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COMPARATIVE SURVIVAL STUDY (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead

2006 Annual Report

BPA Project #199602000

Prepared by

Fish Passage Center and Comparative Survival Study Oversight Committee:

Thomas Berggren and Peter McHugh , Fish Passage Center

Paul Wilson and Howard Schaller, U.S. Fish and Wildlife Service Charlie Petrosky, Idaho Department of Fish and Game

Earl Weber, Columbia River Inter-Tribal Fish Commission Ron Boyce, Oregon Department of Fish and Wildlife

Project Leader: Michele DeHart, Fish Passage Center

Final 11/30/2006

TABLE OF CONTENTS PAGE List of Tables ........................................................................................................................ iii List of Figures ....................................................................................................................... ix Acknowledgements .............................................................................................................. xiv Executive Summary ............................................................................................................. xvi Chapter 1 – Introduction ....................................................................................................... 1 Chapter 2 – Methods ............................................................................................................ 4

Chapter 3 – SARs, T/C ratio, and D for Wild and Hatchery Chinook ................................. 8 Chapter 4 – SARs, T/C ratio, and D for Wild and Hatchery Steelhead ............................... 27 Chapter 5 – Relationships between wild and hatchery Chinook salmon smolt-to-adult survival and inriver, estuary/early ocean, and off-shore marine environmental conditions ................................................................................................................................................. 41

Chapter 6 – Associations between smolt outmigration experience and adult Chinook salmon Bonneville-to-Lower-Granite-Dam apparent survival rates ...................................... 50 Chapter 7 – Upstream-downstream comparisons: Differential mortality for upriver and downriver PIT-tagged wild and hatchery sp/su Chinook ...................................................... 60 Chapter 8 – Upstream-downstream comparisons: contrasting smolt life histories between Snake River and John Day River stream-type Chinook salmon populations ............................................................................................................................. 68 Chapter 8 Appendix – Redd density estimation .................................................................. 79 Chapter 9 – Understanding the implications of smolt size—detection probability relationships for CSS study-group comparisons ......................................................................80 Chapter 10 – Computer program to create simulated PIT tag input files for testing robustness of CJS survival estimates .......................................................................................88 References ...............................................................................................................................100 Appendix A – Formula of parameters used in CSS analyses .................................................105 Appendix B – Estimated number of smolts per study category with associated 90% confidence interval and number of returning adults per study category ..................................113

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Appendix C – Reach survival estimates with bootstrap 95% confidence intervals ...............121 Appendix D – Age distribution of returning adult Chinook and steelhead detected at Lower Granite Dam (or Bonneville Dam for downriver populations) ....................................129 Appendix E – Number of PIT-tagged smolts transported at each collector dam (plus estimated number if tagged fish had been transported in same proportion as the untagged population) and site-specific SAR estimates ..........................................................................132 Appendix F – Data used in estimating the annual weighted SARs for wild and hatchery Chinook and steelhead ............................................................................................................137 Appendix G – PIT-tagged hatchery Chinook release numbers and relation to production ...............................................................................................................................140 Appendix H – Release sites of PIT-tagged wild Chinook and wild & hatchery steelhead (each release site is not present for every migration year) .......................................142 Appendix I – Regional review comments and CSS Oversight Committee responses .................................................................................................................................148

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LIST OF TABLES PAGE Table 1. Number of PIT-tagged wild Chinook parr/smolts from the four tributaries above Lower Granite Dam and Snake River trap used in the CSS analyses for migration years 1994 to 2004. .............................................................................8 Table 2. Estimated SARLGR-to-LGR (%) for PIT-tagged wild Chinook in annual aggregate for each study category from 1994 to 2004 (with 90% confidence intervals). .................................................................................................................................10 Table 3. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged wild Chinook for migration years 1994 to 2004 (with 90% confidence intervals). .................................................................................................................................12 Table 4. Number of PIT-tagged hatchery Chinook parr/smolts from key hatcheries located above Lower Granite Dam used in the CSS analyses for migration years 1997 to 2004. .................................................................................................13 Table 5. Estimated SARLGR-to-LGR (%) for PIT-tagged spring Chinook from Rapid River Hatchery for each study category from 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................15 Table 6. Estimated SARLGR-to-LGR (%) for PIT-tagged spring Chinook from Dworshak Hatchery for each study category from 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................16 Table 7. Estimated SARLGR-to-LGR (%) for PIT-tagged spring Chinook from Catherine Creek AP for each study category from 2001 to 2004 (with 90% confidence intervals). ...............................................................................................................17 Table 8. Estimated SARLGR-to-LGR (%) for PIT-tagged summer Chinook from McCall Hatchery for each study category from 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................18 Table 9. Estimated SARLGR-to-LGR (%) for PIT-tagged summer Chinook from Imnaha River AP for each study category from 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................19 Table 10. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Rapid River Hatchery spring Chinook for 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................21 Table 11. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Dworshak Hatchery spring Chinook for 1997 to 2004 (with 90% confidence intervals). .................................................................................................................................22

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Table 12. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Catherine Creek AP spring Chinook for 2001 to 2004 (with 90% confidence intervals). ...............................................................................................................22 Table 13. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged McCall Hatchery summer Chinook for 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................22 Table 14. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Imnaha AP summer Chinook for 1997 to 2004 (with 90% confidence intervals). ...............................................................................................................23 Table 15. Number of PIT-tagged wild steelhead smolts from the four tributaries above Lower Granite Dam (plus Snake River trap) used in the CSS for migration years 1997 to 2003. .................................................................................................27 Table 16. Estimated SARLGR-to-LGR (%) for PIT-tagged wild steelhead in annual aggregate for each study category from 1997 to 2003 (with 90% confidence intervals). ...............................................................................................................29 Table 17. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged wild steelhead for migration years 1997 to 2003 (with 90% confidence intervals). ...............................................................................................................31 Table 18. Number of PIT-tagged hatchery steelhead smolts from the four tributaries above Lower Granite Dam (plus mainstem Snake River) used in the CSS for migration years 1997 to 2003. ....................................................................................34 Table 19. Estimated SARLGR-to-LGR (%) for PIT-tagged hatchery steelhead in annual aggregate for each study category from 1997 to 2003 (with 90% confidence intervals). ...............................................................................................................36 Table 20. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged hatchery steelhead for migration years 1997 to 2003 (with 90% confidence intervals). ...............................................................................................................38 Table 21. Model selection results for SAR–environmental variable regression models fitted using 1994-2004 MY PIT-tag-based annual weighted SARs. The bold-faced entry corresponds to the model with the lowest AICc value (corrected for sample size) score. Q is discharge, WTT is water transit time, CUI-April is April upwelling, CUI-Oct is October upwelling, and PDO is Pacific decadal oscillation. .......................................................................................................45

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Table 22. Model selection results for SAR–environmental variable regression models fitted using 1964-1984 and 1991-2001 MY run-reconstruction-based SARs. The bold-faced entry corresponds to the model with the lowest AICc value (corrected for sample size) score. See Table 1 description for variable definitions. ..............................................................................................................................45 Table 23. Least-squares slope parameter estimates (+/- 95% CIs) for bivariate regressions between PIT-tag- (‘Contemp.’ in table) and run-reconstruction-based (‘Historic’ in table) SARs and environmental factors. Bold-faced cell entries correspond to those estimates differing significantly from zero. .............................................47 Table 24. Counts of hatchery Chinook salmon adults that failed (‘F’) or were successful (‘S’) in surviving their BON-LGR migration in return years 2002- 2006, grouped by migration year and outmigration experience (see Methods for group definitions). There was evidence for a significant association between transport history and migration success where sufficient observations-per-cell were available (see Table 26 for details). .........................................................................................51 Table 25. Counts of wild Chinook salmon adults that failed (‘F’) or were successful (‘S’) in surviving their BON-LGR migration in return years 2002- 2006, grouped by migration year and outmigration experience (see Methods for group definitions). There was evidence for a significant association between transport history and migration success where sufficient observations- per-cell were available (i.e., > 5; MY2002: χ2 = 8.74, df = 2, P = 0.013; Combined: χ2 = 7.94, df = 2, P = 0.019; MY2001, MY2003-4, not applicable). .........................................................................................................................51 Table 26. Summary of MY-, RY-, and hatchery-specific χ2-tests for hatchery Chinook salmon. The P-values listed are not corrected for multiple tests. The success rate ranking corresponds to the ordering of % successful upstream migrants by juvenile outmigration history. The entry ‘NA’ corresponds to table values that are not applicable because either a test was not performed due to low cell counts (i.e., RY2002) or the resulting test statistic was not significant (α = 0.05). df = 2 for all tests. ...............................................................................53 Table 27. Logistic regression model-selection results for CSS hatchery Chinook salmon. Note, Y = P(Success | X), where X is the variable in question. The bold-faced model was the one most supported by the data, however those with a ΔAIC < 2 can be considered nearly equivalent. K is the number of estimated parameters (inclusive of variance). ..................................................55 Table 28. Parameter estimates for the top logistic regression model describing BON-LGR migration success for CSS hatchery Chinook salmon returning in 2002-2006. ...........................................................................................................55

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Table 29. Logistic regression model-selection results for CSS wild Chinook salmon. Note, Y = P(Success | X), where X is the variable in question. The bold-faced model was the one most supported by the data, however those with a ΔAIC < 2 were viewed as equivalent. K is the number of estimated parameters (inclusive of variance). ..........................................................................................56 Table 30. Parameter estimates for the top logistic regression model describing BON-LGR migration success for CSS wild Chinook salmon returning from 2002-2006. ...............................................................................................................................56 Table 31. Number of PIT-tagged Carson Hatchery Chinook released in the Wind River, estimated survival and resulting smolt population arriving Bonneville Dam in migration years 2000 to 2004 (with 90% confidence intervals) with detected adults at BOA. ..........................................................................................................................61 Table 32. PIT-tag detections of returning adult Chinook (ages 2- and 3-salt) at Bonneville and Lower Granite dams with percentage of fish undetected at Bonneville Dam – returns from smolts that outmigrated in 2001 to 2004. ................................................62 Table 33. Estimates of SAR from first dam encountered1 as smolts to Bonneville Dam (BOA) as adults2 for the upriver PIT-tagged wild Chinook aggregate and the downriver PIT-tagged John Day River wild Chinook that outmigrated in 2000 to 2004. ...................................................................................................63 Table 34. Number of PIT-tagged wild Chinook released in John Day River basin, estimated survival and resulting smolt population arriving John Day Dam in migration years 2000 to 2004 (with 90% confidence intervals) with detected adults at BOA. ..........................................................................................................................64 Table 35. Estimates of SAR from first dam encountered1 as smolts to Bonneville Dam (BOA) as adults2 for the upriver PIT-tagged wild Chinook aggregate and the downriver PIT-tagged John Day River wild Chinook that outmigrated in 2000 to 2004. ...................................................................................................65 Table 36. Conversion of estimated upriver/downriver ratios to differential mortality rates for comparison to differential mortality rates computed by spawner-recruit analyses, 95% confidence intervals shown with each method. .....................66 Table 37. Summary statistics for wild Chinook salmon smolts captured, tagged, and released at CSS trap sites between March 15 and May 20 during migration years 2000-2005. ...............................................................................................................................70 Table 38. Results from an ANCOVA-based comparison of smolt size across upstream and downstream release sites, using redd density as a covariate. ............................................72

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Table 39. Results from an ANOVA evaluating smolt size variation across release sites and migration years. .........................................................................................................73 Table 40. Dates of 50% passage (i.e., median emigration date) for Chinook salmon captured, tagged, and released at CSS-affiliated trap sites during MYs 2000-2006. ...............................................................................................................................74 Table 41. Median estuary arrival (i.e., BON detection) dates for Chinook salmon smolts captured, tagged, and released at CSS-affiliated trap sites during MYs 2000-2006. ..............77 Table 42. Redd abundance and surveyed kilometers for production areas upstream of CSS trap sites used to contrast smolt size between upstream and downstream populations. ..............................................................................................................................79 Table 43. Sample sizes for PIT-tagged release groups (sum of SNKTRP and CLWTRP releases between 11 April and 10 May) used in our estimation of P(det | FL) relationships (1999, 2000, 2002, 2005-6) and comparison of size between detected and undetected study categories, by migration year (MY). Bold-faced values correspond to MYs included in our survival/detection probability modeling exercise. ...................................................................................................................81 Table 44. Candidate detection probability (p) models fitted for fish groups released in migration years 1999-2000, 2002, and 2005-6. For detection-probability model selection, the survival (φ) model structure was held constant based on the recommendations of Lebreton et al. (1992), in the most global form [i.e., φ(site × FL, all), survival varies across sites as a site-specific function of length]. ....................................................................82 Table 45. Model-selection results for wild Chinook salmon release groups with sufficient tags for survival and recapture probability estimation (i.e., >1,000), by migration year. ΔAIC values appear in cells. Top models (i.e., those with the lowest AIC value) are identified with bold-faced font and underlining; near-top models (i.e., those with a ΔAIC value < 2) also appear as underlined, but in italics. See Table 2 for description of survival and detection probability model structures. ........................................83 Table 46. Maximum likelihood slope parameter estimates from detection probability—fork length relationships for wild Chinook salmon captured, PIT- tagged, and released at the Snake River and Clearwater River smolt traps (rel_site = SNKTRP, CLWTRP). Bold-faced values correspond to those parameters with point estimates that were greater than twice the value of their standard errors (after Zabel et al. 2005). Estimates delineated by ‘NOAA’ correspond to the values reported in Zabel et al., ‘CSS’ corresponds to our upstream-of-LGR release analysis. .......................................................................................................................85

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Table 47. Summary statistics for detected and undetected wild Chinook salmon captured, tagged, and released from the Snake River and Clearwater River smolt traps during MYs 1998-2006. Rows with bold-faced font are those MYs where a significant difference (α = 0.05) was detected between categories using a t-test. ...........................................................................................................86 Table 48. Comparison of simulated “true” survival rates S2, S3 and VC, and number of smolts in study categories T0, C0 and C1 using default input parameters of Figures 42 to 48 and the resulting estimated parameter values obtained with the bootstrap program. ...................................................................................................................98 Table 49. Comparison of mean and 90% confidence intervals of parameters S2, S3, VC, T0, C0, and C1 of simulated samples from common underlying population and the estimates obtained with the bootstrap program. ..........................................................99

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LIST OF FIGURES PAGE Figure 1. Salmonid life cycle in the Snake River and lower Columbia River basins (source: Marmorek et al. 2004. ................................................................................................1 Figure 2. Trend in proportion of PIT-tagged wild Chinook transported at each Snake River collector dam, 1994 to 2004. ..........................................................................................9 Figure 3. Estimated SARLGR-to-LGR for PIT-tagged wild Chinook aggregate in transport and inriver study categories for migration years 1994 to 2003 (only 2-salt adult returns for 2004). ............................................................................................................10 Figure 4. Trend in estimated annual SAR (with 90% confidence intervals for 1995-2004) for wild Chinook based on PIT-tagged Chinook SARs in transport and inriver study categories weighted by estimated proportion of run-at-large in each study category for migration years 1994 to 2004 (only 2-salt adult returns for 2004). ...................................11 Figure 5. Trend in proportion of PIT-tagged hatchery Chinook transported at each Snake River collector dam, 1997-2004. ...................................................................................14 Figure 6. Trend in estimated transport and inriver SARs for Rapid River Hatchery spring Chinook for migration years 1997 to 2004 (only 2-salt adult returns for 2004). .....................................................................................................................16 Figure 7. Estimated transport and inriver SARs for PIT-tagged Dworshak Hatchery spring Chinook for migration years 1997 to 2004 (only 2-salt adult returns for 2004). ....................................................................................................................17 Figure 8. Estimated transport and inriver SARs for PIT-tagged Catherine Creek Acclimation Pond spring Chinook for migration years 2001 to 2004 (only 2-salt adult returns for 2004). .....................................................................................................................18 Figure 9. Estimated transport and inriver SARs for PIT-tagged McCall Hatchery summer Chinook for migration years 1997 to 2004 (only 2-salt adult returns for 2004). .......19 Figure 10. Estimated transport and inriver SARs for PIT-tagged Imnaha River acclimation Pond summer Chinook for migration years 1997 to 2004 (only 2-salt adult returns for 2004). .....................................................................................................................20 Figure 11. Trend in estimated annual SARLGR-to-LGR for hatchery and wild sp/su Chinook based on PIT-tagged sp/su Chinook SARs in transport and inriver study categories weighted by estimated proportion of run-at-large in each study category for migration years 1994 to 2004 (only 2-salt adult returns for 2004). ..................................................................................................................................20

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Figure 12. Trend in in-river survival (Vc) for PIT-tagged Snake River wild and hatchery spring/summer Chinook in migrations years 1994 to 2004. ..............................23 Figure 13. Trend in ratio of SAR2(T0)/SAR(C0) (log-transformed) for PIT- tagged Snake River hatchery and wild Chinook in migration years 1994 to 2004. ...........................................................................................................................24 Figure 14. Trend in D (log-transformed) for PIT-tagged Snake River hatchery and wild Chinook in migration years 1993-2004. ...................................................................24 Figure 15. Trend in proportion of PIT-tagged wild steelhead transported at each Snake River collector dam, 1997-2003. ...................................................................................28 Figure 16. Estimated transport and inriver SARs (with 90% confidence intervals) for PIT-tagged wild steelhead aggregate for migration years 1997 to 2003 (incomplete returns for 2003). .....................................................................................................................30 Figure 17. Estimated annual SAR for wild steelhead compared to wild Chinook based on PIT-tagged steelhead SARs in transport and inriver study categories weighted by estimated proportion of run-at-large in each study category for migration years 1997 to 2003 (incomplete returns for 2003). ........................................................................................30 Figure 18. Trend in in-river survival (Vc) for PIT-tagged Snake River wild steelhead and wild Chinook for migration years 1997 to 2003. ..............................................32 Figure 19. Trend in ratio of SAR2(T0)/SAR(C0) (log-transformed) for PIT-tagged Snake River wild steelhead and wild Chinook in migration years 1997 to 2003. ...................32 Figure 20. Trend in D (log-transformed) for PIT-tagged Snake River wild steelhead and wild Chinook in migration years 1997-2003. ....................................................33 Figure 21. Trend in proportion of PIT-tagged hatchery steelhead transported at each Snake River collector Dam, 1997-2003. ..................................................................................35 Figure 22. Estimated transport and inriver SARs for PIT-tagged hatchery steelhead aggregate for migration years 1997 to 2003 (incomplete returns for 2003). ...........................37 Figure 23. Trend in estimated annual SAR for hatchery and wild steelhead with associated 90% confidence intervals based on respective PIT-tagged steelhead SARs in transport and inriver study categories weighted by estimated proportion of run-at-large in each study category for migration years 1997 to 2003 (incomplete returns for 2003). .....................................................................................................................37

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Figure 24. Trend in in-river survival (Vc) for PIT-tagged Snake River hatchery and wild steelhead for migration years 1997 to 2003. .............................................................39 Figure 25. Trend in ratio of SAR2(T0)/SAR(C0) (log-transformed) for PIT-tagged Snake River hatchery and wild steelhead in migration years 1997 to 2003. ......................................39 Figure 26. Trend in D (log-transformed) for PIT-tagged Snake River hatchery and wild steelhead in migration years 1997-2003. .................................................................................40 Figure 27. Time series plot of annual weighted PIT-tag SARs for wild (‘Wild-PIT’) and hatchery (‘Hatch-PIT’, hatchery averaged) Chinook salmon across migration years 1994-2004. Run-reconstruction-based SARs (from Scheuerell and Williams 2005; ‘Wild-RR’) extending from 1964-1984 and 1991-2001 are presented for comparison. Note, SARs were interpolated between 1984 and 1991 for illustrative purposes only. ..........................................................................................................................42 Figure 28. Time series plots of inriver (Water transit time; Columbia River discharge) and estuary/ocean environmental variables (PDO, CUI-April, CUI-October) across migration years 1964 to 2004. See text and Table 21 caption for variable definitions. ...............................................................................................................................44 Figure 29. Scatter plots of hatchery and wild PIT-tag annual weighted SARs versus discharge during outmigration, April upwelling, and summer PDO. ......................................46 Figure 30. Scatter plots of PIT-tag- (‘Contemp.’) and run-reconstruction-based (‘Historic’) bivariate SAR–environmental variable (discharge and WTT during outmigration, April upwelling, and summer PDO). ................................................................48 Figure 31. Bar chart of the percent of hatchery (left) and wild (right) Chinook salmon that were successful in migrating from BON to LGR for inriver, LGR, and LGS-down outmigration histories across return years 2002-2006. ............................................................54 Figure 32. Box-and-whisker plot of BON-LGR travel times for hatchery (left) and wild (right) Chinook salmon, by outmigration experience (pooled across RYs 2002-2006). ..............................................................................................................................57 Figure 33. Trend in differential mortality ΔM=-ln(U/D) for hatchery Chinook (Snake River basin stocks [U] versus Carson NFH stock [D]) for smolt migration years 2000 to 2004. ..................................................................................................................64 Figure 34. Differential mortality estimates from the Deriso et al. (2001) model updated through smolt year 2000 (Marmorek et al. 2004) compared to estimates based on SARs of wild Snake River and John Day River sp/su Chinook, smolt migration years 2000-2004. ...........................................................................................66

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Figure 35. Trend in differential mortality ΔM=-ln(U/D) for wild Chinook (Snake River basin stocks [U] versus John Day stocks [D]) and hatchery Chinook (Snake River basin stocks [U] versus Carson NFH stock [D]) for smolt migration years 2000 to 2004. ..............67 Figure 36. Wild Chinook salmon smolt size (mean fork length +/- 1 SD) for those fish captured, tagged, and released at CSS trap sites during migration years 2000-2005 (between 15 March and 20 May). From left to right, release sites are: CLWTRP = Clearwater River Trap, GRNTRP = Grande Ronde River Trap, IMNTRP = Imnaha River Trap, JDAR1 = John Day River Trap, SALTRP = Salmon River Trap, SNKTRP = Snake River Trap. Note: there were no wild Chinook smolt size data available for CLWTRP prior to 2002. .....................................................................................71 Figure 37. Scatter plot of mean fork length (mm) against redd density (redds / km) for wild Chinook salmon smolts collected, tagged, and released at CSS trap sites during migration years 2000-2005 (between 15 March and 20 May). See Figure 36 caption for release site abbreviation definitions. ........................................................................................73 Figure 38. 6-year mean trap passage (i.e., emigration) distributions for JDAR1, SNKTRP, SALTRP, CLWTRP, IMNTRP, and GRNTRP release sites. Note: Julian date 75 is March 16th, 100 is April 10th, 125 is May 5th, and 150 is May 30th. See Figure 36 caption for release site abbreviation definitions. .....................................................74 Figure 39. Wild Chinook salmon smolt downstream migration rates (km / d, +/- 1 SD) for those fish captured, tagged, and released at CSS trap sites during migration years 2000-2005 (between 15 March and 20 May). See Figure 36 caption for release site abbreviation definitions. Note, CLWTRP operations did not begin until 2002; also, too few tags were available for SNKTRP estimation in 2001, 2004-2005. ...................................75 Figure 40. Scatter plot of first-to-third dam migration duration as a function of water travel time. Each dot reflects the mean value for a year-site combination. See Figure 36 caption for release site abbreviation definitions… ..............................................................76 Figure 41. 6-year mean estuary arrival (measured at BON) timing distributions for JDAR1, SNKTRP, SALTRP, CLWTRP, IMNTRP, and GRNTRP release sites. Note: Julian date 100 is April 10th, 125 is May 5th, 150 is May 30th, and 175 is June 24th. See Figure 36 caption for release site abbreviation definitions. ....................................77

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Figure 42. Estimated fork length (mm)—detection probability relationships for wild Chinook salmon at LGR for MYs 1999, 2000, 2002, 2005, and 2006. ...................................84 Figure 43. First input screen of simulator program – initial settings including release number and survival to LGR, travel time related parameters, and assumed SAR levels. .......89 Figure 44. Second simulator input screen – arrival population characteristics, collection efficiency and removal rates at LGR, and smolt travel time and survival to LGS. .................90 Figure 45. Third simulator input screen – collection efficiency and removal rates at LGS, and smolt travel time and survival to LMN. ..................................................................90 Figure 46. Fourth simulator input screen – collection efficiency and removal rates at LMN, and smolt travel time and survival to MCN. .................................................................91 Figure 47. Fifth simulator input screen – collection efficiency and removal rates at MCN, and smolt travel time and survival to JDA. ..................................................................91 Figure 48. Sixth simulator input screen – collection efficiency and removal rates at JDA, and smolt travel time and survival to BON. ............................................................................92 Figure 49. Seventh simulator input screen – collection efficiency and removal rates at BON, smolt travel time to trawl site, and trawl collection rate (joint survival-collection efficiency). ...............................................................................................................................92 Figure 50. Simulated arrival distribution of smolts at LGR and daily collection efficiency, based on default parameter inputs. .........................................................................94 Figure 51. Passage timing of smolts at each dam and lower Columbia trawl site for fish returned-to-river at each site (upper plot) and transported (lower plot), based on default parameter inputs. ......................................................................................................................95 Figure 52. Reach survival rate from LGR to LGS for use with daily passing (undetected or detected and returned-to-river) smolts at LGR, based on default parameter inputs. ...........96

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ACKNOWLEDGEMENTS

The Comparative Survival Study (CSS) relies on cooperation of multiple agencies and individuals to ensure that the major tasks of marking, handling, releasing, and recovery of fish in three States and at hatcheries and dams are completed successfully.

PIT-tag detection systems installed at mainstem Columbia and Snake River dams are maintained by PSMFC personnel and enable PIT-tag data to be collected and retrieved on a real-time basis. We commend Carter Stein and his staff for their diligence in repair of PIT-tag equipment in the juvenile and adult fish passage systems and providing the smooth transfer of PIT-tag data to the PIT Tag Operations Center in Portland, OR. We especially thank Dave Marvin of PSMFC, who conducts the routine programming for the “separation-by-code” operations at the dams with CSS study fish.

We extend thanks to the Fish and Wildlife agencies and all hatchery managers and staff for their assistance in the planning, raising of, and recovery of study fish for the CSS at their hatcheries. The agencies include Idaho Department of Fish and Game (IDFG) for Rapid River and McCall hatcheries, U.S. Fish and Wildlife Service (USFWS) for Dworshak and Carson hatcheries, and Oregon Department of Fish and Wildlife (ODFW) for Lookingglass Hatchery’s outplants into Imnaha and Catherine Creek acclimation ponds. These acclimation ponds are operated as a cooperative venture with Nez Perce and Umatilla tribes, respectively. We thank the field supervisors and crews for an excellent job in completing the PIT-tagging operations at these hatcheries. The USFWS’ Dworshak and Vancouver Fisheries Resource Office (FRO) personnel PIT tagged the fish at the USFWS hatcheries. PIT tagging at IDFG hatcheries was completed with supervision provided by the IDFG office in Lewiston, Idaho. Chinook at the Lookingglass complex were PIT-tagged by ODFW personnel from the Northeast District fisheries office in LaGrande, Oregon.

In addition, we extend thanks to all crews PIT tagging wild Chinook and wild and hatchery steelhead in the region. These PIT-tagged fish have provided the opportunity for the CSS to expand our comparative evaluations to these salmonids also. We appreciate and thank the researchers at IDFG, ODFW, Confederated Tribes of Umatilla Indian Reservation (CTUIR), and Shoshone-Bannock Tribes (SHOBAN) who have allowed the CSS to route a proportion of their PIT-tagged smolts to transportation at the Snake River collector dams. The CSS commends the Nez Perce Tribal researchers for routing a portion of their PIT-tagged wild Chinook from the Imnaha and SF Salmon River sub-basins to transportation; this increases representation of those drainages in the wild Chinook PIT-tag aggregate population for SAR estimation.

The Fish Passage Center’s role in the implementation of this program was accomplished through coordination of PIT tagging and field logistics, performing database development, data compilation and preliminary analyses, and overseeing the budgetary aspects of this study. In addition to the coauthors, FPC staff members Michele DeHart and Dona Watson provided valuable contributions to the implementation of this program and Brandon Chockley provided assistance in graphics. A special thanks goes to former FPC staff Henry Franzoni, who programmed the “bootstrap” and “simulator” routines, Sergei Rassk for his contribution to updates and improvements to both the bootstrap and simulator programs, and Paul Wilson (USFWS) for his contribution to the planning and development of both the “simulator” and bootstrap programs. We also thank Nick Bouwes (EcoLogic, Logan UT) for his assistance in the planning phase of the bootstrap program.

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Bonneville Power Administration (BPA Project Number 19660200) funded this project through the Northwest Power Planning Council Fish and Wildlife Program. BPA’s Contract Officer’s Technical Representative (COTR) for the CSS is Tracy Hauser.

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EXECUTIVE SUMMARY

The Comparative Survival Study (CSS) was initiated in 1996 as a multi-year program of

the fishery agencies and tribes to estimate survival rates over different life stages for spring and summer Chinook salmon (hereafter, Chinook) produced in major hatcheries the Snake River basin and from selected hatcheries in the lower Columbia River. Much of the information evaluated in the CSS is derived from fish tagged with Passive Integrated Transponder (PIT) tags. A comparison of survival rates of Chinook marked in different regions (which differ in the number of dams Chinook have to migrate through) provides insight into the effects of the Federal Columbia River Power System (FCRPS, hereafter termed hydrosystem). The CSS compares the smolt-to-adult survival rates (SARs) for Snake River wild and hatchery Chinook that were transported versus those that migrated inriver to below Bonneville Dam. As in 2005, we also computed SARs for wild and hatchery summer steelhead PIT-tagged under other existing programs. These SAR estimates generate information reflecting the relative effects of the current management actions used to recover this listed species.

Scientists and managers have recently emphasized the importance of delayed hydrosystem mortality to long-term management decisions. Delayed hydrosystem mortality may occur for both smolts that migrate inriver and smolts that are transported. The CSS PIT-tag information on inriver survival rates and SARs of both transported and inriver fish are relevant to the estimation of “D”, a parameter which partially describes delayed hydrosystem mortality. It is the differential survival rate of transported fish relative to fish that migrated inriver from below Bonneville Dam as smolts to adults returning to Lower Granite Dam. When D < 1, the transported smolts die at a greater rate after release below Bonneville Dam than smolts that have migrated inriver to below Bonneville Dam.

Major objectives of the CSS include: (1) development of a long-term index of transport SAR to inriver SAR for Snake River hatchery and wild spring/summer Chinook smolts measured at Lower Granite Dam; (2) develop a long-term index of survival rates from release of smolts at Snake River hatcheries to return of adults to the hatcheries; (3) compute and compare the overall SARs for selected upriver and downriver spring and summer Chinook hatchery and wild stocks; and (4) begin a time series of SARs for use in hypothesis testing and in the regional long-term monitoring and evaluation.

The CSS PIT tags and annually releases more than 200,000 smolts from Snake River hatcheries (e.g., Dworshak, McCall, Rapid River, Catherine Creek and Imnaha) and currently 15,000 smolts from a downriver hatchery (Carson NFH). In addition, the CSS provides 23,000 PIT-tags for wild Chinook and wild steelhead to augment various on-going trapping and tagging operations in the Snake River basin. These PIT-tagged smolts from the Snake River are detected in collection systems at Snake and Columbia River dams and diverted into transportation or bypassed to the river according to the annual study design. Beginning in 2002, the CSS increased releases of PIT-tagged wild Chinook in the Snake River basin and coordinated with other researchers to route more detected wild Chinook into transportation for subsequent use in the CSS. Because fewer PIT-tagged wild Chinook are available for study, the CSS continues to evaluate the extent to which the responses of hatchery Chinook to management actions can be used as a surrogate for wild Chinook.

The PIT-tagged wild and hatchery Chinook and steelhead are assigned to study categories based on their route of passage (inriver vs transported) through the hydrosystem. The route of

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passage of individual fish is determined from its PIT-tag detection history through the hydrosystem. The inriver study groups include smolts that were never collected or bypassed at Snake River collector dams (Category C0) and smolts that were collected and bypassed at one or more Snake River collector dams (Category C1). The transport study group (Category T0) includes smolts transported from a Snake River collector dam. Returning PIT-tagged adults detected at Lower Granite Dam are assigned to the appropriate study group. Then SARs, measured from smolts at Lower Granite to adult returns to Lower Granite, are were calculated for transport and inriver groups, along with ratios of transport SAR to inriver SAR (T/C ratios) and parameter D. Bootstrap confidence intervals are computed for all parameter estimates (Chinook: Chapter 3; Steelhead: Chapter 4).

In addition to estimating relevant parameters, the CSS also performs upriver/downriver stock comparisons (Chapter 7). In an upriver/downriver evaluation, estimates of SARs for PIT-tagged wild Chinook from John Day River and hatchery Chinook from Carson NFH (both downriver stocks) are compared with Snake River stocks from the first dam encountered as smolts to Bonneville Dam as adults. In recent years, fisheries scientists have identified potential shortcomings of using an upriver/downriver comparison approach towards evaluating FCRPS effects. New to this year’s report is a section addressing several of these concerns. We compare fish size and other smolt life history attributes between upriver and downriver populations in Chapter 8.

Beyond reporting parameter estimates and summarizing upstream/downstream comparisons, we report on several related questions pursued as part of our 2005-2006 analytical efforts. First, as in 2005, we evaluated “dropout” rates (combined effect of harvest, straying, and mortality) for returning adults between dams with adult PIT-tag monitors to see if differences occur between returning adults based on whether they migrated inriver or were transported as smolts. In addition to describing patterns, however, we provide a formal statistical comparison of dropout (i.e., apparent survival) rates between study groups in this year’s report. Second, given that our wild and hatchery Chinook SAR datasets have reached 11- and 8-years duration, respectively, we provide our first evaluation of relationships between this performance response and large-scale environmental variables believed to influence salmon population productivity. That is, we evaluated associations between inriver, estuary/early ocean, and off-shore marine conditions and annual weighted SARs across study populations of Chinook (Chapter 5). We additionally provide an evaluation of the influence of the size–collection efficiency relationships identified by NOAA-Fisheries on our transport vs. inriver comparative study approach (Chapter 9). Finally, we report on our simulation-based evaluation of the robustness of Cormack-Jolly-Seber (CJS) reach-survival estimates under various estimation methodologies (Chapter 10). Chapter 3 Findings: In Chapter 3, the estimates of SARs by study category, annual overall SAR, T/C ratio, and D, are presented for PIT-tagged wild and hatchery sp/su Chinook originating above LGR:

1. The annual SARs (indexed LGR smolts-to-LGR adults) for wild Snake River sp/su Chinook has been highly variable, rising from below 0.5% before 1997 to highs of 2.4% in 1999 before dropping each year to below 0.35 % in 2003 and 2004 (2-salt returns).

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Current overall annual SARLGR-to-LGR estimates are far below the minimum 2% recommended in the NPCC Fish and Wildlife Program mainstem amendments (NPCC 2003), and estimated as needed for keeping the stocks stable (Marmorek et al. 1998).

2. Transportation provided little or no benefit to wild sp/su Chinook during the conditions

experienced in most years during 1994-2004, except during the severe drought year 2001. The 10-year geometric mean (excluding 2001) SAR ratio transported to inriver migrants (T/C) was 0.98, while in 2001, the T/C was approximately 9-fold higher. The T/C ratio was significantly > 1 in only 2001.

3. Delayed mortality of transported wild sp/su Chinook smolts was substantial most years

relative to that of inriver migrants, based on a 10-yr geometric mean D estimate (excluding 2001) of 0.49, indicating transported smolts died at twice the rate as inriver migrants once they passed BON tailrace. In 2001, D was greater than 2, indicating inriver migrants died at twice the rate of transported smolts in the estuary and ocean.

4. The estimated inriver survival of wild sp/su Chinook from LGR tailrace to Bonneville

Dam (BON) tailrace averaged 0.46 (geometric mean) for 1994-2004 (excluding 2001, when estimated survival was 0.23).

5. During the 11-yr period 1994 to 2004, SAR(C1) averaged approximately 32% lower than

SAR(C0) for wild sp/su Chinook.

6. SARs (LGR-to-LGR) for hatchery Snake River spring/summer Chinook have shown similar patterns as wild Chinook during 1997-2004, although the actual survival rates have differed among hatcheries and between spring and summer runs. For spring Chinook hatcheries, SARs for Rapid River Hatchery have exceeded those of Dworshak Hatchery, and SARs of hatchery summer Chinook (particularly from McCall) have exceeded those of hatchery spring Chinook. SARs of most hatchery Chinook (except Dworshak) have equaled or exceeded the SARs of wild Chinook in migration years 1997-2004.

7. In general, transportation provided benefits most years to Snake River hatchery sp/su

Chinook 1997-2004, however benefits varied among hatcheries. Omitting 2001 (when all T/C ratios exceeded 5), the 7-year geometric mean T/C ranged from 1.08 at Dworshak, 1.46 at Rapid River, 1.50 at Imnaha and 1.54 at McCall hatcheries, indicating a higher return rate for the transported Chinook from these latter three hatcheries. Although having a shorter time series, annual T/C ratios at Catherine Creek AP hatchery Chinook have remained greater than 1.

8. Delayed mortality of transported hatchery spring and summer Chinook smolts was

evident most years relative to that of inriver migrants, based on estimated values of D. Except for 2001 when all D values exceeded 1, the other seven years produced geometric mean D values of 0.62 at Dworshak, 0.78 at Imnaha, 0.81 at Rapid River, and 0.89 at McCall hatcheries.

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9. The 7-yr (1997-2000, 2002-2004) geometric mean of the estimated inriver reach survival rate of hatchery sp/su Chinook from LGR tailrace to BON tailrace ranged from 0.49 to 0.54 across hatcheries. In 2001, the estimated reach survival rate ranged from 0.27 to 0.37 across hatcheries.

10. During the 8-yr period 1997 to 2004, SAR(C1) has remained lower than lower than

SAR(C0) for Chinook from Rapid River, Dworshak, Imnaha, and McCall hatcheries.

11. While wild and hatchery populations demonstrated differences in magnitude for some parameters (T/C, D and SARs), the annual patterns of these parameters were highly correlated among wild and hatchery populations.

Chapter 4 Findings: In Chapter 4, the estimates of SARs by study category, annual overall SAR, T/C ratio, and D, are presented for PIT-tagged wild and hatchery summer steelhead originating above LGR:

1. Wild steelhead from the Snake River basin had higher estimated annual SARs (indexed LGR to LGR) than hatchery steelhead in 6 of the 7 migration years (1997 to 2003). Wild steelhead had four years with annual SARs > 2%.

2. The pattern of decreasing estimated annual SARs for wild steelhead is following that of

the wild Chinook, just not dropping as rapidly over the migration years 1999 to 2003.

3. Transportation seems to provide benefit to wild and hatchery Snake River steelhead; the geometric mean T/C ratio (1997-2000, 2002-2003) was 1.72 wild stocks and 1.46 for hatchery stocks. Migration year 2001 had very high, but imprecise T/C ratios, for both wild and hatchery steelhead.

4. Delayed mortality was evident with transported wild and hatchery steelhead relative to

inriver migrants as the geometric mean D for 1997-2003 (excluding 2001) was 0.80 for wild stocks and 0.64 for hatchery stocks. Migration year 2001 estimated Ds were >1 for wild and hatchery steelhead. Confidence intervals were wide due to small sample size.

5. Given small sample sizes and wide confidence intervals for both wild and hatchery

steelhead, it is premature to conclude whether hatchery steelhead can serve as surrogates for wild steelhead. However, trends in Vc and T/C ratios were similar between wild and hatchery steelhead.

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Chapter 5 Findings: In Chapter 5, we evaluated relationships between environmental conditions existing during outmigration, early ocean, and off-shore salmon life stages for hatchery and wild Chinook salmon using contemporary (based CSS PIT tags) and published historic (based on run reconstructions) data:

1. We found moderate-to-strong relationships between SARs and environmental variables using both contemporary PIT-tag and historic run-reconstruction information. Across populations and datasets examined, SARs varied in direct relation to large-scale marine and near-shore coastal climate indices and a single hydrological variable describing outmigration conditions.

2. SAR–environmental variable relationships were generally convergent for both historic

and contemporary datasets, with some minor exceptions. Specifically, given the larger domain existing for some environmental variables in the complete (1964-2001) time series, more variance in run-reconstruction SARs could be explained by October upwelling and WTT than could be for recent (1994-2004) PIT-tag SARs.

3. Measured SARs were highest for those MYs when fish emigrated during high-flow or

under fast-moving WTT conditions, arrived at the coast during periods of increased upwelling, and completed their off-shore migration under cool-phase PDO conditions.

4. Future analyses will consider transport and inriver SARs independently and explore

possible interactions between outmigration history and environmental effects on performance.

Chapter 6 Findings: In Chapter 6, we quantified statistical associations between Chinook salmon outmigration experience and adult upstream-adult survival across several return years:

1. For both wild and hatchery Chinook salmon, we found a significant effect of outmigration experience on the upstream migration success or apparent survival of returning adults. This effect appeared most pronounced for fish that were transported from LGR as smolts, with these individuals surviving at an approximately 10% lower rate than those with either an inriver or an LGS or LMN transport history.

2. We found that outmigration experience does not affect the timing of adult return (based

on BON detections) or the upstream travel times of those salmon surviving to LGR.

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Chapter 7 Findings: In Chapter 7 the ratio of SARs for upriver and downriver wild Chinook are computed, plus the ratio of SARs for upriver and downriver hatchery Chinook. Additionally, trends in the estimated differential mortality rates are presented:

1. Differential mortality rates (between upstream and downstream populations) estimated

from SAR data appear to correspond well with differential mortality rates estimated from recruit/spawner ratios for wild Chinook populations.

2. Differential mortality estimates based on SAR ratios of hatchery populations were

generally less than those based on SAR ratios of wild populations. Chapter 8 Findings: Chapter 8 analyses address criticisms of an upriver/downriver comparison approach:

1. We observed little evidence indicating that a consistent and/or systematic difference in size-at-migration exists between upstream (Snake above LGR) and downstream (John Day) Chinook salmon smolt life histories. Both production areas yield smolts of similar, but variable (on an inter-annual basis) size. Further, we demonstrate that a portion of fork length variation can be attributed to density-dependent effects.

2. Our analysis of trap-passage timing distributions illustrates that both upstream and

downstream populations depart from natal streams within a similar timeframe.

3. Across the years under consideration, we found that upstream-origin smolts migrated to the estuary at a faster rate (~ twice as fast) than those emigrating from the John Day system.

4. Upstream-origin smolts arrived at the estuary later (~7-10 days) than John Day River

Chinook salmon smolts. Chapter 9 Findings: We evaluated the magnitude and likely influence of size–collection efficiency (i.e., detection probability) relationships on CSS outcomes for wild Chinook salmon in Chapter 9:

1. For LGR, the bypass site where the majority of CSS Chinook are collected and assigned to their respective treatment groups – estimated size–collection efficiency relationships were weak to nonexistent. At LGS and LMN, relationships were quite variable across the 5-year record and of comparable magnitude to those estimated by NOAA-Fisheries.

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2. Based on a comparison of realized size distributions remaining inriver or going into a barge, there were no clear differences between detected and undetected fish, across projects and years. This was especially true at LGR, where sizes were virtually identical for the study groups.

Chapter 10 Findings: Chapter 10 presents a description of the simulator program, including the input parameters, and provides preliminary results from runs of simulated data through the bootstrap program to compare estimated values for key parameters to the simulated “true” values:

1. The simulator software program was enhanced in 2006 with a user-friendly interface for inputting parameter values for different simulation runs.

2. Estimates of number of smolts in the CSS study categories in LGR equivalents and

associated 90% confidence intervals computed with the bootstrap program closely agreed (within 0.5%) with default simulated “true” data sets.

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1

CHAPTER 1

Introduction

Fisheries agencies and tribes have developed a multi-year program, the Comparative Survival Study (CSS), for the purpose of monitoring and evaluating the impacts of the mitigation measures and actions (e.g., flow augmentation, spill, and transportation) under the National Marine Fisheries Service (NMFS) Biological Opinion to recover listed stocks. This annual report covers smolt migration and adult return data for PIT-tagged spring/summer Chinook of wild (1994 to 2004) and hatchery (1997 to 2004) origin. New this year is coverage of PIT-tagged wild and hatchery summer steelhead (1997 to 2003). All study fish used in this report were uniquely identifiable based on a passive integrated transponder (PIT) tag implanted in the body cavity during the smolts life stage and retained through their return as adults. These tagged fish can then be detected as juvenile and adults at several locations of the Snake and Columbia Rivers. Reductions in the number of individuals detected as the tagged fish age provide estimates of survival. This allows comparisons of survival over different life stages between fish with different experiences in the hydrosystem (e.g. transportation vs. inriver migrants and migration through various numbers of dams) as illustrated in Figure 1.

Lower Granite

Lower MonumentalIce Harbor

McNaryJohn Day

The DallesBonneville

Little Goose

Freshwater

Ocean

Directsurvivalthrough

dams Directsurvival

oftransported

fish

SART:C

R/S

Smolts/spawner

Eggs

Estuary

Spawning /RearingHabitatActions

S/S

Har

vest

Man

agem

ent

Wild

Hatchery

Mainstem

D = λ t / λ n

Hydro-systemActions

EstuaryHabitatActions

Figure 1. Salmonid life cycle in the Snake River and lower Columbia River basins (source: Marmorek et al. 2004).

2

The CSS has PIT-tagged large numbers of hatchery Chinook to obtain adequate sample sizes for these different comparisons. In addition, PIT-tagged wild Chinook, wild steelhead, and hatchery steelhead from other regional studies have also been used for survival estimation. Estimates and comparisons include: (i) survival of migrating smolts over different reaches of the hydro system; (ii) smolt-to-adult survival rates (SARs) from either Lower Granite Dam (LGR) back to LGR (i.e., SARLGR-to-LGR) or Bonneville Dam (BON) back to LGR (i.e., SARBON-to-LGR) for fish transported around dams and those migrating inriver; (iii) the ratio of SARLGR-to-LGR of transported fish to SARLGR-to-LGR of inriver migrants (T/Cs); and, (iv) the ratio of SARBON-to-LGR of transported fish to SARBON-to-LGR of inriver fish (Ds).

The objectives of the CSS are as follows:

1. Develop a long-term index of transport to inriver smolt-to-adult survival rates (SARs) for Snake River hatchery and wild spring/summer Chinook and hatchery and wild summer steelhead. This includes computing annual ratios of transport SAR to inriver SAR (measured from LGR to LGR) with associated confidence interval. 2. Develop a long-term index of survival rates from release of yearling Chinook smolts at hatcheries to return of adults to hatcheries. This objective includes partitioning survival rates from (i) hatchery (smolts) to LGR (smolts), (ii) LGR (smolts) to back to LGR (adults), and (iii) LGR (adults) to the hatchery (adults). 3. Compute and compare overall SARs for selected upriver and down-river spring/summer Chinook hatchery and wild stocks. 4. Begin a time series of SARs for use in regional long-term monitoring and evaluation.

One use of the SAR index will be for assessment of temporal changes in patterns of life

cycle survival (e.g., recruit/spawner or R/S residuals; Schaller et al. 1999; Deriso et al. 2001). For Snake River wild spring/summer Chinook, changes in SAR explained most of the changes observed in life cycle survival following Columbia River Basin hydroelectric development and operation (Petrosky et al. 2001). A second application, in combination with SARs from downriver stocks, would be for assessing temporal and spatial changes in life cycle survival. Temporal and spatial R/S patterns indicated survival and productivity of Snake River stocks declined more than downriver stocks following hydrosystem development and operation (Schaller et al. 1999; Deriso et al. 2001; Marmorek et al. 2004). The upriver/downriver SAR comparison (Objective 3) will shed additional light on life stage survival patterns that drives life-cycle survival for Snake River populations. Continuing these assessments with PIT-tagged fish in the CSS will provide an independent measure to past R/S data of survival rates from smolt to adult, which incorporates variation in hydrosystem experiences and environmental conditions in the estuary and (early) ocean. Spatial and temporal contrasts of survival rates from different life stages (adult-to-adult, adult-to-smolt, and smolt-to-adult) provide valuable information to diagnose where in the salmon life cycle mortality rates have increased, and allow indirect inferences about alternative causes. The 2006 CSS Annual Report updates the status of the CSS with the addition of the wild and hatchery sp/su Chinook from the 2004 migration year and wild and hatchery steelhead from

3

the 2003 migration year. This annual report provides new analyses addressing the question raised by NOAA Fisheries in the review of last years annual report, specifically, whether size of smolts may be having an impact on the comparison of SARs between transported and in-river migrants. NOAA researchers have stated that the size distribution of fish collected for transportation tends to be smaller than that of the undetected fish, and assuming a higher survival for larger fish, this could partly explain the lower than expected SARs for transported fish. Additional analyses of have been conducted on the adult returns “drop-out” rate between Bonneville Dam and Lower Granite Dam. Plus evaluation of the adequacy of comparing wild Chinook from upriver stocks to the downriver stock in the John Day River has been undertaken in the report. These analytical methodologies will be applied to other questions of interest to fishery managers and interested public during the preparation of next year’s 10-year CSS Summary Report recommended by the Council’s Independent Scientific Advisory Board (ISAB). The use of Akcakaya (2002) method to remove sampling error from the overall variance estimated from a time series of survival rate data, as covered in the 2005 CSS Annual Report, will be deferred to the 10-year CSS Summary Report and covered in greater detail in that document.

