Kohler • Rodney Burns