1. Annual SARs by Study Category, TIR and D: Patterns and Significance Presenter: Charlie Petrosky CSS Annual Meeting Apr 2 nd 2010

2. Chapter 4 Overview Snake River spring/summer Chinook & steelhead Snake River spring/summer Chinook & steelhead Estimate & compare annual SARs for hatchery & wild groups of smolts with different hydrosystem experiences (T 0, C 0, C 1 ) Estimate & compare annual SARs for hatchery & wild groups of smolts with different hydrosystem experiences (T 0, C 0, C 1 ) Evaluate effectiveness of transportation relative to in-river migration – annual SAR ratios between T 0 & C 0 fish (TIR) Evaluate effectiveness of transportation relative to in-river migration – annual SAR ratios between T 0 & C 0 fish (TIR) Estimate differential delayed mortality (D) between transported (T 0 ) and in-river (C 0 ) fish Estimate differential delayed mortality (D) between transported (T 0 ) and in-river (C 0 ) fish Evaluate effects of bypass via annual SAR ratios between C 0 and C 1 fish Evaluate effects of bypass via annual SAR ratios between C 0 and C 1 fish Evaluate TIR patterns relative to in-river survival (S R ) Evaluate TIR patterns relative to in-river survival (S R )

3. Smolt transportation LGRLGSLMNBON  Pre-2006: transported most collected smolts at LGR, LGS, LMN  2006-2009: bypassed early, transported mid- & late season  1994-2009: wide range of in-river conditions (flow & spill)

4. Study Categories C 0 – Pass all Snake River collector/transport dams (LGR, LGS, LMN) via combination of spill and turbine routes C 0 – Pass all Snake River collector/transport dams (LGR, LGS, LMN) via combination of spill and turbine routes i.e., C 0 fish not detected at any transport dami.e., C 0 fish not detected at any transport dam Pass primarily via spill when spill providedPass primarily via spill when spill provided Represent in-river migrants from run-at-large (most years)Represent in-river migrants from run-at-large (most years) C 1 – Pass one or more transport dams via bypass system C 1 – Pass one or more transport dams via bypass system 2006-2009 management – early migrants2006-2009 management – early migrants Bypass needed to estimate in-river survival (S R )Bypass needed to estimate in-river survival (S R ) T 0 – Transported the first time fish is collected at LGR, LGS or LMN T 0 – Transported the first time fish is collected at LGR, LGS or LMN Represent transport management strategyRepresent transport management strategy

5. SAR by Study Category PIT tag in tributaries or hatcheries upstream of LGR PIT tag in tributaries or hatcheries upstream of LGR SAR = (LGR adults)/(LGR smolts) SAR = (LGR adults)/(LGR smolts) LGR adults ~ count dataLGR adults ~ count data LGR smolts ~ mark-recapture (CJS) estimateLGR smolts ~ mark-recapture (CJS) estimate Bootstrap 90% CIBootstrap 90% CI Wild spring/summer Chinook, 1994-2007 Wild spring/summer Chinook, 1994-2007 Hatchery spring/summer Chinook, 1997-2007 Hatchery spring/summer Chinook, 1997-2007 Spring: Dworshak, Rapid R., Catherine Cr.Spring: Dworshak, Rapid R., Catherine Cr. Summer: Imnaha, McCallSummer: Imnaha, McCall MY 2008 additional hatcheries (LSRCP, IPC)MY 2008 additional hatcheries (LSRCP, IPC) Wild steelhead, 1997-2006 Wild steelhead, 1997-2006 Hatchery Steelhead, 1997-2006 Hatchery Steelhead, 1997-2006 MY 2008 initiated increased marking (LSRCP, IPC)MY 2008 initiated increased marking (LSRCP, IPC)

6. Wild Chinook SARs << NPCC 2%-6% SAR goal Wild Chinook SARs << NPCC 2%-6% SAR goal General pattern: SAR(C 0 ) ~ SAR(T 0 ) > SAR(C 1 ) General pattern: SAR(C 0 ) ~ SAR(T 0 ) > SAR(C 1 ) Exception, low flow, low spill yearsException, low flow, low spill years