4

CHAPTER 2

Methods Sources of study fish

Fish utilized in the CSS are marked with a unique-coded passive integrated transponder (PIT) tag, which was evaluated for use on salmonids by NOAA (Prentice et al. 1986). The computer chips are encapsulated in glass with a 12-mm length and 0.05-mm width. PIT tags are cylindrical in shape and impermeable to water. Individual PIT tags are implanted into the fish’s underbelly using a hand-held syringe with a 12-gauge veterinary needle (PTOC 1999 PIT-Tag Marking Procedures Manual). Tag loss and mortality of PIT-tagged fish are monitored, and the tagging files are transferred to Pacific State Marine Fisheries Commission’s regional PTAGIS database in Portland, OR.

The PIT-tagged wild steelhead, hatchery steelhead, and wild Chinook used in the CSS analyses as aggregate marked populations should be as representative of the untagged population as possible. For wild fish, the collection and tagging occurs over lengthy time periods from parr stages to smolt stages in each sub-basin located above Lower Granite Dam including the Clearwater, Grande Ronde, Salmon, and Imnaha rivers. These wild fish were PIT-tagged by various organizations over a 10 to 12-month period with varied sampling gear including incline-plane (scoop) traps, screw traps, electrofishing, hook and line, and beach seining. At the hatcheries, fish were obtained across as wide a set of ponds and raceways as possible to allow effective representation of production. Most hatchery steelhead releases have a small number of PIT-tagged fish, typically between 200 and 1000 fish per individual hatchery. The aggregate of these PIT-tag releases provided a fairly good cross-section of the hatchery production in each year, although it was not proportional to the magnitude of each hatchery production. Likewise, the number of wild fish PIT-tagged in each tributary is not expected to be proportional to the total population present; however, with PIT tagging occurring across a wide range of the total population, the resulting SARs of this aggregate PIT-tag population should be adequately reflective of the total population. The PIT-tagged wild Chinook, wild steelhead, and hatchery steelhead used in the CSS were initially PIT-tagged to satisfy the goals of several different research studies. At certain times of the year, multiple age classes of fish were being PIT-tagged. To ensure that smolts in our annual aggregate groups were actually migrating out in the respective year of interest, fish detected entirely outside the migratory year of interest were excluded. This was necessary since estimates of collection efficiency and survival must reflect a single year. For wild Chinook, we found that limiting the tagging season to a 10-month period from July 25 to May 20 each year reduced the instances of overlapping age classes. In this 10-month period, few additional fish were excluded due to being detected at the dams or trawl in a year outside the migration year; this was less than 0.1% in all years except 1994 when it was 0.18%. For wild steelhead, we found that size at tagging was a useful parameter for removing a high proportion of fish that reside an extra year or two in freshwater beyond the desired migration year of study (Berggren et al. 2005). Excluding wild steelhead below 130 mm and above 299 mm reduced the instances of multiple age classes and allowed the tagging season to be a full 12-months from July 1 to June 30 each year.

5

Detection of study fish PIT-tagged smolts were detected at six Snake and Columbia River dams, including

Lower Granite (LGR), Little Goose (LGS), Lower Monumental (LMN), McNary (MCN), John Day (JDA), and Bonneville (BON). In addition, PIT-tag detections were obtained at the NOAA Fisheries trawl (TWX) operated in the lower Columbia River half-way between BON and the mouth of the Columbia River. The above juvenile fish detection site abbreviations will be used throughout this document.

When PIT-tagged smolts enter the bypass/collection facility of a dam from which transportation occurs, there are four potential outcomes. The tagged fish may (1) be returned-to-river under the default routing option, (2) be routed to the raceways for transportation if requested by the researcher, (3) be routed to the sample room for anesthetization and handling prior to being routed to transportation, and (4) be seen only on the separator detector coils and therefore have an unknown disposition at that site. For PIT-tagged wild steelhead, hatchery steelhead, and wild Chinook originating above LGR, the number of tagged fish specifically routed to transportation has been very small in most prior years prior to 2002 (wild Chinook) and 2003 (wild steelhead and some hatchery steelhead releases). Since the default operation has been to return PIT-tagged fish to the river at collector dams, the only reason some PIT-tagged wild Chinook, wild steelhead, and hatchery steelhead were transported in the early years was because (1) the daily timed subsampling intervals of the Smolt Monitoring Program over-rides the default return-to-river operation for PIT-tagged fish (sampled fish are usually transported) and (2) the occurrence of periods when equipment malfunctions caused the collected PIT-tagged fish to go to the raceways. Based on the detection history of PIT-tagged smolts at the collector dams, we are able to determine to which CSS study category (defined below) these PIT-tagged fish belong.

PIT-tagged returning adults were detected in the Lower Granite Dam adult fish ladder (GRA) in each year. Beginning in return year 2002, detectors were installed in all the adult fish ladders at Bonneville (BOA) and McNary (MCA) dams, allowing detection of returning PIT-tagged adults at these additional locations. In 2003, Ice Harbor Dam (IHA to 4/1/2005 and ICH thereafter) was fitted with a PIT tag detection system in its fish ladder. Lower Granite Dam has PIT tag detection coils located near the adult trapping facility and at the exit section of the adult fish ladder. As noted last year, the LGR adult PIT-tag detection efficiency is ≥ 98% (Berggren et al. 2005), so no adjustments to the number of detected adult PIT-tagged fish at LGR are necessary. The above adult fish detection site abbreviations will be used throughout this document.

Holdovers within the hydrosystem below Lower Granite Dam

In the estimation of inriver survival rates with the Cormack(1964) – Jolly (1965) – Seber

(1965) method (hereafter termed CJS), it is assumed that all PIT-tagged smolts in a group are outmigrating together in a single migration year. Any PIT-tagged fish detected as a smolt only in a year later than the expected migration year was excluded from the release group. This exclusionary clause was necessary particularly for wild Chinook and wild steelhead, because at times when multiple age classes were being PIT tagged, our constraints of size on steelhead and tagging dates on Chinook were not enough to remove non-migratory fish for the year of interest. However, PIT-tagged fish detected at an upper dam and then holding over within the

6

hydrosystem with subsequent detections occurring the following year, were handled as follows. The capture history code for these fish showed detections at dams only during the year they initiated their outmigration. The detections in the following year were excluded during the estimation of CJS reach survivals and project collection efficiencies. Fortunately, few yearling Chinook and steelhead delayed in the hydrosystem until the following year except for steelhead that began their migration in 2001 (Berggren et al. 2005). No additional holdovers were observed for migration years 2003 (steelhead) and 2004 (Chinook). Annual SARs for each study category

The population of PIT-tagged study fish arriving at LGR is partitioned into three categories of smolts related to the manner of subsequent passage through the hydro system. Fish have the opportunity to either (1) pass inriver through the Snake River collector dams in a non-bypass channel route (spillways or turbines), (2) pass inriver through the dam’s bypass channel, or (3) pass in a truck or barge to below BON. These three ways of hydro system passage is used to define the three study categories, C0, C1 and T0, respectively, of the CSS. Typically, study categories T0 and C0 are the most representative of the run-at-large untagged population (exception is 1997 when most fish collected, tagged and untagged, in April and May at LGS and LMN were bypassed to the river). See Appendix A for the formulas used to estimate the number of smolts in each study category.

The SAR formulas for each study category (i.e., SAR1(T0), SAR2(T0), SAR(C1), and SAR(C0) are provided in Appendix A. As WDFW member of the CSS Oversight Committee, Ryding (2006) provided the concept and detailed analytical rationale (with examples) behind why the smolt numbers estimated for CSS study categories must be in LGR-equivalents so that the ratio of SARs forming the parameter T/C is unbiased in the CSS 2006 Design and Analysis Technical Report. The parameter T/C used throughout the 2006 CSS Annual Report is estimated by SAR2(T0)/SAR(C0). The SAR2(T0) estimate is used in most comparisons since it is the least affected by years in which too few PIT-tagged smolts are being transported at LGS and LMN to provide any returning adults for estimating the site-specific SARs used in computing SAR1(T0). In years when the same proportion of collected PIT-tagged smolts are being routed to transportation at each of the three Snake River collector dams, the two estimators SAR1(T0) and SAR2(T0) are equivalent. Annual estimates of SARLGR-to-LGR reflective of the run-at-large for wild steelhead, hatchery steelhead, wild Chinook, and hatchery Chinook are computed by weighting the estimated study category specific SARs of PIT-tagged fish by the estimated proportion of the run-at-large represented with each respective study category. Ninety-percent confidence interval for number of smolts in each study category, SARs for each study category, T/C ratio, and annual SARs are computed using nonparametric bootstrapping methods (Efron and Tibshirani 1993).

Annual estimates of D The parameter D is the ratio of post-BON survival rate of transported fish to in-river fish. Basically, D is computed as {SAR2(T0)/VT}/{SAR(C0)/VC}. The parameter VC is the overall reach survival from LGR to BON of fish in Category C0. The parameter VT is the overall in-river survival from LGR to the transportation sites and on barges or trucks till released below BON for

7

fish in Category T0. Regardless of whether SAR1(T0) or SAR2(T0) is used in the computation of D, the estimate of VT should be computed as 0.98• (t2 +t3 + t4)/(t2 + t3/S2 + t4/S2S3). In the 2005 CSS Annual Report (Berggren et al. 2005), it was noted that computed VT estimates have ranged between 88 and 98%.

8

CHAPTER 3

SARs, T/C ratio, and D for Wild and Hatchery Chinook Wild spring/summer Chinook

The wild PIT-tagged juvenile Chinook used in the CSS analyses were obtained from all

available marking efforts in the Snake River basin above Lower Granite Dam. Wild Chinook from each tributary (plus fish tagged at the Snake River trap near Lewiston) were represented in the PIT-tag aggregates for migration years 1994 to 2004 (Table 1). A list of the locations within the tributaries where the PIT-tagged wild Chinook were released is provided in Appendix H. Table 1. Number of PIT-tagged wild Chinook parr/smolts from the four tributaries above Lower Granite Dam and Snake River trap used in the CSS analyses for migration years 1994 to 2004.

Number of PIT-tagged wild Chinook utilized in CSS by location of origin Migr. Year

Total PIT Tags

Clearwater River (Rkm 224)

Snake River trap1

(Rkm 225)

Grande Ronde River (Rkm 271)

Salmon River (Rkm 303)

Imnaha River (Rkm 308)

1994 49,659 8,292 1,423 8,828 27,725 3,391 1995 74,640 17,605 1,948 12,330 40,609 2,148 1996 21,523 2,246 913 7,079 7,016 4,269 1997 9,781 671 None 3,870 3,543 1,697 1998 33,836 4,681 921 8,644 11,179 8,411 1999 81,493 13,695 3,051 11,240 43,323 10,184 2000 67,841 9,921 1,526 7,706 39,609 9,079 2001 47,775 3,745 29 6,354 23,107 14,540 2002 67,286 14,060 1,077 9,715 36,051 6,428 2003 103,012 15,106 381 14,057 60,261 13,165 2004 99,743 17,214 541 12,104 56,153 13,731 Average % of total 16.3% 1.8% 15.5% 53.1% 13.3%

1 Snake River trap collects fish originating in Salmon, Imnaha, and Grande Ronde rivers.

Estimated numbers of wild Chinook smolts in each study category are presented in Appendix B Table B-1 along with the estimated population of tagged fish arriving Lower Granite Dam. This appendix table provides a bootstrapped 90% confidence interval around each estimate, along with the number of returning adults in each study category. Most PIT-tagged wild Chinook are in the C1 study category due to the default operation of routing most PIT-tagged fish back to the river at the Snake River collector dams. Until 2002, the number of PIT-tagged wild Chinook actually transported has been relatively small relative to the number of untagged wild Chinook transported (Figure 2 and Appendix E Table E-1). Beginning in 2002, the CSS coordinated with IDFG, ODFW, and CTRUIR research programs to purposely route 50% of the first-time detected PIT-tagged wild Chinook smolts at the Snake River transportation facilities to the raceways for transportation. This action has provided more PIT-tagged wild Chinook smolts in the transportation category in recent years. The individual reach survival estimates used to expand PIT-tag smolt counts in each study category to LGR equivalents are presented in Appendix C Table C-1 for each migration year.

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Proportion of PIT-tagged smolts being transported relative to the untagged fish collected and transported

0.0

0.1

0.2

0.3

0.4

0.5

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004Migration year

Prop

ortio

n

prop(lgr)prop(lgs)prop(lmn)

Figure 2. Trend in proportion of PIT-tagged wild Chinook transported at each Snake River collector Dam, 1994 to 2004.

All SARs for wild Chinook are computed with only returning adults, age 2-salt and older.

The full age composition of the returning jacks and adults for each migration year 1994 to 2004 is shown in Appendix D Table D-1. On average, only about 4.3% of the returning PIT-tagged wild Chinook detected at Lower Granite Dam have been jacks.

The site-specific transportation SAR estimates [e.g., SAR(TLGR), SAR(TLGS), and SAR(TLMN)] used in estimating SAR1(T0) for wild Chinook are presented in Appendix E Table E-2. Because of the low number of PIT-tagged smolts transported and small number of returning adults, this study’s ability to detect potential differences in site-specific SARs will be limited. The 90% confidence intervals of the site-specific SARs are extremely wide and overlapping across all three dams in all years of study. However, this does not impact the conduct of this study since our goal is to create an overall multi-dam estimate of transportation SAR for comparison with the SARs of in-river migrants.

The completion of the adult returns for migration year 2003 and addition of migration year 2004 with 2-salt returns has shown two sequential years with extremely low estimated SARLGR-to-LGR (Table 2, Figure 3), not exceeding 0.35% in any study category. Wild sp/su Chinook appear to be back at the pre-1997 levels, which does not bode well for recovery efforts. Marmorek et al. 1998 recommended levels above 2% to maintain a stable population and levels above 4% for recovery. SAR levels above 2% have recently been estimated in only a few years with specific study categories (e.g., transport T0 Category in 1999 and inriver C0 Category in 1997, 1999, and 2000). Only in migration year 2001 was the transport SAR2(T0) significantly higher than that of the inriver migrants based on non-overlapping 90% confidence intervals.

10

Table 2. Estimated SARLGR-to-LGR (%) for PIT-tagged wild Chinook in annual aggregate for each study category from 1994 to 2004 (with 90% confidence intervals). Mig. Year SAR1(T0) SAR2(T0) SAR(C0) SAR(C1) 1994 NA1 0.45 (0.20 – 0.69) 0.28 (0.11 – 0.51) 0.09 (0.02 – 0.17) 1995 NA 0.35 (0.17 – 0.57) 0.37 (0.19 – 0.56) 0.25 (0.18 – 0.32) 1996 NA 0.50 (0.00 – 1.15) 0.26 (0.10 – 0.47) 0.17 (0.08 – 0.27) 1997 NA 1.74 (0.45 – 3.15) 2.35 (1.39 – 3.50) 0.93 (0.59 – 1.29) 1998 1.16 (0.66 – 1.68) 1.18 (0.71 – 1.69) 1.36 (1.05 – 1.75) 1.08 (0.94 – 1.23) 1999 2.50 (1.76 – 3.41) 2.44 (1.89 – 3.05) 2.13 (1.76 – 2.53) 1.90 (1.76 – 2.04) 2000 1.58 (0.83 – 2.44) 1.43 (0.74 – 2.14) 2.39 (2.08 – 2.72) 2.39 (2.12 – 2.52) 2001 NA 1.28 (0.55 – 2.09) Assume = SAR(C1) 0.14 (0.10 – 0.18) 2002 0.75 (0.49 – 1.07) 0.80 (0.57 – 1.04) 1.22 (0.99 – 1.45) 0.99 (0.84 – 1.14) 2003 0.35 (0.24 – 0.46) 0.34 (0.24 – 0.45) 0.33 (0.23 – 0.43) 0.17 (0.12 – 0.24) 2004 2 0.30 (0.22 – 0.39) 0.30 (0.22 – 0.39) 0.31 (0.13 – 0.52) 0.18 (0.13 – 0.24) 11-yr Avg. Std Error

NA 0.98 0.21

1.10 0.28

0.75 0.24

1 Not applicable since some sites have no adult returns for estimating a site-specific SAR 2 Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006.

Wild Spring/Summer Chinook

0.0000.0050.0100.0150.0200.0250.0300.0350.040

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 3. Estimated SARLGR-to-LGR for PIT-tagged wild Chinook aggregate in transport (sarT0) and inriver (sarC0) study categories for migration years 1994 to 2004 (only 2-salt adult returns for 2004).

The PIT-tagged wild Chinook smolts with a prior detection at a collector dam in the

Snake River (C1 Group) continue to have a lower SAR than those smolts undetected at these dams (C0 Group). During the 11-yr period 1994 to 2004 (Table 2), SAR(C1) averaged approximately 32% lower than SAR(C0).

The trend in annual estimated SARLGR-to-LGR reflective of the wild Chinook run-at-large that outmigrated in 1994 to 2004 is shown in Figure 4 (data used to compute these annual weighted estimates is presented in Appendix F Table F-1). The trend in these estimates over the 11-yr period has been highly variable, rising from below 0.5% before 1997 to highs of 2.4% in 1999 before dropping each year to below 0.35 % in 2003 and 2004 (2-salt returns). Current

11

overall annual SARLGR-to-LGR estimates are far below the minimum 2% recommended in Marmorek et al. (1998) for holding the wild Chinook stocks stable, and the 4% recommended for recovery. SARs are also less than the NPPC interim 2-6% SAR (average 4%) goal (NPCC 2003).

Estimated SARLGR-to-LGR for wild sp/su Chinook

0.00

0.01

0.02

0.03

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

Migration Year

SAR

Sur

viva

l Rat

e

Figure 4. Trend in estimated annual SAR (with 90% confidence intervals for 1995-2004) for wild Chinook based on PIT-tagged Chinook SARs in transport and inriver study categories weighted by estimated proportion of run-at-large in each study category for migration years 1994 to 2004 (only 2-salt adult returns for 2004).

The estimated transport SAR to inriver SAR (T/C) ratio for the PIT-tagged wild sp/su Chinook is presented in Table 3. With the addition of 2004 (2-salt returns), the T/C geometric mean (excluding 2001) remains at last year’s level of 0.99. The T/C ratio for 2001 was 9-fold higher than the geometric mean of other years. The lower limit of the 90% confidence interval for T/C exceeded a value of 1 only in 2001, indicating a significantly higher SAR for transported wild Chinook than in-river fish in that year.

The estimated inriver survival from LGR tailrace to BON tailrace (VC) and delayed mortality D for the PIT-tagged wild spring/summer Chinook aggregate group is also presented in Table 3 for migration years 1994 through 2004. The 10-yr geometric mean (excluding 2001) of VC was 0.46, while the 2001 VC value was half that average at 0.23. With VC averaging under 50%, the geometric mean T/C ratios should have exceeded 2.0 if delayed mortality was no greater for transported wild Chinook smolts after release below BON than for inriver migrants, but that was not the case as was shown earlier. In the absence of this differential delayed mortality, D should average 1. However, for wild Chinook, the 10-yr geometric mean (excluding 2001) of D was 0.48, while the 2001 D estimate was slightly greater than 2. The 90% confidence intervals around the estimated D show relatively low precision in most of the years available, indicating the difficulty of estimating a precise D parameter with small sample sizes of PIT-tagged wild Chinook available. The individual reach survival estimates used to obtain Vc are presented in Appendix C Table C-1 for each migration year.

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Table 3. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged wild Chinook for migration years 1994 to 2004 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1994 0.20 (77% expansion)A 1.62 (0.55 – 4.66) 0.36 (0.16 – 0.97) B

1995 0.41 (51% expansion) 0.95 (0.37 – 2.13) 0.42 (0.17 – 0.99) B

1996 0.44 (77% expansion) 1.92 (0.00 – 7.73) 0.92 (0.06 – 3.55) B

1997 0.51 (77% expansion) 0.74 (0.19 – 1.67) 0.40 (0.10 – 1.02) B

1998 0.61 (25% expansion) 0.87 (0.48 – 1.38) 0.55 (0.30 – 0.87) B

1999 0.59 (0.52 – 0.68) 1.15 (0.83 – 1.54) 0.72 (0.53 – 0.99) B

2000 0.48 (0.41 – 0.58) 0.60 (0.32 – 0.92) 0.32 (0.17 – 0.50) 2002 0.61 (0.52 – 0.76) 0.65 (0.45 – 0.94) 0.44 (0.29 – 0.68) 2003 0.60 (0.52 – 0.69) 1.05 (0.69 – 1.67) 0.68 (0.43 – 1.09) 2004 C 0.40 (0.33 – 0.51) 0.97 (0.53 – 2.37) 0.40 (0.21 – 1.03) Geomean 0.46 0.99 0.49 2001D 0.23 (0.20 – 0.28) 8.96 (3.7 – 16.8) 2.2 (0.9 – 4.2) BA Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1994 to 1999 confidence intervals for D are shifted 0.01 to 0.06 higher than reported in 2005 CSS Annual Report to adjust for the corrected D presented in that report. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006. D For migration year 2001, the SAR(C1) value is used in the denominator of the T/C ratio.

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Hatchery Chinook Yearling spring and summer Chinook were PIT-tagged for the CSS at specific hatcheries

within the four drainages above Lower Granite Dam including the Clearwater, Salmon, Imnaha, and Grande Ronde rivers. Hatcheries that accounted for a major portion of the Chinook production in their respective drainage were selected. Since study inception, the CSS has PIT-tagged juvenile Chinook at McCall, Rapid River, Dworshak, and Lookingglass hatcheries (Table 4). Chinook tagged at Lookingglass Hatchery included an Imnaha River stock released in the Imnaha River drainage and a Catherine Creek stock released in the Grande Ronde River drainage. This latter stock became available to the CSS in 2001 to replace the earlier releases made on-site at Lookingglass Hatchery. The proportion of Chinook production released with PIT-tags at each of the hatcheries listed in Table 4 is presented in Appendix G Table G-1 along with median length at time of tagging.

Table 4. Number of PIT-tagged hatchery Chinook parr/smolts from key hatcheries located above Lower Granite Dam used in the CSS analyses for migration years 1997 to 2004.

Migr. Year

Rapid River H

Dworshak NFH

Catherine Creek AP

McCall H Imnaha AP

1997 40,452 14,080 ----- 52,652 13,378 1998 48,336 47,703 ----- 47,340 19,825 1999 47,812 47,845 ----- 47,985 19,939 2000 47,748 47,744 ----- 47,705 20,819 2001 55,091 55,142 20,915 55,127 20,922 2002 54,908 54,725 20,796 54,734 20,920 2003 54,763 54,708 20,628 74,317 20,904 2004 51,969 51,616 20,994 71,363 20,910

The estimated population numbers (with bootstrapped 90% confidence intervals) of PIT-tagged Chinook smolts arriving at LGR for each CSS hatchery group are presented in Appendix B Tables B-2 to B-4 for spring stocks and Appendix B Tables B-5 to B-6 for summer stocks. The appendix tables also provide the estimated number of smolts (with bootstrapped 90% confidence intervals) occurring in each CSS study category, T0, C0, and C1, along with number of returning adults in each study category. Unlike their wild Chinook counterparts, the PIT-tagged hatchery Chinook populations arriving at LGR were fairly well split across the three study categories in all years except 2001. Few PIT-tagged smolts were in Category C0 in 2001 due to the lack of spill at collector dams and subsequent high collection efficiency allowing for few fish to pass the three Snake River collector dams undetected that year. In the other years there were relatively large numbers in categories T0 and C0. Fish in categories T0 and C0 mimic the untagged population in each year except 1997, when approximately 40% of the inriver migrating hatchery Chinook smolts were of Category C0 and the remaining 60% were of Category C1 due to the bypass protocols implemented during portions of April and May at LGS and LMN that year. The individual reach survival estimates used to expand smolt counts per category to LGR equivalents are presented in Appendix C Tables C-2 to C-6 for each migration year and hatchery.

A portion of the CSS PIT-tagged hatchery Chinook was purposely diverted into transportation at LGR in each of the years 1997 to 2004, but this was not the case at the other

14

two Snake River transportation facilities until 2000 (Appendix E Table E-3 and Figure 5). Since 2000, the proportion of first-time detected fish being diverted to transportation at the three Snake River collector dams was held constant within each year. But for parts of 1998 and 1999 (routing PIT-tagged fish to transportation ended on May 9 in 1998 and commenced on May 10 in 1999), PIT-tagged hatchery Chinook were routed to transportation at LGS for the CSS. The CSS did not route PIT-tagged hatchery Chinook to transportation at LMN until 2000. Again in 2002, the CSS did not route PIT-tagged hatchery Chinook to transportation at LMN because of the non-standard operations implemented that year to reduce the numbers of fish collected and transported in the absence of spill at that site. This non-standard operation included primary bypass without PIT tag detections during most of April and alternating 2-day transport and 1-day primary bypass without PIT tag detections during May and part of June at LMN. Springtime transportation at MCN did not occur in migration years 1997 to 2004.


0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1997 1998 1999 2000 2001 2002 2003 2004Migration year

Prop

ortio

n


Figure 5. Trend in proportion of PIT-tagged hatchery Chinook transported at each Snake River collector Dam, 1997 to 2004.

All SARs for hatchery Chinook are computed with only returning adults, age 2-salt and older. The full age composition of the returning jacks and adults for each migration year 1997 to 2004 is shown in Appendix D Table D-3. The average percentage of the total return that return as jacks was higher for the summer Chinook stocks than for the spring Chinook stocks, and was the highest for Chinook from Imnaha River AP. Throughout this report, we classify the Imnaha River Chinook as a summer stock (contrary to ODFW classification) due to its high return rate of jacks and later timing of its returning adults, which coincides with the summer stock from McCall Hatchery stock. This highly variable jack return rate among the hatcheries and the

15

extremely low jack return rate observed with the wild Chinook is one reason that SARs computed in the CSS report include 2-salt and 3-salt returning adults and no jacks.

The site-specific transportation SAR estimates [e.g., SAR(TLGR), SAR(TLGS), and SAR(TLMN)] used in estimating SAR1(T0) for hatchery Chinook are presented in Appendix E Table E-4. Because of the low number of PIT-tagged smolts transported from LGS prior to 2000 and from LMN in any year, and small number of returning adults from these site’s transported fish, this study’s ability to detect potential differences in site-specific SARs will be limited. The 90% confidence intervals of the site-specific SARs are extremely wide and overlapping across all three dams in all years of study. However, this does not impact the conduct of this study since our goal is to create an overall multi-dam estimate of transportation SAR for comparison with the SARs of in-river migrants.

Estimated SARs for hatchery Chinook in study categories T0, C0, and C1 are presented in Tables 5 to 7 for spring Chinook stocks and Tables 8 to 9 for summer Chinook stocks. When routing the same proportion of first-detected PIT-tagged smolts to transportation at each of the three collector dams as occurred in migration years 2000, 2001, 2003, and 2004, both estimators SAR1(T0) and SAR2(T0) produce the same result, illustrating the benefits of having self-weighting occur across the three dams.

Migration year 2004 (2-salt returns) is producing a very low SARLGR-to-LGR for the second consecutive year for Rapid River Hatchery spring Chinook with all study categories having SARs at or below 0.25% (Table 5). These current estimated SARs are far below the magnitudes of 1998 to 2000 (Figure 6). Relative to the 8-year average SAR(C0) of Rapid River Hatchery Chinook that passed the three collector dams undetected, a 57% higher transportation average SAR2(T0) and 24% lower bypass average SAR(C1) was estimated.

Table 5. Estimated SARLGR-to-LGR (%) for PIT-tagged spring Chinook from Rapid River Hatchery for each study category from 1997 to 2004 (with 90% confidence intervals). Mig. Year SAR1(T0) SAR2(T0) SAR(C0) SAR(C1) 1997 NA1 0.79 (0.57 – 1.02) 0.46 (0.29 – 0.65) 0.53 (0.38 – 0.68) 1998 1.68 (1.47 – 1.93) 2.00 (1.79 – 2.21) 1.20 (0.93 – 1.49) 0.67 (0.54 – 0.78) 1999 2.72 (2.47 – 3.00) 3.05 (2.80 – 3.30) 2.37 (2.07 – 2.69) 1.63 (1.45 – 1.79) 2000 2.10 (1.90 – 2.26) 2.10 (1.91 – 2.27) 1.59 (1.39 – 1.80) 1.35 (1.06 – 1.61) 2001 1.08 (0.96 – 1.21) 1.09 (0.97 – 1.22) {Assume =SAR(C1)} 0.05 (0.02 – 0.08) 2002 1.00 (0.78 – 1.25) 1.01 (0.86 – 1.17) 0.67 (0.55 – 0.79) 0.63 (0.52 – 0.74) 2003 0.25 (0.17 – 0.32) 0.25 (0.17 – 0.32) 0.23 (0.17 – 0.29) 0.16 (0.08 – 0.24) 2004 2 0.26 (0.20 – 0.31) 0.26 (0.20 – 0.31) 0.14 (0.05 – 0.26) 0.09 (0.05 – 0.13) 8-yr Avg. Std_error

1.32 0.347

0.84 0.289

0.64 0.206

1 Not applicable since some sites have no adult returns for estimating a site-specific SAR. 2 Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006.

16

Rapid River Hatchery Spring Chinook

0.000

0.005

0.010

0.015

0.020

0.025

0.030

0.035

1997 1998 1999 2000 2001 2002 2003 2004

MIgration Year

SAR

Est

imat

e

sarT0sarC0

Figure 6. Trend in estimated transport and inriver SARs for Rapid River Hatchery spring Chinook for migration years 1997 to 2004 (latter with 2-salt adult returns).

Migration year 2004 (2-salt returns) is producing a very low SARLGR-to-LGR for the second consecutive year for Dworshak Hatchery spring Chinook with all study categories having SARs at or below 0.22% (Table 6). These current estimated SARs are far below the magnitudes of 1998 to 2000 (Figure 7). Relative to the 8-year average SAR(C0) of Dworshak Hatchery Chinook that passed the three collector dams undetected, a 10% higher transportation average SAR2(T0) and 20% lower bypass average SAR(C1) was estimated. Table 6. Estimated SARLGR-to-LGR (%) for PIT-tagged spring Chinook from Dworshak Hatchery for each study category from 1997 to 2004 (with 90% confidence intervals). Mig. Year SAR1(T0) SAR2(T0) SAR(C0) SAR(C1) 1997 NA1 0.83 (0.52 – 1.19) 0.47 (0.26 – 0.72) 0.36 (0.21 – 0.53) 1998 NA 0.90 (0.78 – 1.03) 1.25 (1.09 – 1.42) 0.91 (0.77 – 1.04) 1999 1.07 (0.86 – 1.28) 1.18 (1.00 – 1.36) 1.19 (1.03 – 1.37) 0.95 (0.84 – 1.08) 2000 1.00 (0.88 – 1.13) 1.00 (0.88 – 1.13) 1.01 (0.87 – 1.16) 0.85 (0.65 – 1.07) 2001 0.37 (0.30 – 0.44) 0.36 (0.30 – 0.44) {Assume =SAR(C1)} 0.04 (0.02 – 0.07) 2002 0.48 (0.35 – 0.63) 0.62 (0.49 – 0.75) 0.50 (0.41 – 0.59) 0.50 (0.41 – 0.60) 2003 0.26 (0.19 – 0.33) 0.26 (0.19 – 0.33) 0.21 (0.16 – 0.27) 0.18 (0.10 – 0.27) 2004 2 0.21 (0.16 – 0.27) 0.21 (0.16 – 0.27) 0.22 (0.13 – 0.32) 0.16 (0.11 – 0.21) 8-yr Avg. Std_error

--- 0.67 0.129

0.61 0.168

0.49 0.130


17

Dworshak Hatchery Spring Chinook

0.000

0.005

0.010

0.015

1997 1998 1999 2000 2001 2002 2003 2004

Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 7. Estimated transport and inriver SARs for PIT-tagged Dworshak Hatchery spring Chinook for migration years 1997 to 2004 (latter with 2-salt adult returns).

Migration year 2004 (2-salt returns) is producing a very low SARLGR-to-LGR for the second consecutive year for Catherine Creek AP spring Chinook with all study categories having SARs at or below 0.35% (Table 7 and Figure 8). Relative to the 4-year average SAR(C0) of Catherine Creek AP Chinook that passed the three collector dams undetected, a 84% higher transportation average SAR2(T0) and 4% higher bypass average SAR(C1) was estimated. Table 7. Estimated SARLGR-to-LGR (%) for PIT-tagged spring Chinook from Catherine Creek AP for each study category from 2001 to 2004 (with 90% confidence intervals). Mig. Year SAR1(T0) SAR2(T0) SAR(C0) SAR(C1) 2001 NA1 0.23 (0.13 – 0.35) {Assume =SAR(C1)} 0.04 (0.00 – 0.11) 2002 NA 0.89 (0.60 – 1.19) 0.49 (0.27 – 0.74) 0.32 (0.16 – 0.50) 2003 NA 0.36 (0.17 – 0.59) 0.25 (0.12 – 0.41) 0.36 (0.14 – 0.64) 2004 2 0.37 (0.17 – 0.57) 0.35 (0.17 – 0.55) 0.20 (0.00 – 0.61) 0.32 (0.11 – 0.56) 4-yr Avg. Std_error

0.46 0.147

0.25 0.093

0.26 0.074


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Catherine Creek Hatchery Spring Chinook

0.000

0.005

0.010

0.015

2001 2002 2003 2004

Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 8. Estimated transport and inriver SARs for PIT-tagged Catherine Creek Acclimation Pond spring Chinook for migration years 2001 to 2004 (latter with 2-salt adult returns).

Migration year 2004 (2-salt returns) is producing a very low SARLGR-to-LGR for the second consecutive year for McCall Hatchery spring Chinook with all study categories having SARs at or below 0.31%, a level lower than last year (Table 8). These current estimated SARs are far below the magnitudes of 1998 to 2000 (Figure 9). Relative to the 8-year average SAR(C0) of McCall Hatchery Chinook that passed the three collector dams undetected, a 77% higher transportation average SAR2(T0) and 15% lower bypass average SAR(C1) was estimated. Table 8. Estimated SARLGR-to-LGR (%) for PIT-tagged summer Chinook from McCall Hatchery for each study category from 1997 to 2004 (with 90% confidence intervals). Mig. Year SAR1(T0) SAR2(T0) SAR(C0) SAR(C1) 1997 1.89 (1.20 – 2.75) 1.52 (1.26 – 1.78) 1.09 (0.87 – 1.31) 1.10 (0.92 – 1.29) 1998 1.95 (1.70 – 2.22) 2.71 (2.46 – 2.97) 1.38 (1.08 – 1.69) 0.73 (0.61 – 0.87) 1999 3.58 (3.10 – 4.07) 3.61 (3.29 – 3.91) 2.40 (2.12 – 2.71) 2.05 (1.83 – 2.26) 2000 3.86 (3.60 – 4.15) 3.91 (3.63 – 4.20) 2.06 (1.83 – 2.29) 2.08 (1.73 – 2.42) 2001 1.25 (1.11 – 1.41) 1.24 (1.10 – 1.39) {Assume =SAR(C1)} 0.04 (0.02 – 0.07) 2002 1.31 (0.92 – 1.74) 1.49 (1.29 – 1.71) 1.03 (0.87 – 1.20) 1.02 (0.88 – 1.17) 2003 0.79 (0.68 – 0.91) 0.79 (0.68 – 0.91) 0.54 (0.46 – 0.63) 0.35 (0.25 – 0.45) 2004 2 NA1 0.31 (0.24 – 0.38) 0.25 (0.09 – 0.43) 0.12 (0.07 – 0.16) 8-yr Avg. Std_error

1.95 0.465

1.10 0.294

0.94 0.282


19

McCall Hatchery Summer Chinook

0.0000.0050.0100.0150.0200.0250.0300.0350.0400.045

1997 1998 1999 2000 2001 2002 2003 2004

Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 9 Estimated transport and inriver SARs for PIT-tagged McCall Hatchery summer Chinook for migration years 1997 to 2004 (latter with 2-salt adult returns).

Migration year 2004 (2-salt returns) is producing a very low SARLGR-to-LGR for the second consecutive year for Imnaha AP spring Chinook with all study categories having SARs at or below 0.35%, a level lower than last year (Table 9). These current estimated SARs are far below the magnitudes of 1999 to 2000 (Figure 10). Relative to the 8-year average SAR(C0) of McCall Hatchery Chinook that passed the three collector dams undetected, a 58% higher transportation average SAR2(T0) and 23% lower bypass average SAR(C1) was estimated. Table 9. Estimated SARLGR-to-LGR (%) for PIT-tagged summer Chinook from Imnaha River AP for each study category from 1997 to 2004 (with 90% confidence intervals). Mig. Year SAR1(T0) SAR2(T0) SAR(C0) SAR(C1) 1997 NA1 1.17 (0.82 – 1.60) 0.86 (0.57 – 1.20) 0.69 (0.47 – 0.92) 1998 NA 0.86 (0.65 – 1.09) 0.55 (0.30 – 0.84) 0.30 (0.19 – 0.41) 1999 2.52 (2.07 – 3.04) 2.72 (2.33 – 3.12) 1.43 (1.06 – 1.81) 1.22 (0.94 – 1.48) 2000 3.13 (2.79 – 3.47) 3.15 (2.80 – 3.49) 2.41 (2.02 – 2.83) 1.64 (1.20 – 2.11) 2001 NA 0.62 (0.48 – 0.78) {Assume =SAR(C1)} 0.06 (0.01 – 0.11) 2002 0.98 (0.53 – 1.45) 0.80 (0.57 – 1.04) 0.45 (0.28 – 0.61) 0.54 (0.38 – 0.72) 2003 0.58 (0.41 – 0.74) 0.58 (0.41 – 0.74) 0.48 (0.34 – 0.62) 0.38 (0.20 – 0.55) 2004 2 0.35 (0.23 – 0.47) 0.35 (0.23 – 0.47) 0.23 (0.07 – 0.46) 0.11 (0.04 – 0.20) 8-yr Avg. Std_ error

1.28 0.373

0.81 0.272

0.62 0.196


20

Imnaha Hatchery Summer Chinook

0.0000.0050.0100.0150.0200.0250.0300.0350.0400.045

1997 1998 1999 2000 2001 2002 2003 2004

Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 10. Estimated transport and inriver SARs for PIT-tagged Imnaha River Acclimation Pond summer Chinook for migration years 1997 to 2004 (latter with 2-salt adult returns).

The trend in annual SARLGR-to-LGR for each hatchery and wild Chinook is presented in Figure 11. These annual SARs are computed using the estimated proportion transported and migrating in-river for the run-at-large as weights with the study specific SARs shown in Appendix F Table F-1. A general pattern of increasing SARs from 1997 to 1999 and decreasing SARs from 1999 to 2001 is shown for hatchery Chinook from McCall, Rapid River, and Dworshak hatcheries. Unlike the other three hatcheries,

SAR(LGR-to-LGR) for Hatchery and Wild Chinook

0.000

0.005

0.010

0.015

0.020

0.025

0.030

0.035

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

SAR

(LG

R-to

-LG

R)

WildDWORRAPHMCCAIMNACATH

Figure 11. Trend in estimated annual SARLGR-to-LGR for hatchery and wild sp/su Chinook; based on SAR estimates in transport and inriver categories weighted by estimated proportion of run-at-large in each category for migration years 1994 to 2004 (only 2-salt adult returns for 2004).

21

the SARs of Imnaha Hatchery Chinook dipped in 1998 and peaked in 2000. The annual trends observed for the PIT-tagged wild sp/su Chinook aggregate was similar to that of Imnaha Hatchery Chinook from 1997 to 1999 and similar to that of Rapid River Hatchery Chinook from 1999 to 2001. A slight increase in annual overall SAR was seen in 2002 after the drought year of 2001, followed by a large drop again in 2003 and low levels continuing in 2004. From the patterns of annual SARs the Rapid River Hatchery Chinook had the most similar trend as the PIT-tagged wild Chinook aggregate across the 8 years of adult returns for the four hatcheries continuously used in the CSS since 1997.

Estimated in-river survival rates from Lower Granite Dam tailrace to Bonneville Dam tailrace (parameter Vc) were low in 2004, ranging between 0.33 and 0.44 for hatchery Chinook from Rapid River, Catherine Creek, Imnaha, and McCall facilities, whereas Dworshak Hatchery Chinook had an in-river survival rate estimate of 0.50 for 2004, which is close in magnitude to its 7-yr geometric mean (0.54) of covering 1997-2000 and 2002-2004 (Tables 10 to 14). Although not as low at the in-river survival estimates during the drought year 2001, the 2004 estimates for the other four hatcheries were well below their 7-yr geometric means ranging between 0.49 and 0.54. The individual reach survival estimates for each migration year and hatchery used to compute Vc are presented in Appendix C Tables C-2 to C-6. Annual trends in Vc over the period 1994 to 2004 (hatchery Chinook beginning 1997) are presented in Figure 12 for both wild and hatchery Chinook.

Table 10. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Rapid River Hatchery spring Chinook for 1997 to 2004 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1997 0.33 (77% expansion)A 1.73 (1.07 – 2.84) 0.61 (0.36 – 1.07) B

1998 0.59 (25% expansion) 1.66 (1.30 – 2.16) 1.01 (0.78 – 1.34) B

1999 0.57 (0.49 – 0.68) 1.28 (1.11 – 1.49) 0.79 (0.66 – 0.98) B

2000 0.58 (0.48 – 0.84) 1.32 (1.13 – 1.55) 0.82 (0.65 – 1.21) B

2002 0.71 (0.60 – 0.85) 1.52 (1.18 – 1.93) 1.14 (0.88 – 1.50) B

2003 0.66 (0.57 – 0.79) 1.07 (0.70 – 1.60) 0.75 (0.48 – 1.18) 2004 C 0.35 (0.27 – 0.52) 1.79 (0.94 – 5.25) 0.65 (0.32 – 2.09) Geometric mean 0.52 1.46 0.81 2001D 0.33 (0.28 – 0.40) 21.7 (13.3 – 46.1) 7.3 (4.5 – 15.8) BA Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1997 to 2002 confidence intervals for D are shifted 0.02 to 0.1 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006. D For migration year 2001, the SAR(C1) value is used in the denominator of the T/C ratio.

22

Table 11. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Dworshak Hatchery spring Chinook for 1997 to 2004 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1997 0.49 (77% expansion)A 1.75 (0.95 – 3.55) 0.88 (0.40 – 2.09) B

1998 0.51 (25% expansion) 0.72 (0.60 – 0.86) 0.37 (0.30 – 0.47) B

1999 0.54 (0.47 – 0.63) 0.99 (0.79 – 1.20) 0.60 (0.47 – 0.75) B

2000 0.48 (0.40 – 0.64) 0.99 (0.82 – 1.20) 0.53 (0.42 – 0.73) B

2002 0.62 (0.54 – 0.72) 1.24 (0.92 – 1.63) 0.84 (0.63 – 1.11) B

2003 0.68 (0.59 – 0.80) 1.20 (0.82 – 1.80) 0.87 (0.58 – 1.36) 2004 C 0.50 (0.40 – 0.69) 0.95 (0.60 – 1.72) 0.49 (0.29 – 0.96) Geometric mean 0.54 1.08 0.62 2001D 0.24 (0.20 – 0.30) 8.76 (5.1 – 20.2) 2.2 (1.2 – 5.3) BA Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1997 to 2002 confidence intervals for D are shifted 0.0 to 0.06 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006. D For migration year 2001, the SAR(C1) value is used in the denominator of the T/C ratio. Table 12. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Catherine Creek AP spring Chinook for 2001 to 2004 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 2002 0.65 (0.45 – 1.06) 1.82 (1.04 – 3.57) 1.23 (0.65 – 2.74) B

2003 0.62 (25% expansion)A 1.44 (0.60 – 3.56) 0.93 (0.38 – 2.29) 2004 C 0.33 (0.20 – 0.89) 1.75 (0.0 – 2.31) 0.59 (0.0 – 1.34) Geometric mean 0.51 1.66 0.88 2001D 0.25 (0.18 – 0.38) 5.32 (0.0 – 12.9) 1.38 (0.03 – 3.75) B

A Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 2001 to 2002 confidence intervals for D are shifted 0.03 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006. D For migration year 2001, the SAR(C1) value is used in the denominator of the T/C ratio. Table 13. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged McCall Hatchery summer Chinook for 1997 to 2004 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1997 0.43 (77% expansion)A 1.39 (1.07 – 1.84) 0.64 (0.45 – 0.95) B

1998 0.56 (25% expansion) 1.97 (1.55 – 2.57) 1.17 (0.92 – 1.54) B

1999 0.52 (0.46 – 0.62) 1.50 (1.29 – 1.72) 0.87 (0.73 – 1.06) B

2000 0.61 (0.51 – 0.91) 1.90 (1.68 – 2.18) 1.25 (1.01 – 1.85) B

2002 0.58 (0.50 – 0.67) 1.45 (1.16 – 1.79) 0.88 (0.69 – 1.14) B

2003 0.70 (0.63 – 0.79) 1.46 (1.17 – 1.81) 1.08 (0.85 – 1.39) 2004 C 0.44 (0.35 – 0.58) 1.23 (0.66 – 2.98) 0.55 (0.30 – 1.31) Geometric mean 0.54 1.54 0.89 2001D 0.27 (0.22 – 0.34) 31.9 (18.3 – 72.7) 9.0 (5.2 – 22.0) B

A Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1997 to 2002 confidence intervals for D are shifted 0.03 to 0.2 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006. D For migration year 2001, the SAR(C1) value is used in the denominator of the T/C ratio.

23

Table 14. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged Imnaha AP summer Chinook for 1997 to 2004 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1997 0.31 (77% expansion)A 1.37 (0.86 – 2.32) 0.45 (0.25 – 0.90) B

1998 0.53 (25% expansion) 1.56 (0.96 – 3.03) 0.87 (0.55 – 1.68) B

1999 0.54 (0.42 – 0.73) 1.90 (1.42 – 2.63) 1.12 (0.82 – 1.70 B

2000 0.57 (0.43 – 0.85) 1.30 (1.06 – 1.59) 0.82 (0.60 – 1.24) B

2002 0.50 (0.41 – 0.67) 1.76 (1.08 – 2.91) 0.96 (0.60 – 1.66) B

2003 0.70 (25% expansion) 1.21 (0.79 – 1.89) 0.91 (0.58 – 1.42) 2004 B 0.37 (0.24 – 0.71) 1.50 (0.48 – 4.80) 0.58 (0.15 – 2.19) Geometric mean 0.49 1.50 0.78 2001C 0.37 (0.27 – 0.58) 10.8 (5.2 – 39.1) 4.2 (1.9 – 14.6) B

A Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1997 to 2002 confidence intervals for D are shifted 0.02 to 0.08 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006. D For migration year 2001, the SAR(C1) value is used in the denominator of the T/C ratio.

Vc for Hatchery and Wild Chinook

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

V c

Vc-WildVc-DWORVc-RAPHVc-MCCAVc-IMNAVc-CATH

Figure 12. Trend in in-river survival (Vc) for PIT-tagged Snake River wild and hatchery spring/summer Chinook in migration years 1994 to 2004.

Excluding migration year 2001, which had T/C ratios exceeding 5 in all hatchery groups,

geometric mean T/C ratios covering the seven years from1997-2000 and 2002-2004 have been around 1.5 for Rapid River, Imnaha, and McCall Hatchery Chinook (Tables 10, 13, and 14). For Dworshak Hatchery Chinook, the 7-yr geometric mean T/C ratio was less than 1.1 (Table 11). Although Catherine Creek AP hatchery Chinook have a shorter time series of data (Table 12), its T/C ratios tend to follow the former three hatcheries closer than Dworshak Hatchery. Trends in T/C ratio (log transformed) are presented in Figure 13. A significant increase in the transport SAR over the inriver SAR is found when the lower limit of the 90% confidence interval of the T/C ratio estimates is greater than 1. This did not occurring with any of the five hatcheries in 2004. In prior years, estimated T/C ratios significantly greater than 1 were observed in most years for Rapid River and McCall hatchery Chinook and about half the time for Imnaha AP

24

hatchery Chinook. Significant T/C ratios have never been observed for Dworshak Hatchery Chinook. In the absence of this differential delayed mortality, D should average close to 1. However, except for 2001 when estimated D was greater than 1 at each hatchery, the remaining years have seen a 7-yr geometric mean D of 0.62 at Dworshak, 0.78 at Imnaha, 0.81 at Rapid River, and 0.89 at McCall hatcheries. Trends in D (log transformed) are presented in Figure 14.

ln(T/C) for Hatchery and Wild Chinook

-1.0

-0.5

0.00.5

1.0

1.5

2.02.5

3.0

3.5

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

ln(T

/C)

ln(T/C)-Wildln(T/C)-DWORln(T/C)-RAPHln(T/C)-MCCAln(T/C)-IMNHln(T/C)-CATH

Figure 13. Trend in ratio of SAR2(T0)/SAR(C0) (log-transformed) for PIT-tagged Snake river hatchery and wild Chinook for migration years 1994 to 2004.

ln(D ) for Hatchery and Wild Chinook

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

ln(D

)

ln(D)-Wildln(D)-DWORln(D)-RAPHln(D)-MCCAln(D)-IMNAln(D)-CATH

Figure 14. Trend in D (log-transformed) for PIT-tagged Snake River hatchery and wild Chinook in migration years 1993-2004.

