1. William P. Young 1, Andrew P. Matala 2, Shawn R. Narum 2 and Jason Vogel 1 1 Nez Perce Tribe Department of Fisheries Resources Management 2 Columbia River Intertribal Fish Commission Hagerman Genetics Lab A demographic evaluation of hatchery- and natural-origin Chinook salmon and its impact on the population genetic structure in the South Fork Salmon River

2. Objective: Evaluate the impacts of management activities and demography on the genetic diversity of Chinook salmon Within the upper SFSR population South Fork Salmon River (SFSR) Major Population Group (MPG) within the South Fork Salmon River (SFSR) Major Population Group (MPG) among MPGs within the Snake River Sp/su Chinook salmon ESU among MPGs within the Snake River Sp/su Chinook salmon ESU Measures of genetic diversity Measures of genetic diversity Spawner abundance Spawner abundance Spawner distribution Spawner distribution Hatchery fraction Hatchery fraction

3. Among MPGs within the Snake River basin ESU Philopatry Landscape/geography Among populations within the SFSR MPG upper SFSR Johnson Creek Secesh River Within the upper SFSR, HOR and NOR spawners 4 sections downstream of a weir 1 section upstream of a weir Effects of management and demography across multiple spatial scales small large

4. Management and demographic structure -upper SFSR Large segregated (H x H) mitigation hatchery programLarge segregated (H x H) mitigation hatchery program Started in 1978, mixed originStarted in 1978, mixed origin 100% marking in 1995100% marking in 1995 Significant hatchery- and natural-origin spawning upstream and downstream of the weirSignificant hatchery- and natural-origin spawning upstream and downstream of the weir Pass all unclipped fish above the weirPass all unclipped fish above the weir Hatchery outplants downstream of the weir and to the EFSFSRHatchery outplants downstream of the weir and to the EFSFSR Significant sport and tribal harvestSignificant sport and tribal harvest

5. Management and demographic structure Johnson Creek - East Fork South Fork Salmon River (EFSFSR) population Supplementation hatchery programSupplementation hatchery program N x N broodstockN x N broodstock Initiated in 1997Initiated in 1997 No AD clip, 100% cwt & VIE marksNo AD clip, 100% cwt & VIE marks Significant natural- and hatchery- origin spawning upstream of a weirSignificant natural- and hatchery- origin spawning upstream of a weir Minimal tribal harvestMinimal tribal harvest

6. Management and demographic structure -Secesh River Managed for natural spawningManaged for natural spawning Minimal hatchery influence (strays)Minimal hatchery influence (strays) Significant natural-origin spawningSignificant natural-origin spawning Minimal tribal harvestMinimal tribal harvest

7. Johnson Creek weirMcCall Hatchery weir Spawning ground surveys Weir captures Methods

8. Annual redd counts 1996 2008 2000 2004 Index of Spawner Abundance - upper SFSR, 1996-2008

9. Stolle Meadows, Sec AW 41.4% Weir to unnamed tributary, Sec 01 & 02 76.4% Natural Hatchery Lodgepole CG to Phoebe Creek, Sec 04 10.2% Hatchery Fraction - upper SFSR, 1996-2008 Poverty Flat, Sec 03 21.2%

10. McCall Hatchery weir Spawner Distribution - Upper SFSR Stolle Meadows (Above weir) Below weir Average redd counts

11. SeceshJC total SFSR Secesh1 JC0.91*1 SFSR0.82*0.73*1 Index of Spawner Abundance – SFSR MPG, 1996 - 2008 SeceshJCUpper SFSR 26% 13% 61% *P < 0.005 Pearson Correlation

12. Secesh River Stray HOR = 4.7% Johnson Creek Stray HOR = 3.4% Endemic HOR = 47% Hatchery Fraction - SFSR MPG, 1996-2008 SFSR Approximate HOR = 40%

13. MPG level Spawner Distribution Major spawning areas in headwatersMajor spawning areas in headwaters Populations are separated by areas of unsuitable spawning habitatPopulations are separated by areas of unsuitable spawning habitat High gradient High gradient Large substrateLarge substrate Likely influenced historic metapopulation structure and diversityLikely influenced historic metapopulation structure and diversity

14. Summary – upper SFSR Spawner abundance - Similar annual redd count variation upstream and downstream of the weir Hatchery Fraction - highest in the two sections just below the weir, significant in all sections, including above the weir. Spawner Distribution - spawning distributed almost continuous. Little to no spawning Chinook salmon in the lower 15 kilometers

15. Conclusions – SFSR MPG Spawner Abundance – high spawner variation across years. Hatchery fraction – minor influence of strays in JC and Secesh Spawner distribution - major spawning areas separated by areas of unsuitable spawning habitat (high gradient, large substrate)

16. Historic genetic relationships between the SFSR MPG other MPGs within the Snake River basin ESU appear to have been conserved. Philopatry Landscape/geography Three distinct populations persist in the SFSR MPG widely varying abundance, composition and distribution. widely varying management intensity De facto hatchery integration in the upper SFSR Leaky weir, ISS supplementation Significant HOR spawners downstream of the weir Spatial Scale small large

17. JC JCsupp SCT01 SCT04 SCT02 SCT03 HAT2001 HAT2002 HAT2000 SCT-AW Secesh Nei: 0.01 98.9 63.8 98.9 GENETIC DISTANCE: Radial tree topology – greater proximity equals greater similarity 2. 3. 4. 5. 1. 1.) Imnaha River 2.) Grande Ronde & Clearwater 3.) SFSR : three upper SFSR groups two Johnson Creek & Secesh River 4.) Middle Fork Salmon River 5.) Upper Salmon River Narum et al. 2007. Transactions of the American Fisheries Society 136:1252-1262. In the context of larger scope Snake River studies.

18. Acknowledgements Nez Perce Tribe Neal Espinosa Mike Blenden Cameron Albee Rick Orme Jay Hesse Ryan Kinzer Craig Rabe Field Crews Idaho Department of Fish and Game John Cassinelli Brian Leth Kim Apperson Field Crews