7. Chinook SAR patterns: SAR(C 0 ): Wild > Hatchery SAR(C 0 ): Wild > Hatchery SAR(C 1 ): Wild > Hatchery SAR(C 1 ): Wild > Hatchery SAR(T 0 ): (MCCA, RAPH, IMNA) > Wild > DNFH SAR(T 0 ): (MCCA, RAPH, IMNA) > Wild > DNFH

8. Wild Steelhead SARs << NPCC 2%-6% SAR goal Wild Steelhead SARs << NPCC 2%-6% SAR goal General pattern: SAR(T 0 ) > SAR(C 0 ) > SAR(C 1 ) General pattern: SAR(T 0 ) > SAR(C 0 ) > SAR(C 1 ) Exceptions, 1998 & 2006Exceptions, 1998 & 2006

9. Overall SARs Wild Chinook and steelhead SARs << NPCC 2%-6% SAR goal Wild Chinook and steelhead SARs << NPCC 2%-6% SAR goal All passage routes combinedAll passage routes combined Are PIT tag SARs < SARs of untagged run-at-large? Are PIT tag SARs < SARs of untagged run-at-large? ~25% bias? (Knudsen et al. 2009)~25% bias? (Knudsen et al. 2009) tag shedding or mortality?tag shedding or mortality? CSS has begun to evaluate run reconstruction and PIT tag SARs CSS has begun to evaluate run reconstruction and PIT tag SARs Assumptions and uncertainty in run reconstruction wild smolt and adult estimatesAssumptions and uncertainty in run reconstruction wild smolt and adult estimates Directed studies at hatcheriesDirected studies at hatcheries

10. SAR Ratios TIR = SAR(T 0 )/SAR(C 0 ) TIR = SAR(T 0 )/SAR(C 0 ) Evaluate relative efficacy of transportation vs. in-river passageEvaluate relative efficacy of transportation vs. in-river passage Based on LGR smolts and LGR adultsBased on LGR smolts and LGR adults D = [SAR(T 0 )*S T ]/[SAR(C 0 )*S R ] D = [SAR(T 0 )*S T ]/[SAR(C 0 )*S R ] Evaluate relative post-Bonneville survival of transport vs. in-riverEvaluate relative post-Bonneville survival of transport vs. in-river Based on BON smolts and LGR adultsBased on BON smolts and LGR adults Requires estimate of in-river survival (S R ) from LGR to BON and survival in bargeRequires estimate of in-river survival (S R ) from LGR to BON and survival in barge SAR(C 0 )/SAR(C 1 ) SAR(C 0 )/SAR(C 1 ) Evaluate relative survival effect of bypass vs. combined spill and turbine passage through LGR, LGS & LMNEvaluate relative survival effect of bypass vs. combined spill and turbine passage through LGR, LGS & LMN Bootstrapped 90% CI for all annual SAR ratios Bootstrapped 90% CI for all annual SAR ratios

11. Chinook TIR General patterns: Wild – transportation relatively ineffective Wild – transportation relatively ineffective TIR > 1.0 in 2001, 2005 TIR 1.0 in 2001, 2005 TIR < 1.0 in 2000, 2002 (p<0.10) Hatchery – greater relative effectiveness than for wild Hatchery – greater relative effectiveness than for wild Varies by hatchery & yearVaries by hatchery & year TIR > 1 for ~ half of annual estimatesTIR > 1 for ~ half of annual estimates Wild & Hatchery TIR track closely across years Wild & Hatchery TIR track closely across years