25

While wild and hatchery populations demonstrated differences in magnitude for some parameters (T/C, D, and SARs), the annual patterns of these parameters were similar among wild and hatchery populations. In-river survival (Vc) of the wild population tracked closely with survival of hatchery populations across years (Figure 12). While T/C ratios were higher for Snake River hatcheries than for wild fish, the T/C pattern for the wild population tracked well with those of the hatchery populations across years (Figure 13). Similarly, Snake River hatchery fish had higher D values than wild fish, but wild and hatchery Ds also tracked well across years (Figure 14). SARs for wild Snake River spring/summer Chinook were intermediate to the different hatcheries, but like other metrics, hatchery SARs tracked wild SAR patterns (Figure 11).

Given the high variability in survival for Snake River Chinook populations, we will most likely encounter future years when the abundance of wild juveniles is too low for generating a reliable SAR estimate. In that situation, we will need to rely on surrogate estimates from hatchery-produced fish. This provides a rationale for establishing the relationship between survival of wild and hatchery populations under similar migration, climate, and ocean conditions. CONCLUSIONS

1. The annual SARs (indexed LGR smolts-to-LGR adults) for wild Snake River sp/su Chinook has been highly variable, rising from below 0.5% before 1997 to highs of 2.4% in 1999 before dropping each year to below 0.35 % in 2003 and 2004 (2-salt returns). Current overall annual SARLGR-to-LGR estimates are far below the minimum 2% recommended in the NPCC Fish and Wildlife Program mainstem amendments (NPCC 2003), and estimated as needed for keeping the stocks stable (Marmorek et al. 1998).

2. Transportation provided little or no benefit to wild sp/su Chinook during the conditions

experienced in most years during 1994-2004, except during the severe drought year 2001. The 10-year geometric mean (excluding 2001) SAR ratio transported to inriver migrants (T/C) was 0.98, while in 2001, the T/C was approximately 9-fold higher. The T/C ratio was significantly > 1 in only 2001.

3. Delayed mortality of transported wild sp/su Chinook smolts was substantial most years

relative to that of inriver migrants, based on a 10-yr geometric mean D estimate (excluding 2001) of 0.49, indicating transported smolts died at twice the rate as inriver migrants once they passed BON tailrace. In 2001, D was greater than 2, indicating inriver migrants died at twice the rate of transported smolts in the estuary and ocean.

4. The estimated inriver survival of wild sp/su Chinook from LGR tailrace to Bonneville

Dam (BON) tailrace averaged 0.46 (geometric mean) for 1994-2004 (excluding 2001, when estimated survival was 0.23).

5. During the 11-yr period 1994 to 2004, SAR(C1) averaged approximately 32% lower than

SAR(C0) for wild sp/su Chinook.

26

6. SARs (LGR-to-LGR) for hatchery Snake River spring/summer Chinook have shown similar patterns as wild Chinook during 1997-2004, although the actual survival rates have differed among hatcheries and between spring and summer runs. For spring Chinook hatcheries, SARs for Rapid River Hatchery have exceeded those of Dworshak Hatchery, and SARs of hatchery summer Chinook (particularly from McCall) have exceeded those of hatchery spring Chinook. SARs of most hatchery Chinook (except Dworshak) have equaled or exceeded the SARs of wild Chinook in migration years 1997-2004.

7. In general, transportation provided benefits most years to Snake River hatchery sp/su

Chinook 1997-2004, however benefits varied among hatcheries. Omitting 2001 (when all T/C ratios exceeded 5), the 7-year geometric mean T/C ranged from 1.08 at Dworshak, 1.46 at Rapid River, 1.50 at Imnaha and 1.54 at McCall hatcheries, indicating a higher return rate for the transported Chinook from these latter three hatcheries. Although having a shorter time series, annual T/C ratios at Catherine Creek AP hatchery Chinook have remained greater than 1.

8. Delayed mortality of transported hatchery spring and summer Chinook smolts was

evident most years relative to that of inriver migrants, based on estimated values of D. Except for 2001 when all D values exceeded 1, the other seven years produced geometric mean D values of 0.62 at Dworshak, 0.78 at Imnaha, 0.81 at Rapid River, and 0.89 at McCall hatcheries.

9. The 7-yr (1997-2000, 2002-2004) geometric mean of the estimated inriver reach survival

rate of hatchery sp/su Chinook from LGR tailrace to BON tailrace ranged from 0.49 to 0.54 across hatcheries. In 2001, the estimated reach survival rate ranged from 0.27 to 0.37 across hatcheries.

10. During the 8-yr period 1997 to 2004, SAR(C1) has remained lower than lower than

SAR(C0) for Chinook from Rapid River, Dworshak, Imnaha, and McCall hatcheries.

11. While wild and hatchery populations demonstrated differences in magnitude for some parameters (T/C, D and SARs), the annual patterns of these parameters were highly correlated among wild and hatchery populations.

27

CHAPTER 4

SARs, T/C ratios, and D for Wild and Hatchery Steelhead Wild Steelhead

The wild PIT-tagged juvenile steelhead used in the CSS analyses are obtained from all

available marking efforts in the Snake River basin above Lower Granite Dam. Wild steelhead smolts from each tributary (plus fish tagged at the Snake River trap near Lewiston) were represented in the PIT-tag aggregates for migration years 1997 to 2003 (Table 15). A list of the locations within these tributaries where the PIT-tagged wild steelhead were released is provided in Appendix H. Table 15. Number of PIT-tagged wild steelhead smolts from the four tributaries above Lower Granite Dam (plus Snake River trap) used in the CSS for migration years 1997 to 2003.

Number of PIT-tagged wild steelhead (>130 mm) utilized in CSS by location of origin Migr. Year

Total PIT Tags


Snake River trap1

(Rkm 225)




1997 7,703 5,518 68 248 1,158 711 1998 10,512 4,131 1,032 887 1,683 2,779 1999 15,763 5,095 886 1,628 5,569 2,585 2000 24,254 8,688 1,211 3,618 6,245 4,492 2001 24,487 8,845 867 3,370 7,844 3,561 2002 25,183 10,206 2,368 3,353 6,136 3,120 2003 24,284 5,885 1,197 4,261 6,969 5,972 Average % of total 36.6% 5.8% 13.1% 26.9% 17.6%

1 Snake River trap located at Lewiston, ID, collects wild steelhead originating in Grande Ronde, Salmon, and Imnaha rivers.

The estimated number of PIT-tagged wild steelhead smolts (with bootstrapped 90% confidence intervals) arriving at LGR for each CSS study category, T0, C0, and C1, is presented in Appendix B Table B-7 along with the associated number of returning adults in each study category. Through migration year 2002, few PIT-tagged wild steelhead are in the T0 study category due to the default operation of routing most PIT-tagged fish back to the river at the Snake River collector dams. Until 2003, the number of PIT-tagged wild steelhead actually transported has been relatively small relative to the number of untagged wild steelhead transported (Figure 15 and Appendix E Table E-5). Beginning in 2003, more PIT-tagged wild steelhead have become available in the transport group as state and tribal research programs allowed a portion of their PIT-tagged wild steelhead smolts to be routed to the raceways at Snake River transportation facilities.

28


0.00

0.05

0.10

0.15

0.20

0.25

0.30

1997 1998 1999 2000 2001 2002 2003Migration year

Prop

ortio

n


Figure 15. Trend in proportion of PIT-tagged wild steelhead transported at each Snake River collector dam, 1997 to 2003.

The age breakdown of the returning wild steelhead adults detected at Lower Granite Dam adult fish ladder from smolts outmigrating in 1997 to 2003 is shown in Appendix D Table D-4. For migration years 1997 to 2003, the average age of return to Lower Granite Dam is 42.7% 1+-salt, 55.0% 2+-salt, and 2.3% 3+-salt (hereafter the “+” notation on age will be dropped in both text and tables). Steelhead returning in the fall of the same year that they migrate to the ocean are not included in the adult return data. Because of the small percentage of age-3 salt returning wild steelhead, the return data for migration year 2003 should be close to complete with regard to computing SARs, T/C ratios, or D estimates for that migration year.

Obtaining a valid estimate of the number of PIT-tagged wild steelhead in Category C0 in 2001 is problematic due to apparent large amount of residualism that year. This is based on the finding that most inriver migrants with an adult return were hold-overs. Six of the eight adult returns of Category C1 wild steelhead from migration year 2001 were actually detected in the lower river in 2002. For the three PIT-tagged wild steelhead adult returns with no detection in 2001, it was more likely these fish either completed their smolt migration in 2002 or passed undetected into the raceways during a computer outage in mid-May at LGR than traversed the entire hydrosystem undetected in 2001, when <1% of the wild steelhead run-at-large was estimated to be “destined” to ever pass all three Snake River collector dams through turbines (no spill route available). Because of the uncertainty in passage route and timing of the undetected PIT-tagged wild steelhead smolts in 2001, the in-river SAR utilizing fish from Category C1 rather than Category C0 will be used in comparisons with the transport SARs that year.

29

The site-specific transportation SAR estimates [e.g., SAR(TLGR), SAR(TLGS), and SAR(TLMN)] used in estimating SAR1(T0) for wild steelhead are presented in Appendix E Table E-6. Because of the low number of PIT-tagged smolts transported and small number of returning adults, this study’s ability to detect potential differences in site-specific SARs was limited. The 90% confidence intervals of the site-specific SARs are extremely wide and overlapping across all three dams in all years of study. However, this does not impact the conduct of this study since our goal is to create an overall multi-dam estimate of transportation SAR for comparison with the SARs of in-river migrants.

The SARs for wild steelhead from migration year 2003 remained in the 2% vicinity for transported fish, but was around 0.5% for the in-river migrants (Table 16). These differences were significant based on non-overlapping 90% confidence intervals. Significant differences in estimated SARs between transported and in-river migrants were also observed for migration years 2001 and 2002 (Figure 16). Relative to the 7-year average SAR(C0) of wild steelhead that passed the three collector dams undetected, a 138% higher transportation average SAR2(T0) and 27% lower bypass average SAR(C1) was estimated.

Table 16. Estimated SARLGR-to-LGR (%) for PIT-tagged wild steelhead in annual aggregate for each study category from 1997 to 2003 (with 90% confidence intervals). Mig. Year

SAR1(T0) SAR2(T0) SAR(C0) SAR(C1)

1997 NA1 1.45 (0.36 – 2.68) 0.66 (0.0 – 1.35) 0.23 (0.10 – 0.39) 1998 NA 0.21 (0.0 – 0.61) 1.07 (0.51 – 1.69) 0.23 (0.13 – 0.35) 1999 3.39 (1.75 – 5.31) 3.07 (1.75 – 4.62) 1.35 (0.79 – 1.93) 0.77 (0.60 – 0.95) 2000 3.05 (1.65 – 4.58) 2.79 (1.55 – 4.03) 1.92 (1.40 – 2.51) 1.82 (1.60 – 2.04) 2001 NA 2.49 (0.94 – 4.52) {Assume =SAR(C1)} 0.07 (0.03 – 0.10) 2002 2.75 (1.37 – 4.44) 2.84 (1.52 – 4.43) 0.67 (0.46 – 0.90) 0.94 (0.77 – 1.11) 20032 2.01 (1.50 – 2.54) 1.99 (1.49 – 2.49) 0.48 (0.30 – 0.68) 0.52 (0.38 – 0.66)

7-yr Avg. Std_error

2.12 0.382

0.89 0.231

0.65 0.228

1 Not applicable since some sites have no adult returns for estimating a site-specific SAR. 2 Migration year 2003 is incomplete until 3-salt adult returns occur at GRA.

30

Wild Steelhead

0.00

0.01

0.02

0.03

0.04

0.05

1997 1998 1999 2000 2001 2002 2003Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 16. Estimated transport and inriver SARs (with 90% confidence intervals) for PIT-tagged wild steelhead aggregate for migration years 1997 to 2003 (incomplete 2003 returns).

Annual estimates of SARLGR-to-LGR for Snake River wild steelhead have dropped each

year from the high of 2.86% estimated in 1999 to 1.57% estimated in 2003. Although the wild steelhead estimated annual SARs for migration years 1999 to 2002 were at or above the NPCC interim objective for a minimum SAR of 2%, they remain below the recommended average of 4% SAR (Appendix F Table F-4 and Figure 17). The pattern of decreasing estimated annual SARs for wild steelhead is following that of the wild Chinook, just not dropping as rapidly over the migration years 1999 to 2003.

Estimated Annual SARLGR-toLGR for Wild Steedhead Compared to Wild Chinook

0.00

0.01

0.02

0.03

0.04

0.05

1997 1998 1999 2000 2001 2002 2003

Migration Year

Ann

ual S

AR E

stim

ate

SteelheadChinook

Figure 17. Estimated annual SAR for wild steelhead compared to wild Chinook with 90% confidence intervals; based on SAR estimates in transport and inriver categories weighted by estimated proportion of run-at-large in each category for migration years 1997 to 2003.

31

The estimated inriver survival from LGR tailrace to BON tailrace (VC), transport SAR to inriver SAR (T/C) ratio, and delayed mortality D for the PIT-tagged wild steelhead aggregate group are presented in Table 17 for migration years 1997 to 2003. The individual reach survival estimates for each migration year used to obtain VC are presented in Appendix Table C Table C-7. The geometric mean of VC for 1997 to 2002, excluding 2001, was 0.44. Over these same six years, the wild Chinook VC estimates had a geometric mean of 0.56, which was 27% higher. Figure 18 shows the tend in annual Vc estimates for wild steelhead compared to wild Chinook for 1997-2003. A T/C estimate > 2 with a corresponding D estimate > 1 occurred in 5 of 7 years for PIT-tagged wild steelhead (3 of the 5 T/C ratios and 2 of the 5 D estimates were significant based on the lower limit of the 90% confidence interval). Whereas the PIT-tagged wild Chinook had only a single T/C estimate > 2 (and significant) for drought year 2001, but the corresponding D estimate, though > 1, was not significant based on the lower limit of the 90% confidence intervals (Figures 19 and 20). Excluding 2001, the geometric mean T/C of 1.72 for wild steelhead was double that computed for wild Chinook over these same six years (geometric mean of 0.82). The resulting D estimates for 1997-2000 and 2002-2003 had a geometric mean of 0.80 for wild steelhead and 0.50 for wild Chinook (trend across years shown in Figure 20). These data suggest a very different response to transportation as a recovery tool for listed wild Chinook and wild steelhead. Table 17. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged wild steelhead for migration years 1997 to 2003 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1997 0.52 (25% expansion)A 2.20 (0.0 – 8.30) 1.18 (0.23 – 5.87) B

1998 0.54 (25% expansion) 0.20 (0.0 – 0.71) 0.11 (0.0 – 0.40) B

1999 0.45 (0.38 – 0.55) 2.28 (1.19 – 4.78) 1.07 (0.56 – 2.23) B

2000 0.30 (25% expansion) 1.45 (0.75 – 2.42) 0.50 (0.29 – 0.80) B

2002 0.52 (0.41 – 0.69) 4.25 (2.12 – 7.67) 2.24 (1.09 – 4.25) 2003C 0.37 (0.31 – 0.44) 4.13 (2.62 – 6.80) 1.64 (1.01 – 2.72) Geometric Mean

0.44 1.72 0.80

2001 0.038 (0.026 – 0.059) 37.0 (11.6 – 98.8) 1.46 (0.44 – 4.28) B

A Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1997 to 2001 confidence intervals for D are shifted 0.0 to 0.05 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2003 is incomplete until 3-salt adult returns occur at GRA.

32

Vc for Wild Steelhead Compared to Wild Chinook

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

1997 1998 1999 2000 2001 2002 2003

V c

SteelheadChinook

Figure 18. Trend in in-river survival (Vc) for PIT-tagged Snake River wild steelhead and wild Chinook for migration years 1997 to 2003.

ln(T/C) for Wild Steelhead Compared to Wild Chinook

-2

-1

0

1

2

3

4

5

1997 1998 1999 2000 2001 2002 2003

ln(T

/C)

SteelheadChinook

Figure 19. ln(SAR2(T0)/SAR(C0)) for PIT-tagged wild steelhead and wild Chinook from migration years 1997 to 2003.

33

ln(D ) for Wild Steelhead Compared to Wild Chinook

-2.5

-2.0

-1.5

-1.0

-0.5

0.0

0.5

1.0

1997 1998 1999 2000 2001 2002 2003

ln(D

)

SteelheadChinook

Figure 20. Trend in D (log-transformed) for PIT-tagged Snake River wild steelhead and wild Chinook in migration years 1997-2003.

34

Hatchery Steelhead

The PIT-tagged hatchery steelhead used in the CSS are obtained from all available marking efforts in the Snake River basin above Lower Granite Dam. Hatchery steelhead from each tributary, plus PIT-tag releases in the mainstem Snake River at the Lewiston trap and below Hells Canon Dam, were represented in the PIT-tag aggregates for migration years 1997 to 2003 (Table 18). A list of the locations within the tributaries where the PIT-tagged hatchery steelhead were released is provided in Appendix H. The hatchery steelhead comprising the PIT-tag aggregate appear to be well spread across the drainages above LGR. Table 18. Number of PIT-tagged hatchery steelhead smolts from the four tributaries above Lower Granite Dam (plus mainstem Snake River) used in the CSS for migration years 1997 to 2003.

Number of PIT-tagged hatchery steelhead utilized in CSS by location of origin Migr. Year

Total PIT Tags


Snake River trap1

(Rkm 225)




Snake River at Hells Canyon Dam (Rkm 397)1

1997 35,705 12,872 725 6,039 9,394 6,379 296 1998 30,913 8,451 4,209 4,904 8,457 4,604 288 1999 36,968 11,486 3,925 5,316 9,132 6,808 301 2000 32,000 8,488 3,290 5,348 8,173 6,436 265 2001 29,099 9,155 3,126 4,677 7,859 3,995 287 2002 26,573 7,819 4,722 3,888 7,011 2,839 294 2003 26,379 4,912 4,171 3,113 7,764 6,123 296 Average % of total 29.0% 11.1% 15.3% 26.6% 17.1% 0.9%

1 Snake River trap located at Lewiston, ID, collects hatchery steelhead released in Grande Ronde, Salmon, and Imnaha rivers, and below Hells Canyon Dam.

The estimated number of PIT-tagged wild steelhead smolts (with bootstrapped 90% confidence intervals) arriving at LGR for each CSS study category, T0, C0, and C1, is presented in Appendix B Table B-7 along with the associated number of returning adults in each study category. Through migration year 2002, few PIT-tagged wild steelhead are in the T0 study category due to the default operation of routing most PIT-tagged fish back to the river at the Snake River collector dams. Until 2003, the number of PIT-tagged hatchery steelhead actually transported has been relatively small relative to the number of untagged hatchery steelhead transported (Figure 21 and Appendix E Table E-7). Beginning in 2003, more PIT-tagged wild steelhead have become available in the transport group as hatchery research programs started routing a portion of their PIT-tagged hatchery steelhead smolts to the raceways at Snake River transportation facilities.

35


0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

1997 1998 1999 2000 2001 2002 2003Migration year

Prop

ortio

n


Figure 21. Trend in proportion of PIT-tagged hatchery steelhead transported at each Snake River collector Dam, 1997 to 2003.

The age breakdown of the returning hatchery steelhead adults detected at Lower Granite

Dam adult fish ladder from smolts outmigrating in 1997 to 2003 is shown in Appendix D Table D-5. For migration years 1997 to 2003, the average age of return to Lower Granite Dam is 55.8% 1+-salt, 43.9% 2+-salt, and 0.3% 3+-salt (hereafter the “+” notation on age will be dropped in both text and tables). Steelhead returning in the fall of the same year that they migrate to the ocean are not included in the adult return data. Because of the small percentage of age-3 salt returning hatchery steelhead, the return data for migration year 2003 should be close to complete with regard to computing SARs, T/C ratios, or D estimates for that migration year.

Obtaining a valid estimate of the number of PIT-tagged hatchery steelhead in Category C0 in 2001 is problematic due to residualism just as it was for PIT-tagged wild steelhead. One of the 3 adult returns of Category C1 hatchery steelhead from migration year 2001 was actually detected in the lower river in 2002. There were two PIT-tagged hatchery steelhead adult returns with no smolt detection in 2001. As noted with wild steelhead, these two “never detected” hatchery steelhead also were more likely to have completed their smolt migration in 2002 or have been inadvertently transported from Lower Granite Dam without detection there. Because of the uncertainty in passage route and timing of the undetected PIT-tagged hatchery steelhead smolts in 2001, fish from Category C1 will be used in the transport versus inriver migration comparisons for that year.

The site-specific transportation SAR estimates [e.g., SAR(TLGR), SAR(TLGS), and SAR(TLMN)] used in estimating SAR1(T0) for hatchery steelhead are presented in Appendix E Table E-8. Because of the low number of PIT-tagged smolts transported and small number of

36

returning adults, this study’s ability to detect potential differences in site-specific SARs was limited. The 90% confidence intervals of the site-specific SARs are extremely wide and overlapping across all three dams in all years of study. However, this does not impact the conduct of this study since our goal is to create an overall multi-dam estimate of transportation SAR for comparison with the SARs of in-river migrants.

The SARs for hatchery steelhead from migration year 2003 was 1.81% for transported fish, but below 0.7% for the in-river migrants (Table 19). These differences were significant based on non-overlapping 90% confidence intervals. Significant differences in estimated SARs between transported and in-river migrants were also observed for migration years 2001 and 2002 (Figure 22). Relative to the 7-year average SAR(C0) of hatchery steelhead that passed the three collector dams undetected, a 72% higher transportation average SAR2(T0) and 31% lower bypass average SAR(C1) was estimated. The pattern and relative magnitude of these differences between the study categories was similar for both the wild and hatchery steelhead (Figure 23).

Table 19. Estimated SARLGR-to-LGR (%) for PIT-tagged hatchery steelhead in annual aggregate for each study category from 1997 to 2003 (with 90% confidence intervals). Mig. Year

SAR1(T0) SAR2(T0) SAR(C0) SAR(C1)

1997 NA1 0.52 (0.23 – 0.84) 0.24 (0.11 – 0.39) 0.17 (0.12 – 0.22) 1998 0.53 (0.23 – 0.90) 0.51 (0.22 – 0.85) 0.89 (0.61 – 1.19) 0.22 (0.17 – 0.28) 1999 NA 0.90 (0.51 – 1.35) 1.04 (0.79 – 1.32) 0.59 (0.51 – 0.68) 2000 2.37 (1.41 – 3.53) 2.10 (1.23 – 3.11) 0.95 (0.73 – 1.21) 1.05 (0.92 – 1.17) 2001 NA 0.94 (0.23 – 1.77) {Assume =SAR(C1)} 0.016 (0.005 – 0.03) 2002 NA 1.06 (0.32 – 2.11) 0.70 (0.54 – 0.88) 0.73 (0.61 – 0.85) 20032 1.80 (1.48 – 2.13) 1.81 (1.50 – 2.14) 0.68 (0.52 – 0.85) 0.37 (0.26 – 0.47)

7-yr Avg. Std_error

1.12 0.232

0.65 0.144

0.45 0.137

1 Not applicable since some sites have no adult returns for estimating a site-specific SAR. 2 Migration year 2003 is incomplete until 3-salt adult returns occur at GRA.

37

Hatchery Steelhead

0.00

0.01

0.02

0.03

0.04

1997 1998 1999 2000 2001 2002 2003

Migration Year

SAR

Est

imat

e

sarT0sarC0

Figure 22. Estimated transport and inriver SARs for PIT-tagged hatchery steelhead aggregate for migration years 1997 to 2003 (incomplete returns for 2003).

The 2003 overall estimate of SARLGR-to-LGR for Snake River hatchery steelhead was 1.46%, which is not as high as the estimate for 2000, but still above the other five years since 1997 (Appendix F Table F-4 and Figure 23). The annual time series of aggregate hatchery steelhead SARs were lower than the corresponding annual time series of aggregate wild steelhead SARs in all but one year between 1997 and 2002 (Figure 23), but only significantly lower in 1999 based on non-overlapping 90% confidence intervals (Appendix F Tables F-3 and F-4).

SAR(LGR-to-LGR) for Hatchery and Wild Steelhead

0.00

0.01

0.02

0.03

0.04

0.05

1997 1998 1999 2000 2001 2002 2003

SAR

(LG

R-to

-LG

R)

WildHatchery

Figure 23. Trend in estimated annual SAR for hatchery and wild steelhead with 90% confidence intervals; based on SAR estimates in transport and inriver categories weighted by estimated proportion of run-at-large in each category for migration years 1997 to 2003 (incomplete 2003 returns).

38

The estimated inriver survival from LGR tailrace to BON tailrace (VC), transport SAR to

inriver SAR (T/C) ratio, and delayed mortality D for the PIT-tagged hatchery steelhead aggregate group are presented in Table 20 for migration years 1997 to 2003. The individual reach survival estimates for each migration year used to obtain VC are presented in Appendix Table C Table C-8. The geometric mean of VC for 1997 to 2002, excluding 2001, was 0.41, similar to what was estimated for wild steelhead. Figure 24 shows the tend in annual Vc estimates for wild steelhead compared to hatchery steelhead for 1997-2003. A T/C estimate > 2 with corresponding estimated D >1 occurred in 2 of 7 years for PIT-tagged hatchery steelhead (only 2003 was significant based on the lower limit of the 90% confidence interval) (Figures 25 and 26). Migration year 2001 had very large estimated T/C and D, but the precision in these estimates was extremely low. Excluding 2001, the geometric mean T/C of 1.46 for hatchery steelhead was approximately 15% lower than that estimated for wild steelhead. The D estimates for 1997-2000 and 2002-2003 had a geometric mean of 0.64 for hatchery steelhead, approximately 20% lower than the geometric mean D of 0.80 estimated for wild steelhead. Although differences arise between the estimates for wild and hatchery steelhead, these data suggest that steelhead as a whole have a very different response to transportation as a recovery tool than do the listed wild Chinook.

Table 20. Estimated inriver survival LGR to BON (VC), T/C ratio, and D of PIT-tagged hatchery steelhead for migration years 1997 to 2003 (with 90% confidence intervals). Mig. Year VC SAR2(T0)/SAR(C0) D 1997 0.40 (25% expansion)A 2.21 (0.92 – 5.92) 0.92 (0.38 – 2.88) B

1998 0.64 (0.47 – 0.97) 0.58 (0.23 – 1.05) 0.39 (0.15 – 0.85) B

1999 0.45 (0.39 – 0.53) 0.87 (0.46 – 1.41) 0.41 (0.22 – 0.67) B

2000 0.22 (25% expansion) 2.20 (1.27 – 3.47) 0.55 (0.32 – 0.85) B

2002 0.37 (0.29 – 0.49) 1.51 (0.38 – 3.33) 0.60 (0.14 – 1.38) 2003 C 0.51 (0.43 – 0.62) 2.65 (1.99 – 3.74) 1.43 (1.02 – 2.10) Geometric Mean

0.41 1.46 0.64

2001 0.038 (0.022 – 0.089) 59.7 (0.0 – 228.5) 2.40 (0.08 – 10.8) B

A Expansion shows percent of reach with a constant “per/mile” survival rate applied. B Migration year 1997 to 2001 confidence intervals for D are shifted 0.01 to 0.08 higher than reported in 2005 CSS to adjust for the corrected D presented in that report. C Migration year 2003 is incomplete until 3-salt adult returns occur at GRA.

39

Vc for Hatchery and Wild Steelhead

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

1997 1998 1999 2000 2001 2002 2003

V c

WildHatchery

Figure 24. Trend in in-river survival (Vc) for PIT-tagged Snake River hatchery and wild steelhead for migration years 1997 to 2003

ln(T/C) for Hatchery and Wild Steelhead

-2

-1

0

1

2

3

4

5

1997 1998 1999 2000 2001 2002 2003

ln(T

/C)

WildHatchery

Figure 25. Trend in ratio of SAR2(T0)/SAR(C0) (log-transformed) for PIT-tagged Snake River hatchery and wild steelhead in migration years 1997 to 2003

40

ln(D ) for Hatchery and Wild Steelhead

-2.5-2.0

-1.5-1.0

-0.50.0

0.51.0

1.5

1997 1998 1999 2000 2001 2002 2003

ln(D

)

WildHatchery

Figure 26. Trend in D (log-transformed) for PIT-tagged Snake River hatchery and wild steelhead in migration years 1997-2003. CONCLUSIONS

1. Wild steelhead from the Snake River basin had higher estimated annual SARs (indexed LGR to LGR) than hatchery steelhead in 6 of the 7 migration years (1997 to 2003). Wild steelhead had four years with annual SARs > 2%.

2. The pattern of decreasing estimated annual SARs for wild steelhead is following that of

the wild Chinook, just not dropping as rapidly over the migration years 1999 to 2003.

3. Transportation seems to provide benefit to wild and hatchery Snake River steelhead; the geometric mean T/C ratio (1997-2000, 2002-2003) was 1.72 wild stocks and 1.46 for hatchery stocks. Migration year 2001 had very high, but imprecise T/C ratios, for both wild and hatchery steelhead.

4. Delayed mortality was evident with transported wild and hatchery steelhead relative to

inriver migrants as the geometric mean D for 1997-2003 (excluding 2001) was 0.80 for wild stocks and 0.64 for hatchery stocks. Migration year 2001 estimated Ds were >1 for wild and hatchery steelhead. Confidence intervals were wide due to small sample size.

5. Given small sample sizes and wide confidence intervals for both wild and hatchery

steelhead, it is premature to conclude whether hatchery steelhead can serve as surrogates for wild steelhead. However, trends in Vc and T/C ratios were similar between wild and hatchery steelhead.

41

CHAPTER 5

Relationships between wild and hatchery Chinook salmon smolt-to-adult survival and inriver, estuary/early ocean, and off-shore marine environmental conditions

Introduction

Patterns observed in recruits-per-spawner (R/S) and smolt-to-adult survival (SAR) data collected as part of the CSS, as well as studies done by other researchers (e.g., Pyper et al. 2005), indicate that strong covariation in performance exists among anadromous salmon populations in the Pacific Northwest. Such synchronized population behavior is believed to be driven primarily by large-scale climate variables or ‘year’ effects. Thus, towards a more complete understanding of factors influencing inter-annual patterns in PIT-tag-based SARs and other performance measures used by the CSS (i.e., T/C ratios and D), we evaluated relationships between SARs and selected environmental parameters for our 2006 report. In doing this analysis, our goal was to lay a foundation for future study-group comparisons that will explicitly consider the role of environmental drivers in determining population performance. We provide an analysis of wild and hatchery Chinook salmon SAR (Lower Granite-to-Lower Granite) variation due to inriver, estuary/early ocean, and off-shore marine environmental conditions. Further, in order to determine whether or not CSS SAR–environmental variable relationships are consistent with and representative of those existing for wild Snake River spring/summer Chinook salmon historically, we simultaneously analyzed relationships between run-reconstruction-based SARs and environmental factors. Methods SAR estimates -- For PIT-tagged Chinook, we quantified relationships between environmental variables and smolt-to-adult survival using annual weighted SAR estimates for both wild and hatchery fish (Tables F-1 and F-2, Appendix F). These values incorporate SARs of both transported (T0) and inriver (C0, C1) study groups, with the contribution of each category to the overall estimate being weighted by its relative abundance in the run at large (during outmigration). SARs for wild salmon are derived from PIT-tag releases occurring in natal streams and at smolt traps. The wild Chinook SAR time series extends from migration year (MY) 1994 to 2004 (11 years). SARs were estimated for hatchery Chinook salmon populations based on PIT-tag releases occurring at Dworshak National Fish Hatchery, Imnaha Hatchery, McCall Hatchery, and the Rapid River Hatchery. Our hatchery Chinook salmon SAR time series extends from MY 1997 to 2004 (8 years). Though hatchery and wild Chinook salmon SAR estimates are not statistically independent across populations, they were treated as such in our analysis (i.e., n = 43).

In addition, we included historical run-reconstruction-based SARs in our analysis. These values were taken from the appendix of Scheuerell and Williams (2005), which incorporate information on smolt and spawner abundance from Raymond (1988), Petrosky et al. (2001), and Williams et al. (2005), and represent an aggregate of all wild Snake River spring/summer Chinook populations. In contrast to Scheuerell and Williams (2005), however, we did not use

42

those years when estimated smolt abundance was based on spawner-recruit model predictions (i.e., MYs 1985-1991); thus, our historical time-series extends from 1964-1984 and 1992-2001 (i.e., n = 31 years). A time series plot of contemporary (PIT-tag-based) and historic (run-reconstruction-based) SARs appears in Figure 27.

1960 1970 1980 1990 2000 2010MY

0

1

2

3

4

5SA

R (%

)

Wild-RRWild-PITHatch-PIT

Groups

Figure 27. Time series plot of annual weighted PIT-tag SARs for wild (‘Wild-PIT’) and hatchery (‘Hatch-PIT’, hatchery averaged) Chinook salmon across migration years 1994-2004. Run-reconstruction-based SARs (from Scheuerell and Williams 2005; ‘Wild-RR’) extending from 1964-1984 and 1991-2001 are presented for comparison. Note, SARs were interpolated between 1984 and 1991 for illustrative purposes only. Environmental variables -- Though we could have selected many environmental variables for this analysis, we focused on two classes of variables – inriver variables (flow and water transit time) and ocean environment variables (indices describing coastal upwelling intensity and sea surface temperature/atmospheric pressure anomalies). We did this for two reasons: 1) pre-existing knowledge on factors influencing ocean salmon production and downstream migration survival provide a clear basis for a priori screening of possible variables; and 2) our dataset was relatively small, effectively supporting an evaluation of models containing only a few variables. Additionally, among the multitude of possible inriver and ocean variables available for analysis, preliminary analyses narrowed our focus to these particular descriptors.

Given that outmigrant survival and the potential delayed consequences of outmigration experience may be flow- and migration-duration-related, we described inriver migration conditions based on river discharge and water-particle transit time (WTT). Thus, using flow measurements (in kcfs) made by the USGS on the mainstem Columbia River (at the Dalles Dam, USGS site 14105700), we described outmigration flow conditions as the two month (April-May) average for each MY. Similarly, using dam-specific April-May mean discharge values for dams occurring between the Snake Basin and the Columbia River estuary (i.e., from LGR to BON) and existing discharge–velocity conversions, we estimated the time (in days; WTT) for water to travel from the Clearwater-Snake confluence to below Bonneville Dam.

43

We included in our analysis two variables describing environmental conditions existing during the early-ocean phase of Chinook salmon. First, after Scheuerell and Williams (2005), we described conditions existing immediately off shore using an index of coastal upwelling intensity (i.e., the Bakun Index , CUI hereafter) estimated at 45°N and 125°W during the months of April (i.e., approximately when Snake River spring/summer Chinook arrive at sea) and October. Upwelling in April and downwelling in October have been associated with increased primary productivity and recruitment of juvenile anadromous salmonids in their early ocean phase. CUI data were obtained from NOAA (Pacific Fisheries Environmental Lab website, http://www.pfeg.noaa.gov).

Second, we described conditions existing in the off-shore marine environment using the Pacific decadal oscillation index (PDO hereafter), given existing knowledge on associations between salmon production and PDO regimes (e.g., Hare et al. 1999). PDO is a large-scale ocean-climate index based on sea surface temperature and pressure anomalies measured at stations in the North Pacific Ocean (poleward of 20°N). Negative values indicate cold-PDO and positive values warm-PDO phases; production of Columbia River salmon is believed to be greatest during cold-PDO phases due to the increased primary production encountered by these fish while at sea. We obtained a PDO time series from University of Washington and NOAA’s Joint Institute for the Study of the Atmosphere and Ocean website (http://jisao.washington.edu/pdo/PDO.latest). As used in our analysis, PDO values represent mean summer (June-August) values for the MY of ocean entry. See Figure 28 for time series plots of all environmental variables for the period extending from 1964-2004. Data analysis -- We explored relationships between contemporary and historic SARs (ln-transformed for normalization) and inriver and estuary/early ocean environmental conditions, separately, through a multi-stage linear regression modeling exercise. That is, we fit several models (Tables 21 and 22) to both PIT-tag- and run-reconstruction-based SAR–environmental variable datasets in order to identify the most parsimonious model accounting for the greatest degree of variance in SARs. Thus, we started with a set of bivariate single-predictor inriver models (i.e., selecting between discharge and WTT) and single-predictor ocean environment models (i.e., distinguishing between CUI-April, CUI-October, and PDO) and progressively built towards our most fully parameterized model – one including a single inriver and 2 marine variables (i.e., including the best upwelling variable and PDO). Additionally, because data were available for both hatchery and wild Chinook salmon in our CSS PIT-tag dataset, we also added a group variable to our analysis to determine whether or not both groups respond similarly to inter-annual variation in environmental conditions.

For each dataset, we completed all analyses using linear regression and distinguished between candidate models at each stage using the least-squares version of

44

1960 1970 1980 1990 2000 2010MY

0

10

20

30

40

Wat

er T

rans

it Ti

me

( day

s)

1960 1970 1980 1990 2000 2010MY

100

200

300

400

Dis

c har

ge (k

cfs)

1960 1970 1980 1990 2000 2010MY

-2

-1

0

1

2

3

Pac

ific

Dec

adal

Osc

illat

ion

1960 1970 1980 1990 2000 2010MY

-100

-50

0

50

100

April

Upw

ellin

g

1960 1970 1980 1990 2000 2010MY

-100

-50

0

50

Oct

ober

Upw

ellin

g

Figure 28. Time series plots of inriver (Water transit time; Columbia River discharge) and estuary/ocean environmental variables (PDO, CUI-April, CUI-October) across migration years 1964 to 2004. See text and Table 21 caption for variable definitions. Akaike’s Information Criterion (AICc; also corrected for small sample size), following the information-theoretic approach advocated by Burnham and Anderson (2002). Although we completed a separate model selection and fitting exercise for both historic (i.e., run-reconstruction-based) and contemporary (i.e., PIT-tag-based) SAR datasets, we ultimately contrasted results between groups in order to understand the generality of patterns existing in each. To do this, we qualitatively compared model selection results, contrasted bivariate slope parameters (i.e., estimates +/- 95% CIs), and examined associated scatter plots. All analyses were completed using SYSTAT version 9. Results PIT-tag-based contemporary SARs -- Both SARs and inriver and marine environmental conditions varied considerably across migration years 1994-2004 (Figures 27 and 28). SARs spanned a range of over an order of magnitude across observations (min to max: 0.21 to 3.28 %). Further, SARs were highly correlated across PIT-tag release groups (mean pair-wise Pearson correlation, R = 0.88, range: 0.80-0.96), and when evaluated on a group-by-group basis, with the same environmental variables in the same manner (Figure 29). There was no statistical evidence suggesting that separating hatchery and wild Chinook salmon PIT-tag groups was warranted; both AICc-based model selection and regression parameter estimates identify the group effect as being negligible (i.e., models lacking group effects ranked better using AICc; across models, the

45

group parameter did not differ from zero [P > 0.40 in all cases]). Thus, only aggregate hatchery-wild results are presented and discussed from here on. Table 21. Model selection results for SAR–environmental variable regression models fitted using 1994-2004 MY PIT-tag-based annual weighted SARs. The bold-faced entry corresponds to the model with the lowest AICc value (corrected for sample size) score. Q is discharge, WTT is water transit time, CUI-April is April upwelling, CUI-Oct is October upwelling, and PDO is Pacific decadal oscillation.

Contemporary Models K AICc ΔAICc R2

SAR = Q 3 -4.3 11.7 0.12 SAR = WTT 3 -3.9 12.1 0.10 SAR = CUI-Apr 3 -7.4 8.7 0.25 SAR = CUI-Oct 3 -2.0 14.1 0.00 SAR = PDO 3 -4.3 11.7 0.12 SAR = Q + CUI-Apr 4 -8.3 7.7 0.38 SAR = Q + CUI-Apr + PDO 5 -16.0 0.0 0.64

Our PIT-tag SAR model-selection exercise indicated that among bivariate relationships, discharge and WTT described survival variation comparably (though discharge slightly better); also, both April upwelling and PDO bivariate models received greater support than October upwelling based on ΔAICc (Table 21). Overall, the best regression (inclusive of bivariate and multivariate possibilities) was a three-variable model including discharge, April upwelling, and PDO effects (Table 21). Based on slope parameter estimates for this model, SARs tended to be highest in those MYs characterized by high flows during outmigration, coastal upwelling during ocean entry, and cool-phase PDO conditions during a Chinook’s first summer at sea. Table 22. Model selection results for SAR–environmental variable regression models fitted using 1964-1984 and 1991-2001 MY run-reconstruction-based SARs. The bold-faced entry corresponds to the model with the lowest AICc value (corrected for sample size) score. See Table 21 description for variable definitions.

Model description K AICc ΔAICc R2

SAR = Q 3 3.3 5.3 0.02 SAR = WTT 3 0.7 2.7 0.19 SAR = CUI-Apr 3 -0.9 1.1 0.28 SAR = CUI-Oct 3 0.2 2.2 0.23 SAR = PDO 3 -0.2 1.8 0.25 SAR = WTT + CUI-Apr 4 -2.0 0.0 0.46 SAR = WTT + CUI-Apr + PDO 5 -0.9 1.1 0.52

Run-reconstruction-based historic SARs -- Historic SAR estimates based on run reconstruction varied considerably from 1964 to 2001, ranging between 3-5% in the late 1960s to less than

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0.5% in the early 1990s. Also, estimates were highly correlated with (R = 0.93) and were comparable to those measured using PIT-tags (i.e., 1994-1998; Figure 27), though there was some deviation past 1999. Environmental variables, especially WTT and both month-specific upwelling indices, exhibited much greater variation across the complete 1964-2004 time series than over the 1994-2004 contemporary window; thus, the domain for these variables was greater in the historic than the PIT-tag SAR analysis. Run-reconstruction SAR model-selection results indicate that among bivariate relationships: 1) WTT described survival variation better (ΔAICc > 2) than discharge; and 2) April and October upwelling and summer PDO similarly described SAR variability, with April CUI–SAR regression having the lowest AICc value of the three models (Table 22). Of all models fitted, the best of all was a two-variable function including WTT and April upwelling. This result suggests that from 1964-2001, SARs were highest in MYs with short travel times and positive upwelling conditions. When PDO was added as a predictor (i.e., the 3-variable model in Table 22), it indicates that SARs are lowest in those MYs with warm-phase PDO conditions.

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Contemporary vs. historic SAR–environment relationships -- Generally speaking, Snake River spring/summer Chinook salmon smolt-to-adult survival varied as a function inriver and ocean conditions in a similar manner during both historic and contemporary time periods (Figure 30; Table 23). There were, however, some subtle differences. First, given its minimal variation from 1994-2004 (compared to the longer time series), October upwelling explained little variation in PIT-tag-based SARs; for the historic time series, however, October upwelling was a significant predictor of SARs (Table 23). Additionally, whereas discharge was a significant predictor of contemporary survival, it was not for the historic time series – either by itself (Table 23) or relative to WTT (Table 22). However, WTT accounted for a significant portion of SAR variation in the historic time series. Despite these differences, however, both historic and contemporary slope parameter estimates were comparable (i.e., they had overlapping 95% CIs and similar point estimates; Table 23). Both analyses suggest that SARs vary as a positive function of discharge/WTT, April upwelling, and as a negative function of PDO and October upwelling. Table 23. Least-squares slope parameter estimates (+/- 95% CIs) for bivariate regressions between PIT-tag- (‘Contemp.’ in table) and run-reconstruction-based (‘Historic’ in table) SARs and environmental factors. Bold-faced cell entries correspond to those estimates differing significantly from zero.

β1 estimate Variable Contemp. Historic Discharge 0.004 0.002 (0.001 to 0.007) (-0.003 to 0.006) WTT -0.043 -0.053 (-0.082 to -0.003) (-0.094 to -0.012) CUI-April 0.026 0.019 (0.012 to 0.040) (0.008 to 0.031) CUI-Oct. -0.005 -0.022 (-0.032 to 0.023) (-0.037 to -0.006) PDO -0.255 -0.427

(-0.473 to -0.038) (-0.708 to -0.145) Discussion and Conclusions

We found moderate-to-strong and convergent relationships between Chinook salmon smolt-to-adult survival and both inriver and ocean environmental conditions across contemporary (1994-2004) and historic (1964-2001) time periods. Further, we documented similar environmental variable–SAR relationships for stocks of different origin (i.e., hatchery and wild populations) and based on datasets generated using different survival estimation techniques (PIT-tag mark-recapture vs. run reconstruction). Based on both historic and contemporary datasets, SARs were highest for those MYs when fish emigrated rapidly and/or during high-flow conditions, arrived at the coast during periods of increased upwelling, and completed their off-shore migration under cool-phase PDO conditions.

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Figure 30. Scatter plots of PIT-tag- (‘Contemp.’) and run-reconstruction-based (‘Historic’) bivariate SAR–environmental variable (discharge and WTT during outmigration, April upwelling, and summer PDO).

The relationships we document herein are consistent with those reported for previous evaluations of environmental controls on stock productivity based on other metrics. For example, R/S residual– (Schaller and Petrosky In Review) and fishery catch–based (Hare et al. 1999) evaluations suggest that these measures of stock productivity respond similarly to upwelling and PDO trends. The associations between both discharge and WTT and SARs, similarly, are in agreement with the results of Schaller and Petrosky (In Review) who found that increased WTT – a function of discharge and reservoir volume existing between Lower Granite Pool and Bonneville Dam tailrace – was associated with a decrease in an estimated survival-rate index. In sum, it appears that observed inter-annual patterns in PIT-tag-based SARs, as estimated for the CSS, are robust.

In addition to the analyses described in this section of our report, we plan to further analyze relationships between SARs and environmental variables for our upcoming 10-year report. Planned analyses include: 1) as the data permit, we will consider other and more complex model structures, including those using study-category-specific SARs with associated model effects (i.e., T0 vs. C0 dummy variables) and interactions (e.g., study category × water travel time) in a model-selection framework; 2) we will evaluate relationships between reach survival estimates (i.e., Vc’s) and inriver migration conditions across our 11+ migration year (MY)

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dataset; and 3) as more MYs become available for wild and hatchery steelhead, we will pursue similar analyses for these fish.

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CHAPTER 6

Associations between smolt outmigration experience and adult Chinook salmon Bonneville-

to-Lower-Granite-Dam apparent survival rates

Introduction

Given that estimates of T/C ratios and D both rely on smolt-to-adult survival rates (SARs) based on adult detections at Lower Granite Dam (LGR), these values include both an ocean mortality component and one occurring during upstream migration (i.e., between Bonneville Dam, BON, and LGR) in the year of adult return. Using data collected at PIT-tag interrogation systems on adult fishways, the latter quantity can be directly estimated and compared between CSS’s transport (T0 and T1) and inriver (C0 and C1) study categories. By quantifying upstream survival rates, it may be possible to more precisely identify mechanisms responsible for a portion of the observed study-category SAR differential. Accordingly, we initiated an analysis/comparison of the inter-dam ‘drop out’ (i.e., mortality) rates of hatchery and wild Chinook salmon for our 2005 annual report. For the present report, we extended analyses reported in 2005 in several ways: 1) we updated our dataset with return year (RY) 2006 adult PIT-tag detections; 2) we quantified adult migration (BON-LGR) survival for both study groups; and 3) we formally tested for differences in adult migration survival, timing, and duration between groups. Additionally, we evaluated the role of environmental factors (i.e., flow, spill, and temperature) on the upstream survival of adult salmon. Methods Approach -- We tested for an effect of juvenile transportation on upstream adult migration timing, duration, and success for Chinook salmon through three separate analyses: 1) we tested whether or not BON-LGR migration success was independent of juvenile outmigration history using χ2-tests (Note: given the ~100% detection probability at LGR, we take detection at LGR [i.e., BON-LGR migration success] to be synonymous with upstream-migration apparent survival [i.e., inclusive of both mortality and straying]); 2) we modeled individual survival, a binary response, using logistic regression; within this analysis, we tested for transportation and environmental variables effects using an Akaike’s Information Criterion (AIC)-based model-selection exercise and based on significance tests for fitted model parameters and associated odds ratios; 3) we contrasted adult return timing (i.e., arrival at BON) and BON-LGR upstream travel time (i.e., passage duration, in days) across outmigration histories using analysis of variance. Dataset description -- We evaluated relationships between outmigration experience and upstream survival and migration characteristics for hatchery and wild Chinook salmon, separately. For hatchery Chinook salmon, we used available adult PIT-tag detections for fish released from Catherine Creek (CATH), Dworshak (DWOR), Imnaha (IMNA), McCall (MCCA), and Rapid River (RAPH) hatcheries; for wild salmon, we relied on PIT-tag releases

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from CSS-affiliated smolt traps and from tagging efforts occurring in natal streams throughout the Snake River Basin. We included in our analysis >1-salt adults (i.e., we excluded jacks) from MYs 2001-2004 that were detected as adults at BON, McNary (MCN), Ice Harbor (IHR), and LGR PIT-tag interrogation sites in RYs 2002-2006. Also, we excluded those adult that were not initially detected at BON during their respective upstream migration. We determined each adult’s juvenile outmigration experience based its smolt capture history and grouped individuals in a manner similar to Marsh et al. (2005). Thus, we included categories for the following juvenile outmigration histories: 1) inriver outmigrants (i.e., undetected or detected but bypassed = ‘inriver’ group hereafter); 2) transported individuals that were collected at and transported from LGR (‘LGR’ group hereafter); and 3) transported individuals that were collected at and transported from LGS or another downstream project (‘LGSdown’ group hereafter). Sample sizes, by migration year, transport history, and BON-LGR passage success are provided in Tables 24 (hatchery; aggregate n = 3,649) and 25 (wild; aggregate n = 539). Table 24. Counts of hatchery Chinook salmon adults that failed (‘F’) or were successful (‘S’) in surviving their BON-LGR migration in return years 2002-2006, grouped by migration year and outmigration experience (see Methods for group definitions). There was evidence for a significant association between transport history and migration success where sufficient observations-per-cell were available (see Table 26 for details).

