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Demographic Evaluation of Hatchery and Natural-Origin Chinook Salmon and its Impact on Population Genetic Structure in t

This study evaluates the effects of management activities and demography on the genetic diversity of Chinook salmon in the South Fork Salmon River. It examines the population genetic structure within the river and among different population groups. The study also analyzes the impact of management and demographic factors on genetic diversity across multiple spatial scales.

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Demographic Evaluation of Hatchery and Natural-Origin Chinook Salmon and its Impact on Population Genetic Structure in t

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  1. A demographic evaluation of hatchery- and natural-origin Chinook salmon and its impact on the population genetic structure in the South Fork Salmon River William P. Young1, Andrew P. Matala2, Shawn R. Narum2 and Jason Vogel1 1Nez Perce Tribe Department of Fisheries Resources Management 2Columbia River Intertribal Fish Commission Hagerman Genetics Lab

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

  3. Effects of management and demography across multiple spatial scales large • 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 small

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

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

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

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

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

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

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

  11. Index of Spawner Abundance – SFSR MPG, 1996 - 2008 Pearson Correlation 61% 26% 13% *P < 0.005 Secesh JC Upper SFSR

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

  13. MPG level Spawner • Distribution • Major spawning areas in headwaters • Populations are separated by areas of unsuitable spawning habitat • High gradient • Large substrate • Likely 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. Spatial Scale • 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 large large small

  17. GENETIC DISTANCE: Radial tree topology – greater proximity equals greater similarity In the context of larger scope Snake River studies. JCsupp 4. Secesh 5. HAT2002 3. JC 98.9 98.9 HAT2000 63.8 1. 2. SCT01 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 SCT03 SCT-AW Nei: 0.01 SCT04 HAT2001 SCT02 Narum et al. 2007. Transactions of the American Fisheries Society 136:1252-1262.

  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

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