12. Steelhead TIR General patterns: Wild – relative transport effectiveness Wild – relative transport effectiveness TIR > 1.0 in 6/10 yearsTIR > 1.0 in 6/10 years TIR < 1.0 in 1998 (p<0.10)TIR < 1.0 in 1998 (p<0.10) Hatchery – relative transport effectiveness Hatchery – relative transport effectiveness TIR > 1 in 4/10 yearsTIR > 1 in 4/10 years Wild & Hatchery TIR track closely across years Wild & Hatchery TIR track closely across years

13. Chinook D General patterns: Wild D ~ 0.54 (w/o 2001) Wild D ~ 0.54 (w/o 2001) D < 1.0 in 7/14 yearsD < 1.0 in 7/14 years D > 1 in zero of 14 (p<0.10) Hatchery D – greater than wild D Hatchery D – greater than wild D Varies by hatchery & yearVaries by hatchery & year D < 1 in 11/51 annual estimates D > 1 in 6/51 estimates (p<0.10) (p<0.10) Wild & Hatchery D track closely across years Wild & Hatchery D track closely across years

14. Steelhead D General patterns: Wild D ~ 1.0 Wild D ~ 1.0 D 1 in 3/10 years (p 1 in 3/10 years (p<0.10) Hatchery D – similar wild D Hatchery D – similar wild D D 1 in 1/10 years (p 1 in 1/10 years (p<0.10) Wild & Hatchery D estimates differ somewhat between years Wild & Hatchery D estimates differ somewhat between years

15. Ratio SAR(C 0 )/SAR(C 1 ) General patterns: SAR(C 0 ) > SAR(C 1 ) SAR(C 0 ) > SAR(C 1 ) Negative bypass effect on SARs for Wild & Hatchery Chinook & Steelhead Negative bypass effect on SARs for Wild & Hatchery Chinook & Steelhead

16. Why difference in relative transportation effects between Chinook and steelhead? Is TIR related to in- river conditions and smolt survival? Is TIR related to in- river conditions and smolt survival? Wild Chinook annual S R ~ 50% (range 23% - 61%), 1997-2006Wild Chinook annual S R ~ 50% (range 23% - 61%), 1997-2006 Wild steelhead annual S R ~ 37% (range 4% - 58%), 1997-2006Wild steelhead annual S R ~ 37% (range 4% - 58%), 1997-2006 Regression analysis: association of TIR and S R for wild Chinook & steelhead Regression analysis: association of TIR and S R for wild Chinook & steelhead

17. Relative effectiveness of transportation declines as S R increases Expected TIR 55% Expected TIR 55% Wild ChinookWild Chinook Wild steelheadWild steelhead Chinook S R > steelhead S R Chinook S R > steelhead S R How much can we improve steelhead S R ? How much can we improve steelhead S R ? Wild steelhead S R related to WTT and, particularly, spill (Chapter 3)Wild steelhead S R related to WTT and, particularly, spill (Chapter 3) Chinook Steelhea d Chinook steelhead

18. Chapter 4 Summary Annual SARs << NPCC 2-6% SAR goal Annual SARs << NPCC 2-6% SAR goal Snake River wild Chinook & steelheadSnake River wild Chinook & steelhead T 0, C 0 and C 1 and combinedT 0, C 0 and C 1 and combined Significant negative bypass effect on SARs Significant negative bypass effect on SARs SAR(C 0 ) > SAR(C 1 ), Wild & Hatchery, Chinook & SteelheadSAR(C 0 ) > SAR(C 1 ), Wild & Hatchery, Chinook & Steelhead TIRs of both wild Chinook and steelhead variable across years and associated with in-river survival TIRs of both wild Chinook and steelhead variable across years and associated with in-river survival Relative effectiveness of transportation declines as in-river survival (S R ) increases Relative effectiveness of transportation declines as in-river survival (S R ) increases TIR steelhead > TIR ChinookTIR steelhead > TIR Chinook S R Chinook > S R steelheadS R Chinook > S R steelhead S R is function of in-river conditions (WTT and spill)S R is function of in-river conditions (WTT and spill) How much can we improve S R ?How much can we improve S R ?

19. Questions?