MY2001 MY2002 MY2003 MY2004 Combined Outmigration history F S F S F S F S F S Inriver 12 43 146 789 62 395 40 113 260 1340 LGR 140 560 66 226 53 174 76 142 335 1102 LGSdown 22 89 46 214 20 119 31 71 119 493

Table 25. Counts of wild Chinook salmon adults that failed (‘F’) or were successful (‘S’) in surviving their BON-LGR migration in return years 2002-2006. There was evidence for a significant association between transport history and migration success where sufficient observations-per-cell were available (i.e., > 5; MY2002: χ2 = 8.74, df = 2, P = 0.013; Combined: χ2 = 7.94, df = 2, P = 0.019; MY2001, MY2003-4, not applicable).

MY2001 MY2002 MY2003 MY2004 Combined Outmigration History F S F S F S F S F S Inriver 4 34 30 210 8 53 8 36 50 333 LGR 3 7 7 12 2 15 8 28 20 62 LGSdown 0 5 6 26 0 16 2 19 8 66

Environmental variables -- Within the context of our logistic regression-based assessment of transportation effects, we also wished to account for variation in BON-LGR survival that could be attributed to inriver migration conditions. Specifically, given the results from the University of Idaho’s radio telemetry work (Keefer et al. 2004; Naughton et al. 2006), we quantified the influence of discharge, spill (%), and water temperature on adult passage success. We summarized these variables using records from the Fish Passage Center and USACE’s websites.

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Discharge and temperature data were summarized for Lower Granite (i.e., used as a proxy for Snake River hydrological and thermal conditions) and Bonneville dam (i.e., as a proxy for Columbia River conditions) sites and averaged across 2-week time blocks in each RY. Similarly, spill was summarized as an average Lower Columbia (BON, TDA, JDA, and MCN, averaged) and Lower Snake (IHR, LMN, LGS, and LGR, averaged) value for the same time blocks. Environmental variables were matched with individual fish records based on their Bonneville arrival date. However, given that the majority (hatchery: 570/714 or 80%; wild: 64/78 or 82%) of adults that failed to arrive at LGR dropped out before McNary Dam and that variables are correlated across sites, we used only Lower Columbia environmental variables in our final analysis. Statistical analysis -- For both wild and hatchery Chinook salmon, we analyzed relationships between outmigration experience and adult migration success according to the following steps. First, we ran a separate χ2-test (2 × 3 table; success/failure × inriver/LGR/LGSdown categories) for each migration year (MY) and RY, when sufficient observations per cell were available (i.e., > 5); we also performed a single χ2-test, pooling individuals across years. We additionally performed hatchery-specific tests for hatchery Chinook.

Second, we evaluated the effects of both transportation history and environmental conditions (i.e., Lower Columbia flow, spill, and temperature) on the upstream migration survival of individual fish using logistic regression. Thus, we fit 11 a priori models (Tables 27 and 29) describing an individual’s survival response (0 = unsuccessful; 1 = successful) as a function of a combination of transportation (i.e., dummy variables for LGR and LGSdown histories; intercept = inriver) and/or environmental predictor variables. Thus, we evaluated the possibilities that individual upstream passage success was determined by transportation history or environmental conditions alone, or in combination. We used an AIC-based model selection approach to determine the level of support for different models (i.e., hypotheses) and subsequently assessed slope parameter sign (+/-) and significance (using a t-test), as well as success odds ratio estimates (i.e., OLGR/Oinriver and OLGSdown/Oinriver, where Oi = psuccess/pfail for group i) and associated 95% CIs from our top model.

For the final component of our analysis, we contrasted BON arrival timing (i.e., date of adult return, measured as the Julian calendar date) and BON-LGR upstream travel times (in days, log10-transformed for normality purposes) between inriver, LGR, and LGSdown groups. To do this, we performed ANOVAs on both hatchery and wild Chinook salmon data sets, separately. Factors included in both arrival timing and travel time analyses were transport history (i.e., inriver, LGR, LGSdown groups), RY (i.e., as a blocking factor), and their interaction. We evaluated model-effect significance based on F-tests (Type-III sums-of-squares) and subsequently contrasted responses between categories using Tukey’s HSD test.

All statistical analyses were performed using SYSTAT v. 9 (SPSS 1998). We evaluated statistical significance at α = 0.05.

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Table 26. Summary of MY-, RY-, and hatchery-specific χ2-tests for hatchery Chinook salmon. The P-values listed are not corrected for multiple tests. The success rate ranking corresponds to the ordering of % successful upstream migrants by juvenile outmigration history. The entry ‘NA’ corresponds to table values that are not applicable because either a test was not performed due to low cell counts (i.e., RY2002) or the resulting test statistic was not significant (α = 0.05). df = 2 for all tests.

Table P-value Success Rate Ranking Aggregate <0.001 Inriver > LGSdown > LGR MY2001 0.946 NA MY2002 0.022 Inriver > LGSdown > LGR MY2003 0.004 Inriver > LGSdown > LGR MY2004 0.200 NA RY2002 NA NA RY2003 0.009 Inriver > LGSdown > LGR RY2004 0.005 Inriver > LGSdown > LGR RY2005 0.029 Inriver > LGSdown > LGR RY2006 0.126 NA CATH 0.015 Inriver > LGR > LGSdown DWOR <0.001 LGSdown > Inriver > LGR IMNA 0.092 NA MCCA 0.383 NA RAPH 0.009 Inriver > LGSdown > LGR

Results Hatchery Chinook χ2 tests -- The results from the aggregate, MY-, RY-, and hatchery-specific χ2-tests are summarized in Table 26. Though there was some variability in which of these tests indicated a significant departure from the null expectation (i.e., that migration success was independent of outmigration experience), on average 77% of LGR adults passed from BON to LGR; in contrast, 81% and 84% of all LGSdown and inriver outmigrants, respectively, made a successful BON-LGR migration (Figure 31). This pattern was generally consistent across χ2-tests conducted on a MY, RY, or aggregate basis. Hatchery-specific χ2-tests also suggest a transportation effect. However, there appeared to be a distance-to-LGR effect on the results for the different hatcheries. That is, the disparity in migration success between inriver and LGR adults was generally less for those individuals originating from hatcheries that were further upstream (Pearson R = -0.61, correlation between the LGR vs. inriver success-rate difference and distance from release to LGR). Also worth noting is the possible role of race type in survival patterns. χ2-tests for IMNA and MCCA hatcheries – the only two releasing summer-run Chinook smolts – were not significant. The association between outmigration experience and adult migration success for spring-run Chinook hatcheries, in contrast, was statistically significant across all sites. Wild Chinook χ2 tests -- Given the small sample size for wild CSS Chinook salmon adults, we focused primarily on the pooled χ2-test for inferential purposes (i.e., MY2002 was the only year

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with >5 observations per cell for all MY- and RY-specific analyses). Consistent with our findings for hatchery salmon, this analysis (see Table 2 caption for test-statistic details) suggests that wild adult Chinook salmon BON-LGR migration success is influenced by outmigration experience. Specifically, adults that were transported from LGR as smolts were consistently less successful at returning to their upstream tributaries than those that emigrated as inriver or LGSdown smolts (P = 0.019). Whereas only about 10% of inriver and LGSdown smolts did not survive (inclusive of mortality and straying) from BON and LGR, approximately 25% of those collected and transported from LGR as smolts did not reach LGR (Figure 31).

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Figure 31. Bar chart of the percent of hatchery (left) and wild (right) Chinook salmon that were successful in migrating from BON to LGR for inriver, LGR, and LGS-down outmigration histories across return years 2002-2006 (i.e., combined counts). Error bars correspond 95% confidence intervals. Hatchery Chinook logistic regression analysis -- Consistent with hatchery χ2 findings, our AIC-based model-selection exercise also demonstrates an effect of transportation history on upstream adult migration success. The best model describing individual migration success included transport, temperature, and spill effects (Table 28). Model evidence ratios (i.e., wi-best overall model / wi-best environmental variables-only model; Table 27) indicate that the top model, which contained a combination of transportation and environmental effects, was > 6,000 times more likely than the best environmental variables-only model. Thus, based on these data and candidate models evaluated, there is clear evidence suggesting that patterns in individual survival are due to a combination of transportation history and environmental conditions.

Considering the top logistic regression model in greater detail (i.e., the transport + temperature + spill model), all parameters differed significantly from zero, except for the dummy variable identifying an LGSdown-group effect (P = 0.085; Table 28). Parameter estimates indicate that the probability of an individual fish migrating successfully from BON to LGR was less for LGR individuals than for either inriver outmigrants and LGSdown individuals. Additionally, parameter estimates suggest that upstream migration success was lessened during periods characterized by high spill and cold temperatures in the Lower Columbia River. Further, the odds ratio estimate for the LGR group (estimate: 0.64; 95% CI: 0.53-0.77) indicates that these adults had significantly lower odds of surviving their BON-LGR migration than inriver

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outmigrants (i.e., the 95% CI did not include 1). The odds ratio for the LGSdown parameter did not differ from 1 (estimate: 0.81; 95% CI: 0.64-1.03), suggesting that these individuals had a similar likelihood of making it to LGR as inriver-outmigrant adults. Table 27. Logistic regression model-selection results for CSS hatchery Chinook salmon. Note, Y = P(Success | X), where X is the variable in question. The bold-faced model was the one most supported by the data, however those with a ΔAIC < 2 can be considered nearly equivalent. K is the number of estimated parameters (inclusive of variance).

Model K AIC ΔAIC wi

Y = Spill 3 3612.9 24.3 0.00 Y = Flow 3 3612.3 23.7 0.00 Y = Temperature 3 3608.7 20.2 0.00 Y = Spill + Temperature 4 3606.2 17.6 0.00 Y = Flow + Temperature 4 3606.7 18.1 0.00 Y = Transport 5 3593.7 5.2 0.04 Y = Transport + Spill 6 3595.0 6.4 0.02 Y = Transport + Flow 6 3595.4 6.9 0.02 Y = Transport + Temperature 6 3590.9 2.3 0.18 Y = Transport + Spill + Temperature 7 3588.6 0.0 0.57 Y = Transport + Flow + Temperature 7 3591.1 2.5 0.16

Table 28. Parameter estimates for the top logistic regression model describing BON-LGR migration success for CSS hatchery Chinook salmon returning in 2002-2006.

Parameter Estimate SE t P-value Intercept 1.410 0.285 4.95 <0.001 LGR -0.446 0.092 -4.84 <0.001 LGSdown -0.212 0.123 -1.73 0.085 Spill -0.016 0.008 -2.04 0.041 Temperature 0.057 0.020 2.87 0.004

Wild Chinook logistic regression analysis -- Our wild Chinook logistic regression analysis also demonstrates an effect of transportation history on upstream adult migration success. The best model describing individual migration success included transport effects alone (Table 29); every one of the closest competing models (i.e., those models with ΔAIC < 2) also included transportation effects. Model evidence ratios (i.e., wi-best model / wi-best environmental variable-only model; Table 29) indicate that a transport-effects-only model is 4 times more likely than the best environmental variables-only model. Thus, based on these data and candidate models, there is stronger support for a transportation-legacy hypothesis than any environmental conditions-only hypotheses. Of parameters estimated for our top model, only the LGR parameter differed significantly from zero (P = 0.003; Table 30). As expected, the probability of an individual fish migrating successfully from BON to LGR was lower for LGR individuals than for either inriver outmigrants or LGSdown individuals. At 0.46 (95% CI: 0.26-0.84), the odds ratio estimate for this group indicates that LGR salmon were about half as likely to survive their migration from BON to LGR than inriver outmigrants. Similar to hatchery

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models logistic regression results, the odds ratio for LGSdown adults did not differ from 1 (estimate: 1.24; 95% CI: 0.56-2.73). Table 29. Logistic regression model-selection results for CSS wild Chinook salmon. Note, Y = P(Success | X), where X is the variable in question. The bold-faced model was the one most supported by the data, however those with a ΔAIC < 2 were viewed as equivalent. K is the number of estimated parameters (inclusive of variance).

Model K AIC ΔAIC wi

Y = Spill 3 451.6 3.1 0.07 Y = Flow 3 451.1 2.5 0.09 Y = Temperature 3 451.4 2.8 0.08 Y = Spill + Temperature 4 453.2 4.7 0.03 Y = Flow + Temperature 4 452.9 4.4 0.03 Y = Transport 5 448.6 0.0 0.31 Y = Transport + Spill 6 450.4 1.8 0.13 Y = Transport + Flow 6 450.4 1.9 0.12 Y = Transport + Temperature 6 450.2 1.6 0.14 Y = Transport + Spill + Temperature 7 451.7 3.1 0.06 Y = Transport + Flow + Temperature 7 452.1 3.5 0.05

Table 30. Parameter estimates for the top logistic regression model describing BON-LGR migration success for CSS wild Chinook salmon returning from 2002-2006.

Parameter Estimate SE t P-value Intercept 1.896 0.152 12.5 <0.001 LGR -0.765 0.299 -2.6 0.010 LGSdown 0.214 0.404 0.5 0.596

Hatchery Chinook arrival and travel time ANOVAs -- Analysis of variance results for hatchery Chinook salmon suggest that no consistent trend exists in either BON arrival date or BON-LGR travel time across the three outmigration histories, though there was considerable variation in both responses across RYs. Significant effects in the arrival date ANOVA include RY (F = 35.1, P < 0.001) and its interaction with outmigration history (F = 6.2, P < 0.001). The model effect outmigration by itself did not account for a significant portion of arrival date variation (F = 2.2, P = 0.12). Given the significant RY × outmigration history interaction effect, we evaluated differences between groups within years using Tukeys’ HSD test. Of all within-year, across-group comparisons, the only significant difference observed was between LGR and inriver fish during 2003 (P < 0.001); in this case, LGR fish arrived at BON 10 days earlier than inriver adults. Across years, however, all groups returned to BON within a 3-day window of each other, with inriver, LGR, and LGSdown mean arrival dates being 21-May, 23-May, and 19-May, respectively.

Similar to BON arrival timing, travel times varied significantly across years (RY F-test, F = 71.7, P < 0.001) and there were some differences between study categories that varied by year (RY × outmigration history F-test, F = 3.3, P = 0.001). However, the outmigration effect by itself was not significant (F = 0.4, P = 0.662). As with arrival timing, the only significant within-year difference was between LGR and inriver fish in 2003; inriver migrants passed from BON to LGR 2 days faster than LGR study fish. All other year-group comparisons indicate

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negligible differences occur in upstream travel times due to outmigration history, though LGR fish tended towards a more skewed distribution (i.e., at the slow end of travel times; Figure 32). On average, all groups passed from BON to LGR in 14 days. Wild Chinook arrival and travel time ANOVAs -- Similar to the hatchery Chinook BON arrival timing and BON-LGR travel time analysis, there was considerable variability in both responses across RYs but not groups. For the BON arrival timing ANOVA, the only significant model effect was RY (F = 7.1, P <0.001), with arrival dates tending to be earlier in 2004-6 than 2002-3. Arrival dates averaged later than those for hatchery Chinook, with inriver, LGS, and LGSdown adults groups averaging 30-May, 27-May, and 28-May across the 5-year record, respectively. Thus, return timing did not differ as a function of outmigration experience. Similarly, BON-LGR travel times varied considerably (and slightly increasing in time) across years (RY F-test, F = 8.0, P < 0.001), but not as a function of outmigration experience, either across or within years (outmigration history F-test, F = 0.5, P = 0.623; RY*outmigration history F-test, F = 1.3, P = 0.247). All study groups migrated upstream at a similar rate (i.e., in 14.8, 14.0, and 13.3 days, aggregate means for LGR, LGSdown, and inriver groups, respectively); however, as with hatchery Chinook, there was a tendency towards a more skewed and slower travel time distribution for LGR adults (Figure 32).

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Figure 32. Box-and-whisker plot of BON-LGR travel times for hatchery (left) and wild (right) Chinook salmon, by outmigration experience (pooled across RYs 2002-2006). Lower and upper box bounds correspond to 25th and 75th percentiles, respectively; the mid line represents the median; the upper and lower whiskers encompass 1.5 times the inter-quartile range (IQR); values beyond 3 times the IQR appear as circles, those within as asterisks. Discussion and Conclusions

For both wild and hatchery Chinook salmon, our analysis demonstrates a significant effect of outmigration experience on the upstream migration success or apparent survival of returning adults. However, our analysis also illustrates that this effect was most pronounced for fish that were transported from LGR as smolts, with these individuals surviving at an approximately 10% lower rate than those with either an inriver or LGSdown smolt history.

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Further, our results suggest that outmigration experience does not affect the timing of adult return (based on all BON detections) or the upstream travel times of those salmon surviving to LGR.

Previous research suggests that transportation can affect adult apparent survival rates in the direction we observed in several ways. First, it has been suggested that smolt transportation can disrupt the imprinting process, which typically occurs during smoltification (e.g., Quinn 2005), and thus lead to increased straying of spawners upon return (e.g., Pascual et al. 1995; Bugert et al. 1997; Chapman et al. 1997). In the case where successful migration is defined by an individual’s arrival at LGR, inter-dam straying is equivalent to mortality. Additionally, elevated fallback rates and extensive downstream forays by adult salmon have been attributed to juvenile transportation (Keefer et al. 2006). Given that mortality can increase with the number of fallback events and reascension attempts that are made by individuals (Keefer et al. 2005), transport-related fallback may also explain a portion of the observed disparity between study categories. Though less clear, other possible mechanisms may account for the mortality differential we observed. For instance, if increased fallback and impaired homing increase an individual’s residence time between BON and MCN dams, transported fish may be more vulnerable to the zone-6 tribal fishery. This possibility, however, has not been evaluated to any great extent.

Regardless of the precise mechanisms involved, our results have important implications worth noting: 1) A portion of deviation in both T/C and D from their null expectations may be attributed to survival differences occurring in the mainstem Columbia and Snake rivers after adults return to the freshwater environment to spawn. As a simple example, if we alter wild Chinook SAR(T0) and SAR(C0) values for MY2004 to represent a marine-only post-BON mortality component (i.e., using the average BON-LGR survival for adults with LGR (0.76) and inriver (0.87) outmigration histories), T/C ratios change from 0.97 to 1.11 and D from 0.39 to 0.45. 2) The effect of outmigration experience on upstream adult survival appears to be tempered by a distance-from-release effect. Although we provide only a preliminary analysis of this issue in the present report, we observed two results supporting this conclusion: a) in contrast to LGR-transported fish, the differential between transported and inriver outmigrants was considerably less for those fish collected and transported from LGS or sites even further downstream (i.e., LMN, MCN); and b) the survival discrepancy between LGR and inriver outmigrants tended to be less for hatcheries existing higher in the watershed. This finding is consistent with the results Solazzi et al. (1991), who documented an increase in the straying rates of adult coho salmon that were transported and released as smolts at differing distances from their hatchery rearing site. Further, the lack of a transportation effect on homing for adults transported from IHR as smolts (Ebel et al. 1973) prior to the completion of LGR suggests that sufficient distance for imprinting may exist between LGR and IHR. 3) Finally, using project-specific PIT-tag detections has become the standard for estimating inter-dam conversion rates for use in in-season fisheries management. While a PIT-tag approach has permitted managers to avoid some of the pitfalls associated with traditional count-based approaches towards conversion rate estimation (Dauble and Mueller 2000), our data suggest that such estimates may be biased (relative to the run at large) if transportation history is not

59

considered in the estimation process. For example, if upstream survival is greater for inriver than transported groups – as we demonstrate here – and the majority of the untagged run-at-large was transported as smolts, a raw PIT-tag estimate of adult conversion rates will be biased relative to the run-at-large.

While we intend to further explore these conclusions, their implications, as well as perform additional supporting analyses for future reports, we document a clear inriver, upstream-migrant mortality effect resulting from different juvenile outmigration experiences.

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CHAPTER 7

Upstream-downstream comparisons: Differential mortality for upriver and downriver

PIT-tagged wild and hatchery sp/su Chinook Background

The upstream/downstream stock comparison was initiated primarily to provide information relevant to the patterns observed in recruit/spawner patterns between upriver and downriver stream-type Chinook (e.g., Schaller et al. 1999, Deriso et al. 2001). The PATH comparison of R/S patterns indicated Snake River stocks productivity and survival rates declined coincident with development and operation of the FCRPS. The R/S comparisons also provided evidence of delayed mortality of inriver migrants from the Snake River, after accounting for direct mortality, differential delayed mortality of transported smolts (D), and the common year effect (CSS Delayed Mortality Workshop proceedings, Marmorek et al. 2004). Analyses by coauthors Schaller and Petrosky in the 2005 CSS Annual Report showed that the differential mortality rates (between upstream and downstream populations) from migration years 2000 to 2002 estimated from PIT-tag SAR data corresponded with differential mortality rates estimated from historic recruit/spawner ratios covering smolt migration years 1993 to 2000. They found that differential mortality between Snake River and downriver stocks averaged 1.47; thus Snake River populations survived only 1/4 (i.e., e-1.47) as well as the downriver populations since hydrosystem completion in the mid-1970s.

In the current annual report, we will add two additional migration years to the time series of PIT-tagged fish generated SARs for upriver and downriver stocks. SARs computed with upriver wild and hatchery Chinook stocks from LGR as smolts to BOA as adults, downriver wild Chinook from JDA as smolts to BOA as adults, and downriver hatchery Chinook from BON as smolts to BOA as adult. The downriver wild Chinook originate in John Day River and the downriver hatchery Chinook originate at Carson NFH on the Wind River. Rather than compare the downstream SAR to upriver fish in the transport and in-river study categories separately as was done last year, we have used an overall weighted SAR for the upriver stocks, where the study-specific SARs get weighted by their estimated proportion in the overall run-at-large. Recovery year 2002 is the first year when BOA had sufficient coverage of all fish ladders with PIT-tag detectors. Therefore, all comparisons of upriver and downriver stocks will be limited to migration years 2000 and later. We do not attempt to expand the BOA counts for any harvest occurring below Bonneville Dam and assume that any harvest occurring will be affecting the upriver and downriver stocks equally. Carson NFH Spring Chinook Although the CSS has PIT-tagged a given number of Carson Hatchery production in each year since 1997 (see Appendix G Table G-2 for the number of Carson NFH Chinook PIT-tagged, median length, and percentage of production tagged in each year from 1997 to 2004), an adult PIT-tag system was not fully installed at BON until the 2002 return season. Therefore, we will limit discussion in the annual report of Carson Hatchery PIT-tag releases to migration years

61

2000 to 2004 for purpose of the upriver and downriver SAR comparison. SAR data from 1997 to 1999 may be seen in the 2005 CSS Annual Report (Berggren et al. 2005).

For Carson Hatchery spring Chinook, BON is the primary evaluation site. BON is the only project these fish pass on their way to the ocean, and juvenile survival estimates must rely on a recapture site(s) below the project to estimate survival to Bonneville Dam and thereby the number of PIT-tagged Carson Hatchery Chinook smolts index at that dam. NOAA Fisheries operates a trawl located at River KM 74 near Clatskanie, OR, that is equipped with PIT-tag detection equipment in the cod-end of the net. Only a specific amount of sets can be made during the season, and catch rate will vary based on river flow, velocity of the flow, and debris and other factors that might reduce sampling time during a given year. Since these recapture numbers can be low, we explored in the 2003/04 CSS Annual Report (Berggren et al. 2005) the additional use of PIT tags decoded from the tern and cormorant nesting sites at Rice Island (Rkm 34) and East Sand Island (Rkm 8) in the lower Columbia River estuary. We found that the CJS reach survival estimate from Carson Hatchery to BON for migration years 1998 to 2002 were more stable (fluctuating only 10 percentage points over these years) when both the tag detections at the trawl and tag recoveries on the bird colonies as two final recovery sites below BON. However, along with utilizing the PIT-tags recovered from bird colony comes the unproven assumption that the birds did not capture PIT-tagged fish above Bonneville Dam. Table 31 presents the resulting survival estimates to BON.

Table 31. Number of PIT-tagged Carson Hatchery Chinook released in the Wind River, estimated survival and resulting smolt population arriving Bonneville Dam in migration years 2000 to 2004 (with 90% confidence intervals) with detected adults at BOA. Migration year

Release number

Survival rate A

Estimate (95% CI) Smolt est. at BON

Smolts at BON 90% CI

Adults at BOA

2000 14,992 0.863 (0.69 – 1.03) 12,945 11,015 – 15,531 427 2001 14,978 0.835 (0.72 – 0.95) 12,506 11,244 – 14,150 223 2002 14,983 0.824 (0.60 – 1.02) 12,349 10,096 – 15,432 151 2003 14,983 0.848 (0.68 – 1.02) 12,709 10,855 – 15,275 34 2004B 14,973 Estimate > 1, so use

0.843 (avg of 2000–2003) 12,622 NA 79

A Survival estimates and 95% confidence intervals from hatchery to Bonneville Dam (BON) tailrace based on trawl site and bird colony sites as the downstream PIT-tag detection sites. B Migration year 2004 is incomplete with jacks and Age 2-salt adult returns through 8/9/2006; including 226 PIT tags found on East Sand Island bird colony, estimated release-to-BON survival >1 was obtained, so average survival rate of prior 4 years is used for 2004.

In determining SARs indexed on adult returns at (BOA), we need an estimate of the

number of smolts passing BON and number of PIT-tagged adults passing BOA in the fish ladders. Only 2-salt and older adult returns are used in the computations of the SARs (the full age composition of the returning jacks and adults for each migration year is shown in Appendix Table D-4). Beginning with return year 2002 there was the capability to detect nearly all PIT-tagged adult fish passing the three ladders at BOA. However, since a portion of the fish swim over the weir crests and don’t pass through the orifices where the detection equipment is installed, the detection rate for PIT-tagged adult fish at BON remains less than 100%. To expand the number of adult PIT-tag detections at BON to account for “missed” fish, we computed BOA

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adult PIT-tag detection efficiency estimates for migration years 2000 (see Table 46 of Berggren et al. 2005) and 2001 to 2004 (Table 32). The combined hatchery/wild detection efficiency estimates were used for all wild and hatchery Chinook groups in the estimation of SARs. Table 32. PIT-tag detections of returning adult Chinook (ages 2- and 3-salt) at Bonneville and Lower Granite dams with percentage of fish undetected at Bonneville Dam – returns from smolts that outmigrated in 2001 to 2004.

Age 2-and 3-Salt Returning Adult Chinook Smolt Migr. Year

Dam for adult detections1 Hatchery

Chinook2Wild Chinook3

Combined Chinook

BOA GRA, MCA, IHA

616 626

45 46

631 642

2001

BOA detection efficiency5 98.4% 97.8% 98.3 % BOA GRA, MCA, IHA

1,026 1,065

232 240

1,258 1,305

2002

BOA detection efficiency5 96.3% 96.7% 96.4 % BOA GRA, MCA, IHA/ICH

514 543

84 90

598 633

20034

BOA detection efficiency5 94.7% 93.3% 94.5 % BOA GRA, MCA, ICH

318 326

86 88

404 414

20044

BOA detection efficiency5 97.5% 97.7% 97.6% 1 BOA covers Bonneville Dam ladders (detectors BO1, BO2, and BO3), MCA covers McNary Dam ladders (detectors MC1 and MC2), IHA/ICH covers Ice Harbor Dam ladders, and GRA covers the Lower Granite Dam ladder. 2 Hatchery Chinook contains the combination of PIT-tagged fish from Rapid River, Dworshak, Catherine Creek AP, Imnaha AP, and McCall hatcheries. 3 Wild Chinook contain the aggregate of PIT-tagged fish originating above LGR used in the CSS. 4 Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006. 5 Calculated as p = (N detected at BOA) / (N detected at BOA + N passing BOA undetected that were later detected upstream)

The SARs from first-dam encountered as smolts to Bonneville Dam as adults was higher across migration years 2000 to 2004 for Carson NFH Chinook (downriver group) than for the upriver spring Chinook hatchery releases, but not always higher for the upriver summer Chinook (Table 33). The SAR computations used BOA adult numbers expanded by the reciprocal of the PIT-tag detection efficiency estimated for that site. The PIT-tag hatchery Chinook from the upriver Snake River hatcheries and the downriver hatchery both had a decreasing trend in SARs from migration year 2000 to 2004. The ratio of the upriver SAR to downriver SAR ranged was highest among all five upriver hatcheries in migration year 2003, and lowest in 2001 for Dworshak, Catherine Creek, and Imnaha hatcheries and lowest in 2004 for Rapid River and McCall hatcheries (Table 33). The higher upriver/downriver ratios in 2003 were significant higher than prior years based on non-overlapping 90% confidence intervals for the two summer stocks (McCall and Imnaha hatcheries). Confidence intervals were not available for migration year 2004 data, because the estimation of the population of PIT-tagged smolts at BON for that year could only be indirectly estimated using the average survival rate from release to BON tailrace of the prior four years (see Table 31).

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Table 33. Estimates of SAR from first dam encountered1 as smolts to Bonneville Dam (BOA) as adults2 for the upriver PIT-tagged wild Chinook aggregate and the downriver PIT-tagged John Day River wild Chinook that outmigrated in 2000 to 2004.

Upriver Hat. Chinook 3

SARLGR-to-BOA

Carson NFH Chinook SARBON-to-BOA

Upriver/Downriver Ratio

Hatchery Run Type

Migr. Year Est.

% 90% CI

% Est. %

90% CI % Est. 90% CI

2000 2.71 2.53 – 2.87 3.44 2.82 – 4.07 0.79 0.65 – 0.96 2001 1.38 1.24 – 1.52 1.81 1.53 – 2.09 0.76 0.63 – 0.93 2002 1.06 0.94 – 1.18 1.27 0.97 – 1.60 0.83 0.65 – 1.12 2003 0.34 0.28 – 0.41 0.28 0.20 – 0.38 1.21 0.86 – 1.79

RAPH Sp Ch

2004 4 0.32 0.26 – 0.39 0.64 N/A 0.50 N/A 2000 1.58 1.45 – 1.70 3.44 2.82 – 4.07 0.46 0.38 – 0.57 2001 0.44 0.37 – 0.51 1.81 1.53 – 2.09 0.24 0.19 – 0.30 2002 0.75 0.66 – 0.85 1.27 0.97 – 1.60 0.59 0.45 – 0.78 2003 0.31 0.26 – 0.37 0.28 0.20 – 0.38 1.11 0.77 – 1.67

DWOR Sp Ch

2004 4 0.40 0.34 – 0.46 0.64 N/A 0.63 N/A 2001 0.37 0.23 – 0.51 1.81 1.53 – 2.09 0.20 0.19 – 0.30 2002 1.11 0.83 – 1.41 1.27 0.97 – 1.60 0.87 0.60 – 1.22 2003 0.35 0.22 – 0.50 0.28 0.20 – 0.38 1.25 0.72 – 2.03

CATH Sp Ch

2004 4 0.42 0.25 – 0.62 0.64 N/A 0.66 N/A 2000 3.76 3.53 – 3.99 3.44 2.82 – 4.07 1.09 0.91 – 1.34 2001 1.46 1.30 – 1.62 1.81 1.53 – 2.09 0.81 0.67 – 0.99 2002 1.72 1.54 – 1.91 1.27 0.97 – 1.60 1.35 1.05 – 1.81 2003 0.81 0.72 – 0.89 0.28 0.20 – 0.38 2.85 2.08 – 4.15

MCCA Su Ch

2004 4 0.44 0.37 – 0.51 0.64 N/A 0.69 N/A 2000 3.61 3.29 – 3.93 3.44 2.82 – 4.07 1.05 0.87 – 1.30 2001 0.81 0.66 – 0.99 1.81 1.53 – 2.09 0.45 0.34 – 0.59 2002 0.92 0.73 – 1.13 1.27 0.97 – 1.60 0.73 0.52 – 0.99 2003 0.71 0.58 – 0.84 0.28 0.20 – 0.38 2.50 1.76 – 3.77

IMNA Su Ch

2004 4 0.50 0.38 – 0.63 0.64 N/A 0.78 N/A 1 First dam encounter is LGR for upriver wild Chinook and JDA for downriver wild Chinook 2 Estimated SARs use adults detected at BOA that have been expanded by reciprocal of the PIT-tag detection efficiency estimates of 0.960 for migration year 2000 from Table 46 in Berggren et al. 2005, and 0.983, 0.964, 0.945, and 0.976 for migration years 2001 to 2004 from Table 32 in this chapter. 3 Upriver SAR is weighted average of study-specific SARs when weight is estimated proportion of study group in run-at-large for migration year. 4 Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

Estimates of differential mortality, calculated as ΔM = -ln(SARsnake/SARdownriver), for each of the five PIT-tagged hatchery Chinook upriver population relative to the Carson NFH Chinook downriver population are graphically presented in Figure 33. Although the estimated ΔM differ among hatcheries, there is a common annual pattern among the five upriver hatcheries.

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Differential mortality upriver/downriver stocks of hatchery sp/su Chinook

-1.5

-0.5

0.5

1.5

2.5

2000 2001 2002 2003 2004

Migration year

- ln(U

/D)

DWORRAPHMCCAIMNACATH

Figure 33. Trend in differential mortality ΔM=-ln(U/D) for hatchery Chinook (Snake River basin stocks [U] versus Carson NFH stock [D]) for smolt migration years 2000 to 2004. John Day River Wild Chinook

In the lower Columbia River basin, the CSS utilizes the PIT-tagged wild spring Chinook from John Day River (tagged under a separate contract between ODFW and BPA) for the upstream/downstream comparison. ODFW crews have PIT-tagged the following number of juvenile Chinook within the John Day River basin (methods and locations of this PIT-tagging are found in Carmichael et al. [2002]).

Estimating SAR from first dam encountered as smolts to BOA as adults requires an estimate of the number of PIT-tagged John Day River wild Chinook smolts passing JDA. This smolt estimate (Table 34) was obtained by multiplying the tag release number by estimated survival from release to JDA tailrace. In estimating this survival, we did not include the PIT-tag recoveries from the bird colonies, since the detections at BON and the trawl alone provided sufficient precision in the survival estimate to JDA tailrace. The number of adult returns (2-salt and older) detected at BOA are also shown in Table 34 (the full age composition of returning jacks and adults for each migration year is shown in Appendix Table D-2).

Table 34. Number of PIT-tagged wild Chinook released in John Day River basin, estimated survival and resulting smolt population arriving John Day Dam in migration years 2000 to 2004 (with 90% confidence intervals) with detected adults at BOA. Migration year

Release number

Survival estimateA

Survival 90% CI

Smolt est. at JDA

JDA # 90% CI

Adults at BOA

2000 1,851 0.709 0.648 – 0.784 1,312 1,199 – 1,451 140 2001 3,881 0.701 0.674 – 0.730 2,721 2,617 – 2,835 106 2002 3,999 0.639 0.570 – 0.724 2,555 2,279 – 2,894 95 2003 6,122 0.687 0.640 – 0.737 4,203 3,919 – 4,512 123 2004B 4,372 0.630 0.540 – 0.756 2,755 2,359 – 3,304 68 A Survival of aggregate from release sites to John Day Dam (JDA) tailrace based on Bonneville Dam and trawl sites as downstream PIT-tag detection sites. B Migration year 2004 is incomplete with jacks and Age 2-salt adult returns through 8/9/2006.

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The SARs from first-dam encountered as smolts to Bonneville Dam as adults was

substantially higher across migration years 2000 to 2004 for the John Day River wild Chinook (downriver group) than aggregate Snake River stocks (upriver group)(Table 35). The SAR computations used BOA adult numbers expanded by the reciprocal of the PIT-tag detection efficiency estimated for that site. The PIT-tag aggregate of wild Chinook from the John Day River and the PIT-tag aggregate of wild Chinook from the Snake River basin above LGR both had a decreasing trend in SARs from migration year 2000 to 2004. The ratio of the upriver SAR to downriver SAR was significantly higher for migration years 2001 and 2002 compared to 2003 and 2004 based on non-overlapping 90% confidence intervals. The U/D ratio for migration year 2000 was intermediate to the other years.

Table 35. Estimates of SAR from first dam encountered1 as smolts to Bonneville Dam (BOA) as adults2 for the upriver PIT-tagged wild Chinook aggregate and the downriver PIT-tagged John Day River wild Chinook that outmigrated in 2000 to 2004.

Upriver Wild Chinook Downriver Wild Chinook Ratio Upriver/Downriver Migr.

Year Weighted 3

SAR % SARLGR-to-BOA

90% CI % Estimated

SAR % SARJDA-to-BOA

90% CI % Estimated U/D Ratio

U/D Ratio 90% CI

2000 2.70 2.03 – 3.35 11.11 9.27 – 12.98 0.24 0.18 – 0.32 2001 1.84 0.93 – 2.87 3.96 3.29 – 4.58 0.47 0.23 – 0.75 2002 1.19 0.97 – 1.39 3.86 3.12 – 4.60 0.31 0.23 – 0.40 2003 0.36 0.28 – 0.45 3.10 2.61 – 3.62 0.12 0.09 – 0.15 2004 4 0.39 0.30 – 0.48 2.53 1.87 – 3.20 0.15 0.11 – 0.22 1 First dam encounter is LGR for upriver wild Chinook and JDA for downriver wild Chinook 2 Estimated SARs use adults detected at BOA that have been expanded by reciprocal of the PIT-tag detection efficiency estimates of 0.960 for migration year 2000 from Table 46 in Berggren et al. 2005, and 0.983, 0.964, 0.945, and 0.976 for migration years 2001 to 2004 from Table 32 in this chapter. 3 Upriver SAR is weighted average of study-specific SARs when weight is estimated proportion of study group in run-at-large for migration year. 4 Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

Estimates of differential mortality, calculated as ΔM = -ln(SARsnake/SARdownriver), for the

six years of SAR data (smolt migration years 2000 to 2004) from PIT-tagged wild populations (Snake and John Day rivers) are presented in Table 36 with associated 95% confidence intervals for comparison with the historic differential mortality estimates from Deriso et al. (2001). Wider confidence intervals (95% instead of 90%) are used to match those of the historic data set. In the one year of overlap between the two data series, the PIT-tag wild Chinook SAR-based differential mortality estimate (ΔM) for 2000 agreed well with the differential mortality estimated from the spawner-recruit analysis (Figure 34). A benefit of the SAR-based ΔM estimate appears to be a much narrower 95% confidence interval than obtained from the spawner-recruit analysis – see the trend in confidence interval spread from 2000 to 2004.

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Table 36. Conversion of estimated upriver/downriver ratios to differential mortality rates for comparison to differential mortality rates computed by spawner-recruit analyses, 95% confidence intervals shown with each method.

Ratio Upriver/Downriver Differential Mortality (ΔM) Migr. Year Estimated

U/D Ratio U/D Ratio 95% CI

Estimated -ln(U/D)

-ln(U/d) 95% CI

2000 0.243 0.165 – 0.340 1.41 1.08 – 1.80 2001 0.466 0.194 – 0.802 0.76 0.22 – 1.64 2002 0.308 0.224 – 0.424 1.18 0.86 – 1.50 2003 0.117 0.083 – 0.161 2.15 1.83 – 2.49 2004 4 0.153 0.104 – 0.241 1.88 1.42 – 2.26

Differential mortality

-1.0

0.0

1.0

2.0

3.0

4.0

5.0

1970 1975 1980 1985 1990 1995 2000 2005

Migration year

Diff

eren

tial m

orta

lity

LCL_mumuUCL_muLCL_MM=-ln(SAR ratio)UCLM

Figure 34. Differential mortality estimates from the Deriso et al. (2001) model updated through smolt year 2000 (Marmorek et al. 2004) compared to estimates based on SARs of wild Snake River and John Day River sp/su Chinook, smolt migration years 2000-2004.

Differential mortality estimates (ΔM) between upriver and downriver Chinook stocks

based on the SAR ratios of PIT-tagged fish over the five migration years were greater for the wild Chinook stocks than for the hatchery populations (Figure 35), and showed different annual patterns. The ΔM trend was similar across years for the five upriver hatcheries with the lowest value occurring for migration year 2003. Migration year 2003 produced the lowest overall annual SARs for each upriver hatchery stock and even a lower annual SAR for Carson NFH Chinook. The upriver wild Chinook stocks also had their lowest overall annual SAR estimated for migration year 2003, but the SAR for wild Chinook from John Day River was only slightly lower than the prior three years. CSS has proposed adding more wild and hatchery downriver stocks in future years to aid in the assessment of differential mortality and a common year effect.

67

As the time series of SAR data increases, we should improve our ability to calibrate PIT-tag generated SAR data to the recruit/spawner derived differential mortality, common year effect and other metrics.

Differential mortality upriver/downriver stocks of wild and hatchery Chinook

-1.5

-0.5

0.5

1.5

2.5

2000 2001 2002 2003 2004

Migration year

-ln(U

/D)

WILDDWORRAPHMCCAIMNACATH

Figure 35. Trend in differential mortality ΔM=-ln(U/D) for wild Chinook (Snake River basin stocks [U] versus John Day stocks [D]) and hatchery Chinook (Snake River basin stocks [U] versus Carson NFH stock [D]) for smolt migration years 2000 to 2004. CONCLUSIONS

1. Differential mortality rates (between upstream and downstream populations) estimated

from SAR data appear to correspond well with differential mortality rates estimated from recruit/spawner ratios for wild Chinook populations.

2. Differential mortality estimates based on SAR ratios of hatchery populations were

generally less than those based on SAR ratios of wild populations.

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Chapter 8

Upstream-downstream comparisons: contrasting smolt life histories between Snake River and John Day River stream-type Chinook salmon populations

Introduction

The use of an upstream-downstream stock-comparison approach towards evaluating the effects of the FCRPS on endangered anadromous salmonids (e.g., Chapter 7; Schaller et al. 1999; Deriso et al. 2001; Schaller and Petrosky In Review) has been criticized for a number of reasons (Zabel and Williams 2000; Williams et al. 2005). Critics suggest that downstream stocks, which pass through fewer dams than upstream stocks (i.e., 3 vs. 8 projects), are not appropriate controls for evaluating the effects of hydropower development because a number of confounding issues are at play. For instance, downstream smolts may migrate to sea at a different time than upstream stocks and therefore experience different (more favorable) conditions during estuary/early ocean residence (Zabel and Williams 2000; Williams et al. 2005); also, they may be less exposed to ocean fisheries than their upstream counterparts (Zabel and Williams 2000). More recently, it has been suggested that smolts produced by upstream populations may be smaller than those originating from downstream stocks (Williams et al. 2005), thereby suffering greater (size-selective) mortality at sea (Zabel and Williams 2002). Overall, critics argue that the existence of systematic differences in upstream and downstream population life history attributes precludes the ability to ascribe stock viability differences to the FCRPS.

Previous responses to this criticism (Schaller et al. 2000; Deriso et al. 2001; Budy et al. 2002) have stressed that life-history differences would need to explain the systematic change in relative performance existing for upstream and downstream populations coincident with, but unrelated to, the development and operation of the FCRPS. Thus, the relevant issue is not whether or not genetic or life history differences exist between upstream and downstream groups, but rather whether or not differences (if present) were manifested contemporaneously with the completion of the FCRPS. For this reason, upstream-downstream criticisms may be best evaluated using a historic time series comparison approach (i.e., where parameters describing various life history attributes are contrasted between groups as a function of time). Though we are attempting to assemble such a historical dataset, contemporary data (i.e., from the last decade) are all that is available for a quantitative evaluation.

For our present purpose, we explore whether or not there are any observable (present-time) differences between upriver and downriver populations that could explain the observed differential mortality. We focused on life history characteristics associated with the active outmigrant, or smolt, life stage. For both upstream and downstream populations, we quantified and compared outmigration attributes in order to understand the possible confounding effects of smolt life history differences on the results reported in Chapter 7 and elsewhere (Schaller et al. 1999; Schaller and Petrosky In Review). To do this, we exploited a six-year time series of outmigrant smolt data collected at juvenile traps affiliated with the wild Chinook salmon tagging component of the CSS. We contrasted size-at-tagging (fork length, in mm), emigration timing (using the trap site as a reference point for emigration), downstream migration rates (in km / day, to Bonneville Dam, BON), and estuary arrival timing (taken as arrival at BON) between

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wild/natural Chinook salmon smolts captured, tagged, and released at upstream (above Lower Granite Dam, LGR) trap sites and the John Day River mainstem trap site for migration years (MY) 2000 through 2005. Methods

We used five upstream smolt trap sites in our comparison of upstream-downstream life histories: (1) the Snake River trap (SNKTRP); (2) the Salmon River trap (SALTRP); (3) the Clearwater River trap (CLWTRP); (4) the Grande Ronde River trap (GRNTRP);and (5) the Imnaha River trap (IMNTRP). Our primary downstream reference for wild Chinook salmon smolt collection and tagging is the John Day River mainstem trap site (JDAR1). Our analysis of smolt life history characteristics was based on daily smolt collections for the primary period of juvenile outmigration (March 15th to May 20th; i.e., our evaluation is inclusive of spring outmigrants only) during migration years 2000 to 2005 (Note: CLWTRP operations were not initiated until 2002). Smolt size analysis -- We tested for differences in smolt size across the six release sites under two approaches. First, we tested for differences in size while explicitly accounting for across-site differences in relative abundance (i.e., using per-kilometer redd density as a surrogate measure of abundance to account for density dependent effects; See Chapter 8 Appendix, Table 42 for details) using analysis of covariance (ANCOVA). Second, we used an ANOVA approach where we implicitly accounted for inter-annual variation in in-stream conditions relating to juvenile growth and size (i.e., by incorporating MY as a factor). We evaluated ANOVA and ANCOVA model-effect significance based on F-tests (Type-III sums-of-squares); we contrasted density- and year-adjusted mean fork length between John Day smolts and those collected at other release sites using Tukey’s post-hoc HSD test. To further explore the effects of density on smolt size, we inspected slope parameters and their associated significance tests and examined plots of mean fork length against redd density, for each site. As a final note, because the sample sizes involved were quite large (Table 37) and statistical significance was therefore virtually guaranteed for all tests, we judged biological significance when between-group size differences were greater than 5 mm in magnitude. Outmigration timing -- Assuming that daily tag releases were proportional across the outmigration period and that collected individuals were actively migrating smolts, we estimated passage distribution statistics for each wild/natural Chinook salmon trap site described above. That is, we plotted cumulative passage distributions for each site and MY, as well as for the 6-year average. Additionally, we computed the median passage date for each trap site and MY. Downstream migration rate -- We estimated downstream migration rates, in kilometers per day (km / d) for fish tagged and released at upstream and downstream sites. For distance estimation, the upstream reference was the location of release (i.e., the trap site) and the downstream reference was BON (inclusive of all juvenile interrogation sites); migration duration was estimated for each individual as the difference between release date/time and final date/time of detection at BON (if detected). Migration distances used in computations were 512, 564, 603, 170, 694, and 513 for CLWTRP, GRNTRP, IMNTRP, JDAR1, SALTRP, and SNKTRP release

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sites, respectively. Ultimately, we tested for a difference in migration rates between upstream and downstream populations using ANOVA (as described above for our smolt size evaluation). Table 37. Summary statistics for wild Chinook salmon smolts captured, tagged, and released at CSS trap sites between March 15th and May 20th during migration years 2000-2005.

Release site MY Trap releases (n)

Mean fork length, mm (SD)

BON detections (n)

JDAR1 2000 1,599 113 (9) 280 2001 3,374 104 (8) 694 2002 3,278 99 (9) 256 2003 5,838 104 (10) 722 2004 2,893 109 (10) 167 2005 2,363 105 (9) 307 SNKTRP 2000 1,520 107 (10) 216 2001 29 120 (16) 4 2002 1,076 105 (10) 105 2003 383 102 (11) 34 2004 541 104 (11) 17 2005 339 103 (9) 8 SALTRP 2000 2,022 105 (11) 298 2001 1,768 111 (13) 130 2002 5,429 95 (10) 462 2003 9,133 100 (11) 716 2004 7,216 97 (10) 177 2005 8,974 103 (9) 203 CLWTRP 2000 0 NA NA 2001 0 NA NA 2002 260 99 (9) 21 2003 990 91 (9) 59 2004 1,224 99 (10) 35 2005 1,880 104 (10) 22 IMNTRP 2000 3,450 110 (9) 430 2001 9,315 109 (10) 742 2002 2,142 104 (11) 227 2003 4,832 104 (10) 522 2004 8,549 101 (10) 151 2005 2,572 98 (9) 72 GRNTRP 2000 1,235 118 (10) 158 2001 718 121 (11) 50 2002 1,178 113 (9) 99 2003 2,254 111 (12) 166 2004 2,861 112 (11) 98 2005 1,783 113 (12) 43

Given the different distances traveled by upstream and downstream fish prior to reaching

downstream detection sites and the distance–acceleration relationships that have been documented for Snake-origin spring/summer Chinook salmon (i.e., migration speeds increase as fish progress through the hydrosystem; Williams et al. 2005), we also compared migration rates between populations for a comparable (developmentally speaking) segment of their mainstem FCRPS hydrosystem migration corridor, on an exploratory basis. As dictated for downstream detection opportunities for JDAR1 fish, we compared mean first-to-third dam (John Day Dam-Bonneville Dam for downstream, LGR-Lower Monumental Dam for upstream fish) migration

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durations (in days) between populations. Because different river reaches (of comparable length JDA-BON = 116 km; LGR-LMN = 158 km) had to be used for this analysis by design, we evaluated whether or not populations differed as a function of reach- and/or year-specific water velocities, as measured water travel time values (WTT; the average duration in days it takes water particles to travel from the upstream end of a reservoir to the tailrace of another dam; a function of observed river flow and estimated reservoir volume). Estuary arrival timing -- Using the same methods as for outmigration timing, we quantified arrival timing distribution statistics for those fish detected at BON, assuming that passage at this site is equivalent to estuary arrival. That is, for those fish that survived and were detected at BON, we plotted cumulative passage distributions and estimated dates of 50% passage (i.e., median passage dates) for both upstream and downstream release groups.

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Figure 36. Wild Chinook salmon smolt size (mean fork length +/- 1 SD) for fish tagged and released during migration years 2000-2005 (between 15 March and 20 May). From left to right, trap sites are: CLWTRP = Clearwater R., GRNTRP = Grande Ronde R., IMNTRP = Imnaha R., JDAR1 = John Day R., SALTRP = Salmon R., SNKTRP = Snake R. Note: there were no wild Chinook smolt size data available for CLWTRP prior to 2002. As a final note, due to the small number of fish released and subsequently detected at BON in 2001 (n = 4), 2004 (n = 17), and 2005 (n = 8) for the SNKTRP site, we did not estimate migration rate or estuary arrival timing for this site in these years (Table 37). Additionally, to understand the potential influence of disparate mortality levels imposed upon upstream- relative

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to downstream-originating smolts prior to BON arrival, we computed the BON detection rate as a proxy for survival (i.e., n BON detects / n released at trap site). Results Summary -- In total, we evaluated differences between upstream and downstream smolt life histories based on a sample of over 100,000 individual fish collected across the 6-year time series. Based on these data, we observed that smolt size and outmigration timing were generally similar across upstream and downstream sites. However, we also observed that upstream-originating smolts that survived to and were detected at BON migrated downstream at a faster rate but arrived in the estuary at a later time later than downstream-origin smolts. Of JDAR1 fish tagged and released, 13% were detected at BON; 7% of upstream-origin smolts were detected at BON. Smolt size analysis -- Our analysis demonstrates that smolt size varies considerably across migration years, both within and across sites (Table 37; Figure 36). Within these data, however, there was no clear indication of a systematic size difference between the John Day fish relative to those captured at upstream trap sites. During some years, JDAR1 smolts were larger than those captured at upstream sites whereas in other years they were considerably smaller. The only clear and consistent trend indicated that those fish captured at the GRNTRP site were generally the largest whereas those captured at the CLWTRP site were the smallest of all sites in question. More importantly, with the exception of GRNTRP and CLWTRP sites, JDAR1 fish were generally within 5 mm of upstream sites. Table 38. Results from an ANCOVA-based comparison of smolt size across upstream and downstream release sites, using redd density as a covariate. Effect Sum-of-squares df MSS F P Rel_site 311,305 5 62,260.9 561.703 < 0.001 Redds 48,801 1 48,801.3 440.273 < 0.001 Rel_site*Redds 137,368 5 27,473.6 247.86 < 0.001 Error 11,417,500 103,006 110.843

Analysis of Covariance (ANCOVA) results indicate that fork length varies across sites,

but as a site-specific function of redd density (Table 38). With the exception of GRNTRP, smolt size—redd density regressions all had negative, non-zero (P < 0.001 for all parameter significance tests) slopes (Figure 37). Given that the density effect was site specific, we contrasted least-squares adjusted mean fork length between release sites at both the average density and at 4 redds per km – a level of abundance common to all sites (i.e., to avoid extrapolating for low-escapement sites). At an average level of density (8.9 redds per km), density-adjusted mean fork lengths differed significantly between all release sites (P < 0.001 for all pairwise contrasts); values were 74, 121, 106, 106, 100, and 100 mm for CLWTRP, GRNTRP, IMNTRP, JDAR1, SALTRP, and SNKTRP fish. At 4 redds per km, density-adjusted sizes for the same release groups (respectively) were 90, 117, 108, 107, 100, and 104 mm. Thus, though there is evidence for statistically significant differences between fish across release sites, the magnitude of departure may not be biologically profound. However, it should be noted that

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this model accounted for only a minor proportion of fork length variation and that the majority was due to the release site effect (not redd density).

In addition to explicitly incorporating density effects, we also contrasted fork lengths between release sites using ANOVA with MY as a factor. This approach accounted for a greater proportion of overall fork length variation than the density-specific model (i.e., Table 39 vs. Table 38). Similar to the ANCOVA results, ANOVA results indicate that significant differences exist among release sites, but that the general pattern varies depending on the migration year in question (Tables 38 and 39; Figure 36). Post-hoc pair-wise comparisons indicate the rank of JDAR1 fish size relative to

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Figure 37. Scatter plot of mean fork length (mm) against redd density (redds / km) for wild Chinook salmon smolts collected, tagged, and released at CSS trap sites during migration years 2000-2005 (between 15 March and 20 May). See Figure 36 caption for release site abbreviation definitions.

upstream sites varied across years (P < 0.001 for all contrasts): 1) in 2000, JDAR1 fish were between 2 and 8 mm larger than those collected at upstream sites; 2) in 2001, they were between 5 and 17 mm smaller than those captured at all other sites; 3) JDAR1 smolts were smaller than all but SALTRP and CLWTRP fish in 2002; 4) excluding CLWTRP and GRNTRP in 2004 and GRNTRP and IMNTRP in 2005, JDAR1 fish were within 5 mm of those collected at upstream sites in both of these years.

Table 39. Results from an ANOVA evaluating smolt size variation across release sites and migration years. Effect Sum-of-squares df MSS F P Rel_site 1,145,889 5 229,177.8 2,266.934 <0.001 my 93,338 5 18,667.6 184.652 <0.001 Rel_site*my 704,810 23 30,643.9 303.117 <0.001 Error 10,411,300 102,984 101.1

Outmigration timing -- Outmigration timing varied considerably across sites and migration years, particularly so for upstream-origin smolts. In most years, the 50% passage date occurred in mid

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April, but was as early as March 27th (SALTRP, MY 2004) and as late as May 17th (SNKTRP, MY 2005). Variability in JDAR1 outmigration timing was considerably less than that observed for upstream release groups. Table 40 details median passage dates for each site and migration year. Despite the wide range of variability in outmigration timing, there was no evidence for any systematic difference between upstream and downstream populations – that is, in some years downstream populations emigrated earlier than upstream populations whereas in other years they emigrated later. Despite the variability within sites across years, it appears that upstream and downstream populations initiate emigration from tributary streams within a similar time window, on average (Figure 38); both the upstream aggregate (i.e., all traps together) and the JDAR1 6-year average date of 50% passage was April 13th (across 2000-2005). Thus, in terms of trap catch data, we found no evidence for a disparity in outmigration timing for upstream and downstream groups. Table 40. Dates of 50% passage (i.e., median emigration date) for Chinook salmon captured, tagged, and released at CSS-affiliated trap sites during MYs 2000-2006. Median emigration date

Site 2000 2001 2002 2003 2004 2005 6-y

mean JDAR1 18-Apr 11-Apr 14-Apr 11-Apr 13-Apr 15-Apr 13-Apr SNKTRP 20-Apr 27-Apr 16-Apr 17-Apr 28-Apr 17-May 25-Apr SALTRP 12-Apr 25-Apr 9-Apr 4-Apr 27-Mar 12-Apr 9-Apr CLWTRP NA NA 2-May 31-Mar 29-Mar 3-Apr 8-Apr IMNTRP 1-Apr 28-Mar 19-Apr 4-Apr 12-Apr 10-Apr 7-Apr GRNTRP 20-Apr 19-Apr 17-Apr 3-Apr 12-Apr 29-Apr 16-Apr

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Figure 38. 6-year mean trap passage (i.e., emigration) distributions for JDAR1, SNKTRP, SALTRP, CLWTRP, IMNTRP, and GRNTRP release sites. Note: Julian date 75 is March 16th, 100 is April 10th, 125 is May 5th, and 150 is May 30th. See Figure 36 caption for release site abbreviation definitions. Downstream migration rates -- Based on those fish tagged, released, and later detected at BON, we also estimated total downstream migration rates (km / d) and compared them between upstream and downstream populations. This comparison demonstrates that smolts from

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upstream populations actually migrated faster than downstream-origin smolts, once their differing migration distances were accounted for. As illustrated in Figure 39, JDAR1 fish migrated to the estuary at a rate of approximately 5-10 km / d whereas upstream fish did so at twice the rate (10-20 km / d). Further, the across-site pattern was consistent and statistically significant (ANOVA with my, rel_site, and my*rel_site effects, P < 0.001 for all F-tests, and for all pair-wise contrasts between JDAR1 and upstream sites) for the MYs in question. As an aside, CLWTRP fish were

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Figure 39. Wild Chinook salmon smolt downstream migration rates (km / d, +/- 1 SD) for those fish captured, tagged, and released at CSS trap sites during migration years 2000-2005 (between 15 March and 20 May). See Figure 36 caption for release site abbreviation definitions. Note, CLWTRP operations did not begin until 2002; also, too few tags were available for SNKTRP estimation in 2001, 2004-2005. the slowest of all upstream-origin smolts and had the migration rate closest to that of JDAR1 fish. It should re-emphasized, however, that relative survival to BON differed between upstream and downstream release groups by ~6% (Table 37) and that relative detection rates (i.e., non-CJS estimates) at BON were low for both groups (upstream: 7%, downstream: 13%).

Despite their different overall trap-BON migration rates, we found evidence of similar and WTT-influenced first-to-third dam migration lengths (in days) for both upstream and downstream populations (Figure 40). In particular, analysis of covariance (with site and WTT effects) suggests a strong positive influence of WTT (F1,27 = 71.3, P < 0.001) but no effect of release site on migration duration, once upstream-downstream WTT differences are considered

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(F5,27 = 0.9, P = 0.485). The mean (WTT-adjusted) first-to-third dam migration duration (+ 2SE) for JDAR1 was 12+2 days; for upstream populations, durations averaged 10+2 days. Given that this statistical comparison relied partially on extrapolation for both upstream and downstream populations (Figure 40), however, this result can only be taken as suggestive. Estuary arrival timing – Despite the contemporaneous natal stream departure schedule and the faster downstream migration rate of upstream relative to downstream fish, upstream-origin smolts generally reached the estuary (taken as BON) later than downstream fish (Table 41; Figure 41). That is, while upstream release groups reached BON within roughly a day of each other on average (based on 6-year average of 50% passage date), they arrived 9-10 days after the downstream release group. On average, downstream fish arrived at the estuary on May 9th whereas upstream fish arrived on May 18th. Further, this pattern of delayed arrival was consistent across years.

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Figure 40. Scatter plot of first-to-third dam migration duration as a function of water travel time. Each dot reflects the mean value for a year-site combination. See Figure 36 caption for release site abbreviation definitions.

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Table 41. Median estuary arrival (i.e., BON detection) dates for Chinook salmon smolts captured, tagged, and released at CSS-affiliated trap sites during MYs 2000-2006. Median estuary arrival date

Site 2000 2001 2002 2003 2004 2005 6-y

mean JDAR1 8-May 10-May 11-May 14-May 7-May 5-May 9-May SNKTRP 12-May NA 18-May 16-May NA NA 15-May SALTRP 12-May 5-Jun 19-May 15-May 15-May 18-May 19-May CLWTRP NA NA 28-May 22-May 18-May 17-May 21-May IMNTRP 8-May 2-Jun 22-May 18-May 17-May 18-May 19-May GRNTRP 14-May 4-Jun 19-May 9-May 16-May 23-May 19-May

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Figure 41. 6-year mean estuary arrival (measured at BON) timing distributions for JDAR1, SNKTRP, SALTRP, CLWTRP, IMNTRP, and GRNTRP release sites. Note: Julian date 100 is April 10th, 125 is May 5th, 150 is May 30th, and 175 is June 24th. See Figure 36 caption for release site abbreviation definitions. Discussion and Conclusions

Our comparison of upstream and downstream Chinook salmon population-specific life history attributes yielded several important results: 1) We found no evidence for a consistent and/or systematic difference in size-at-migration existing between upstream and downstream populations. That is, both upstream and downstream production areas yielded smolts of similar, but variable (on an inter-annual basis) size. We also demonstrated that a portion of fork length variation could be attributed to density-dependent effects. 2) Our analysis of trap-passage timing distributions illustrates that both upstream and downstream populations depart from natal streams within a similar timeframe. We also found evidence for greater variation in outmigration timing for upstream relative to downstream

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populations. This finding is consistent with that of Williams et al. (2005), who reported greater variation in passage timing (at BON) for unmarked, upstream-origin yearling Chinook salmon. 3) Across all years in question, we found that upstream-origin smolts migrated to the estuary at a faster rate (~ twice as fast) than those emigrating from the John Day system. This result was not surprising given that upstream-origin fish spend a greater amount of time en route to sea (i.e., they travel from 3-4 times as far away as downstream stocks) and that smoltification status increases and travel times decrease as an increasing function of time spent in migration (e.g., Berggren and Filardo 1993; Williams et al. 2005). 4) Based on a comparison of migration rates between upstream and downstream populations for similar sections of their respective mainstem migration corridors (i.e., between the first and third dams encountered by each group), we found that hydrosystem migration rates did not differ between groups but were strongly influenced by water travel time. 5) Despite their similar size, similar emigration timing, and faster downstream migration rate, upstream-origin smolts arrived at the estuary later (~7-10 days) than John Day River Chinook salmon smolts. Given conclusions 2, 3, and 4 above and the historical increase in water transit times due to hydropower dam development, however, the observed discrepancy in arrival timing at BON is more likely a result of the FCRPS than some innate life history difference existing between upstream and downstream Chinook populations.

In summary, our analysis illustrates that although subtle differences occur within and across Chinook salmon populations, there is no indication that a systematic smolt life history difference exists between upstream and downstream production areas. Thus, while our use of an upstream-downstream comparison relies on a ‘natural experiment’ approach and is therefore imperfect by design, the analysis we present here illustrates that the potential confounding effects due to life history differences are negligible, if not non-existent. However, to address these matters further, we will conduct additional analyses for our 10-year report.

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Chapter 8 Appendix Redd Density Estimation

In order to account for the effects of density on smolt size, we used wild and natural

Chinook salmon redd counts as an index of the relative abundance of juveniles emigrating in a given migration year. To do this, we summed redd counts from the majority of trend-monitoring reaches occurring upstream of each of the CSS-affiliated traps. For Oregon sites (JDAR1, IMNTRP, GRNTRP), we acquired redd count data from ODFW reports (Wilson et al. 2005) and unpublished data sources (accessed via Streamnet); for Idaho sites (SALTRP, CLWTRP), we compiled redd abundance data from Brown (2002) and unpublished IDFG sources. For the SNKTRP site, we summed counts compiled for sites upstream of IMNTRP, GRNTRP, and SALTRP. In each case, we also estimated the total stream length surveyed (in km) so that density estimates could be standardized across sites. Survey-length information was obtained directly from reports when available; otherwise, it was accessed via queries of Streamnet’s database.

This approach is meant to provide a coarse, but relative picture of juvenile density across the different production areas and years. However, it relies on several assumptions. Among the more important ones are: 1) there is a strong relationship between spawner abundance and juvenile production and rearing density; and 2) trend monitoring areas are where the majority of spawning/production occurs, or if not, they approximate redd density in non-indexed reaches. The redd data, their sources, and some minor comments/clarifications appear in Table 42. Table 42. Redd abundance and surveyed kilometers for production areas upstream of CSS trap sites used to contrast smolt size between upstream and downstream populations.

Counts by brood year (migration year - 2) Trap Site km 1998 1999 2000 2001 2002 2003 Comments John Day 82 357 370 1411 1411 1500 1021 Inclusive of all indexed reaches

that are reported in Wilson et al. (2005) and upstream of trap site.

Salmon 6341 1264 518 1533 3345 3718 4043 Inclusive of all indexed reaches that are reported in Brown (2002) and upstream of trap.

Clearwater 1981 107 24 316 778 304 194 Inclusive of all indexed reaches that are reported in Brown (2002) and upstream of trap.

Snake 654 1315 605 1619 3529 4076 4315 Sum of survey lengths and redd numbers from reaches associated Salmon, Imnaha, and Grande Ronde traps.

Imnaha 16 39 87 82 182 352 269 Accessed via Streamnet. Grande Ronde

5 12 0 4 2 6 3 Accessed via Streamnet; does not include the Vey Meadows area, nor other production areas in the Grande Ronde Basin upstream of the trap (due to data limitations).

1. Lengths were estimated based on the maps presented in Brown (2002) and a query of Streamnet’s database for transect details; thus, a minor amount of measurement error exists in these values.

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CHAPTER 9

Understanding the implications of smolt size—detection probability relationships for CSS

study-group comparisons Introduction

Recent analyses demonstrate the existence of negative relationships between wild and hatchery Chinook salmon and steelhead smolt size (fork length, FL, in mm) and detection probabilities at Little Goose (LGS) and Lower Monumental (LMN) dams (Williams et al. 2005; Zabel et al. 2005). Given that the primary opportunity for smolts to be detected at these projects is via bypass systems, the implications of consistent size–detection probability relationships for studies relying on bypassed (i.e., inclusive of C1 and T0 study groups) and inriver (i.e., undetected, C0) outmigrant categories for drawing inference on the effects of the FCRPS on salmon may be considerable. Specifically, in their discussion Zabel et al. (2005) suggest that a study design like that used by CSS is inherently confounded; because smolt-to-adult survival (SAR) is size-dependent (e.g., Zabel and Williams 2002) and individuals may be sorted into transported and inriver treatment groups on the basis of size (i.e., larger fish stay inriver, smaller individuals end up in the bypass system), it may not be possible to separate the effects of the ‘treatment’ (i.e., bypass and/or transport) from the pre-existing effect of size on performance.

Before size-related confounding can be concluded, several issues need to be considered. First, while Zabel et al. (2005) demonstrate significant size–detection probability relationships for LGS and LMN collection and transport sites, the majority (>50%, Appendix E, Table 1) of CSS transport-group fishes are collected at Lower Granite Dam (LGR). Thus, the strength and sign (i.e., +/-) of size–detection probability association at LGR, which have not been previously quantified, are perhaps most influential on any realized size-related confounding. Secondarily, the practical (i.e., biological) significance of LGS-, LMN-, and LGR-specific size–detection probability relationships needs to be evaluated. For instance, while Zabel et al.’s relationships for wild steelhead were consistent, those estimated for both hatchery and wild Chinook salmon appeared to be weaker and more variable. Thus, it may be necessary to estimate the realized size discrepancy between study categories to fully appreciate the influence of size–detection probability relationships on studies like the CSS. Based on the results of Zabel et al. (2005) and on NOAA’s comments on our 2005 annual report (Appendix D in Berggren et al. 2005), we consider these issues in detail in this section of our report. In doing so, we focused exclusively on wild Chinook salmon for our evaluation, given that this group exhibits the largest transport vs. inriver post-Bonneville differential delayed mortality difference (i.e., D = SARBON-

LGR(T0)/SARBON-LGR(C0); Chapter 3) of all species and rearing type combinations evaluated as part of the CSS. Our approach relied on the following steps:

1) Using an AIC-based model-selection procedure, we evaluated the level of empirical support for size–detection probability relationships at LGR, LGS, and LMN among smolts tagged and released immediately upstream of Lower Granite pool during migration years 1998-2006 as part of the CSS;

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2) We estimated size–detection probability function parameters (i.e., the slope and intercept of fitted logistic functions) and their associated uncertainty for LGR, LGS, and LMN bypass/collection sites;

3) We contrasted FL (at release) between detected and undetected smolts (minus known removals made at upstream projects) through year and project-specific t-tests.

In the following pages, we detail the methods and results associated with each of these

steps. We conclude with a brief discussion about the implications of our findings and those of Zabel et al. for current and future efforts of CSS. Also, we identify other analyses that we hope to complete in order to more fully evaluate size–detection probability relationship issues in the future. Methods Dataset details -- We evaluated the level of empirical support for fork length–detection probability relationships using a dataset consisting of wild Chinook salmon smolts that were measured, PIT-tagged, and released at the Snake River trap (SNKTRP) and Clearwater River trap (CLWTRP) during migration years (MY) 1998-2006. Because fish size was a variable of primary concern, we selected these sites to ensure that size-at-release could be reasonably assumed (i.e., given their close proximity to LGR) to reflect that existing at dam arrival and/or bypass opportunity. Initially, we queried PIT-tag releases occurring in a period encompassing the peak of smolt outmigration and tagging at the SNKTRP and CLWTRP release sites (15 March-20 May) so as to obtain as large of a sample size as possible (minimum used for survival-detection modeling, n = 1,000). However, due to the existence of temporal trends in discharge, spill, and fish size-at-release within migration years, we limited our analysis to the 30-day period extending from 11 April-10 May. Based on preliminary analyses, both hydrological variables and size were reasonably stable across this period during the years in question. Table 43. Sample sizes for PIT-tagged release groups (sum of SNKTRP and CLWTRP releases between 11 April and 10 May) used in our estimation of P(det | FL) relationships (1999, 2000, 2002, 2005-6) and comparison of size between detected and undetected study categories, by migration year (MY). Bold-faced values correspond to MYs included in our survival/detection probability modeling exercise.

Species/rear type MY n wild Chinook 1998 532 wild Chinook 1999 1,592 wild Chinook 2000 1,320 wild Chinook 2001 26 wild Chinook 2002 1,150 wild Chinook 2003 507 wild Chinook 2004 617 wild Chinook 2005 1,026 wild Chinook 2006 2,022

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Based on the above restrictions, we obtained data for use in our evaluation of wild Chinook salmon survival and recapture probabilities for five of the eight years queried (1999, 2000, 2002, 2005-6; Table 43); for detected vs. undetected t-tests, we included all years available (i.e., 1998-2006). Using PIT-tag detections made at mainstem Snake and Columbia river dam sites, we constructed 5-digit binary (0 = not detected; 1 = detected) capture histories for each individual, with the initial digit corresponding to the SNKTRP release site, the second to LGR, the third to LGS, the fourth to LMN, and the fifth to a combined McNary-John Day-Bonneville Dam (MCN-BON) detection site (i.e., 3 detection opportunities were collapsed into a single one to bolster sample sizes; after Zabel et al. 2005). Also, fork length measurements made at the trap site were paired with individual capture histories. Analytical approach -- Using the dataset described above, we evaluated relationships between individual sizes and bypass probability using a three-tiered approach. First, we modeled survival and recapture probabilities for marked fish as a function of individual size and site effects using a modified Cormack-Jolly-Seber (CJS) framework. While maintaining a constant survival probability structure (see Table 44 caption for details), we fit eight candidate models, reflecting various hypotheses about whether or not size influenced individual recapture probability, and if so at which projects (Table 44). Note that our approach did not consider size effects for the final joint survival-detection probability (i.e., for MCN-BON) parameter, given that it was a pooled 3-site estimate and that we were interested in site-specific effects only. We evaluated the level of empirical support for competing hypotheses using an information-theoretic approach (Burhnam and Anderson 2002); we ranked models according to their ΔAIC values, and considered the model with the lowest AIC score to be our top model. If the best detection probability model included size effects and was measurably better than closely competing models (i.e., separated by > 2.0 ΔAIC units), we concluded that evidence existed for a relationship between FL and detection probability. Table 44. Candidate detection probability (p) models fitted for fish groups released in migration years 1999-2000, 2002, and 2005-6. For detection-probability model selection, the survival (φ) model structure was held constant based on the recommendations of Lebreton et al. (1992), in the most global form [i.e., φ(site × FL, all), survival varies across sites as a site-specific function of length].

Model structure Description of associated biological hypothesis p(.) p is constant across sites and does not vary as a function of size. p(site only) p varies by site, but irrespective of size. p(site × FL, LGR,LGS,LMN) p varies across sites as a site-specific function of size. p(site × FL, LGR, LGS) p varies across sites, but as a function of size at LGR and LGS only. p(site × FL, LGR,LMN) p varies across sites, but as a function of size at LGR and LMN only. p(site × FL, LGS,LMN) p varies across sites, but as a function of size at LGS and LMN only. p(site × FL, LGR) p varies across sites, but as a function of size at LGR only. p(site × FL, LGS) p varies across sites, but as a function of size at LGS only. p(site × FL, LMN) p varies across sites, but as a function of size at LMN only.

Independent of the results from our model-selection phase, we also evaluated fitted slope

parameters (and SEs) for site-specific (i.e., LGR, LGS, LMN) size–detection probability

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functions. To do this, we assessed the sign and precision of all slope parameters and inspected plots of size–detection probability relationships. We also computed across-year slope estimates using a meta-analysis framework. That is, for each collection site we estimated a pooled slope as βpool = [Σβi*wi]/Σwi, where wi = 1/σi

2 (i.e., inverse of variance around βi) and i is one of the study years; standard errors were computed as SE(βpool) = √(1/Σwi). For all slope estimates, we deemed statistical significance (i.e., H0: β = 0) when the absolute value of estimates exceeded two standard errors, after Zabel et al. (2005). Further, we contrasted our estimates with those reported previously by NOAA-Fisheries in order to understand the generality of patterns seen across years and sites common to both our datasets. Finally, it should be noted that while we did estimate survival and detection probabilities at LGR, LGS, LMN, and MCN-JDA projects, we relied on a modest trap-release dataset for doing so and thus emphasize primarily those results for our upper-most sites only, particularly LGR.

In addition to estimating size–detection probability relationships at LGR and downstream, we also compared the size distributions of detected and undetected wild Chinook salmon that were tagged and released at the CLWTRP and SNKTRP sites. For LGR, LGS, and LMN, we compared log10-transformed FLs between groups using t-tests, on a MY-by-MY basis. However, we excluded individuals that were known to be removed (i.e., placed in a barge) at an upstream site for subsequent downstream comparisons. Note that while we could account for known removals in this process, this approach did not allow us to account for inter-dam mortality.

All survival/detection probability analyses were completed using Program MARK. Other statistical analyses were completed using SYSTAT, version 9. We evaluated significance at α = 0.05. Table 45. Model-selection results for wild Chinook salmon release groups with sufficient tags for survival and recapture probability estimation (i.e., >1,000), by migration year. ΔAIC values appear in cells. Top models (i.e., those with the lowest AIC value) are identified with bold-faced font and underlining; near-top models (i.e., those with a ΔAIC value < 2) also appear as underlined, but in italics. See Table 44 for description of survival and detection probability model structures.

Model structure 1999 2000 2002 2005 2006 p(.) 443.4 82.4 183.2 47.9 245.8 p(site) 2.9 0.0 0.0 0.3 2.0 p(site × FL, all) 1.9 2.5 3.8 3.2 0.0 p(site × FL, LGR, LGS) 0.3 2.0 1.2 3.3 1.1 p(site × FL, LGR,LMN) 1.6 3.3 2.0 2.0 1.7 p(site × FL, LGS,LMN) 4.7 1.0 1.3 1.2 2.3 p(site × FL, LGR) 0.0 1.5 1.2 2.3 0.7 p(site × FL, LGS) 3.0 0.4 0.1 1.3 1.4 p(site × FL, LMN) 4.5 0.4 0.8 0.0 1.0

Results Detection probability modeling exercise -- Based on fish tagged and released above LGR, our survival-detection probability model-selection exercise provided no clear indication of a strong relationship between individual size and detection probability at LGR, or any site downstream

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(Table 45). In two of the five years analyzed (2000 and 2002), the model lacking FL effects (i.e., the null case) at all sites was the top model, though not unambiguously so; in two other years (2005 and 2006), the non-size model was virtually equivalent to any containing FL effects. The only year with measurable support for a size–detection probability relationship was 1999, during which the top model indicated a positive relationship exists between FL and detection probability at LGR (Figure 42). In contrast to site versus site–size model ambiguity, separation between a constant detection probability model (i.e., p(.)) and all others was unequivocal.

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Figure 42. Estimated fork length (mm)—detection probability relationships for wild Chinook salmon at LGR for MYs 1999, 2000, 2002, 2005, and 2006.

Our evaluation of site-specific size–detection probability slope parameter estimates resulting from our most fully specified models matched model-selection results. The only slope parameter differing significantly from zero out of all MY-site combinations was that for the 1999 LGR size–detection probability relationship. Estimates from all other years, though of similar magnitude to those reported for LGS and LMN by NOAA (i.e., where comparison was possible; Table 46), did not differ significantly from zero on a year-specific basis. However, given the limited amount of data available for estimation below LGR, we most emphasize our LGR findings. At this site, relationships varied qualitatively from positive to negative to neutral across the MYs in question (Figure 42). Further, pooled slope values (βLGR = 0.001, SE(βLGR) = 0.003; βLGS = - 0.010, SE(βLGS) = 0.004; βLMN = -0.002, SE(βLMN) = 0.004) – based on an inverse-variance-weighted, meta-analysis estimation – corroborate year-specific patterns; only LGS had a non-zero significant (and negative) pooled size–detection probability slope value. Thus, overall there was no strong evidence for a consistent size-related bias in detection probability for our primary transport site (LGR), but some evidence for an effect at LGS. Detected vs. undetected FL contrasts -- t-tests comparing size distributions between detected and undetected smolts after release at SNKTRP and CLWTRP provide an additional indication that size-sorting is not a major concern for CSS wild Chinook salmon (Table 47). For LGR, detected fish had significantly greater log10-transformed FLs than did undetected fish (by 2 mm, based on back-transformed means) in two years (1998, 1999). At LGS and LMN, detected fish were significantly smaller than undetected fish in 1 and 2 years, respectively. In all cases, size

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differences between detected and undetected fish, where statistically significant, were less than or equal to 2 mm; in all other years, median sizes of detected and undetected fish were virtually identical and not statistically distinguishable (Table 47). It should be noted that even though we could not directly account for mortality in this analysis, if survival was positively and detection probability (and subsequent removal) was negatively size dependent, we would expect size differences to progressively increase in a downstream direction. However, this is not the case. Thus, these results conservatively indicate differences existing in size distributions between detected and undetected fish are virtually nonexistent. Table 46. Maximum likelihood slope parameter estimates from detection probability—fork length relationships for wild Chinook salmon captured, PIT-tagged, and released at the Snake River and Clearwater River smolt traps (rel_site = SNKTRP, CLWTRP). Bold-faced values correspond to those parameters with point estimates that were greater than twice the value of their standard errors (after Zabel et al. 2005). Estimates delineated by ‘NOAA’ correspond to the values reported in Zabel et al., ‘CSS’ corresponds to our upstream-of-LGR release analysis.

p2 (LGS) p3 (LMN) MY slope SE slope SE 1999-NOAA 0.004 0.005 -0.017 0.006 2000-NOAA -0.008 0.003 -0.007 0.005 2002-NOAA -0.023 0.004 0.003 0.007 mean -0.009 -0.007 1999-CSS -0.009 0.007 -0.004 0.007 2000-CSS -0.010 0.008 -0.010 0.009 2002-CSS -0.010 0.008 0.008 0.009 mean -0.010 -0.002

Discussion and Conclusions

Despite its limitations, this analysis suggests that on average size–detection probability relationships are likely of negligible importance for wild Chinook salmon study group comparisons currently made as part of the CSS. The following observations support this conclusion: 1) First, model-selection results provided only marginal support for any size–detection probability relationship, across sites and MYs. For LGR in particular, the bypass site where the majority of our study fish are collected and assigned to their respective treatment groups – estimated relationships were weak to nonexistent. At LGS and LMN, relationships were quite variable across the 5-year record and of comparable magnitude to those estimated by Zabel et al. (2005). Given the high survival values estimated for release to LGR (φ1 = 90-95% in all MYs) and high detection probabilities estimated for lower-river sites (>60-70% at LGS, LMN, MCN-BON), we are confident that this result is not simply a statistical power issue. This contention is supported by the fact that the data clearly discriminated between site-specific and constant detection probability (i.e., p(.)) models in all MYs.

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Table 47. Summary statistics for detected and undetected wild Chinook salmon captured, tagged, and released from the Snake River and Clearwater River smolt traps during MYs 1998-2006. Rows with bold-faced font are those MYs where a significant difference (α = 0.05) was detected between categories using a t-test.

Detected Undetected Site Year n median SD n median SD LGR 1998 286 111 11 246 109 10 1999 441 105 9 1151 105 9 2000 430 106 10 890 106 10 2001 20 118 18 6 115 10 2002 246 102 11 904 104 10 2003 209 98 10 298 98 10 2004 426 102 10 191 102 10 2005 720 103 9 306 103 9 2006 667 105 9 1355 105 9 LGS 1998 263 110 9 251 111 12 1999 952 105 9 592 105 9 2000 520 106 10 781 107 10 2001 20 117 7 5 116 9 2002 398 103 10 644 104 10 2003 131 98 9 282 98 10 2004 266 102 9 163 102 9 2005 355 103 9 215 104 9 2006 895 105 9 699 106 10 LMN 1998 205 109 10 281 111 10 1999 752 105 9 784 105 10 2000 300 105 9 978 106 10 2001 12 117 8 12 117 7 2002 337 104 9 546 103 11 2003 38 94 9 330 98 10 2004 93 101 8 291 102 9 2005 150 104 10 326 103 9 2006 475 106 9 694 105 10

2) Considering realized size distributions, there were no clear differences between detected and undetected fish, across projects and years. This is especially true at LGR, the site for which our data are most reliable, where sizes were virtually identical for both groups. For downstream sites (LGS, LMN), our t-test results similarly suggest a lack of size separation.

In sum, both survival/detection probability modeling results and basic comparisons of

size distributions between detected and undetected wild Chinook salmon suggest that realized size differences between transported and inriver study groups are negligible. While this section constitutes our first attempt at addressing size-sorting issues in the CSS, we plan to conduct additional analyses to further understand the confounding effects of size–detection probability relationships on our results to date. Specifically, we intend to perform simulations evaluating realized distributions of fish entering bypass and remaining inriver given the range of possible size-related detection and survival probability functions (and associated uncertainty)

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demonstrated herein and in Zabel et al. (2005). Also, we intend to compare SARs between study groups containing fish that were detected and not detected in the Lower Snake (conditioned upon being seen at a site in the Lower Columbia River), as an explicit function of length (e.g., using ANCOVA), in order to evaluate this issue on a total life-cycle basis. Also, we intend to explore similar analyses for other species and rear types used in the CSS. With this information, we hope that we will be able to separate the effects of transport from those due to a size-related treatment-group assignment bias, if such a phenomenon indeed exists for these other study groups.

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CHAPTER 10

Computer program to create simulated PIT tag input files

for testing robustness of CJS survival estimates

The CJS methodology assumes that all members of a tagged group of interest have a common underlying probability of survivability and collectability. When these conditions (along with other assumptions mentioned in Appendix A) are met, the CJS estimates for reach survival between dams and collection efficiency at dams will be unbiased with minimum variance. A key purpose of the simulation studies will be to determine how unequal the underlying survivability and collectability may become among members of a population before the CJS estimates are compromised. An initial demonstration of how the simulation program may be used to investigate this question is conducted in this chapter using a set of default values for parameter inputs (described below). These default values were established to reflect the variable conditions of survivability and collectability occurring with “real” populations of migrating smolts. In the 2002/03 CSS Annual Report (Berggren et al. 2005), we discussed the need to conduct simulation studies to evaluate the robustness of the CJS inriver survival estimates. Also, we wanted to compare the results of using the CJS on a population from the “full” season to weighted survival rates created by running the CJS on temporal subsamples of tagged fish from the season (i.e., subcohorts). Since then, development and refinement of a sophisticated computer program to create simulated data sets as an input to the bootstrap program has been underway. The resulting simulator program will provide simulated data sets for investigating the extent to which changing survival and detection probabilities may impact CJS estimates computed for “full” season samples. It does not allow the post-stratifying, based on date of detection at LGR, of this “full” season sample into temporal blocks for assessing the “subcohort” method, which was attempted, but abandoned in earlier CSS reports. Early on, it became apparent that a large sample size of PIT-tagged fish was needed to estimate in-river survival rates from Lower Granite Dam to Bonneville Dam and so applying the CJS method to the full sample rather than subcohorts was essential.

The simulator creates a single population of tagged fish that moves through the hydrosystem experiencing “user defined” changing patterns of survivability and collectability over the migration season. The simulator program accounts for travel time and temporal spread of the passage distributions of migrating fish as they move thorough the hydrosystem in order to reflect how real fish pass the monitored dams. Capture history codes are created as these fish are split between undetected, detected and bypassed, or detected and transported routes of passage at these dams. The resulting simulated population of fish with associated capture history codes may then be run through the bootstrap program to obtain the CJS reach survival estimates. Estimates of reach survival rates between Lower Granite and Lower Monumental dams are used in expanding study category smolt numbers to Lower Granite Dam equivalents. Estimates of in-river survival rates between Lower Granite Dam and Bonneville dams are used in calculating the Vc term in the computation of D.

In contract year 2006, there have been accomplishments in this direction, and some preliminary simulation results will be presented herein. However, the major activity in 2006 has been in the area of continued computer program enhancements to make it more efficient for the

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end-user when multiple scenarios of changing survival and capture probabilities are being run. Additionally, a new shell program is being developed to allow the end-user to create many (1000 or multiples of 1000) independent dataset as random draws from a specific underlying population defined by a unique set of input parameters to produce an environment in which temporally changing survival and capture probabilities and smolt inter-dam travel times occurs. This later enhancement is needed to address whether the confidence intervals created by the bootstrapping program for the various survival rate parameters and combinations of these parameters presented in the CSS closely approximate the nominal coverage around the point estimate of interest. Simulator Input Running the simulator program creates a dataset that may then become the input file to the bootstrap program. To demonstrate how this program works, I will first start with the default set of input parameter values and show examples of samples drawn from the population of fish defined by the default parameter values. The default parameter values were calibrated to reflect conditions seen with real data of past years (particularly smolt migration year 2000). Figures 43 to 49 show the default parameter values entered into the seven input screens of the simulator program for an individual simulator run. Figure 43. First input screen of simulator program – initial settings including release number and survival to LGR, travel time related parameters, and assumed SAR levels.

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Figure 44. Second simulator input screen – arrival population characteristics, collection efficiency and removal rates at LGR, and smolt travel time and survival to LGS. Figure 45. Third simulator input screen – collection efficiency and removal rates at LGS, and smolt travel time and survival to LMN.

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Figure 46. Fourth simulator input screen – collection efficiency and removal rates at LMN, and smolt travel time and survival to MCN. Figure 47. Fifth simulator input screen – collection efficiency and removal rates at MCN, and smolt travel time and survival to JDA.

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Figure 48. Sixth simulator input screen – collection efficiency and removal rates at JDA, and smolt travel time and survival to BON. Figure 49. Seventh simulator input screen – collection efficiency and removal rates at BON, smolt travel time to trawl site, and trawl collection rate (joint survival-collection efficiency).

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In the second input screen, there are parameters that define the midpoint and breadth of the Gaussian Distributed (Normal) arrival population of smolts in Lower Granite Dam forebay. This spreads the population of smolts over a span of time similar to that observed historically for wild Chinook at Lower Granite Dam. On this screen and the subsequent six screens, there are parameters to describe the travel time for smolts to migrate between successive dams where PIT-tag detectors are present. At these dams, there are parameters to describe a daily collection efficiency that may (or may not) change over time as defined by the analyst. In the river reaches between dams where PIT-tag detectors are located, there are parameters to describe a daily survival rate that may (or may not) change over time also. Smolt travel time, collection efficiency, and reach survival all may change across the days of the migration season to reflect “real-life” situations where smolt travel time decreases as the season progress (e.g., fish may migrate faster as their physiological smoltification development advances over time), collection efficiency decreases as flows and spill levels increase during the peak of the annual freshet, and reach survival rates decrease as one moves further from the peak of the migration distribution. The simulator program allows the analyst to vary the amount of change by adjusting slopes of the linear and quadratic terms in each relation. The resulting values for travel time estimates are then fed into a gamma distribution while the collection efficiency and reach survival rates are fed into a binomial distribution.

Additional day-to-day variability (natural noise) may be added by allowing the probability term of the binomial distribution to vary as a beta distributed term. Therefore, the analyst has the option to use beta-binomial or simple binomial distributed probabilities of collection efficiency or survival rates (this is also true of the removal probabilities at each dam). These set of daily varying parameters are applied to the pool of smolts that have arrived in the forebay of a specific dam on a specific day. The smolts arriving on a specific day at an upstream site and continuing in-river to the next site will have their passage timing at the next downstream site spread out based on their travel times, but up to a maximum width of 10 days (analyst may specify a lower width). For the fish arriving in the forebay of a particular dam on a specific day, random draws based on the outcome from the collection efficiency curve on that day will determine which fish are collected at that site and which fish pass undetected. For this dam’s collected fish on that given day, random draws based of the outcome of the removal probability determination for that day will determine which smolts are removed for transportation or bypassed back-to-river.

As fish are moving downstream through the hydrosystem, they get defined a capture-history code based on their outcome at each dam. Once they pass the trawl site, they have all the required digits in their capture-history code to define how they passed through the system, or died in route. The total number of fish released, each with their associated capture-history code, become the input dataset for the bootstrap program for evaluation of questions regarding the robustness of the CJS survival rate estimates under conditions of changing survivability and collect-ability.

The default distribution of arrival and default collection efficiency at LGR is presented in Figure 50. The maximum range of dates in the simulation program runs from March 22 to June 30 at LGR. But by calibrating the input parameters to reflect typical wild Chinook passage timing at LGR, the dates of arrival fall between April 4 and June 15 with the middle 80% passage occurring between April 29 and May 23. The default arrival timing was used in the preliminary simulation runs for this report.

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Arrival smolt population at LGR and daily collection efficiency

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The resulting distribution of smolt detected at each dam and trawl and returned-to-river at

that site are presented in upper plot of Figure 51. The lower plot shows the timing of the transported fish at each dam. These plots show the effect of the default travel time parameters in shifting the distribution later at each successive detection site to closer mimic real fish populations.

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Figure 51. Passage timing of smolts at each dam and lower Columbia trawl site for fish returned-to-river at each site (upper plot) and transported (lower plot), based on default parameter inputs.

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The default survival rates applied daily to fish passing LGR undetected or detected in

bypass and returned-to-river from LGR to LGS are presented in Figure 52. This plot illustrates the quadratic shape of the survival relation with default parameter inputs and the variability achieved with application of the beta variation at a standard deviation of 0.05 (note that this plot simply shows the outcome from a single run with beta variation applied, and so future runs may fluctuate differently around the quadratic curve). The analyst has the choice of setting the beta variation to levels lower or higher than the default value of 0.05, or even to zero to disengage adding the beta variation in a given run. This type of relation, with differing values based on historic reach survival data, is possible for each successive reach survival estimate used in the simulator. When applied to the number of fish starting the reach of interest, this survival probability is used to obtain binomial draw of number of fish surviving that reach.

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Figures 50 to 52 illustrate the basic features of the simulator program by showing how

the arriving smolt population is handled at LGR, and at subsequent downstream sites. Input parameters that define the daily smolt travel times between dams allow analysts to create realistic migration timing distributions through the hydrosystem. The ability to modify survival rates and collection efficiencies with daily relations that may be quadratic, linear, or constant with

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differing levels of day-to-day variation allows the analyst to select input parameters that best represent the species or population of salmonids of interest. In the preliminary analyses presented next in this report, we will maintain the LGR arrival distribution as show in Figure 50 and travel time inputs used to create the migration timing shown in Figure 51. The removal probability for first-time detected fish at LGR, LGS, and LMN for transportation will held at 0.667 to reflect the current routing of two-thirds of collected PIT-tagged CSS study fish to transportation at those locations. The removal probability is constant across each day of collection in the binomial draws.

Simulator output files as input to Bootstrap Program Table 48 shows twelve simulations conducted with the default input parameters (including the default beta variation) from Figures 43 to 49. Each simulated run may be viewed as a random sample drawn from a common underlying population. The variability in the “true” survival rates and collection efficiency rates among the simulated runs show the influence of the beta-binomial draws for determining the numbers of fish surviving daily through each reach and collected daily for transportation and bypass and movement of fish through the hydrosystem as influenced by their migration rates. Six key parameters are presented in this table including estimates of S2 (survival LGR-LGS), S3 (survival LGS-LMN), VC (survival LGR-BON), and smolt numbers in LGR-equivalents for study categories T0 (transport), C0 (undetected at LGR, LGS, or LMN), and C1 (bypassed at LGR, LGS, and/or LMN).

The mean and 90% confidence intervals around the 12 simulated runs (Table 49) show close agreement for parameter S2 between simulated “true” values and the bootstrap estimates, but there appeared a trend toward higher mean estimates (and wider 90% confidence intervals) for the bootstrap results as more downstream reaches were considered. The largest difference was for VC, which is the product of the five reaches S2 to S6. With only two reaches required for expansions to LGR-equivalents, the number of smolts in each study category was within one-half of one percent between simulated “true” values and bootstrap estimate results for both the mean and 90% confidence intervals. This indicates close agreement of the bootstrap estimates to the simulated “true” values for number of smolts in the CSS study categories. This finding is encouraging since the estimates of smolt numbers is integral to each subsequent parameter of interest, such as SARs, T/C ratios, and D.

This exercise also illustrates the need to create many randomly drawn (independent) datasets from a common underlying population (i.e., hold all input parameters unchanged for the multiple data sets created), when we begin to evaluate whether confidence intervals estimated around the SARs, T/C ratios, and D are providing the proper coverage for the α-level desired. For the 10-year Summary Report, we plan to add programming features to the simulator program, whereby we may create 1000 (or more) data sets from a common underlying set of conditions for comparing bootstrapped 95%, 90%, and 80% confidence limits coverage properties.

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Table 48. Comparison of simulated “true” survival rates S2, S3 and VC, and number of smolts in study categories T0, C0 and C1 using default input parameters of Figures 42 to 48 and the resulting estimated parameter values obtained with the bootstrap program. Parameter “true” value Estimate Parameter “true” value Estimate

Sim# 810626 S2 0.938 0.945 T0 16,122 16,033 S3 0.929 0.938 C0 6,307 6,310 Vc 0.61 0.686 C1 7,885 7,812

Sim# 436487 S2 0.916 0.930 T0 16,234 16,129 S3 0.927 0.923 C0 6,209 6,321 Vc 0.59 0.624 C1 7,911 7,852

Sim# 374513 S2 0.929 0.922 T0 16,169 16,194 S3 0.936 0.946 C0 6,353 6,358 Vc 0.61 0.560 C1 7,946 7,945

Sim# 372932 S2 0.936 0.938 T0 16,296 16,323 S3 0.934 0.918 C0 6,230 6,224 Vc 0.60 0.600 C1 7,916 7,928

Sim# 371387 S2 0.940 0.943 T0 16,286 16,230 S3 0.941 0.951 C0 6,225 6,328 Vc 0.62 0.590 C1 7,849 7,807

Sim# 363900 S2 0.939 0.947 T0 16,246 16,130 S3 0.932 0.947 C0 6,222 6,297 Vc 0.62 0.564 C1 8,018 7,963

Sim# 362081 S2 0.934 0.917 T0 16,259 16,336 S3 0.936 0.957 C0 6,322 6,365 Vc 0.61 0.762 C1 7,853 7,906

Sim# 360565 S2 0.935 0.934 T0 16,244 16,202 S3 0.935 0.956 C0 6,223 6,159 Vc 0.62 0.608 C1 8,006 7,971

Sim# 357567 S2 0.942 0.931 T0 16,244 16,282 S3 0.932 0.950 C0 6,225 6,259 Vc 0.61 0.620 C1 7,872 7,869

Sim# 355331 S2 0.926 0.918 T0 16,094 16,136 S3 0.934 0.944 C0 6,465 6,471 Vc 0.61 0.628 C1 7,946 7,991

Sim# 349675 S2 0.935 0.922 T0 16,153 16,215 S3 0.931 0.946 C0 6,364 6,381 Vc 0.60 0.645 C1 7,866 7,894

Sim# 351288 S2 0.925 0.939 T0 16,150 16,093 S3 0.930 0.910 C0 6,340 6,346 Vc 0.61 0.629 C1 7,989 7,935

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Table 49. Comparison of mean and 90% confidence intervals of parameters S2, S3, VC, T0, C0, and C1 of simulated samples from common underlying population and the estimates obtained with the bootstrap program.

Parameter

Statistic1

Simulated “true” value

(A)

Bootstrap estimate

(B)

Estimate % change bootstap from “true” values

(B-A)/A 90% LL 0.929 0.927 -0.22 Mean 0.933 0.932 -0.11 S2

90% UL 0.937 0.938 0.11

90% LL 0.931 0.933 0.21 Mean 0.933 0.941 0.86

S3

90% UL 0.935 0.948 1.39

90% LL 0.604 0.598 -0.99 Mean 0.609 0.626 2.79

VC

90% UL 0.614 0.655 6.68

90% LL 16,173 16,144 -0.18 Mean 16,208 16,192 -0.10

T0

90% UL 16,243 16,240 -0.02

90% LL 6,248 6,277 0.46 Mean 6,290 6,318 0.45

C0

90% UL 6,332 6,359 0.43

90% LL 7,890 7,874 -0.20 Mean 7,921 7,906 -0.19

C1

90% UL 7,952 7,938 -0.18 1 Lower limit (LL) and upper limit (UL) of 90% CI use t(α=0.10; 11 df) of 1.796. CONCLUSIONS

1. The simulator software program was enhanced in 2006 with a user-friendly interface for inputting parameter values for different simulation runs.

2. Estimates of number of smolts in the CSS study categories in LGR equivalents and

associated 90% confidence intervals computed with the bootstrap program closely agreed (within 0.5%) with default simulated “true” data sets.

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APPENDIX A

CSS Statistical Framework and Equations

Introduction

This appendix provides the statistical framework of the CSS and formulas used to estimate the parameters of reach survivals, numbers of smolts in study categories T0, C0, and C1, SAR(C0), SAR(C1), SAR1(T0), SAR2(T0), T/C and U/D ratios, and D, plus the annual SARs. A detailed description of the analytical basis for estimating unbiased T/C ratios of the form SAR2(T0)/SAR(C0) is presented in the 2006 CSS Design and Analysis Report (Ryding 2006). The Design and Analysis Report illustrates why it is critical to compute SARs for CSS study categories in LGR-equivalents in order to obtain T/C ratios that are unbiased.

Key Assumptions

In Ryding (2006) a list and discussion of twelve assumptions that are key to tag-recapture methods of survival rate estimation and the use of T/C ratios. These twelve assumptions, reproduce below, are integral to the estimation approaches utilized in the CSS.

1. Tagged fish in the study are representative of the population. 2. All fish in a release group have equal detection and survival probabilities. 3. All fish in a release group have equal probabilities of a particular capture history. 4. Fates of individual fish are independent. 5. Previous detections have no influence on subsequent survival or detection probabilities. 6. Release numbers, capture histories, and PIT tag codes are accurately recorded and

known. 7. Only detected fish are subject to transport. 8. Tagged fish removed for use in other studies are known and accurately recorded. 9. All tagged fish in a cohort release migrate through the Snake and Columbia Rivers within

the same season and while the bypass facility and transport systems are operational, i.e., there is no delayed migration of tagged fish.

10. Transported fish and in-river migrants experience the same estuary and ocean conditions. 11. Harvest survival is the same for transported and in-river categories. 12. River conditions for same-age returns of a cohort are the same for the and

categories. 0T C

Statistical Framework and Computational Equations of the CSS The basic statistical framework of the CSS is the utilization of the CJS methodology for estimation of in-river reach survival rates, collection efficiency at monitored dams, and the reduced M-matrix for numbers of first-time detected smolts at Lower Granite, Little Goose, and Lower Monumental dams. Three groupings of smolts into specific study categories are made: (1) Transportation Group T0, (2) In-River Undetected Group C0, and (3) In-River Detected Group C1, where detection status refers only to the Snake River collector dams where

106

transportation takes place. Being detected at lower Columbia River dams or the estuary trawl does not preclude fish from Category C0. The first row of the reduce M-matrix (see Figure 1 for partial display) gives the number of first-time detected fish at Lower Granite Dam (m12), Little Goose Dam (m13), Lower Monumental Dam (m14), McNary Dam (m15), John Day Dam (m16), Bonneville Dam (m17), and the estuary trawl (m18). The notation for the complete reduced M-matrix is mjk, where the jth subscript refers to cohort number and the kth subscript refers to site, where 1 is reserved for release site, and 2 to 8 are used to designate each subsequent downstream detection locations). Cohort 1 is the initial release and provides the tallies by site of all possible capture histories first-detected at that site; the sum across these tallies equating to the total number of tagged fish detected from a given initial release. Cohort 2 is made up of the fish returned-to-river at Lower Granite Dam and m2k gives the summary tallies of these prior detected fishes’ subsequent first-detection at a downstream dam. This process is continued through Cohort 7, which is made up of the fish returned-to-river at Bonneville Dam and the tally of its fish subsequently detected at the estuary trawl is given by m78. Ratios of various sums across different cohorts provide the ingredients for the CJS survival estimates as depicted in Figure 1 (note: this figure is only a partial depiction of all sites and cohorts, so the various mj column tallies, zk tallies and rj row tallies will span more cohorts and sites than shown here: e.g., z2 = m13 + m14 + m15 + m16 + m17 + m18 and r2 = m23 + m24 + m25 + m26 +m27 + m28). The estimate of collection efficiency for the kth site is obtained by dividing the numerator from the Φk-1 survival estimate in Figure 1 into the mk tally.

As stated previously, the mjk’s are tallies of capture histories reflecting were tagged fish are detected or not detected. An eight-digit binary code represents the status of detection (1) or non-detection (0) at each recovery site following initial release (1 in code’s first position), so that code 10010001 would show detections at Lower Monumental Dam (4th digit) and the estuary trawl (8th digit). If a detected fish is not returned-to-river, it will instead receive a digit 2 if transported (e.g., 10020000 if first-time detected fish is transported from Lower Monumental Dam ) or 3 if “other” removal types such as taken for use in other studies (e.g., sacrificed for physiological research [Congleton 1999 to 2003] or inadvertently collected during NOAA tagging activities Lower Monumental or John Day Dam and re-released elsewhere with those fish in some years). The notation X10020000 is used to represent the tally of fish with the capture history shown in the subscript. The tallies of first-time detected fish that are transported are X10020000, X10020000, and X10020000 for Lower Granite, Little Goose, and Lower Monumental dams, respectively. First-time detected fish that are returned-to-river at the kth site are tallied as “m1k - dk”, where dk is the sum of fish removed at the kth site. The removal sum dk includes transported (at collector dams) and “other” removal fish.

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Figure 1. Schematic of key part of reduced M-matrix used in CJS survival rate estimation and CSS study category smolt number estimation – complete reduced M-matrix of CSS includes three more sites (JDA, BON, and TWX) and three more cohorts (# 5, 6, and 7). In estimating SARs from Lower Granite Dam as smolts to Lower Granite Dam as adults for each of the three study categories, it is necessary to convert the tallies of detected fish at sites below Lower Granite Dam into the number necessary to start at Lower Granite Dam (termed LGR-equivalents in this report) in order to produce the observed detected number at the downstream sites of Little Goose and Lower Monumental dams. Ryding (2006) demonstrates the necessity of converting detections at Little Goose and Lower Monumental Dam into LGR-equivalents before computing T/C ratios. In that report, known probabilities of survival, collection efficiency, and transportation if collected from two scenarios are utilized to compute expected numbers of smolts in Study Categories T0 and C0 in LGR-equivalents to make this case. In practice, estimates of these parameters of survival rate and collection efficiency are obtained with the CJS methodology, which uses the reduced M-matrix as presented above to summarize the observed detection data from which maximum likelihood estimated parameters of survival and collection efficiency are generated. In estimating the number of smolts in each of the three CSS study categories, the number of detections at Lower Granite (m12), Little Goose (m13), and Lower Monumental (m14) dams from the reduced M-matrix, and estimated survival rates from release to Lower Granite Dam tailrace (S1) to get starting population at Lower Granite Dam, Lower Granite Dam tailrace to Little Goose Dam tailrace (S2), and Little Goose Dam tailrace to Lower Monumental Dam tailrace (S3) from the CJS model output are key components. In addition, data at the kth site on number of PIT-tagged smolts transported (nk for tally of PIT-tagged fish and tk for estimated number of PIT-tag that would have occurred if the PIT-tagged fish had been routed to transportation at the same rate as the untagged run-at-large) and number of PIT-tagged smolts returned-to-river (m1k - dk) at each Snake River collector dam (k = 2 [LGR], 3 [LGS], and 4 [LMN]) is used to complete the estimation of smolt numbers in Study Categories T0 and C1.

Lastly, there is a small adjustment made to the estimated numbers of smolts in C0 and C1 categories to reflect known removals occurring at monitoring sites downstream of Lower Monumental Dam. Fish were considered removed (not returned-to-river) at McNary Dam when detected on raceway or sample room monitors or only on the separator monitor during the summer transportation season, or when collected and removed at John Day or Bonneville Dam for other research purposes. For example, samples of CSS hatchery Chinook from Rapid River, McCall, and Dworshak hatcheries were collected and sacrificed at John Day and/or Bonneville dams during migration years 1999 to 2003 for physiological (blood chemistry) evaluation (Dr. Congleton, University of Idaho Fish and Wildlife Unit). Because most removals occurred at John Day and Bonneville dams for other research purposes, we settled on a fixed 50% Lower Granite to Bonneville Dam survival rate for each removed fish in order to subtract these fish in LGR-equivalents from the estimated number of smolts in Categories C0 and C1. Most survival rates from Lower Granite Dam to Bonneville Dam from 1995 to 2004 (excluding 2001 when extremely low in-river reach survival rates and few returning adults occurred on in-river migrants) have been averaging around 50%. In 1994, the wild Chinook in-river survival rate from Lower Granite Dam to McNary Dam was estimated at 47%, with most removals occurring at McNary Dam due to no operational return-to-river diversion route present that year.

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The following list of 25 items show the computational formulas used in the CSS. The observed detections from the reduced M-matrix and estimated parameter of survival and collection efficiency from the CJS (parameters in bold type) are used to estimate smolt numbers in each study category along with their expectations. Tallies of adult returns for each study category are used with their corresponding estimated number of smolts to arrive at smolt-to-adult survival rates (SARs). Additionally, a ratio of transport SAR to inriver SAR, delayed mortality D, and overall annual SAR are computed as shown below:

1. Observed first-time detection tally at Lower Granite Dam (LGR) is m12 and expectation of E(m12) = R1· S1 · p2

2. Observed first-time detection tally at Little Goose Dam (LGS) is m13 and expectation of

E(m13) = R1· S1· (1- p2) · S2 · p3 3. Observed first-time detection tally at Lower Monumental Dam (LMN) is m14 and

expectation of E(m14) = R1· S1· (1- p2) · S2 · (1- p3) · S3 · p4

4. Observed transportation tally of PIT-tag smolts at LGR is n2 = X12000000 and expectation of E(n2) = E(m12) · Pn2 where Pn2 is the proportion of collected PIT-tagged smolts transported at LGR

5. Observed transportation estimate of run-at-large smolts at LGR is t2 =

(LGR run-at-large transported/LGR run-at-large collected) · m12 and expectation of E(t2) = E(m12) · Pt2 where Pt2 is the proportion of run-at-large (total fish at level of species and rearing type from Smolt Monitoring Program) transported at LGR

6. Observed transportation tally of PIT-tag smolts at LGS is n3 = X10200000 and expectation

of E(n3) = E(m13) · Pn3 where Pn3 is the proportion of collected PIT-tagged smolts transported at LGS

7. Observed transportation estimate of run-at-large smolts at LGS is t3 =

(LGS run-at-large transported/LGS run-at-large collected) · m13 and expectation of E(t3) = E(m13) · Pt3 where Pt3 is the proportion of run-at-large (total fish at level of species and rearing type from Smolt Monitoring Program) transported at LGS

8. Observed transportation tally of PIT-tag smolts at LMN is n4 = X10020000 and expectation

of E(n4) = E(m14) · Pn4 where Pn4 is the proportion of collected PIT-tagged smolts transported at LMN

9. Observed transportation estimate of run-at-large smolts at LMN is t4 =

(LMN run-at-large transported/LMN run-at-large collected) · m14 and expectation of E(t4) = E(m14) · Pt4 where Pt4 is the proportion of run-at-large (total fish at level of species and rearing type from Smolt Monitoring Program) transported at LMN

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10. Observed return-to-river tally of PIT-tag smolts at LGR is m12-d2 = m12· (1-Pd2) and expectation of E(m12-d2) = E(m12) · (1-Pd2) where Pd2 is proportion of collected PIT-tagged smolts not returned-to-river at LGR

11. Observed return-to-river tally of PIT-tag smolts at LGS is m13-d3 = m13· (1-Pd3) and

expectation of E(m13-d3) = E(m13) · (1-Pd3) where Pd3 is proportion of collected PIT-tagged smolts not returned-to-river at LGS

12. Observed return-to-river tally of PIT-tag smolts at LMN is m14-d4 = m14· (1-Pd4) and

expectation of E(m14-d4) = E(m14) · (1-Pd4) where Pd4 is proportion of collected PIT-tagged smolts not returned-to-river at LMN

13. Estimated number of PIT-tag smolts expanded to LGR-equivalents that are transported

from the three Snake River collector dams

T0 = X12000000 + X10200000/S2 + X10020000/S2S3 and expectation of E(T0) = E(n2) + E(n3)/S2 + E(n4)/S2S3

14. Estimated number of PIT-tag smolts expanded to LGR-equivalents that would have been transported if the PIT-tag smolts had been transported at the same proportion as the run-at-large from the three Snake River collector dams

T0

* = t2 + t3/S2 + t4/S2S3 and expectation of E(T0

* ) = E(t2) + E(t3)/S2 + E(t4)/S2S3

15. Estimated number of PIT-tag smolts expanded to LGR-equivalents that are return-to-

river at each collector dam and remain in-river to below LMN C1 = (m12 – d2) + (m13 – d3)/S2 + (m14 – d4)/S2S3 – 2·d1 and expectation of E(C1) = E(m12)·(1-Pd2) + [E(m13)·(1-Pd3)]/S2 + [E(m14)·(1-Pd4)]/S2S3 – 2·d1 The subtraction of 2·d1 fish from the estimate of Category C1 smolts was to account for fish from this category being removed below LMN. The numbers removed were expanded to LGR-equivalents with a fixed 50% survival rate.

16. Estimated number of PIT-tag smolts expanded to LGR-equivalents that are not detected

at any of the three Snake River collector dams

C0 = R1S1 – (m12 + m13/S2 + m14/S2S3) – 2·d0 and expectation of E(C0) = R1S1 – [E(m12) +E(m13)/S2 + E(m14)/ S2S3] – 2·d0E(C0) = R1·S1· (1- p2) · (1- p3) · (1- p4) – 2·d0 The subtraction of 2·d0 fish from the estimate of Category C0 smolts was to account for fish from this category being removed below LMN. The numbers removed were expanded to LGR-equivalents with a fixed 50% survival rate.

111

17. Numbers of returning adults used in SAR estimates are tallies of PIT-tag adults (age 2-salt and older for Chinook; age 1-salt and older for steelhead) detected at Lower Granite Dam adult monitors (GRA), which have near 100% detection efficiency. Some analyses use Bonneville Dam adult detections (BOA), which have been expanded by estimated detection efficiency at that site.

ATLGR = tally of adults of smolts transported at LGR, capture history “12000000” ATLGS = tally of adults of smolts transported at LGS, capture history “10200000” ATLGR = tally of adults of smolts transported at LGR, capture history “10020000”

AC0 = tally of adults of smolts that passed the three Snake River collector dams undetected (capture histories “1000AAAA” where A=0 signifies not being detected and A=1 signifies detection and return-to-river at a downstream site.

AC1 = tally of adults of smolts that passed the three Snake River collector dams with at least one detection (capture histories “11AAAAAA” or “101AAAAA” or “1001AAAA” where the A=0 signifies not being detected and B=1 signifies detection and return-to-river at a downstream site.

18. Site-specific transportation SAR (nk is observed number smolts at kth dam that is not

expanded to LGR-equivalents):

SAR(TLGR) = ATLGR / n2 SAR(TLGS) = ATLGS / n3SAR(TLMN) = ATLMN / n4

19. Overall transportation SAR where site-specific SARs are weighed by the proportion of PIT-tag smolts that would have been transported from each site (expanded in LGR-equivalents) if the PIT-tag smolts had been transported in the same proportion as the run-at-large at each collector dam

SAR1(T0) = {t2 • SAR(TLGR) + (t3/S2) • [S2•SAR(TLGS)]

+ t4/S2S3) • [S2S2•SAR(TLMN)]}/ {t2 + (t3/S2) + (t4/S2S3)} SAR1(T0) = {t2•SAR(TLGR) + t3•SAR(TLGS)

+ t4•SAR(TLMN)}/{t2 + (t3/S2) + (t4/S2S3)}

20. Overall transportation SAR where site-specific SARs are weighed by actual proportion of PIT-tag smolts transported at each collector dam (expanded in LGR-equivalents)

SAR2(T0) = {n2 • SAR(TLGR) + (n3/S2) • [S2•SAR(TLGS)]

+ n4/S2S3) • [S2S2•SAR(TLMN)]}/ {n2 + (n3/S2) + (n4/S2S3)} SAR2(T0) = {n2 • (ATLGR / n2) + (n3 • (ATLGS)/n3)

112

+ n4 • (ATLMN / n4)}/ {n2 + (n3/S2) + (n4/S2S3)}

SAR2(T0) = {ATLGR + ATLGS + ATLMN }/ {n2 + (n3/S2) + (n4/S2S3)}

21. In-river SAR for smolts not detected at the Snake River collector dams SAR(C0) = AC0 / C0

22. In-river SAR for smolts detected at one or more Snake River collector dam

SAR(C1) = AC1 / C1

23. Estimated T/C ratio T/C = SAR2(T0) / SAR(C0)

24. Estimate delayed mortality parameter D

D = [SAR2(T0) / VT] / [SAR(C0) / VC ] where VT = 0.98 * [t2 + t3 + t4] / [t2 + (t3/S2) + (t4/S2S3)] VC = S2•S3•S4•S5•S6

25. Estimate of annual SARs computed by weighting each study category SAR by the

estimated proportion of the run-at-large (in LGR-equivalents) each represents

SARANNUAL = w(T0*) •SAR2(T0) + w(C0) •SAR(C0) + w(C1

*) •SAR(C1)

where T0

* = t2 + (t3/S2) + (t4/S2S3) and C1* = (T0 + C1) – T0

* reflect the number of PIT-tag smolts in transport and bypass categories, respectively, if collected PIT-tag smolts had been routed to transportation in the same proportion as the run-at-large w(T0

*) = T0*/ (T0

* + C0 + C1*) is transported smolt proportion

w(C0) = C0 / (T0* + C0 + C1

*) is non-detected (LGR, LGS, LMN) smolt proportion w(C1*) = 1- [w(T0

*) + w(C0)] is bypass (LGR, LGS, LMN) smolt proportion

113

Appendix B

Estimated number of smolts per study category with associated 90% confidence interval

and number of returning adults per study category Appendix Table B-1. Estimated number of PIT-tagged wild Chinook (aggregate of fish tagged in 10-month period between July 25 and May 20) arriving Lower Granite Dam in each of the three study categories from 1994 to 2004 (with 90% confidence intervals), with detected adults at Lower Granite (GRA) and Bonneville (BOA) adult ladders.

Detected adults (2-salt & older)

Migr.Year

Estimated smolts starting in LGR population (with 90% CI)

Study category

Estimated smolt numbers in each study category (with 90% CI) GRA BOA

1994 15,260 (15,008 – 15,520)

T0C0C1

2,002 (1,926 – 2,087) 1,801 (1,694 – 1,911) 4,372 (4,192 – 4,549)

9 5 4

1995 20,206 (19,950 – 20,457)

T0C0C1

2,283 (2,204 – 2,363) 2,709 (2,603 – 2,818) 14,206 (13,994 – 14,411)

8 10 36

1996 7,868 (7,682 – 8,070)

T0C0C1

400 (368 – 436) 1,917 (1,803 – 2,033) 5,209 (5,060 – 5,360)

2 5 9

1997 2,898 (2,784 – 3,024)

T0C0C1

230 (207 – 257) 680 (614 – 749) 1,936 (1,842 – 2,039)

4 16 18

1998 17,363 (17,172 – 17,562)

T0C0C1

1,271 (1,215 – 1,332) 3,081 (2,971 – 3,189) 12,276 (12,114 – 12,446)

15 42 133

1999 33,662 (33,343 – 33,988)

T0C0C1

1,764 (1,690 – 1,835) 4,469 (4,355 – 4,600) 26,138 (25,864 – 26,412)

43 95 497

2000 25,053 (24,721– 25,397)

T0C0C1

839 (790 – 890) 6,494 (6,321 – 6,686) 16,833 (16,574 – 17,087)

12 155 392

21 184 456

2001 22,415 (22,234 – 22,595)

T0C0C1

547 (512 – 588) 231 (209 – 251)

20,306 (20,125 – 20,489)

7 1A

29

10 1A

32 2002 23,356

(22,995 – 23,697) T0C0C1

3,886 (3,775 – 3,995) 6,218 (6,042 – 6,395) 12,687 (12,455 – 12,922)

31 76 125

41 86 137

2003 31,093 (30,744 – 31,490)

T0C0C1

8,713 (8,560 – 8,873) 8,879 (8,660 – 9,094) 12,694 (12,499 – 12,910)

30 29 22

29 33 22

2004B 32,546 (32,296 – 32,828)

T0C0C1

12,887 (12,722 – 13,058) 2,252 (2,168 – 2,354) 16,504 (16,313 – 16,725)

39 7 30

49 8 35

A One returning adult with no detections may have inadvertently been transported so inriver SARs based solely on Category C1 fish in 2001. B Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

114

Appendix Table B-2. Estimated number of PIT-tagged spring Chinook from Rapid River Hatchery arriving Lower Granite Dam in each of the three study categories from 1997 to 2004 (with 90% confidence intervals), with detected adults at Lower Granite (GRA) and Bonneville (BOA) adult ladders.


Migr. Year


Study category

Estimate smolt numbers in each study category (with 90% CI) GRA BOA

1997 15,765 (15,246 – 16,439)

T0C0C1

4,321 (4,204 – 4,451) 4,176 (3,889 – 4,506) 6,843 (6,477 – 7,254)

34 19 36

1998 32,148 (31,801 – 32,473)

T0C0C1

12,862 (12,659 – 13,057) 4,402 (4,232 – 4,563) 13,597 (13,344 – 13,841)

257 53 91

1999 35,895 (35,272 – 36,542)

T0C0C1

12,833 (12,602 – 13,078) 7,040 (6,799 – 7,323) 14,456 (14,123 – 14,810)

391 167 235

2000 35,194 (34,652 – 35,769)

T0C0C1

16,588 (16,321 – 16,855) 11,046 (10,650 – 11,422) 5,248 (5,112 – 5,389)

349 176 71

492 201 90

2001 38,026 (37,822 – 38,211)

T0C0C1

19,090 (18,903 – 19,267) 966 (917 – 1,016)

15,990 (15,808 – 16,184)

207 2A

8

265 2A

12 2002 41,471

(40,785 – 42,099) T0C0C1

11,589 (11,375 – 11,795) 13,625 (13,296 – 13,960) 14,854 (14,526 – 15,178)

117 91 94

132 106 104

2003 37,911 (37,317 – 38,562)

T0C0C1

13,353 (13,138 – 13,586) 16,858 (16,398 – 17,331) 7,055 (6,897 – 7,212)

33 39 11

52 41 11

2004B 36,178 (35,955 – 36,406)

T0C0C1

19,519 (19,332 – 19,719) 3,484 (3,350 – 3,616) 12,776 (12,615 – 12,946)

50 5 11

66 5 11

A Two returning adults with no detections may have inadvertently been transported so inriver SARs based solely on Category C1 fish in 2001. B Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

115

Appendix Table B-3. Estimated number of PIT-tagged spring Chinook from Dworshak Hatchery arriving Lower Granite Dam in each of the three study categories from 1997 to 2004 (with 90% confidence intervals), with detected adults at Lower Granite (GRA) and Bonneville (BOA) adult ladders.


Migr. Year


Study category


1997 8,175 (7,735 – 8,683)

T0C0C1

1,931 (1,856 – 2,015) 2,529 (2,283 – 2,798) 3,613 (3,344 – 3,938)

34 19 36

1998 40,218 (39,660 – 40,742)

T0C0C1

14,708 (14,486 – 14,927) 11,151 (10,770 – 11,483) 13,128 (12,831 – 13,412)

132 139 119

1999 40,804 (39,771 – 41,948)

T0C0C1

9,783 (9,549 – 10,022) 10,484 (10,109 – 10,930) 19,081 (18,473 – 19,705)

115 125 182

2000 39,412 (38,782 – 40,101)

T0C0C1

18,317 (17,977 – 18,650) 13,075 (12,635 – 13,556) 5,416 (5,268 – 5,561)

183 132 46

296 172 56

2001 41,251 (41,068 – 41,446)

T0C0C1

21,740 (21,542 – 21,930) 886 (840 – 936)

16,872 (16,675 – 17,072)

79 0 7

96 0 8

2002 45,233 (44,268 – 46,304)

T0C0C1

9,668 (9,461 – 9,906) 19,008 (18,457 – 19,581) 14,914 (14,493 – 15,324)

60 95 74

80 113 80

2003 38,612 (37,984 – 39,274)

T0C0C1

13,205 (12,984 – 13,447) 17,697 (17,237 – 18,153) 6,715 (6,573 – 6,881)

34 38 12

44 45 12

2004A 45,505 (42,223 – 42,788)

T0C0C1

21,657 (21,443 – 21,897) 6,280 (6,100 – 6,468) 14,009 (13,822 – 14,189)

46 14 22

88 18 36

A Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

116

Appendix Table B-4. Estimated number of PIT-tagged spring Chinook from Catherine Creek Acclimation Pond arriving Lower Granite Dam in each of the three study categories from 2001 to 2004 (with 90% confidence intervals), with detected adults at Lower Granite (GRA) and Bonneville (BOA) adult ladders.


Migr. Year


Study category


2001 10,885 (10,747 – 11,021)

T0C0C1

4,790 (4,681 – 4,896) 379 (347 – 412)

4,642 (4,533 – 4,750)

11 0 2

18 0 3

2002 8,435 (8,181 – 8,709)

T0C0C1

2,688 (2,596 – 2,787) 2,445 (2,313 – 2,592) 3,120 (2,979 – 3,258)

24 12 10

33 11 10

2003 7,202 (6,932 – 7,487)

T0C0C1

2,494 (2,397 – 2,592) 3,201 (3,010 – 3,421) 1,403 (1,333 – 1,478)

9 8 5

10 8 6

2004A 5,348 (5,225 – 5,465)

T0C0C1

2,877 (2,790 – 2,970) 503 (455 – 551) 1,869 (1,797 – 1,938)

10 1 6

13 0 7

A Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

117

Appendix Table B-5. Estimated number of PIT-tagged summer Chinook from McCall Hatchery arriving Lower Granite Dam in each of the three study categories from 1997 to 2004 (with 90% confidence intervals), with detected adults at Lower Granite (GRA) and Bonneville (BOA) adult ladders.


Migr. Year


Study category


1997 22,381 (21,588 – 23,224)

T0C0C1

6,001 (5,859 – 6,138) 6,761 (6,339 – 7,214) 9,272 (8,779 – 9,795)

91 74 102

1998 27,812 (27,474 – 28,141)

T0C0C1

10,080 (9,916 – 10,258) 3,849 (3,685 – 4,006) 12,816 (12,537 – 13,075)

273 53 94

1999 31,571 (30,816 – 32,358)

T0C0C1

10,457 (10,200 – 10,710) 8,407 (8,081 – 8,734) 11,391 (11,037 – 11,782)

377 202 233

2000 31,825 (31,170 – 32,466)

T0C0C1

12,807 (12,532 – 13,066) 13,064 (12,578 – 13,593) 4,485 (4,352 – 4,611)

497 269 93

584 299 101

2001 36,784 (36,578 – 36,994)

T0C0C1

16,706 (16,530 – 16,893) 1,000 (950 – 1,057) 15,537 (15,351 – 15,730)

206 3A

6

246 3A

7 2002 32,599

(32,042 – 33,229) T0C0C1

8,842 (8,659 – 9,030) 10,280 (9,987 – 10,599) 12,315 (12,022 – 12,612)

131 106 126

164 127 154

2003 43,144 (42,527 – 43,752)

T0C0C1

14,006 (13,782 – 14,233) 19,696 (19,221 – 20,166) 8,669 (8,503 – 8,845)

111 107 30

124 122 32

2004B 40,150 (39,912 – 40,408)

T0C0C1

20,858 (20,667 – 21,062) 2,359 (2,262 – 2,453) 16,297 (16,094 – 16,500)

65 6 19

92 7 31

A Three returning adults with no detections may have inadvertently been transported so inriver SARs based solely on Category C1 fish in 2001. B Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

118

Appendix Table B-6. Estimated number of PIT-tagged summer Chinook from Imnaha River Acclimation Pond arriving Lower Granite Dam in each of the three study categories from 1997 to 2004 (with 90% confidence intervals).


Migr. Year


Study category

Estimated smolt numbers in each study category (with 90% CI) GRA BOA

1997 8,254 (7,814 – 8,740)

T0C0C1

2,135 (2.050 – 2,223) 2,219 (1,993 – 2,478) 3,785 (3,475 – 4,091)

25 19 26

1998 13,577 (13,327 – 13,833)

T0C0C1

4,773 (4,648 – 4,895) 1,995 (4,884 – 2,104) 6,335 (6,156 – 6,523)

41 11 19

1999 13,244 (12,829 – 13,687)

T0C0C1

4,779 (4,616 – 4,955) 2,869 (2,690 – 3,050) 5,084 (4,871 – 5,327)

130 41 62

2000 14,267 (13,926 – 14,650)

T0C0C1

6,786 (6,609 – 6,975) 4,402 (4,151 – 4,679) 2,254 (2,164 – 2,347)

211 106 37

262 114 41

2001 15,650 (15,531 – 15,763)

T0C0C1

7,730 (7,611 – 7,849) 366 (335 – 396)

6,939 (6,817 – 7,042)

48 1A

4

61 4A

4 2002 13,962

(13,560 – 14,380) T0C0C1

3,912 (3,787 – 4,050) 4,637 (4,427 – 4,838) 5,135 (4,953 – 5,335)

31 21 28

41 27 33

2003 14,948 (14,532 – 15,377)

T0C0C1

5,189 (5,044 – 5,345) 6,683 (6,358 – 6,999) 2,908 (2,801 – 3,015)

30 32 11

39 38 13

2004B 12,867 (12,709 – 13,013)

T0C0C1

6,927 (6,801 – 7,049) 1,302 (1,221 – 1,381) 4,456 (4,349 – 4,554)

24 3 5

35 5 6

A One returning adult with no detections may have inadvertently been transported so inriver SARs based solely on Category C1 fish in 2001. B Migration year 2004 is incomplete with 2-salt adult returns as of 8/9/2006.

119

Appendix Table B-7. Estimated number of PIT-tagged wild steelhead (aggregate of tagged fish >130 mm released in 12-month period between July 1 and June 30) arriving Lower Granite Dam in each of the three study categories from 1997 to 2003 (with 90% confidence intervals). Migr.Year


Study category

Estimated smolt numbers in each study category (with 90% CI)

LGR detected returning adults

1997 3,830 (3,744 – 3,920)

T0C0C1

275 (248 – 302) 454 (415 – 495) 2,984 (2,910 – 3,067)

4 3 7

1998 7,109 (7,010 – 7,208)

T0C0C1

480 (445 – 517) 750 (700 – 800) 5,148 (5,047 – 5,245)

1 8 12

1999 8,820 (8,695 – 8,960)

T0C0C1

391 (359 – 424) 1,113 (1,054 – 1,172) 6,992 (6,875 – 7,121)

12 15 54

2000 13,609 (13,418 – 13,818)

T0C0C1

466 (428 – 506) 1,871 (1,783 – 1,967) 10,616 (10,457 – 10,778)

13 36 193

2001A 12,929 (12,810 – 13,066)

T0C0C1

201 (180 – 226) 103 (86 – 121) 11,892 (11,764 – 12,031)

5 3B

8 2002C 13,378

(13,148 – 13,598) T0C0C1

317 (289 – 346) 4,045 (3,908 – 4,197) 8,726 (8,552 – 8,891)

9 27 82

2003C 12,926 (12,696 – 13,153)

T0C0C1

2,210 (2,140 – 2,293) 3,320 (3,185 – 3,459) 7,132 (6,979 – 7,292)

44 16 37

A Estimates of number of smolts in study categories in 2001 are approximate due to potentially high holdover rate in lower Snake River affecting reach survival estimates and ultimately the smolt estimates in LGR-equivalents for each study category. B Three returning adults with no detections may have inadvertently been transported or held-over to the following year so inriver SARs based solely on Category C1 fish in 2001

C Migration year 2003 is incomplete until 3-salt returns occur at GRA.

120

Appendix Table B-8. Estimated number of PIT-tagged hatchery steelhead (aggregate of tagged fish released in 3-month period between April 1 and June 30) arriving Lower Granite Dam in each of the three study categories from 1997 to 2003 (with 90% confidence intervals). Migr.Year


Study category

Estimated smolt numbers in each study category (with 90% CI)

LGR detected returning adults

1997 24,710 (24,477 – 24,933)

T0C0C1

1,729 (1,654 – 1,795) 3,390 (3,263 – 3,523) 19,095 (18,883 – 19,304)

9 8 32

1998 23,507 (23,325 – 23,685)

T0C0C1

1,365 (1,303 – 1,431) 2,926 (2,820 – 3,024) 17,958 (17,783 – 18,126)

7 26 40

1999 27,193 (26,959 – 27,426)

T0C0C1

1,336 (1,275 – 1,397) 3,952 (3,831 – 4,073) 20,975 (20,759 – 21,187)

12 41 124

2000 24,565 (24,280 – 24,847)

T0C0C1

668 (621 – 715) 4,408 (4,236 – 4,595) 18,804 (18,580 – 19,010)

14 42 197

2001A 20,877 (20,739 – 21,031)

T0C0C1

427 (390 – 463) 372 (333 – 406) 19,132 (18,986 – 19,279)

4 2B

3 2002 20,681

(20,328 – 21,037) T0C0C1

284 (256 – 313) 6,129 (5,917 – 6,338) 14,038 (13,764 – 14,322)

3 43 102

2003C 21,400 (21,067 – 21,732)

T0C0C1

4,595 (4,475 – 4,719) 6,459 (6,248 – 6,671) 10,118 (9,918 – 10,320)

83 44 37

A Estimates of number of smolts in study categories in 2001 are approximate due to potentially high holdover rate in lower Snake River affecting reach survival estimates and ultimately the smolt estimates in LGR-equivalents for each study category. B Two returning adults with no detections may have inadvertently been transported or held-over to the following year so inriver SARs based solely on Category C1 fish in 2001

C Migration year 2003 is incomplete until 3-salt returns occur at GRA

121

Appendix C

Reach Survival Estimates with Bootstrap 95% Confidence Intervals

Appendix Table C-1. In-river smolt survival rate estimates through hydrosystem for the PIT-tag aggregate of wild spring/summer Chinook in migration years 1994 to 2004.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit

1994 S2 (lgr-lgs) S3 (lgs-lmn)

0.822 0.836

0.796 0.807

0.846 0.866

1995 S2 (lgr-lgs) S3 (lgs-lmn) S4 (lmn-mcn)

0.895 0.951 0.764

0.880 0.924 0.659

0.911 0.978 0.923


0.908 0.911

0.869 0.850

0.946 0.977


0.922 0.931

0.859 0.822

0.990 1.057

1998 S2 (lgr-lgs) S3 (lgs-lmn) S4 (lmn-mcn) S5 (mcn-jda)

1.003 0.850 0.940 0.854

0.986 0.824 0.889 0.763

1.021 0.874 0.993 0.965

1999 S2 (lgr-lgs) S3 (lgs-lmn) S4 (lmn-mcn) S5 (mcn-jda) S6 (jda-bon)

0.958 0.924 0.889 0.889 0.845

0.948 0.914 0.869 0.854 0.734

0.967 0.934 0.908 0.927 1.000


0.897 0.868 0.977 0.734 0.866

0.880 0.842 0.934 0.674 0.708

0.915 0.893 1.022 0.804 1.097


0.930 0.772 0.684 0.714 0.663

0.925 0.762 0.670 0.669 0.553

0.936 0.782 0.698 0.763 0.827


0.901 0.996 0.810 0.873 0.967

0.883 0.975 0.785 0.826 0.780

0.920 1.016 0.837 0.927 1.268


0.893 0.878 0.990 0.798 0.962

0.877 0.852 0.955 0.759 0.803

0.910 0.905 1.023 0.841 1.146


0.970 0.830 0.878 0.744 0.756

0.960 0.810 0.841 0.667 0.581

0.979 0.849 0.917 0.843 1.021

122

Appendix Table C-2. In-river smolt survival rate estimates from hatchery to LGR and through reaches in the hydrosystem for PIT-tagged Rapid River Hatchery spring Chinook in migration years 1997 to 2004.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit

1997 S1 (rel-lgr) S2 (lgr-lgs) S3 (lgs-lmn)

0.390 0.964 0.803

0.376 0.903 0.746

0.406 1.027 0.867

1998 S1 (rel-lgr) S2 (lgr-lgs) S3 (lgs-lmn) S4 (lmn-mcn) S5 (mcn-jda)

0.665 1.005 0.847 0.982 0.798

0.658 0.986 0.826 0.924 0.713

0.672 1.024 0.869 1.045 0.897

1999 S1 (rel-lgr) S2 (lgr-lgs) S3 (lgs-lmn) S4 (lmn-mcn) S5 (mcn-jda) S6 (jda-bon)

0.751 0.923 0.957 0.906 0.945 0.750

0.738 0.901 0.937 0.875 0.882 0.622

0.765 0.943 0.977 0.939 1.022 0.923


0.737 0.846 1.127 0.823 0.945 0.782

0.724 0.813 1.016 0.721 0.760 0.546

0.752 0.882 1.255 0.937 1.250 1.171


0.690 0.958 0.856 0.698 0.924 0.618

0.686 0.951 0.843 0.683 0.854 0.497

0.694 0.965 0.867 0.715 1.013 0.802


0.755 0.947 0.981 0.841 0.953 0.951

0.741 0.923 0.959 0.819 0.895 0.770

0.769 0.972 1.004 0.863 1.018 1.191


0.692 0.916 0.875 0.964 0.902 0.947

0.680 0.881 0.809 0.885 0.834 0.788

0.706 0.950 0.949 1.050 0.976 1.195


0.696 0.999 0.754 0.880 0.766 0.696

0.691 0.985 0.709 0.812 0.667 0.478

0.702 1.013 0.807 0.950 0.897 1.120

123

Appendix Table C-3. In-river smolt survival rate estimates from hatchery to LGR and through reaches in the hydrosystem for PIT-tagged Dworshak Hatchery spring Chinook in migration years 1997 to 2004.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit


0.581 1.047 0.810

0.547 0.959 0.725

0.613 1.148 0.908


0.843 1.071 0.765 0.931 0.782

0.832 1.043 0.740 0.891 0.696

0.855 1.098 0.790 0.976 0.891


0.853 0.887 0.952 0.875 0.899 0.816

0.832 0.862 0.935 0.848 0.849 0.684

0.873 0.914 0.968 0.901 0.959 1.010


0.825 0.807 1.036 0.834 0.944 0.730

0.809 0.777 0.955 0.754 0.804 0.543

0.843 0.839 1.124 0.920 1.145 1.007


0.748 0.941 0.839 0.694 0.693 0.636

0.744 0.934 0.828 0.681 0.654 0.510

0.752 0.947 0.849 0.707 0.739 0.839


0.827 0.917 0.978 0.810 0.931 0.910

0.803 0.884 0.950 0.787 0.877 0.758

0.849 0.953 1.007 0.834 0.995 1.086


0.706 0.905 0.897 0.983 0.856 0.990

0.692 0.874 0.854 0.934 0.804 0.833

0.722 0.933 0.947 1.038 0.908 1.217


0.823 0.977 0.969 0.779 0.790 0.858

0.817 0.964 0.912 0.723 0.701 0.640

0.830 0.990 1.031 0.839 0.910 1.270

124

Appendix Table C-4. In-river smolt survival rate estimates from hatchery to LGR and through reaches in the hydrosystem for PIT-tagged Catherine Creek Acclimation Pond spring Chinook in migration years 2001 to 2004.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit


0.520 0.945 0.814 0.659 0.768 0.639

0.513 0.931 0.787 0.624 0.654 0.419

0.528 0.961 0.840 0.699 0.901 1.101


0.406 0.949 1.013 0.808 0.928 0.896

0.391 0.899 0.954 0.743 0.779 0.562

0.421 0.998 1.073 0.887 1.125 1.726


0.349 0.972 0.855 1.093 0.764

0.334 0.894 0.743 0.937 0.641

0.366 1.056 1.004 1.282 0.918


0.255 0.976 0.921 0.900 0.704 0.579

0.248 0.942 0.827 0.743 0.513 0.271

0.262 1.010 1.047 1.072 1.040 2.149

125

Appendix Table C-5. In-river smolt survival rate estimates from hatchery to LGR and through reaches in the hydrosystem for PIT-tagged McCall Hatchery summer Chinook in migration years 1997 to 2004.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit


0.425 0.935 0.882

0.411 0.889 0.820

0.441 0.987 0.954


0.588 0.991 0.843 0.942 0.824

0.580 0.971 0.820 0.884 0.738

0.595 1.012 0.867 1.007 0.930


0.658 0.908 0.936 0.913 1.086 0.622

0.642 0.880 0.908 0.872 0.989 0.514

0.675 0.939 0.961 0.957 1.206 0.766


0.667 0.867 0.917 1.034 1.307 0.570

0.650 0.813 0.807 0.911 0.904 0.323

0.685 0.932 1.036 1.181 2.258 0.887


0.667 0.928 0.771 0.647 0.862 0.674

0.663 0.920 0.756 0.628 0.784 0.531

0.672 0.937 0.786 0.666 0.954 0.924


0.596 0.964 0.990 0.837 1.051 0.688

0.583 0.936 0.964 0.809 0.969 0.583

0.609 0.992 1.016 0.869 1.144 0.840


0.581 0.921 0.884 1.014 0.907 0.929

0.570 0.892 0.838 0.964 0.858 0.804

0.590 0.949 0.933 1.070 0.960 1.082


0.563 0.938 0.993 0.754 0.893 0.696

0.559 0.927 0.942 0.695 0.780 0.515

0.567 0.949 1.052 0.812 1.039 0.993

126

Appendix Table C-6. In-river smolt survival rate estimates from hatchery to LGR and through reaches in the hydrosystem for PIT-tagged Imnaha Acclimation Pond summer Chinook in migration years 1997 to 2004.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit


0.617 0.994 0.768

0.586 0.909 0.693

0.654 1.082 0.856


0.685 0.978 0.843 0.956 0.784

0.673 0.951 0.812 0.894 0.685

0.697 1.006 0.872 1.035 0.907


0.664 0.921 0.954 0.876 0.944 0.740

0.645 0.885 0.920 0.825 0.840 0.548

0.686 0.957 0.989 0.931 1.075 1.103


0.685 0.822 1.008 0.885 0.893 1.013

0.665 0.774 0.869 0.717 0.677 0.570

0.707 0.877 1.201 1.081 1.293 2.469


0.748 0.958 0.892 0.751 0.853 0.678

0.742 0.950 0.877 0.729 0.763 0.462

0.755 0.968 0.908 0.776 0.958 1.226


0.667 0.951 0.947 0.858 0.828 0.788

0.645 0.910 0.911 0.817 0.753 0.603

0.691 0.994 0.984 0.904 0.914 1.120


0.715 0.901 0.905 0.914 1.027

0.691 0.845 0.815 0.809 0.913

0.739 0.952 1.020 1.021 1.163


0.615 0.964 0.910 0.834 0.878 0.576

0.607 0.943 0.831 0.731 0.701 0.333

0.624 0.986 1.001 0.966 1.126 1.274

127

Appendix Table C-7. In-river smolt survival rate estimates through reaches in the hydrosystem for the PIT-tag aggregate of wild summer steelhead in migration years 1997 to 2003.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit


0.984 0.975 0.886 0.721

0.948 0.902 0.685 0.368

1.017 1.060 1.233 2.096


0.969 0.843 0.889 0.868

0.945 0.807 0.805 0.746

0.995 0.879 1.000 1.009


0.974 0.910 0.835 1.040 0.580

0.956 0.888 0.785 0.937 0.473

0.991 0.934 0.890 1.148 0.761


0.790 0.910 0.860 0.659

0.771 0.878 0.800 0.594

0.807 0.943 0.931 0.729


0.834 0.716 0.288 0.230 0.958

0.823 0.694 0.267 0.191 0.618

0.845 0.741 0.312 0.281 1.714


0.943 1.164 0.522 0.960 0.939

0.921 1.122 0.493 0.886 0.720

0.965 1.215 0.553 1.083 1.269


0.908 0.914 0.729 0.913 0.664

0.884 0.875 0.679 0.826 0.552

0.934 0.958 0.784 1.21 0.818

128

Appendix Table C-8. In-river smolt survival rate estimates through reaches in the hydrosystem for the PIT-tag aggregate of hatchery summer steelhead in migration years 1997 to 2003.

Migr Year

Reach of Survival

Survival Estimate

95% CI Lower Limit

95% CI Upper Limit


0.954 0.853 0.938 0.656

0.937 0.823 0.814 0.440

0.972 0.888 1.104 1.187


0.950 0.854 0.820 1.058 0.915

0.936 0.834 0.775 0.970 0.642

0.963 0.875 0.868 1.148 1.543


0.966 0.895 0.801 1.044 0.622

0.955 0.880 0.769 0.985 0.519

0.978 0.909 0.837 1.111 0.772


0.693 0.812 0.803 0.705

0.673 0.778 0.735 0.614

0.717 0.854 0.877 0.820


0.693 0.678 0.284 0.353 0.805

0.682 0.650 0.262 0.286 0.418

0.705 0.707 0.311 0.463 2.455


0.908 0.970 0.570 0.937 0.777

0.887 0.943 0.536 0.830 0.604

0.930 1.001 0.610 1.051 1.067


0.949 0.935 0.710 0.954 0.842

0.927 0.900 0.664 0.856 0.695

0.972 0.971 0.761 1.056 1.049

129

Appendix D

Age Distribution of Returning Adult Chinook and Steelhead Detected at Lower Granite Dam

(or Bonneville Dam for Downriver Populations) Appendix Table D-1. Age composition of returning PIT-tagged wild Chinook jacks and adults detected at Lower Granite Dam that were PIT-tagged during the 10-month period from July 25 to May 20 for each migration year between 1994 and 2004.

Migration Year

Jacks 1-salt

Adults 2-salt

Adults 3-salt

Percent 1-salt

Percent 2-salt

Percent 3-salt

1994 1 11 11 4.3 47.8 47.8 1995 1 38 20 1.7 64.4 33.9 1996 0 11 5 0.0 68.8 31.3 1997 2 33 5 5.0 82.5 12.5 1998 17 148 47 8.0 69.8 22.2 1999 25 517 144 3.6 75.4 21.0 2000 9 259 312 (1B) 1.5 44.6 53.7 (0.2 B) 2001 2 30 15 4.3 63.8 31.9 2002 26 197 38 10.0 75.5 14.6 2003A 3 61 24 3.4 69.3 27.3 2004A 3 86 NA -- -- -- Average 4.2 66.2 29.6

A Migration year 2004 is incomplete until 3-salt returns occur at GRA; not included in average. B One 4-salt adult shown in parenthesis in 3-salt column.

Appendix Table D-2. Age composition of returning PIT-tagged John Day River wild Chinook jacks and adults detected at Bonneville Dam for fish that outmigrated in 2000 to 2004.

Migration Year

Jacks 1-salt

Adults 2-salt

Adults 3-salt

Percent 1-salt

Percent 2-salt

Percent 3-salt

2000 3 112 31 2.1 76.7 21.2 2001 7 90 15 6.3 80.4 13.4 2002 5 86 9 5.0 86.0 9.0 2003 5 110 13 3.9 85.9 10.2 2004A 5 68 NA -- -- -- Average 4.3 82.3 13.4

A Migration year 2004 is incomplete until 3-salt returns occur at BOA; not included in average.

130

Appendix Table D-3. Number of returning PIT-tagged hatchery Chinook adults and jacks detected at Lower Granite Dam that migrated as smolts in 1997 to 2004 and percent of total return.

Hatchery (run)

Migration Year

Jacks 1-salt

Adults 2-salt

Adults 3-salt

Percent 1-salt

Percent 2-salt

Percent 3-salt

RAPH (spring) Average

1997 1998 1999 2000 2001 2002 2003

2004 A

2 32 43 8 21 60 20 4

86 390 787 371 206 298 75 67

7 23 31 256 13 5 8 NA

2.1 7.2 5.0 1.3 8.8 16.5 19.4 -- 8.6

90.5 87.6 91.4 58.4 85.8 82.1 72.8 -- 81.2

7.4 5.2 3.6 40.3 5.4 1.4 7.8 -- 10.2

MCCA (summer) Average

1997 1998 1999 2000 2001 2002 2003 2004 A

21 108 119 144 62 116 129 25

263 394 722 635 200 347 222 91

11 37 113 239 (1B) 23 18 27 NA

7.1 20.0 12.5 14.1 21.8 24.1 34.1 -- 19.1

89.2 73.1 75.7 62.3 70.2 72.1 58.7 -- 71.6

3.7 6.9 11.8 23.5 (0.1B) 8.1 3.7 7.1 -- 9.3

DWOR (spring) Average

1997 1998 1999 2000 2001 2002 2003 2004 A

1 51 14 3 14 52 5 1

36 372 393 180 79 222 73 85

6 23 44 197 10 8 12 NA

2.3 11.4 3.1 0.8 13.6 18.4 5.6 -- 7.9

83.7 83.4 87.1 47.4 76.7 78.7 81.1 -- 76.9

14.0 5.2 9.8 51.8 9.7 2.8 13.3 -- 15.2

IMNA (summer) Average

1997 1998 1999 2000 2001 2002 2003 2004 A

24 54 81 149 30 46 93 9

63 69 226 289 49 81 71 33

7 2 12 79 4 2 2 NA

25.5 43.2 25.4 28.8 36.1 35.7 56.0 -- 35.8

67.0 55.2 70.8 55.9 59.0 63.8 42.8 -- 59.2

7.4 1.6 3.8 15.3 4.8 1.6 1.2 -- 5.1

CATH (spring) Average

2001 2002 2003 2004 A

2 11 5 2

13 45 22 17

0 1 0 NA

13.3 19.3 18.5 -- 17.0

86.7 79.0 81.5 -- 82.4

0.0 1.8 -- 0.6

A Migration year 2004 is incomplete until 3-salt returns occur at GRA; not included in average. B One 4-salt adult shown in parenthesis in 3-salt column.

131

Appendix Table D-4. Age composition of returning PIT-tagged Carson NFH Chinook jacks and adults detected at Bonneville Dam for fish that outmigrated in 2000 to 2004.

Migration Year

Jacks 1-salt

Adults 2-salt

Adults 3-salt

Percent 1-salt

Percent 2-salt

Percent 3-salt

2000 5 302 124 (1A) 1.2 69.9 28.7 (0.2A) 2001 3 205 18 1.3 90.7 8.0 2002 5 148 3 3.2 94.9 1.9 2003 0 32 2 0 94.1 5.9 2004B 4 79 NA -- -- -- Average 1.4 87.4 11.2

A One 4-salt adult Chinook shown in parenthesis in 3-salt column. B Migration year 2004 is incomplete until 3-salt returns occur at BOA; not included in average. Appendix Table D-5. Age composition of returning PIT-tagged wild steelhead adults detected at Lower Granite Dam that were PIT-tagged during the 12-month period from July 1 to June 30 for each migration year between 1997 and 2003.

Migration Year

Age 1-salt

Age 2-salt

Age 3-salt

Percent 1-salt

Percent 2-salt

Percent 3-salt

1997 4 10 0 28.6 71.4 0 1998 16 8 0 66.7 33.3 0 1999 33 51 2 38.4 59.3 2.3 2000 132 131 3 49.6 49.3 1.1 2001 5 14 2 23.8 66.7 9.5 2002 59 60 1 49.2 50.0 0.8 2003A 38 63 NA (37.6) (62.4) -- Average 42.7 55.0 2.3

A Migration year 2003 is incomplete until 3-salt returns occur at GRA; not included in average. Appendix Table D-6. Age composition of returning PIT-tagged hatchery steelhead adults detected at Lower Granite Dam that migrated as smolts in 1997 to 2003.

Migration Year

Age 1-salt

Age 2-salt

Age 3-salt

Percent 1-salt

Percent 2-salt

Percent 3-salt

1997 1998 1999 2000 2001 2002 2003A

Average

34 45 85 178 3 99 90

15 32 96 89 8 49 77

1 1 1 NA

69.4 58.4 46.7 66.4 27.3 66.4 (53.9) 55.8

30.6 41.6 52.7 33.2 72.7 32.9 (46.1) 43.9

0 0 0.5 0.4 0 0.7 -- 0.3

A Migration year 2003 is incomplete until 3-salt returns occur at GRA; not included in average.

132

Appendix E

Number of PIT-tagged smolts transported at each collector dam

(plus estimated number if tagged fish had been transported in same proportion as the untagged population) and site-specific SAR estimates

Appendix Table E-1. Number of PIT-tagged wild Chinook actually transported from each dam and estimate (ti) of total PIT-tagged wild Chinook that would have been transported if all tagged fish were transported at same rate as the untagged run-at-large, 1994 to 2004.

Lower Granite Dam Little Goose Dam Lower Monumental Dam Migr. Year Actual t2 Actual t3 Actual t41994 1,051 6,851 387 2,094 330 1,308 1995 1,702 9,657 356 3,626 156 1,490 1996 268 2,269 85 1,749 32 927 1997 185 1,064 30 335 11 171 1998 820 7,669 359 4,002 79 1,632 1999 1,107 8,183 319 14,213 287 4,594 2000 327 7,095 244 6,603 187 2,095 2001 452 18,062 72 2,904 13 278 2002 1,640 4,813 1,856 6,505 167 3,705 2003 5,098 11,694 2,548 6,634 599 1,495 2004 8,951 20,367 2,812 6,552 834 1,849 Average Percent1 56.7% 32.0% 11.3% 1 11-yr average percentage of total transported population transported at each Snake River dam. Appendix Table E-2. Estimated dam-specific transportation SARs (%) of the PIT-tagged wild Chinook aggregate for migration years 1994 to 2004 (with 90% confidence intervals). Migr. Year

SAR(TLGR) % (CI%)

Adult #

SAR(TLGS) % (CI%)

Adult #

SAR(TLMN) % (CI%)

Adult #

1994 0.67 (0.28 – 1.12) 7 0.52 (0.0 – 1.11) 2 NA None 1995 0.41 (0.18 – 0.68) 7 0.28 (0.0 – 0.84) 1 NA None 1996 0.37 (0.0 – 1.10) 1 1.18 (0.0 – 3.41) 1 NA None 1997 1.08 (0.0 – 2.37) 2 6.67 (0.0 – 14.8) 2 NA None 1998 1.34 (0.72 – 2.01) 11 0.84 (0.0 – 1.66) 3 1.27 (0.0 – 3.53) 1 1999 2.53 (1.82 – 3.28) 28 2.82 (1.49 – 4.47) 9 2.09 (0.72 – 3.58) 6 2000 1.22 (0.31 – 2.27) 4 2.46 (0.87 – 4.29) 6 1.07 (0.0 – 2.38) 2 2001 1.33 (0.46 – 2.23) 6 1.39 (0.0 – 4.11) 1 NA None 2002 0.61 (0.30 – 0.95) 10 1.08 (0.70 – 1.53) 20 0.60 (0.0 – 1.79) 1 2003 0.31 (0.18 – 0.45) 16 0.51 (0.28 – 0.77) 13 0.17 (0.0 – 0.49) 1 2004A 0.30 (0.21 – 0.40) 27 0.28 (0.14 – 0.46) 8 0.48 (0.12 – 0.92) 4 A Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006.

133

Appendix Table E-3. Number of PIT-tagged hatchery Chinook actually transported from each dam and estimate (ti) of total PIT-tagged hatchery Chinook that would have been transported if all PIT-tagged fish had been transported at same rate as the untagged run-at-large.

Lower Granite Dam

Little Goose Dam

Lower Monumental Dam

Migr. Year

Hatchery

Actual t2 Actual t3 Actual t4 1997

RAPH MCCA DWOR IMNA

4,135 5,851 1,864 2,074

5,365 7,428 2,351 2,603

132 105 52 45

1,618 2,241 970 954

38 31 15 12

949 1,153 517 487

1998

RAPH MCCA DWOR IMNA

11,279 8,988 11,096 4,036

15,274 12,178 14,350 5,621

1,359 896 3,574 606

7,578 6,970 9,326 3,749

197 157 225 97

3,100 3,073 3,887 1,354

1999

RAPH MCCA DWOR IMNA

7,385 4,730 4,930 2,160

9,488 6,374 6,346 2,785

4,724 4,986 3,798 2,293

12,750 10,584 14,602 5,129

290 203 484 114

3,818 3,515 5,304 1,428

2000

RAPH MCCA DWOR IMNA

10,367 8,496 9,805 3,862

14,386 11,734 13,399 5,447

4,181 2,821 4,911 1,812

6,123 4,086 7,206 2,705

1,213 776 2,030 530

1,625 1,279 2,539 713

2001

RAPH MCCA DWOR IMNA CATH

15,385 13,093 16,567 5,734 3,375

28,122 27,575 28,345 10,629 7,356

2,846 2,643 4,091 1,604 1,096

5,874 5,119 8,490 3,380 2,143

582 500 639 246 195

1,076 892 1,177 483 373

2002


5,339 4,284 4,088 1,616 1,464

8,475 6,729 6,417 2,531 2,286

5,312 4,140 4,348 1,953 1,112

8,852 6,951 7,274 3,271 1,826

572 200 734 194 50

8,534 7,305 9,673 2,814 1,586

2003


8,391 8,334 7,031 3,094 1,564

12,925 13,604 10,747 4,764 2,416

3,887 4,242 4,345 1,557 698

6,115 7,094 6,926 2,547 1,141

574 866 1,113 299 176

874 1,391 1,695 464 291

2004


13,511 16,455 12,725 4,754 2,078

21,806 28,896 20,489 7,583 3,292

5,271 3,877 8,154 1,916 700

8,775 6,879 13,623 3,230 1,181

550 251 552 162 73

946 439 888 292 188

Average percentage1 52 % 32 % 16% 1 Average percentage of total transported population transported at each Snake River dam.

134

Appendix Table E-4. Estimated dam-specific transportation SAR percentages of PIT-tagged hatchery spring/summer Chinook that outmigrated in 1997 to 2004 (with 90% confidence intervals).

Mig_Yr HatcheryA

SAR(TLGR) % (CI%)

Adult #

SAR(TLGS) % (CI%)

Adult #

SAR(TLMN) % (CI%)

Adult #

‘97RAPH 0.80 (0.58 – 1.02) 33 NA None 2.63 (0.0 – 7.89) 1 ‘97MCCA 1.49 (1.21 – 1.76) 87 2.86 (0.85 – 5.83) 3 3.23 (0.0 – 9.52) 1 ‘97DWOR 0.86 (0.54 – 1.23) 16 NA None NA None ‘97IMNA 1.21 (0.84 – 1.66) 25 NA None NA None ‘98RAPH 2.12 (1.89 – 2.35) 239 1.18 (0.75 – 1.72) 16 1.02 (0.0 – 2.29) 2 ‘98MCCA 2.93 (2.65 – 3.22) 263 1.00 (0.46 – 1.62) 9 0.64 (0.0 – 1.88) 1 ‘98DWOR 0.99 (0.85 – 1.14) 110 0.62 (0.41 – 0.85) 22 NA None ‘98IMNA 0.92 (0.69 – 1.18) 37 0.66 (0.17 – 1.22) 4 NA None ‘99RAPH 3.20 (2.89 – 3.52) 236 3.22 (2.79 – 3.64) 152 1.03 (0.31 – 2.13) 3 ‘99MCCA 4.36 (3.88 – 4.83) 206 3.23 (2.82 – 3.65) 161 4.93 (2.26 – 7.58) 10 ‘99DWOR 1.26 (1.01 – 1.53) 62 1.29 (0.99 – 1.59) 49 0.83 (0.21 – 1.62) 4 ‘99IMNA 3.43 (2.82 – 4.08) 74 2.31 (1.80 – 2.86) 53 2.63 (0.0 – 5.31) 3 ‘00RAPH 2.34 (2.10 – 2.58) 243 1.89 (1.52 – 2.30) 79 2.23 (1.43 – 3.06) 27 ‘00MCCA 4.54 (4.18 –4.94) 386 3.26 (2.69 – 3.83) 92 2.45 (1.61 – 3.36) 19 ‘00DWOR 1.18 (1.01 – 1.37) 116 1.08 (0.83 – 1.32) 53 0.69 (0.40 – 1.03) 14 ‘00IMNA 3.99 (3.50 – 4.48) 154 2.48 (1.91 – 3.09) 45 2.26 (1.18 – 3.36) 12 ‘01RAPH 1.18 (1.04 – 1.33) 182 0.74 (0.49 – 1.00) 21 0.69 (0.17 – 1.29) 4 ‘01MCCA 1.41 (1.23 – 1.58) 184 0.76 (0.49 – 1.05) 20 0.40 (0.00 – 0.91) 2 ‘01DWOR 0.36 (0.29 – 0.44) 60 0.44 (0.27 – 0.60) 18 0.16 (0.00 – 0.47) 1 ‘01IMNA 0.73 (0.56 – 0.92) 42 0.37 (0.13 – 0.64) 6 NA None ‘01CATH 0.33 (0.18 – 0.50) 11 NA None NA None ‘02RAPH 1.14 (0.91 – 1.39) 61 0.94 (0.72 – 1.17) 50 1.05 (0.37 – 1.74) 6 ‘02MCCA 1.63 (1.31 – 1.95) 70 1.43 (1.14 – 1.74) 59 1.00 (0.0 – 2.21) 2 ‘02DWOR 0.64 (0.44 – 0.83) 26 0.74 (0.54 – 0.96) 32 0.27 (0.0 – 0.60) 2 ‘02IMNA 0.74 (0.38 – 1.12) 12 0.82 (0.51 – 1.19) 16 1.55 (0.00 – 2.97) 3 ‘02CATH 1.09 (0.66 – 1.53) 16 0.72 (0.29 – 1.18) 8 NA None ‘03RAPH 0.32 (0.22 – 0.43) 27 0.13 (0.05 – 0.23) 5 0.17 (0.0 – 0.51) 1 ‘03MCCA 0.82 (0.65 – 0.97) 68 0.85 (0.63 – 1.08) 36 0.81 (0.35 – 1.37) 7 ‘03DWOR 0.28 (0.19 – 0.39) 20 0.28 (0.16 –0.42) 12 0.18 (0.0 – 0.43) 2 ‘03IMNA 0.58 (0.38 – 0.80) 18 0.64 (0.32 – 1.00) 10 0.67 (0.0 – 1.59) 2 ‘03CATH 0.32 (0.12 – 0.57) 5 0.57 (0.14 – 1.07) 4 NA None ‘04RAPH 0.28 (0.21 – 0.36) 38B 0.21 (0.10 – 0.32) 11B 0.18 (0.00 – 0.55) 1B

‘04MCCA 0.33 (0.26 – 0.40) 54B 0.28 (0.15 – 0.43) 11B NA None ‘04DWOR 0.13 (0.08 – 0.18) 16B 0.34 (0.24 – 0.46) 28B 0.36 (0.00 – 0.86) 2B

‘04IMNA 0.32 (0.19 – 0.45) 15B 0.37 (0.16 – 0.63) 7B 1.23 (0.00 – 2.91) 2B

‘04CATH 0.24 (0.05 – 0.43) 5B 0.57 (0.14 – 1.09) 4B 1.37 (0.00 – 4.11) 1B

A Abbreviations: RAPH=Rapid River H; MCCA=McCall H; DWOR=Dworshak NFH; IMNA=Imnaha AP; and CATH=Catherine Ck AP. B Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006.

135

Appendix Table E-5. Number of PIT-tagged wild steelhead actually transported from each dam and estimate (ti) of total PIT-tagged wild steelhead that would have been transported if all PIT- tagged fish had been transported at same rate as the untagged run-at-large.

Lower Granite Dam Little Goose Dam Lower Monumental Dam Migr. Year Actual t2 Actual t3 Actual t41997 214 2,112 33 344 26 184 1998 294 4,246 100 1,164 68 595 1999 223 2,910 90 3,134 67 1,129 2000 200 6,264 89 2,643 110 971 2001 162 11,126 23 833 7 139 2002 128 3,804 62 2,896 135 2,154 2003 1,215 4,705 655 2,958 227 991 Average Percent1 64 % 25 % 11 % 1 Estimated percentage of total transported population transported at each Snake River dam. Appendix Table E-6. Estimated dam-specific transportation SAR percentages of PIT-tagged wild steelhead in the annual aggregate groups for 1997 to 2003 (with 90% confidence intervals). Migr. Year

SAR(TLGR) %

Adult #

SAR(TLGS) %

Adult #

SAR(TLMN) %

Adults #

1997 1.87 (0.47 – 3.59) 4 NA None NA None 1998 0.34 (0.0 – 1.00) 1 NA None NA None 1999 2.69 (0.98 – 4.65) 6 4.44 (1.12 – 8.43) 4 2.99 (0.0 – 7.04) 2 2000 3.50 (1.51 – 5.64) 7 3.37 (0.0 – 6.86) 3 2.73 (0.74 – 5.36) 3 2001 3.09 (1.16 – 5.59) 5 NA None NA None 2002 3.91 (1.55 – 6.82) 5 1.61 (0.0 – 4.92) 1 2.22 (0.65 – 4.41) 3 2003A 1.73 (1.16 – 2.36) 21 2.75 (1.67 – 3.90) 18 2.20 (0.82 – 3.88) 5 A Migration year 2003 is incomplete until 3-salt returns occur at GRA.

136

Appendix Table E-7. Number of PIT-tagged hatchery steelhead actually transported from each dam and estimate (ti) of total PIT-tagged hatchery steelhead that would have been transported if all PIT- tagged fish had been transported at same rate as the untagged run-at-large.

Lower Granite Dam

Little Goose Dam

Lower Monumental Dam

Migr. Year

Actual t2 Actual t3 Actual t41997 1,521 12,445 104 1,128 81 883 1998 795 13,080 358 4,264 157 2,127 1999 779 9,169 291 8,845 221 3,402 2000 399 14,023 73 2,091 92 1,472 2001 331 17,696 43 950 16 205 2002 124 4,951 64 4,101 79 4,278 2003 2,068 6,459 1,510 4,817 829 2,730 Average Percent1 65 % 22 % 13 % 1 Estimated percentage of total transported population transported at each Snake River dam. Appendix Table E-8. Estimated dam-specific transportation SAR percentages of PIT-tagged hatchery steelhead in the annual aggregate groups for 1997 to 2003 (with 90% confidence intervals). Migr. Year

SAR(TLGR) %

Adult #

SAR(TLGS) %

Adult #

SAR(TLMN) %

Adult #

1997 0.59 (0.27 – 0.96) 9 NA None NA None 1998 0.63 (0.24 – 1.13) 5 0.28 (0.0 – 0.84) 1 0.64 (0.0 – 1.91) 1 1999 1.03 (0.50 – 1.69) 8 1.37 (0.34 – 2.57) 4 NA None 2000 3.01 (1.74 – 4.56) 14 1.37 (0.0 – 3.90) 1 1.09 (0.0 – 3.09) 1 2001 1.21 (0.30 – 2.32) 4 NA None NA None 2002 2.42 (0.70 – 4.93) 3 NA None NA None 2003A 1.98 (1.51 – 2.54) 41 2.12 (1.54 – 2.73) 32 1.21 (0.60 – 1.85) 10 A Migration year 2003 is incomplete until 3-salt returns occur at GRA.

137

Appendix F

Data used in estimating the annual weighted SARs

for wild and hatchery Chinook and steelhead Appendix Table F-1. Study-specific SARs and weights (estimated proportion of run-at-large reflected by each study category) used to estimate the annual SARs for wild Chinook.

Population proportion in study categoryA

SAR for study category (%)

Migr. Year T0 C0 C1 SAR2(T0) SAR(C0) SAR(C1)

Weighted SARLGR-to-LGR (%)

(90% CI) 1994 0.886 0.114 0.45 0.28 0.43 1995 0.851 0.149 0.35 0.37 0.35 1996 0.735 0.265 0.50 0.26 0.44 1997 0.572 0.239 0.189 1.74 2.35 0.93 1.73 (0.96 – 2.55) 1998 0.815 0.185 1.18 1.36 1.21 (0.83 – 1.63) 1999 0.863 0.137 2.44 2.13 2.40 (1.92 – 2.93) 2000 0.709 0.269 0.022 1.43 2.39 2.34 1.71 (1.22 – 2.24)

2001B 0.989 0.011 1.28 Assume= SAR(C1) 0.14

1.27 (0.55 – 2.07)

2002 0.709 0.273 0.018 0.80 1.21 0.99 0.92 (0.75 – 1.10) 2003 0.694 0.293 0.013 0.34 0.33 0.17 0.34 (0.26 – 0.42) 2004C 0.929 0.071 0.30 0.31 0.30 (0.22 – 0.39) A Estimated proportion of total smolt population (tagged and untagged) at LGR in each study category. B Migration year 2001 uses SAR(C1) with the C0 population proportion in the weighted SAR computation. C Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006.

138

Appendix Table F-2. Study-specific SARs and weights (estimated proportion of run-at-large reflected by each study category) used to estimate the annual SARs for hatchery Chinook.

Population proportion in study category2


Migr. Year

Hatchery Code1

T0 C0 C1 SAR2(T0) SAR(C0) SAR(C1)

Weighted SARLGR-to-LGR

3 (%) (90% CI)

DWOR 0.481 0.313 0.205 0.83 0.47 0.36 0.62 IMNA 0.516 0.273 0.211 1.17 0.86 0.69 0.98 MCCA 0.509 0.307 0.184 1.89 1.09 1.10 1.50

1997 RAPH 0.539 0.272 0.189 0.79 0.46 0.53 0.65

DWOR 0.714 0.286 0.90 1.25 1.00 IMNA 0.848 0.152 0.86 0.55 0.81 MCCA 0.856 0.144 2.71 1.38 2.52

1998 RAPH 0.857 0.143 2.00 1.20 1.89

DWOR 0.735 0.265 1.18 1.20 1.19 IMNA 0.777 0.223 2.72 1.43 2.43 MCCA 0.725 0.275 3.61 2.40 3.28

1999 RAPH 0.797 0.203 3.05 2.37 2.91

DWOR 0.660 0.340 1.00 1.01 1.00 IMNA 0.686 0.314 3.15 2.41 2.92 MCCA 0.580 0.420 3.91 2.06 3.13

2000 RAPH 0.679 0.321 2.10 1.59 1.94

DWOR 0.978 0.022 0.36 0.04 0.35 IMNA 0.976 0.024 0.62 0.06 0.61 MCCA 0.972 0.028 1.24 0.04 1.21 RAPH 0.974 0.026 1.09 0.05 1.06

2001 CATH 0.964 0.036 0.23

Assume SAR(C1) value 0.04 0.22

DWOR 0.569 0.431 0.62 0.50 0.57 (0.49 – 0.65) IMNA 0.662 0.338 0.80 0.45 0.68 (0.52 – 0.85) MCCA 0.678 0.322 1.49 1.03 1.34 (1.19 – 1.50) RAPH 0.665 0.335 1.01 0.67 0.90 (0.79 – 1.00)

2002

CATH 0.706 0.294 0.89 0.49 0.77 (0.56 – 1.00) DWOR 0.537 0.463 0.26 0.21 0.24 (0.19 – 0.28) IMNA 0.550 0.450 0.58 0.48 0.53 (0.42 – 0.64) MCCA 0.539 0.461 0.79 0.54 0.68 (0.61 – 0.75) RAPH 0.551 0.449 0.25 0.23 0.24 (0.19 – 0.29)

2003

CATH 0.552 0.448 0.36 0.25 0.31 (0.20 – 0.44) DWOR 0.843 0.150 0.007 0.21 0.22 0.16 0.21 (0.17 – 0.26) IMNA 0.888 0.103 0.009 0.35 0.23 0.11 0.33 (0.23 – 0.45) MCCA 0.929 0.060 0.011 0.31 0.25 0.12 0.31 (0.24 – 0.37) RAPH 0.890 0.097 0.013 0.26 0.14 0.09 0.24 (0.19 – 0.30)

2004 4

CATH 0.898 0.096 0.006 0.35 0.20 0.32 0.33 (0.18 – 0.52) 1 Hatchery coding: DWOR=Dworshak H; IMNA=Imnaha AP; MCCA=McCall H; RAPH=Rapid River H; CATH=Catherine Creek AP. 2 Estimated proportion of total smolt population (tagged and untagged) at LGR in each study category. 3 Estimated overall weighted SARLGR-to-LGR is obtained by taking proportion of total population of smolts (tagged and untagged) at Lower Granite Dam in each study category and multiplying by the respective study category’s SARLGR-to-LGR (see text for exception in 2001). 4 Migration year 2004 is incomplete with Age 2-salt adult returns through 8/9/2006.

139

Appendix Table F-3. Study-specific SARs and weights (estimated proportion of run-at-large reflected by each study category) used to estimate the annual SARs for wild steelhead.




Weighted SARLGR-to-LGR (%) (90% CI)

1997 0.715 0.122 0.163 1.45 0.66 0.23 1.16 (0.37 – 2.12) 1998 0.892 0.108 0.21 1.07 0.30 (0.07 – 0.66) 1999 0.869 0.131 3.07 1.35 2.84 (1.68 – 4.19) 2000 0.846 0.144 0.009 2.79 1.92 1.82 2.66 (1.62 – 3.72)

2001B 0.992 0.008

2.49 Assume SAR(C1) 0.07 2.47 (0.97 – 4.49)

2002 0.675 0.309 0.016 2.84 0.67 0.94 2.14 (1.24 – 3.21) 2003C 0.723 0.262 0.015 1.99 0.48 0.52 1.57 (1.21 – 1.94) A Estimated proportion of total smolt population (tagged and untagged) at LGR in each study category. B Migration year 2001 uses SAR(C1) with the C0 population proportion in the weighted SAR computation. C Migration year 2003 is incomplete until 3-salt returns occur at GRA. Appendix Table F-4. Study-specific SARs and weights (estimated proportion of run-at-large reflected by each study category) used to estimate the annual SARs for hatchery steelhead.




Weighted SARLGR-to-LGR (%) (90% CI)

1997 0.608 0.140 0.252 0.52 0.24 0.17 0.39 (0.22 – 0.59) 1998 0.873 0.127 0.51 0.89 0.56 (0.30 – 0.85) 1999 0.848 0.150 0.002 0.90 1.04 0.59 0.92 (0.59 – 1.30) 2000 0.817 0.183 2.10 0.95 1.89 (1.18 – 2.70)

2001B 0.979 0.019 0.003 0.94 Assume SAR(C1) 0.016 0.92 (0.24 – 1.74)

2002 0.700 0.300 1.06 0.70 0.95 (0.40 – 1.72) 2003C 0.690 0.305 0.005 1.81 0.68 0.37 1.46 (1.24 – 1.70) A Estimated proportion of total smolt population (tagged and untagged) at LGR in each study category. B Migration year 2001 uses SAR(C1) with the C0 population proportion in the weighted SAR computation. C Migration year 2003 is incomplete until 3-salt returns occur at GRA.

140

Appendix G

PIT-tagged hatchery Chinook release numbers and relation to production

Appendix Table G - 1. Hatchery Chinook PIT-tagged and released in Snake River basin specifically for CSS (long time series), 1997 to 2004.

Hatchery Migration Year

Hatchery Release

Fish # / lb

Median Length at Tagging (mm)

PIT Tags Released

PIT Tag Proportion

Rapid River H (RAPH)

1997 1998 1999 2000 2001 2002 2003 2004

85,838 896,170 2,847,283 2,462,354 736,601 2,669,476 2,330,557 2,762,058

20.5 20.3 17.9 19.2 18.8 19.8 18.8 24.5

100A

117 120 119 118 122 119 (no lengths taken)

40,452 48,336 47,812 47,747 55,085 54,908 54,763 51,969

0.4713 0.0539 0.0168 0.0194 0.0748 0.0206 0.0235 0.0188

Dworshak H (DWOR)

1997 1998 1999 2000 2001 2002 2003 2004

53,078 973,400 1,044,511 1,017,873 333,120 1,000,561 1,033,982 1,078,923

12.7 20.9 21.0 24.0 19.7 20.1 21.4 20.2

118 121 116 112 121 119 120 113

14,080 47,703 47,845 47,743 55,139 54,725 54,708 51,616

0.2653 0.0490 0.0458 0.0469 0.1655 0.0547 0.0529 0.0478

Catherine Ck AP (CATH)

2001 2002 2003 2004

136,833 180,343 105,292 162,614

19.7 18.6 12.8 23.2

117A

115A

123A

109A

20,915 20,796 20,628 20,994

0.1529 0.1153 0.1959 0.1291

McCall H (MCCA)

1997 1998 1999 2000 2001 2002 2003 2004

238,647 393,872 1,143,083 1,039,930 1,076,846 1,022,550 1,053,660 1,088,810

17.1 17.5 23.9 23.3 19.4 23.0 21.1 20.9

128 126 117 117 129 122 121 (no lengths taken)

52,652 47,340 47,985 47,705 55,124 54,734 74,317 71,363

0.2206 0.1202 0.0420 0.0459 0.0512 0.0535 0.0705 0.0655

Imnaha AP (IMNA)

1997 1998 1999 2000 2001 2002 2003 2004

50,911 93,108 184,725 179,797 123,014 303,737 268,426 398,469

17.0 21.1 18.5 19.1 16.0 14.1 16.3 26.1

122 122 117A

113A

121A

121A

123A

98A

13,378 19,825 19,939 20,819 20,922 20,920 20,904 20,910

0.2628 0.2129 0.1079 0.1158 0.1701 0.0689 0.0779 0.0525

A Tagged in fall ~5 months before release; otherwise tagged in spring 1-2 months before release.

141

Appendix Table G - 2. Carson NFH Chinook PIT-tagged and released in lower Columbia River basin specifically for CSS (full time series), 1997 to 2004. Migration Year

Dates of Release

# Release from Hatchery

# Fish per Pound

Median Fork Length1 at Tagging (mm)

# of PIT Tags Released

% PIT Tags in Hatchery Release

1997 4/17 907,708 15.5 119 4,983 0.55 1998 4/20 1,734,188 16.6 115 7,491 0.43 1999 4/20 1,415,744 12.6 120 12,977 0.92 2000 4/20 1,430,022 15.6 116 14,992 1.05 2001 4/19-21 1,608,684 14.9 108 14,978 0.93 2002 4/16-17 1,449,361 15.6 116 14,983 1.03 2003 4/16-17 1,673,255 17.1 111 14,983 0.90 2004 4/14 -16 1,417,986 17.3 111 14,973 1.06 1 Fork length taken at time of tagging in early January approx. 3 months before release.

142

Appendix H

Release sites of PIT-tagged wild Chinook and wild & hatchery steelhead (each release site is not present for every migration year)

WILD SP/SU CHINOOK Release River KM Release Site Rel_site Code CLEARWATER RIVER SUB-BASIN 522.224 Clearwater River CLWR 522.224.010 Clearwater Trap CLWTRP 522.224.087 Lolo Creek LOLOC 522.224.120.004 Clear Creek CLEARC 522.224.120.037 Lochsa River LOCHSA 522.224.120.037 Selway River SELWYR 522.224.120.037.003 Pete King Creek PETEKC 522.224.120.037.029 Gedney Creek GEDNEC 522.224.120.037.031 Meadow Creek, Selway R. MEADOC 522.224.120.037.039 Fish Creek FISHC 522.224.120.037.039.002 Fish Creek Trap FISTRP 522.224.120.037.042 Boulder Creek Trap BOUTRP 522.224.120.037.065 Moose Creek, Selway R. MOOS2C 522.224.120.037.096 Squaw Creek SQUAWC 522.224.120.037.105 Papoose Creek PAPOOC 522.224.120.037.113 Colt Kill Creek (Replaces WHITSC) COLTKC 522.224.120.037.113.003 Crooked Fork Creek Trap CFCTRP 522.224.120.037.113.011 Brushy Fork Creek BRUSHC 522.224.120.037.113.016 Storm Creek STORMC 522.224.120.037.264 White Cap Creek WHITCC 522.224.120.084 Newsome Creek NEWSOC 522.224.120.094 Crooked River CROOKR 522.224.120.094.001 Crooked River Trap CROTRP 522.224.120.101 American River AMERR 522.224.120.101 Red River REDR 522.224.120.101.006 Red River Trap REDTRP SNAKE RIVER TRAP AT LEWISTON 522.225 Snake Trap SNKTRP GRANDE RONDE RIVER SUB-BASIN 522.271 Grande Ronde R (km 131-325) GRAND2 522.271 Grande Ronde R (archaic) GRANDR 522.271.002 Grande Ronde River Trap GRNTRP 522.271.073 Wenaha River WENR 522.271.073.035 North Fork Wenaha River WENRNF 522.271.073.035 South Fork Wenaha River WENRSF

143

Release River KM Release Site Rel_site Code 522.271.131 Wallowa River WALLOR 522.271.131.016 Minam River MINAMR 522.271.131.042 Lostine River LOSTIR 522.271.137 Lookingglass Creek LOOKGC 522.271.232 Catherine Creek CATHEC SALMON RIVER SUB-BASIN 522.303 Salmon R (archaic) SALR 522.303.103 Salmon Trap SALTRP 522.303.215 SF Salmon River SALRSF 522.303.215.000 Lower SF Salmon River Trap LSFTRP 522.303.215.059 Secesh River SECESR 522.303.215.059.045 Lake Creek LAKEC 522.303.215.060 EF South Fork Salmon R. SAEFSF 522.303.215.060.024 Johnson Creek JOHNSC 522.303.215.060.024.007 Johnson Creek Trap JOHTRP 522.303.215.115 SF Salmon River Trap SFSTRP 522.303.215.125 Stolle Pond STOLP 522.303.282 Chamberlain Creek CHAMBC 522.303.282.024 WF Chamberlain Ck CHAMWF 522.303.319 MF Salmon River (km - ) SALMF2 522.303.319 MF Salmon River (archaic) SALRMF 522.303.319.029 Big Creek, MF Salmon R. BIG2C 522.303.319.029.011 Rush Creek, MF Salmon R. RUSHC 522.303.319.057 Camas Creek, MF Salmon R. CAMASC 522.303.319.073 Loon Creek LOONC 522.303.319.150 Sulphur Creek, MF Salmon R. SULFUC 522.303.319.170 Bear Valley Creek BEARVC 522.303.319.170 Marsh Creek MARSHC 522.303.319.170.010 Capehorn Creek CAPEHC 522.303.319.170.011 Marsh Creek Trap MARTRP 522.303.319.170.014 Elk Creek ELKC 522.303.381 NF Salmon River SALRNF 522.303.416 Lemhi River LEMHIR 522.303.416.049 Lemhi River Weir LEMHIW 522.303.489 Pahsimeroi River PAHSIR 522.303.489.002 Pahsimeroi River Trap PAHTRP 522.303.552 EF Salmon River SALREF 522.303.552.014 Herd Creek HERDC 522.303.552.029 EF Salmon River Trap SALEFT 522.303.552.030 EF Salmon River Weir SALEFW 522.303.591.011 WF Yankee Fork YANKWF 522.303.609 Valley Creek VALEYC 522.303.615 Redfish Lake Creek REDFLC 522.303.615.003 Redfish Lake Ck Trap RLCTRP 522.303.617 Sawtooth Trap SAWTRP 522.303.622 Williams Creek WILLIC 522.303.624 Huckleberry Creek HUCKLC

144

Release River KM Release Site Rel_site Code 522.303.633 Alturas Lake Creek ALTULC 522.303.633.002 Pettit Lake Creek PETTLC 522.303.642 Beaver Creek BEAVEC 522.303.644 Smiley Creek SMILEC 522.303.647 Frenchman Creek FRENCC IMNAHA RIVER SUB-BASIN 522.308 Imnaha River IMNAHR 522.308.007 Imnaha Trap IMNTRP 522.308.074 Imnaha River Weir IMNAHW WILD STEELHEAD Release River KM Release Site Rel_site Code

CLEARWTER RIVER SUB-BASIN 522.224.018.016 Mission Creek MISSC 522.224.024 Potlatch River POTR 522.224.087 Lolo Creek LOLOC 522.224.120.004 Clear Creek CLEARC 522.224.120.037 Lochsa River LOCHSA 522.224.120.037 Selway River SELWYR 522.224.120.037.012 O'Hara Creek, Selway R. OHARAC 522.224.120.037.016 Deadman Creek, Lochsa R. DEADMC 522.224.120.037.029 Gedney Creek, Selway R. GEDNEC 522.224.120.037.029.005 West Fork Gedney Creek GEDCWF 522.224.120.037.031 Meadow Creek, Selway R. MEADOC 522.224.120.037.039 Fish Creek, Lochsa R. FISHC 522.224.120.037.039.002 Fish Creek Trap FISTRP 522.224.120.037.042 Boulder Creek, Lochsa R. BOULDC 522.224.120.037.042.001 Boulder Creek Trap BOUTRP 522.224.120.037.051 Three Links Creek, Selway R. 3LINKC 522.224.120.037.065.006 North Fork Moose Creek, Selway R. MOOS2N 522.224.120.037.092 Warm Springs Creek, Lochsa R. WARMSC 522.224.120.037.096 Squaw Creek, Lochsa R. SQUAWC 522.224.120.037.113 Colt Kill Creek (Replaces WHITSC) COLTKC 522.224.120.037.113.003 Crooked Fork Creek Trap CFCTRP 522.224.120.037.113.011 Brushy Fork Creek, Lochsa R. BRUSHC 522.224.120.037.113.016 Storm Creek STORMC 522.224.120.037.253 Running Creek RUNNIC 522.224.120.056 Johns Creek JOHNC 522.224.120.076 Tenmile Creek TENMIC 522.224.120.084 Newsome Creek NEWSOC 522.224.120.094 Crooked River CROOKR 522.224.120.094.001 Crooked River Trap CROTRP

145

Release River KM Release Site Rel_site Code 522.224.120.101 American River AMERR 522.224.120.101 Red River REDR 522.224.120.101.006 Red River Trap REDTRP SNAKE RIVER TRAP AT LEWISTON 522.225 Snake Trap SNKTRP GRANDE RONDE RIVER SUB-BASIN 522.271 Grande Ronde R (km 131-325) GRAND2 522.271 Grande Ronde R (Archaic) GRANDR 522.271.002 Grande Ronde River Trap GRNTRP 522.271.131 Wallowa River WALLOR 522.271.131.016 Minam River MINAMR 522.271.131.042 Lostine River LOSTIR 522.271.137 Lookingglass Creek LOOKGC 522.271.232 Catherine Creek CATHEC 522.271.232.044 Little Catherine Creek LCATHC 522.271.232.052 North Fork Catherine Creek CATCNF 522.271.232.052 South Fork Catherine Creek CATCSF SALMON RIVER SUB-BASIN 522.303.086 Whitebird Creek WBIRDC 522.303.103 Salmon Trap SALTRP 522.303.106 Slate Creek SLATEC 522.303.140 Little Salmon River LSALR 522.303.140.007 Rapid River, Little Salmon River RAPIDR 522.303.140.007.006 Rapid River Hatchery RAPH 522.303.140.007.007 Rapid River Trap RPDTRP 522.303.140.007.012 West Fork Rapid River RAPIWF 522.303.140.031 Hazard Creek HAZARC 522.303.140.031.002 Hard Creek HARDC 522.303.177 Wind River WINDR 522.303.200 Crooked Creek CROOC 522.303.215 SF Salmon River SALRSF 522.303.215.000 Lower SF Salmon River Trap LSFTRP 522.303.215.059 Secesh River SECESR 522.303.215.059.008 Lick Creek LICKC 522.303.215.059.045 Lake Creek LAKEC 522.303.215.060 EF South Fork Salmon R. SAEFSF 522.303.215.060.024 Johnson Creek JOHNSC 522.303.215.060.024.007 Johnson Creek Trap JOHTRP 522.303.215.115 SF Salmon River Trap SFSTRP 522.303.255 Bargamin Creek BARGAC 522.303.282 Chamberlain Creek CHAMBC 522.303.282.024 WF Chamberlain Ck CHAMWF 522.303.301 Horse Creek HORSEC

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Release River KM Release Site Rel_site Code 522.303.319.029 Big Creek, MF Salmon R. BIG2C 522.303.319.029.011 Rush Creek, MF Salmon R. RUSHC 522.303.319.057 Camas Creek, MF Salmon R. CAMASC 522.303.319.150 Sulphur Creek, MF Salmon R. SULFUC 522.303.319.170 Bear Valley Creek BEARVC 522.303.319.170 Marsh Creek MARSHC 522.303.319.170.011 Marsh Creek Trap MARTRP 522.303.319.170.014 Elk Creek ELKC 522.303.338 Panther Creek PANTHC 522.303.416 Lemhi River LEMHIR 522.303.416.049 Lemhi River Weir LEMHIW 522.303.489 Pahsimeroi River PAHSIR 522.303.489.002 Pahsimeroi River Trap PAHTRP 522.303.552 EF Salmon River SALREF 522.303.552.014 Herd Creek HERDC 522.303.591.011 WF Yankee Fork YANKWF 522.303.609 Valley Creek VALEYC 522.303.617 Sawtooth Trap SAWTRP 522.303.642 Beaver Creek BEAVEC IMNAHA RIVER SUB-BASIN 522.308 Imnaha River IMNAHR 522.308.007 Imnaha Trap IMNTRP 522.308.008 Lightning Creek LITNGC HATCHERY STEELHEAD Release River KM Release Site Rel_site Code CLEARWTER RIVER SUB-BASIN 522.224 Clearwater River CLWR 522.224.031 Cottonwood Creek COTNWC 522.224.042 Bedrock Creek BEDRKC 522.224.047 Jacks Creek JACKSC 522.224.057 Big Canyon Creek BIGCAC 522.224.065 Dworshak National Fish Hatchery DWOR 522.224.065 Dworshak H, mainstem Clearwater R DWORMS 522.224.065.000 Dworshak NFH, NF Clearwater R DWORNF 522.224.087 Lolo Creek LOLOC 522.224.120 South Fork Clearwater River CLWRSF 522.224.120.004 Clear Creek CLEARC 522.224.120.037.096 Squaw Creek, Lochsa R. SQUAWC 522.224.120.069.003 Twentymile Creek Trap TWNMIT 522.224.120.084 Newsome Creek NEWSOC 522.224.120.094 Crooked River CROOKR 522.224.120.094.015 Crooked River Pond CROOKP

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Release River KM Release Site Rel_site Code 522.224.120.101 American River AMERR 522.224.120.101 Red River REDR 522.224.120.101.027 Red River Rearing Pond REDP SNAKE RIVER TRAP AT LEWISTON 522.225 Snake Trap SNKTRP GRANDE RONDE RIVER SUB-BASIN 522.271 Grande Ronde R (km 131-325) GRAND2 522.271 Grande Ronde R (Archaic) GRANDR 522.271.002 Grande Ronde River Trap GRNTRP 522.271.046 Cottonwood Acclimation Pond COTP 522.271.131.016 Minam River MINAMR 522.271.131.018.001 Big Canyon Facility, Wallowa R. BCANF 522.271.131.063.001 Wallowa Hatchery WALH SALMON RIVER SUB-BASIN 522.303 Salmon R (Archaic) SALR 522.303.103 Salmon Trap SALTRP 522.303.140 Little Salmon River LSALR 522.303.140.031 Hazard Creek HAZARC 522.303.381 North Fork Salmon River SALRNF 522.303.416 Lemhi River LEMHIR 522.303.489 Pahsimeroi River PAHSIR 522.303.489.002 Pahsimeroi River Trap PAHTRP 522.303.489.002 Pahsimeroi Weir PAHSIW 522.303.552.014 Herd Creek, EF Salmon R. HERDC 522.303.552.030 East Fork Salmon River Weir SALEFW 522.303.564 Squaw Creek SQAW2C 522.303.564.001 Squaw Creek Acclimation Pond SQUAWP 522.303.591 Yankee Fork YANKFK 522.303.591.011 WF Yankee Fork YANKWF 522.303.617 Sawtooth Hatchery SAWT 522.303.617 Sawtooth Trap SAWTRP IMNAHA RIVER SUB-BASIN 522.308 Imnaha River IMNAHR 522.308.007 Imnaha Trap IMNTRP 522.308.008 Lightning Creek LITNGC 522.308.032 Big Sheep Creek BSHEEC 522.308.032.005.008 Little Sheep Facility LSHEEF SNAKE RIVER BELOW HELLS CANYON DAM 522.397 Hells Canyon Dam HCD

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Appendix I

Regional Review Comments and CSS Oversight Committee Responses

149

Department of Energy

Bonneville Power Administration

P.O. Box 3621 Portland, Oregon 97208-3621

ENVIRONMENT, FISH AND WILDLIFE

November 20, 2006 In reply refer to: KEW-4

Fish Passage Center 1827 NE 44th Ave., Suite 240 Portland, Oregon 97213 Dear Ms. Michelle DeHart, and Mr. Thomas Berggren: Thank you for the opportunity to comment on the Comparative Survival Study (CSS) 2006 Annual Report, BPA Contract 19960200. We summarize our major points below and provide a more detailed analysis including our concerns with the 2006 CSS Report in the enclosure. We request that the authors of the report provide greater background and detail for their statistical methods:

• Please provide your statistical methods for estimating SARs, Transport-control and D.

• Ryding’s design and analysis report provides a framework for the T/C estimator; please explain its use with the available data.

• Please provide the underlying statistical framework used in the CSS annual report and explain how stated assumptions are used throughout the report.

Our review describes important population attributes that we believe the CSS report must address. These include:

• The age structure of the returning adults. • Data on the size of all PIT-tagged fish from hatcheries and other release sites

(ISAB review comments on the 2007-2009 CSS proposal). The March 15, 2006 ISAB review of the 2005 CSS Annual Report (ISAB 2006-3) pointed out that “Fish size is generally not accorded much significance in the CSS studies despite a well-known survival advantage for larger fish.”

We believe these two omissions alone could likely explain differential survival among PIT-tagged populations, particularly the factors that could help explain any difference in SARs of up and down river stocks. We believe the overriding issue for CSS is reproducibility. It refers to the ability of a test to be accurately reproduced or replicated by independent researchers to see if their analysis gives similar results to those reported by the original group. As pointed out in the ISAB 2005 CSS review, the review of the ISAB on the 2007-2009 CSS Proposal, and the Review of the 2006 Annual Report attached herein dated November 7, 2006, the 2006 CSS Annual Report requires additional supporting data as well as more detailed method descriptions to allow a disinterested third party to reproduce the analysis and conclusions contained in the CSS 2006 Annual Report. Please let us know if you have any questions or require further clarification on our comments. As we stated in our 2005 comment, it is critical that the issues raised be addressed in this Annual Report because of their importance for the continuing work described in the proposal for the 2007-2009 funding period. Sincerely, Robert J. Austin for William C. Maslen

Enclosure cc Mr. Brian Lipscomb, Columbia Basin Fish and Wildlife Authority Mr. Randy Fisher, Pacific States Marine Fisheries Commission Mr. Larry Cassidy, Northwest Power and Conservation Council Mr. John Ferguson, NOAA Fisheries Mr. Tim Peone Upper Columbia River Basin Tribes Mr. Pete Hassemer, Idaho Department of Fish and Game Ms. Liz Hamilton, Northwest Sportfishing Industry Association Ms. Shauna McReynolds, Pacific Northwest Utilities Conference Committee Mr. Rob Lothrop, Columbia River Inter-Tribal Fish Commission

150

A Review of The Comparative Survival Study (CSS) of

PIT-Tagged Spring/Summer Chinook Salmon and PIT-Tagged Summer Steelhead: 2006 Annual Report

November 7, 2006

by Bonneville Power Administration

Fish and Wildlife

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Overview The 2006 Comparative Survival Study (CSS) annual report is a technical analysis of juvenile and adult PIT-tag data generated from brood years 1997-2003 (2004). The report includes the typical juvenile smolt inriver survival estimates, upriver adult survival, smolt-to-adult ratio (SAR), and estimates of D, a differential post-Bonneville survival rate, as in previous reports. The 2006 report also includes analyses of relationships between SAR and river/ocean covariates (Chapter 5), relationships between smolt transport history and upriver migration success (Chapter 6), and effects of smolt size on detection probabilities (Chapter 9). Chapters 7 and 8 continue the upstream-downstream comparisons that concerned the Independent Scientific Advisory Board (ISAB) (2005). Chapter 10 provides some limited computer simulation studies of the robustness of the survival estimation procedures. The statistical methods for estimating SARs, transport-control (T/C), and D, as reported in the CSS 2006 design and analysis report (Ryding 2006), have not changed from 2005. The authors have not augmented their statistical methods with greater detail, as suggested by the ISAB (2005) review. Although Ryding (2006) has provided a document explaining the nature of the T/C (also referred to as T/I, or Transport-Inriver Ratio) estimator in terms of “Lower Granite equivalents,” she does not explain how to estimate T/I using the available data, and the CSS annual report does not use her equations (see Appendix AA). The CSS authors state that Ryding’s (2006) document provides the “analytical basis” for using Lower Granite (LGR) equivalents in estimating T/I, and “illustrates” the need to use LGR equivalents in estimating the SARs for the CSS study categories. However, Ryding’s document merely illustrates how to use LGR equivalents to estimate the SARs and the T/C ratio, and does not demonstrate the necessity of using LGR equivalents. Additionally, the CSS annual report includes many expressions that are not addressed in the Ryding (2006) document, and which are neither developed nor defended in the CSS annual report. As in previous years, it is unclear what underlying statistical framework was used in the CSS annual report. Although statistical assumptions are listed, it is not clear that those assumptions are used throughout the report. The CSS study relies upon the methods of Burnham et al. (1987) and the Cormack-Jolly-Seber (CJS) model, but it is not clear to what extent. Apparently the authors use the CJS model (equivalently, Burnham et al. 1987) to estimate juvenile migration parameters, including inriver survival, detection, and transportation proportions. This is acceptable. However, it is not clear how they estimate adult survival or otherwise estimate the number of adults returning to either Bonneville or Lower Granite in Chapter 3. The discussion should be expanded to better describe how the age structure of returning adults was addressed, and the model to estimate ocean and upriver survival. The CSS authors attempt in Appendix AA to estimate SAR and T/C values for certain groups of fish, namely the C0 (undetected) and T0 (transported at first detection) groups, with the rationale that these groups more realistically represent the migration experience of untagged fish. This is necessary only if the survival rates of the C0 and T0

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groups are systematically different from the survival rates of the more general non-transported and transported groups, respectively. However, the CSS estimates the sizes of the C0 and T0 groups using estimates from the CJS model, which is based on the assumptions that (1) all fish have common survival and detection probabilities, and (2) detection has no effect on subsequent survival and detection probabilities. These two assumptions are counter to the reasons for restricting attention to the C0 and T0 groups in the first place. Thus, the CSS approach is inconsistent. There are different ways of conceptualizing and expressing SARs and T/C, particularly at the systemwide level. The CSS approach, as described in the Ryding (2006) document, is one option. It is based on estimating the SARs of the C0 and T0 groups in terms of LGR equivalents. The T/C defined in the Ryding (2006) document is the ratio of two conditional return rates from LGR as smolts to LGR as adults: the return rate for fish that reach LGR and are “destined” for transport, and the return rate for fish that reach LGR and are “destined” for inriver migration:

[ ]

[ ]Pr Return to LGR | Destined to be transported

T/CPr Return to LGR | Destined for inriver

= .

If the desired inference is to fish that are “destined” for a particular migration method, then the Ryding (2006) definition of T/C is reasonable. However, it does not appear the CSS annual report actually uses the definition provided by Ryding (see Appendix AA). The expressions for the sizes of the C0 and C1 groups (Appendix AA, page 113) include a constant of 2, “to offset the typical 50% survival rate to the lower Columbia River of fish starting at Lower Granite Dam.” However, survival from Lower Granite to the lower Columbia River is rarely 50% (see Figures 12, 18, and 24). It is unnecessary to make the assumption of 50% survival, because inriver survival between Lower Granite and McNary is estimated (i.e., S2S3S4), (and used elsewhere in the estimators of C0 and C1.) In Appendix AA, the CSS authors introduce quantities not addressed by Ryding (2006), i.e., SAR1(T0), SAR2(T0), SAR(C0) (different expressions than Ryding’s), SAR(C1), D, and SARAnnual, as well as SAR(TLGR), SAR(TLGS), and SAR(TLMN). SAR1(T0) appears to agree in expectation with the expression for SAR(T0) from Ryding’s (2006) document. However, the CSS report remains impossible to fully assess without knowing the statistical framework and the conceptual definitions of SAR and D, this would facilitate the technical review of methods. In explaining trends in SARs in Figures 11, 17, and 23 and Chapter 5, consideration of the effects of harvest should be discussed. Changes in harvest mortality in the ocean or Columbia/Snake River can also affect SAR values, but this factor does not appear to have been considered in the analysis. Harvest numbers from the mouth of the Columbia River to Lower Granite have been relatively stable from 1997 to 2005 for steelhead. However, for Chinook salmon (spring, summer, and fall), harvest numbers have increased approximately three-fold from 1997-2000 to 2001-2005 (see figure

153

below) (data provided by DART). This suggests that consideration of harvest is important for understanding of the factors influencing SAR and recovery.

Year

Har

vest

in N

umbe

rs

2005200420032002200120001999199819971996

270000

240000

210000

180000

150000

120000

90000

60000

30000

0

ChinookSteelhead

Specific Comments

Chapter 1

1. Page 2, last sentence. Although the report indicates that survival from different life stages provides “valuable information to diagnose where in the salmon life cycle mortality rates have increased,” it is not clear how the relative contributions of inriver smolts, ocean (Bonneville-to-Bonneville) conditions, and upriver survival to overall SARs were considered. Ocean survival (i.e., Bonneville-to-Bonneville) is a major driving force behind annual changes in the SARs, and needs to be discussed.

Chapter 3

2. Page 11, first paragraph under Figure 4. In replicated studies (e.g., Figure 4), the individual confidence interval lengths are relatively less meaningful than if in a single point estimate was presented. Confidence interval (CI) length is a function of sample size, so the number of 90% CI that exceed the value 1 is more a reflection of sampling precision than overall performance. One should use a weighted t-test to assess

154

o

a

H : 1

vs.H : 1

T C

T C

μ

μ

≤

> using the between-year variability in T/C values.

3. Pages 21-22. Across-year averages of VC, T/C, and D are reported as geometric means (e.g., Tables 10-14), while SARs are reported as arithmetic means (e.g., Tables 5-9). No explanation is provided for the difference in computations. Geometric means by construct will have lower values than arithmetic means. The report should justify distributionally the need for different estimates of central tendency. Alternatively, the arithmetic mean is an appropriate estimator of expected value.

Chapter 4

4. Page 30, central paragraph. The conclusion, “the outlook for recovery may be poor,” seems to be stretching the interpretation of the steelhead data. First, the 2003 SAR is incomplete; second, the four years of steelhead data (1999-2002) have point estimates >2%; third, the wide confidence intervals would not suggest a significant linear downward trend.

5. Page 31, Table 17, lines 8-11 of first paragraph. Formal meta-analysis using the replicate years of data should be performed rather than simply counts of how often values of CI exceeded specific values. One approach is to test, for example,

o

a

H : 1vs.

H : 1

D

D

≤

> for each year and compute observed P-values. The individual P-values could be combined as follows to provided an overall test of significance:

22

1

2 ln n

n ii

Pχ=

= − ∑ ,

where 22nχ is the chi-square statistic with 2n degrees of freedom.

Another approach is to use a weighted t-test, weighing inversely proportional to variances. It would be useful if CSS were to compute standard errors (SE) for their estimates—which would enhance the ability to perform such tests.

6. Page 38, line 8-10. See previous comment 5.

7. Page 40, conclusion #10. Figures 24 and 24 illustrate a very high correlation between VC and T/C ratios between wild and hatchery steelhead (r2 not computed). Are high correlation and similar values sufficient to conclude

155

hatchery steelhead may be used as a surrogate for wild steelhead? It not, what are the criteria for such a determination?

Chapter 5

8. Page 41, section titled SAR estimates. With part of the goals of the regression analysis to examine the relationship between SARs and inriver covariates (i.e., flow and water transit time), It is unclear why the transport (T0) fish included these fish by virtue of being transported were not subject to inriver conditions. Analysis should also look at C0 and C1 fish only to confirm the pooled results. Water temperature has also been associated with inriver migration success and should be considered in the modeling (it was considered later in Chapter 6).

Chapter 6

9. Page 53, section titled Statistical analysis and Table 1(p. 59). To perform an across-year analysis of homogeneity between transported and nontransported hatchery adults, one approach is to sum the four independent chi-square statistics across years (i.e., 0.1109 + 7.6023 + 11.0768 +3.2190 = 22.0090 with df = 8 for a P = 0.0049). Another approach is to use a Poisson log-linear analysis of a three-dimensional contingency table (i.e., R × C × T = 3 × 2 × 4).

10. Page 54, section titled Hatchery chinook χ2 tests, last sentence. Wording unclear; “ . . . in contrast, was statistically across all sites.”

11. Page 55, first sentence. The lower success rate of “LGR” fish may be due to greater mortality or increased straying.

12. Page 55, section titled Wild Chinook logistic regression analysis. Logistic regression doesn’t estimate the quantity “odds ratio” but, rather, the log odds ratio

i.e., ln1

pp

⎡ ⎤⎛⎢ ⎜ −⎝ ⎠⎣ ⎦

⎞⎥⎟ . It appears the authors have misinterpreted the regression

results, “At 0.46 the odds ratio estimate for this group indicates that LGR salmon were about half as likely to survive their migration from BON to LGR than inriver outmigrants.” The more appropriate comparison is the success rate.

Examination of Table 2 (p. 59) indicates the following success rates(p): History 2001 2002 2003 2004

Inriver (pInirver) 0.8947 0.8750 0.8689 0.8882

LGR (pLGR) 0.7000 0.6316 0.8824 0.7777

Ratio pLGR/pInriver 0.7824 0.7218 1.0155 0.8756

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In no year was the ratio pLGR/pInriver < 0.46; the smallest value of 0.7218 occurred in year 2002. Pooling the data, the success rates were 0.8695 and 0.7561 for Inriver- and LGR-type fish for a relative success rate of 0.8986, LGR:Inriver, not 0.46! The same apparent misinterpretation of the logistic regression is also found in the section titled Hatchery Chinook logistic regression analysis. There, the relative success rate for LGR:Inriver fish is 0.7769/0.8375 = 0.9157, using the combined data, and not 0.64 as stated in the text.

13. Page 56, last sentence and Figure 4. It is not obvious that LGR adults have a “more skewed and slower travel time distribution” in examining the box-and-whisker plots (Figure 4). Because different software programs compile box-and-whisker plots differently, it is difficult to interpret the figures. Figure symbols need to be defined.

14. Page 62, Figures 1 and 2. Confidence bounds should be added to the bar chart for greater interpretive value.

Chapter 7

15. Page 65, first paragraph, last sentence. Justify the basis of equation ¼ e−1.47= 0.0594. Are you stating that Snake River population are surviving only 0.0594 times as well as downriver populations?

16. Page 66, first paragraph. Greater justification and description of assumptions using the bird colony PIT-tag recoveries is necessary. Perez-Comas and Skalski (2000) found the bird colony data could severely bias CJS estimates if PIT-tag recoveries occur from fish taken above Bonneville.

17. Page 67, Table 2. The estimates of Bonneville detection probabilities of for adults are negatively biased. The estimator assumes no adult mortality between Bonneville and upstream dams and detection at upstream dams is 100%. However, Chapter 6, Tables 1 and 2, indicate there are indeed losses, assumed to be as high as 25% between Bonneville and Lower Granite dams. The resulting negative biases in Table 2 will underestimate actual arrival abundance of adults at Bonneville; this, in turn, will negatively bias subsequent SARs. See Many and Parr (1968) for estimating detection probabilities from limited capture histories.

18. Page 68, Table 3. First column heading “Migr. Year” appears to be mislabeled.

19. Page 68, first sentence. Mathematical justification for equation

157

snake

downriver

SARlnSAR

M ⎛ ⎞Δ = − ⎜ ⎟⎝ ⎠

is necessary. Assuming S e μ−= where μ is the instantaneous mortality rate, then snake

dowriver downriver snakelneeM

μ

μ μ μ−

−

⎛ ⎞Δ = − = −⎜ ⎟

⎝ ⎠

is the difference in instantaneous morality rates and should be so labeled, not as “differential mortality.”

20. Page 68 and Figure 1 (Page 69). The report states, “Although the estimated MΔ differ using hatcheries, there is a common arrival pattern among the five upriver hatcheries.” Part of this pattern is due to the use of the same denominator (i.e., SARdownriver) and across all hatcheries, i.e., the covariate

H H

downriver downriver

SAR SARCov ln ln

SAR SARij i j

j j

′⎛ ⎞⎛ ⎞ ⎛ ⎞

− −⎜ ⎟⎜ ⎟ ⎜ ⎟⎜ ⎟ ⎜ ⎟⎜ ⎟⎝ ⎠ ⎝ ⎠⎝ ⎠

where = SAR for hatchery i in year j, HSAR

ij

downriverSARj = SAR for downriver stock in year j.

is also a function of downriverSARj and how it varies.

21. Page 68, first sentence. Estimation of differential mortality, as proposed in the CSS study, is a function of the ratio

LGR-BON

BON-BON

SARSAR

,

where = smolt-to-adult ratio (i.e., survival) from Lower Granite as

smolts to Bonneville as adults for Snake River fish, LGR-BONSAR

= smolt-to-adult ratio (i.e., survival) from Bonneville as smolts to Bonneville as adults for Carson Hatchery.

BON-BONSAR

If survival and return processes are homogeneous between stocks, then the ratio has the expected value

LGR-BON LGR-BON BON-BONLGR-BON

BON-BON BON-BON

SAR SARSAR SAR

SE S⋅⎛ ⎞ =⎜ ⎟⎝ ⎠

,

where = smolt survival between Lower Granite and Bonneville. LGR-BONSThere is no reason to expect that ratio to be equal to 1. Instead, interest should focus on whether that ratio of SARs differs appreciably from the smolt survival estimates between Lower Granite and Bonneville. In Table 3, (p. 68), the mean of that ratio is 0.9333—substantially higher than the average smolt survival rate for that reach at 0.52 (Table 10, p. 21) or 0.44 (Table 17, p. 31) reported earlier in the

158

CSS annual report. The differential mortality between the upriver and the one downriver site is thus much lower than expected (i.e., 1 0 9933 0 0067. .− = vs.

or 1 )as explained by survival through the hydro system. 1 0 52 0 48. .− = 0 44 0 56. .− =

Chapter 8

22. The issue of replicability is labeled a “red herring” by Hurlbert (1984). No two things can be identical, and try as we might, we can never prove they are so. The more important issue is replication. As stated in the 2005 ISAB review, additional downstream hatcheries need to be incorporated into the design. In so doing, the between-replicate, within-category variance can be used to compare treatment conditions. Until that additional downstream replication is incorporated, the upstream-downstream comparison is not useful.

Chapter 9

23. Page 87, second paragraph, last sentence. The report states wild Chinook were the focus of the size-detection probability analysis because “this group exhibits the largest transport vs. inriver SAR difference.” Based on the CSS report, geometric mean T/C ratios were 0.99 for wild Chinook (Table 3, p. 12), 1.46 for hatchery Chinook (Table 10, p. 21), 1.46 for hatchery steelhead (Table 20, p. 38), and 1.72 for wild steelhead (Table 17, p. 31). These data indicate wild Chinook have the most similar SARs for transport and inriver fish, while wild steelhead, the most different SAR values. Using the CSS annual report rationale, this suggest that analysis should focus on wild steelhead, not wild Chinook; this needs further explanation.

24. Page 89, second paragraph, Table 4, and Figure 1. A meta-analysis looking at the overall significance of the slope terms for size vs. detection probability should be performed. Multiple annual results in the same direction but not significant may be statistically significant when examined over the multiple-year data set.

Literature Cited Burnham, K.P., Anderson, D.R., White, G.C., Brownie, C., and Pollock, K.H. 1987. Design and

analysis methods for fish survival experiments based on release-recapture. American Fisheries Society Monographs 5.

Hurlbert, S.H. 1984. Pseudoreplication and the design of ecological field experiments. Ecological Monographs 54(2): 187-211.

Independent Scientific Advisory Board for the Northwest Power and Conservation Council, Columbia River Basin Indian Tribes, and National Marine Fisheries Service (N. Huntly, Chair). 2006. ISAB review of the 2005 comparative survival studies’ annual report and applicability of comparative survival studies’ analysis results. Northwest Power and Conservation Council, Portland, Oregon, ISAB 2006-3, http://www.nwcouncil.org/library/isab/isab2006-3.pdf.

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http://www.nwcouncil.org/library/isab/isab2006-3.pdf

Manly, B. F. J., and Parr, M. J. (1968), “A New Method of Estimating Population Size, Survivorship and Birth Rate From Capture-Recapture Data,” in Transactions of the Society for British Entomology, 18, 81-89.

Perez-Comas, J. A, and J. R. Skalski. 2000. Appraisal of system-wide survival estimation of Snake River yearling chinook salmon using PIT-tags recovered from Caspian tern and double-crested cormorant breeding colonies on Rice Island. Volume XIII in the Design and Analysis of Salmonid Tagging Studies in the Columbia Basin. Bonneville Power Administration, Portland, OR.

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FISH PASSAGE CENTER 1827 NE 44th Ave., Suite 240, Portland, OR 97213

Phone: (503) 230-4099 Fax: (503) 230-7559 http://www.fpc.org/

e-mail us at [email protected]

December 12, 2006 William C. Maslen, Director Environment, Fish, and Wildlife Bonneville Power Administration P.O. Box 3621 Portland, Oregon 97208-3621 Re: KEW-4 Dear Mr. Maslen, Thank you and the staff of Bonneville Power Administration’s Environment, Fish, and Wildlife Program for reviewing and commenting on the draft 2006 Comparative Survival Study (CSS) Annual Report. Regional review has been and will continue to be fundamental in our study’s progress and improvement. Overall, the comments provided by the BPA reviewer(s) were both constructive and insightful. In considering the provided comments in detail, we have revised and substantially improved our final 2006 report. Our specific responses to comments provided in your letter dated November 27, 2006 are addressed in the attached document. If you need further clarification of our responses or other aspects of the CSS, please do not hesitate to contact us. Sincerely, Michele DeHart

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http://www.fpc.org/%7Efpc

mailto:[email protected]

RESPONSE TO BPA’S 2006 ANNUAL REPORT COMMENTS Overview comments & responses Reviewer comments: The statistical methods for estimating SARs, transport-control (T/C), and D, as reported in the CSS 2006 design and analysis report (Ryding 2006), have not changed from 2005. The authors have not augmented their statistical methods with greater detail, as suggested by the ISAB (2005) review. Although Ryding (2006) has provided a document explaining the nature of the T/C (also referred to as T/I, or Transport-Inriver Ratio) estimator in terms of “Lower Granite equivalents,” she does not explain how to estimate T/I using the available data, and the CSS annual report does not use her equations (see Appendix AA). The CSS authors state that Ryding’s (2006) document provides the “analytical basis” for using Lower Granite (LGR) equivalents in estimating T/I, and “illustrates” the need to use LGR equivalents in estimating the SARs for the CSS study categories. However, Ryding’s document merely illustrates how to use LGR equivalents to estimate the SARs and the T/C ratio, and does not demonstrate the necessity of using LGR equivalents. Additionally, the CSS annual report includes many expressions that are not addressed in the Ryding (2006) document, and which are neither developed nor defended in the CSS annual report. As in previous years, it is unclear what underlying statistical framework was used in the CSS annual report. Although statistical assumptions are listed, it is not clear that those assumptions are used throughout the report. Response: The reviewer states that the 2006 CSS Annual Report did not provide greater detail on the statistical methods, as suggested by the ISAB (2005) review. Although an appendix listing all equations used to estimate parameter was provided in the draft report, we agreed with the reviewer that a more structured approach to describing the statistical framework utilized in the CSS was needed. Therefore, a fully revised and expanded appendix (Appendix A) was prepared for the final report to replace draft Appendix AA. It shows more details on how the computational formulas used in the CSS were derived, such as how the observed detections from the reduced M-matrix (Burnham el al. 1987) and estimated parameter of survival and collection efficiency from the Cormack-Jolly-Seber (CJS) are used to estimate smolt numbers in each study category, along with their expectations. Coverage was expanded to show how the tallies of adult returns for each study category are used along with estimated smolt numbers to arrive at smolt-to-adult survival rates (SARs). Lastly, more detail was presented on the formulas used to compute ratio of transport SAR to inriver SAR, delayed mortality D, and overall annual SAR. Additionally, a companion document (Ryding 2006) was presented with our 2006 report to address concerns brought up by the ISAB and other reviewers. In particular, Ryding provides a validation that CSS SARs, which are based on smolt counts expressed as Lower Granite Dam equivalents, are unbiased. Regarding the discrepancy between Appendix AA functional forms and those illustrated in Ryding (2006), the companion paper presents equations in terms of expected values whereas the CSS report provides the actual estimators derived from the reduced M-matrix used to estimate numbers of smolts in each study category in LGR-equivalents.

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Reviewer comments: The CSS study relies upon the methods of Burnham et al. (1987) and the Cormack-Jolly-Seber (CJS) model, but it is not clear to what extent. Apparently the authors use the CJS model (equivalently, Burnham et al. 1987) to estimate juvenile migration parameters, including inriver survival, detection, and transportation proportions. This is acceptable. However, it is not clear how they estimate adult survival or otherwise estimate the number of adults returning to either Bonneville or Lower Granite in Chapter 3. The discussion should be expanded to better describe how the age structure of returning adults was addressed, and the model to estimate ocean and upriver survival. Response: The CSS uses the CJS tag-recapture model to estimate the juvenile reach-survival estimates used throughout the report. The numbers of first-time detected PIT-tagged fish at each dam, i.e., the m1k’s, taken from the first row of the reduced M-matrix (Burnham et al. 1987), are used along with the CJS reach survival estimates in the computational equations to determine the number of smolts in each study group. In contrast to juveniles, the number of adults is not modeled with probabilities (with the exception of adults at Bonneville); instead it is simply the count of returning adults with specific capture histories that are part of a specific study group. For example, in draft Appendix AA, the X12000000 is simply the tally of returning tagged adult fish that were transported as smolts from Lower Granite Dam. Since PIT-tag monitors in the adult ladders at Lower Granite Dam have very high detection efficiency, we use the adult tallies with no further adjustments. At Bonneville Dam, lower PIT-tag detection efficiencies occur in the ladders, so we expanded the adult tally by an estimate of the PIT-tag detection efficiency (discussed below, Response 17). Regarding our treatment of adult age-structure issues, we present the age-composition of the returning PIT-tagged fish as 1-salt (jacks for Chinook), 2-salt, and 3-salt for Chinook and steelhead in Appendix D. Only 2-salt and older fish are used for wild and hatchery Chinook return numbers as a single total adult tally. For steelhead, 1-salt, 2-salt, and 3-salt returns are combined into a single total adult tally. The overall adult tallies are divided by the estimated smolts (in LGR-equivalents) to produce the reported SAR estimates. Reviewer comments: The CSS authors attempt in Appendix AA to estimate SAR and T/C values for certain groups of fish, namely the C0 (undetected) and T0 (transported at first detection) groups, with the rationale that these groups more realistically represent the migration experience of untagged fish. This is necessary only if the survival rates of the C0 and T0 groups are systematically different from the survival rates of the more general non-transported and transported groups, respectively. However, the CSS estimates the sizes of the C0 and T0 groups using estimates from the CJS model, which is based on the assumptions that (1) all fish have common survival and detection probabilities, and (2) detection has no effect on subsequent survival and detection probabilities. These two assumptions are counter to the reasons for restricting attention to the C0 and T0 groups in the first place. Thus, the CSS approach is inconsistent. Response: The reviewer felt the CSS approach was inconsistent because the in-river survival rates we used to convert estimated smolt numbers to LGR-equivalents are based on PIT-tagged

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fish which experience more in-river capture histories than do the primary transportation and in-river study groups, T0 and C0, we used in estimating SARs for the T/C ratios. The review listed two key CJS model assumptions: “(1) all fish have common survival and detection probabilities, and (2) detection has no effect on subsequent survival and detection probabilities.” In using the CJS method, it is true that the CSS assumes the in-river survival and collection efficiency rates occurring within each river reach are the same between first-time detected fish and multiple-time detected fish. But the CSS (and supported by NOAA studies) realized early on in the study that SARs of smolts passing multiple bypasses tended to have lower SARs than those passing fewer bypasses. Since the management strategy in each year from 1994 to the present (except in 1997 when the fishery agencies and tribe attempted to reach a 50-50 split in transport to in-river migration by bypassing many smolts at Little Goose and Lower Monumental dams during portions of the season rather than transport them) has been to transport fish if collected at one of the three Snake River collector dams, the CSS wanted to create study groups that most closely reflected what was occurring to the whole population (which consists mostly of untagged fish). Most PIT-tagged fish have been returned-to-river as the default operation at the collector dams, while most untagged fish were being collected and transported. This goal of matching the primary study groups in the CSS to the experiences of most fish that pass through the hydrosystem provides the rationale for creating the T0 and C0 study categories rather than simply lumping all transported and non-transported fish into two study categories as suggested by the reviewer. The reviewer’s suggested approach does not match with how the management operations are implemented for Snake River steelhead and yearling Chinook populations.

In the approach suggested by the reviewer, far more tagged fish would be added to the in-river group than transport group, because of the default return-to-river operations for most non-CSS studies and the separation-by-code (SbyC) operations of CSS PIT-tagged fish that allowed daily updates to the SbyC databases at the dams to return-to-river previously detected PIT-tagged fish. This approach has been used in the CSS through migration year 2005. Beginning in 2006, the CSS has adopted the approach of pre-assigning the tagging files into one group to mimic the operations encountered by the run-at-large (mostly untagged fish) and another group (returned-to-river if collected) to provide all in-river survival rate estimates. For most migration years analyzed to date, the SARs of Category C1 fish have tended to be lower than those of Category C0 fish. So simply combining all non-transported PIT-tagged fish will provide a lower estimate for in-river migrants, but it will be less reflective of what is occurring for the run-at-large (mostly untagged) population of migrating smolts. This forms the basis for using our approach. Reviewer comments: There are different ways of conceptualizing and expressing SARs and T/C, particularly at the systemwide level. The CSS approach, as described in the Ryding (2006) document, is one option. It is based on estimating the SARs of the C0 and T0 groups in terms of LGR equivalents. The T/C defined in the Ryding (2006) document is the ratio of two conditional return rates from LGR as smolts to LGR as adults: the return rate for fish that reach LGR and are “destined” for transport, and the return rate for fish that reach LGR and are “destined” for inriver migration:

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[ ][ ]

Pr Return to LGR | Destined to be transportedT/C

Pr Return to LGR | Destined for inriver= .

If the desired inference is to fish that are “destined” for a particular migration method, then the Ryding (2006) definition of T/C is reasonable. However, it does not appear the CSS annual report actually uses the definition provided by Ryding (see Appendix AA). Response: The expectations of the computational equations shown in Draft CSS 2006 Annual Report Appendix AA for SAR(C0) and SAR2(T0) and T/C ratio of these two SARs are equivalent to what is shown in Ryding (2006). In the report appendix, more detail has been added to show the expectations of numbers of smolts in study categories T0, C0, and C1 and subsequent SARs for these study categories. Reviewer comments: The expressions for the sizes of the C0 and C1 groups (Appendix AA, page 113) include a constant of 2, “to offset the typical 50% survival rate to the lower Columbia River of fish starting at Lower Granite Dam.” However, survival from Lower Granite to the lower Columbia River is rarely 50% (see Figures 12, 18, and 24). It is unnecessary to make the assumption of 50% survival, because inriver survival between Lower Granite and McNary is estimated (i.e., S2S3S4), (and used elsewhere in the estimators of C0 and C1.) Response: The use of a constant offset of 2 times the number of smolts removed below the Snake River collector dams created concern to the reviewer. PIT-tagged fish not confirmed as being returned-to-river at a downstream dam needed to be removed from either the C0 or C1 study groups. Fish were considered as removals at McNary Dam when detected on the raceway or sample room monitors or only on the separator monitor during the summer transportation season, or when collected and removed at John Day or Bonneville Dam for other research purposes. Samples of CSS PIT-tag hatchery Chinook from Rapid River, McCall, and Dworshak hatcheries were collected and sacrificed at John Day and/or Bonneville dams during migration years 1999 to 2003 for physiological (blood chemistry) evaluation (Dr. Congleton, University of Idaho Fish and Wildlife Unit). Because most removals occurred at John Day and Bonneville dams for other research purposes, we settled on a fixed 50% Lower Granite to Bonneville Dam survival rate for each removed fish in order to subtract these fish in LGR-equivalents from the estimated number of smolts in Categories C0 and C1. Most survival rates from Lower Granite Dam to Bonneville Dam from 1995 to 2004 (excluding 2001 when extremely low in-river reach survival rates occurred on in-river migrants) have been averaging around 50%. In 1994, the wild Chinook in-river survival rate from Lower Granite Dam to McNary Dam was estimated at 47%, with virtually all removals occurring at McNary Dam since no operational return-to-river diversion system was present that year, so the fixed 50% expansion to LGR-equivalents on removals was proper in that year also. In post-1994 years, wild Chinook and wild steelhead had relatively small “raw” numbers of PIT-tag fish removed at downstream dams (Table 1).

Table 1. Estimated number of wild Chinook (upper table) and steelhead (lower table) C0 tags and removals across migration years 1994-2003. In most years, the % removed was negligible.

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Wild Chinook 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Pre-adj. C0 Est. #

3621 2725 1919 682 3081 4469 6573 233 6410 9001

Removal # Percent

910

25.1 8 0.29

1 0.05

1 0.15

0 --

0 --

41 0.62

1 0.43

60 0.94

60 0.67

Wild Steelhead 1997 1998 1999 2000 2001 2002 2003 Pre-adj. C0 Est. #

454 776 1113 1871 103 4107 3343

Removal # Percent

0 --

13 1.68

0 --

0 --

0 --

9 0.22

12 0.36

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Overall, the probable effect of applying a fixed 50% survival estimate to expand removals to LGR-equivalents is likely miniscule, given the small number of fish involved. However, this assumption could be more formally validated in the future. Reviewer comments: In Appendix AA, the CSS authors introduce quantities not addressed by Ryding (2006), i.e., SAR1(T0), SAR2(T0), SAR(C0) (different expressions than Ryding’s), SAR(C1), D, and SARAnnual, as well as SAR(TLGR), SAR(TLGS), and SAR(TLMN). SAR1(T0) appears to agree in expectation with the expression for SAR(T0) from Ryding’s (2006) document. However, the CSS report remains impossible to fully assess without knowing the statistical framework and the conceptual definitions of SAR and D, this would facilitate the technical review of methods. Response: The reviewer states it is impossible to fully assess the methods of the CSS without knowing the study’s statistical framework. In the Ryding (2006) report, the number of smolts in the study categories T0 and C0 is estimated using numbers released, probabilities of survival between collector dams, collection efficiencies at collector sites, and transportation probabilities of collected fish. The formula shown in that document provides the expected numbers of first-time detected fish at Lower Granite, Little Goose, and Lower Monumental dams. In the computational formulas used throughout the CSS report, the detections (observed numbers) at these collector dams are utilized along with the CJS survival rates to convert these observed numbers to estimated numbers in LGR-equivalents. The Ryding (2006) document is meant to illustrate why it is necessary to convert the smolt numbers to LGR-equivalents. The Appendix A (formally draft Appendix AA) has been rewritten to include more details on the statistical framework utilized in the CSS. The BPA reviewer had mistakenly presumed that the numerator of the T/C ratio in Ryding (2006) was SAR1(T0), but in fact it was SAR2(T0). Our revised and expanded Appendix A should allow readers to more clearly see the distinction between SAR1(T0) and SAR2(T0). Reviewer comments: In explaining trends in SARs in Figures 11, 17, and 23 and Chapter 5, consideration of the effects of harvest should be discussed. Changes in harvest mortality in the ocean or Columbia/Snake River can also affect SAR values, but this factor does not appear to have been considered in the analysis. Harvest numbers from the mouth of the Columbia River to Lower Granite have been relatively stable from 1997 to 2005 for steelhead. However, for Chinook salmon (spring, summer, and fall), harvest numbers have increased approximately three-fold from 1997-2000 to 2001-2005 (see figure below) (data provided by DART). This suggests that consideration of harvest is important for understanding of the factors influencing SAR and recovery.

Response: Harvest rate changes had only minor effects on SAR patterns (to Lower Granite) for Snake River spring/summer Chinook and steelhead (the CSS study fish) during the study period. The reviewer’s comments showing combined harvest of spring, summer and fall Chinook is misleading because it mixes runs with heavy harvest (fall Chinook) with those used in the CSS study (spring/summer Chinook), which are not heavily harvested relative to fall Chinook. Snake River spring/summer Chinook and steelhead are not intercepted to any degree in ocean fisheries (unlike fall Chinook).

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Figure 1 (below) shows the Columbia River harvest rates affecting Snake River spring/summer Chinook and (wild) steelhead for 1997-2005 (data from ODFW/WDFW Joint Staff Reports, January 18, 2006 and July 18, 2006). Figure 2 shows the survival rates through Columbia River fisheries for the same runs. Snake River spring summer Chinook harvest rates during this period ranged from 0.048 to 0.19 (i.e., survival rates ranged from 0.81 to 0.952). Wild A-run harvest rates ranged from 0.025 to 0.104; wild B-run harvest rates ranged from 0.034 to 0.156. Across years and species analyzed by the CSS, inriver survival and harvest have remained relatively constant over the last several years, even though SARs have varied widely.

Columbia River Harvest Rates (Zones 1-6)

0.0

0.1

0.2

0.3

0.4

0.5

1997 1998 1999 2000 2001 2002 2003 2004 2005

Run year

Har

vest

rate

spring/ summer Chinook

wild A-run steelhead

wild B-run steelhead

Figure 1. Columbia River harvest rates affecting Snake River spring/summer Chinook and (wild) steelhead for 1997-2005 (data from ODFW/WDFW Joint Staff Reports, January 18, 2006 and July 18, 2006).

Survival through Columbia River Fisheries

0.0

0.2

0.4

0.6

0.8

1.0

1997 1998 1999 2000 2001 2002 2003 2004 2005Run year

Har

vest

rate

spring/ summer Chinook

wild A-run steelhead

wild B-run steelhead

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S

Figure 2. Survival rates through Columbia River fisheries for Snake River spring/summer Chinook and (wild) steelhead for 1997-2005 (data from ODFW/WDFW Joint Staff Reports, January 18, 2006 and July 18, 2006).

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Chapter 1 1. Page 2, last sentence. Although the report indicates that survival from different life stages provides “valuable information to diagnose where in the salmon life cycle mortality rates have increased,” it is not clear how the relative contributions of inriver smolts, ocean (Bonneville-to-Bonneville) conditions, and upriver survival to overall SARs were considered. Ocean survival (i.e., Bonneville-to-Bonneville) is a major driving force behind annual changes in the SARs, and needs to be discussed. Response: We agree that analyzing ocean survival patterns more precisely could be a useful and revealing exercise. However, because detection efficiency has been poor (10-20%; Berggren et al. 2003) at Bonneville Dam until return year 2002, we cannot effectively evaluate patterns in Bonneville-to-Bonneville survival for more than the last few years using our approach. It is possible to parse out Bonneville-to-Bonneville survival using a juvenile-to-adult life-cycle CJS model, such as the ROSTER (Buchanan et al. 2006). We will explore this and/or other full-life cycle approaches in the future, thereby allowing us to pursue ocean survival analyses explicitly. Chapter 3 2. Page 11, first paragraph under Figure 4. In replicated studies (e.g., Figure 4), the individual confidence interval lengths are relatively less meaningful than if in a single point estimate was presented. Confidence interval (CI) length is a function of sample size, so the number of 90% CI that exceed the value 1 is more a reflection of sampling precision than overall performance. One should use a weighted t-test

o

a

H : 1

vs.H : 1

T C

T C

μ

μ

≤

>

to assess using the between-year variability in T/C values. Response: The reviewer’s comment describes one statistical approach towards asking the question of whether or not there are benefits to transportation, from a study-wide perspective. We have intentions of addressing this question in our synthesis report and will consider his/her recommendation in doing so. We will also address this study-wide question based on a parameter estimation approach that permits the isolation of sampling and process error (i.e., Akçakaya’s method) and therefore facilitates inference based on environmentally driven survival patterns only (i.e., relative to the expectation of T:C = 1). An initial application of this approach undertaken by the CSS is described in Berggren et al. (2005). 3. Pages 21-22. Across-year averages of VC, T/C, and D are reported as geometric means (e.g., Tables 10-14), while SARs are reported as arithmetic means (e.g., Tables 5-9). No explanation is provided for the difference in computations. Geometric means by construct will

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have lower values than arithmetic means. The report should justify distributionally the need for different estimates of central tendency. Alternatively, the arithmetic mean is an appropriate estimator of expected value. Response: The SARs for each study category approximate normality, as do the individual reach survival rates computed by the CJS method. However, the parameters VC (i.e., the product of S2·S3·S4·S5·S6·S7), the T/C ratio, and D each tend to be lognormal distributed with skewness to the right. For these reasons, the arithmetic mean was used for parameter SAR and the geometric mean was used for the other log-normally distributed parameters. To illustrate the shape of these distributions, histograms of the 1000 iterations from the bootstrap run on wild Chinook from 1999 is presented for parameters S2, VC, SAR2(T0), SAR(C0), T/C ratio, and D (Figure 3).

Distribution of Parameter S2

for Wild Chinook 2000

0

20

4060

80100

120

0.871 0.878 0.885 0.891 0.898 0.905 0.911 0.918 0.925

Value of S2

Freq

uenc

y (1

000

itera

tions

)

Distribution of Parameter Vc for Wild Chinook 2000

020406080

100120140160

0.384 0.434 0.483 0.532 0.582 0.631 0.681 0.730 0.780

Value of Vc

Freq

uenc

y (1

000

itera

tions

)

Distribution of Parameter SAR2(T0)for Wild Chinook 2000

0

20406080

100

120

0.38% 0.73% 1.09% 1.44% 1.80% 2.15% 2.50% 2.86% 3.21%

Value of SAR2(T0)

Freq

uenc

y(1

000

itera

tions

)

Distribution of parameter SAR(C0) for Wild Chinook 2000

020406080

100120

1.85% 1.99% 2.14% 2.29% 2.44% 2.59% 2.74% 2.88% 3.03%

Value of SAR(C0)

Freq

uenc

y(1

000

itera

tions

)

Distribution of Parameter T/C for Wild Chinook 2000

0

20

40

60

80

100

120

0.16 0.30 0.44 0.58 0.73 0.87 1.01 1.15 1.29

Value of T/C

Freq

uenc

y (1

000

itera

tions

)

Distribution of Parameter D for Wild Chinook 2000

020406080

100120140160

0.10 0.20 0.30 0.40 0.51 0.61 0.71 0.81 0.91

Value of D

Freq

uenc

y(1

000

itera

tions

)

Figure 3. Distribution of key parameters of PIT-tag wild Chinook from migration year 1999 to illustrate parameters that are typically Normal distributed (left column) or lognormal distributed (right column).

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Chapter 4 4. Page 30, central paragraph. The conclusion, “the outlook for recovery may be poor,” seems to be stretching the interpretation of the steelhead data. First, the 2003 SAR is incomplete; second, the four years of steelhead data (1999-2002) have point estimates >2%; third, the wide confidence intervals would not suggest a significant linear downward trend. Response: We have toned down the language in the final report draft based on this comment. It should be noted, however, that the NPCC objective is a minimum 2% with a mean of 4% SAR (as stated in the draft report). Thus, the point estimates (and in most cases CIs) of steelhead SARs were all much less than the recommended mean of 4%, rendering our original conclusion accurate but overstated. 5. Page 31, Table 17, lines 8-11 of first paragraph. Formal meta-analysis using the replicate years of data should be performed rather than simply counts of how often values of CI exceeded specific values. One approach is to test, for example,

o

a

H : 1vs.

H : 1

D

D

≤

>

for each year and compute observed P-values. The individual P-values could be combined as follows to provided an overall test of significance:

22

1

2 ln n

n ii

Pχ=

= − ∑ ,

where is the chi-square statistic with 2n degrees of freedom. Another approach is to use a weighted t-test, weighing inversely proportional to

variances. It would be useful if CSS were to compute standard errors (SE) for their estimates—which would enhance the ability to perform such tests. Response: As above in 2, the reviewer’s comment describes one approach towards asking the question of whether or not there are difference in delayed mortality patterns for transported relative to inriver fish, from a study-wide perspective. We have intentions of addressing this question in our synthesis report and will consider his/her recommendations in doing so. We will also apply Akçakaya’s estimation method in our study-wide assessment of D patterns, relative to the H0: D < 1. 6. Page 38, line 8-10. See previous comment 5. Response: See our response to number 5 above. 7. Page 40, conclusion #10. Figures 24 and 24 illustrate a very high correlation between VC and T/C ratios between wild and hatchery steelhead (r2 not computed). Are high correlation and similar values sufficient to conclude hatchery steelhead may be used as a surrogate for wild steelhead? It not, what are the criteria for such a determination?

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Response: The similarity in trend across in Vc and T/C ratios between wild and hatchery steelhead reflects similar responses to migration in-river through the hydrosystem and transportation. This similarity in pattern, in spite of a tendency for the overall SAR for wild steelhead to be higher than that of hatchery steelhead, makes a strong case for the validity of using hatchery steelhead as a surrogate for wild steelhead in years when too few PIT-tagged steelhead would be available. Since both wild and hatchery steelhead groups are comprised of fish tagged at locations spread across tributaries above Lower Granite Dam, they are generally representative of the at-large population emigrating each year. Chapter 5 8. Page 41, section titled SAR estimates. With part of the goals of the regression analysis to examine the relationship between SARs and inriver covariates (i.e., flow and water transit time), It is unclear why the transport (T0) fish included these fish by virtue of being transported were not subject to inriver conditions. Analysis should also look at C0 and C1 fish only to confirm the pooled results. Water temperature has also been associated with inriver migration success and should be considered in the modeling (it was considered later in Chapter 6). Response: As discussed in the final paragraph of our original Chapter 5 (p. 45 in our draft report), we already have plans to pursue the analyses the reviewer describes and recommends for our upcoming synthesis report. Thus, the reviewer’s comments – including the recommendation of including temperature and transport group effects in regression models – will be addressed via future analysis. Chapter 6 9. Page 53, section titled Statistical analysis and Table 1(p. 59). To perform an across-year analysis of homogeneity between transported and nontransported hatchery adults, one approach is to sum the four independent chi-square statistics across years (i.e., 0.1109 + 7.6023 + 11.0768 +3.2190 = 22.0090 with df = 8 for a P = 0.0049). Another approach is to use a Poisson log-linear analysis of a three-dimensional contingency table (i.e., R × C × T = 3 × 2 × 4). Response: Both approaches the reviewer describes are appropriate for our dataset and analytical objectives. However, we did not alter our analysis and results based on this comment for two reasons: 1) the pooling of independent tests would have only been possible for hatchery fish (i.e., due to lower cell frequencies, year-specific tests were generally not possible for wild salmon); and 2) a pooling of year-specific test statistics leads to the same statistical (i.e., P < 0.05) and biological conclusions.

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10. Page 54, section titled Hatchery chinook �2 tests, last sentence. Wording unclear; “ . . . in contrast, was statistically across all sites.” Response: A clarification was made accordingly. 11. Page 55, first sentence. The lower success rate of “LGR” fish may be due to greater mortality or increased straying. Response: In our analysis, we treat successful migration to LGR as being synonymous with apparent survival to LGR (regardless of fate). We’ve updated text according to the reviewer’s comments and added a clarification (in italics) to make this assumption more transparent. 12. Page 55, section titled Wild Chinook logistic regression analysis. Logistic regression doesn’t estimate the quantity “odds ratio” but, rather, the log odds ratio . It appears the authors have misinterpreted the regression results, “At 0.46 the odds ratio estimate for this group indicates that LGR salmon were about half as likely to survive their migration from BON to LGR than inriver outmigrants.” The more appropriate comparison is the success rate.

In no year was the ratio pLGR/pInriver < 0.46; the smallest value of 0.7218 occurred in year 2002. Pooling the data, the success rates were 0.8695 and 0.7561 for Inriver- and LGR-type fish for a relative success rate of 0.8986, LGR:Inriver, not 0.46!

The same apparent misinterpretation of the logistic regression is also found in the section titled Hatchery Chinook logistic regression analysis. There, the relative success rate for LGR:Inriver fish is 0.7769/0.8375 = 0.9157, using the combined data, and not 0.64 as stated in the text. Response: The odds ratio estimates (and associated precision), as presented in the original and revised reports, characterize the likelihood of successful upstream migration (i.e., survival) for transported relative to inriver migrants. Values represent ratios of the odds of success (e.g., OLGR = psuccess / pfailure) for LGR and LGSdown fish, relative to inriver outmigrants (i.e., OLGR / Oinriver and OLGSdown / Oinriver). Although the values presented are based on regression output and are therefore exponentiations of transport-site (LGR, LGSdown) dummy variable regression coefficients (e.g., eβLGR), the reviewer correctly points out that these values can also be estimated from contingency table data. For example, the coefficient-based estimate of 0.465 presented in the original report is equivalent to the contingency table-based odds ratio estimate for wild Chinook salmon (i.e., (0.76/(1-0.76))/(0.87/(1-0.87)) = 0.465). Though we were correct in our original presentation and interpretation, we’ve revised our Chapter 6 results to more precisely define that we are speaking of odds ratios and not relative success rates. 13. Page 56, last sentence and Figure 4. It is not obvious that LGR adults have a “more skewed and slower travel time distribution” in examining the box-and-whisker plots (Figure 4). Because different software programs compile box-and-whisker plots differently, it is difficult to interpret the figures. Figure symbols need to be defined.

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Response: See Figure 32 caption. Box-plot components are now clearly defined. 14. Page 62, Figures 1 and 2. Confidence bounds should be added to the bar chart for greater interpretive value. Response: Upper and lower 95% confidence bounds have been added based on this comment, see Figure 31. Chapter 7 15. Page 65, first paragraph, last sentence. Justify the basis of equation ¼ e�1.47= 0.0594. Are you stating that Snake River population are surviving only 0.0594 times as well as downriver populations? Response: This question was the result of our unclear presentation of that particular result. We have rephrased this part of the final report so as to make it clear that we simply mean the upstream-downstream differential is ~1/4 (i.e., e -1.46). 16. Page 66, first paragraph. Greater justification and description of assumptions using the bird colony PIT-tag recoveries is necessary. Perez-Comas and Skalski (2000) found the bird colony data could severely bias CJS estimates if PIT-tag recoveries occur from fish taken above Bonneville. Response: It is not possible to determine whether or not a portion of Carson Hatchery Chinook PIT-tags recovered at bird colonies include fish killed above Bonneville Dam. Given this, we assume no mortality due to birds occurs upstream of Bonneville Dam. It should be noted, however, that even if a number of Carson Hatchery PIT-tags were taken above Bonneville Dam our findings and conclusions would only be rendered more robust. Specifically, the observed pattern in upriver:downriver hatchery stock SAR ratios (U/D) was such that two-thirds of the cases shown in Table 33 show U/D<1. If PIT-tagged fish were taken by birds before passing Bonneville Dam, this would have led to a positive bias in hatchery-to-Bonneville survival (Perez-Comas and Skalski 2000) and therefore overestimated the Bonneville smolt population size. The resulting SAR for Carson Hatchery Chinook would therefore be biased low and the ratio of upriver SAR (which does not use bird colony PIT-tag recoveries) and downriver Carson Hatchery SAR (which does use bird colony PIT-tag recoveries) would be biased high. Therefore, the estimated U/D for hatchery Chinook could be considered as a conservatively high estimate whenever a significant number of Carson Hatchery PIT-tag fish are taken by birds before they reach Bonneville Dam and then re-deposited on the bird colonies downstream in the estuary. 17. Page 67, Table 2. The estimates of Bonneville detection probabilities of for adults are negatively biased. The estimator assumes no adult mortality between Bonneville and upstream

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dams and detection at upstream dams is 100%. However, Chapter 6, Tables 1 and 2, indicate there are indeed losses, assumed to be as high as 25% between Bonneville and Lower Granite dams. The resulting negative biases in Table 2 will underestimate actual arrival abundance of adults at Bonneville; this, in turn, will negatively bias subsequent SARs. See Many and Parr (1968) for estimating detection probabilities from limited capture histories. Response: In this comment, the reviewer suggests our estimate of Bonneville adult ladder (BOA) detection probability (pBOA) is biased and built on an assumption of 100% upstream-adult survival. We disagree with this comment and suspect the reviewer’s perspective stems from our omission of estimation detail. To address this concern, we now list our BOA detection probability formula in a footnote in Table 32. Also, we briefly describe our approach and explain why it is unbiased.

Our estimator of BOA detection efficiency is equivalent to the proportion of fish passing BOA that were detected and seen upstream (where detection probability is assumed to be 100%) relative to the total number adults detected upstream (inclusive of those seen and unseen at BOA). That is, our parameter estimate is based on the sample of fish passing BOA and surviving to be detected at upstream sites (i.e., is conditioned on upstream detection).

pBOA = (X11) / (X11 + X01), where

X11 = no. seen at BOA and seen upstream; expected value = NpBOAS X01 = no. not seen at BOA, but seen upstream; expected value = N (1- pBOA) S N = size of the adult population passing Bonneville dam; what we want to estimate S = Bonneville to Lower Granite Dam survival

While we can only estimate pBOA based on those fish surviving to upstream sites, it is not built on an assumption of 100% survival. Rather, estimating detection efficiency in this way only assumes that survival and detection probability are equivalent for all individuals (i.e. detected and undetected fish survive at a similar rate); the number of fish actually detected at BOA and upstream sites (i.e., ‘sampled’) will thus vary as a function of survival, but the estimate will not. In contrast to this approach, one based on all BOA detections regardless of their upstream fate would in fact be positively biased (and lead to a negative SAR bias), as there would be no way to account for fish that are not detected at BOA and die before upstream detection. We suspect our omission of a pBOA equation led the reviewer to believe we used this latter approach. 18. Page 68, Table 3. First column heading “Migr. Year” appears to be mislabeled. Response: Revised accordingly. 19. p. 68, first sentence. Mathematical justification for equation ΔM = -ln(SARsnake/SARdownriver)

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is necessary… [ΔM] is the difference in instantaneous morality [sic] rates and should be so labeled, not as” differential mortality.” Response: This comment appears to be primarily about semantics, as the reviewer presented equivalent expressions of the same formula in the comments. We refer the reviewer to Deriso et al. (2001) who interchangeably used the terminology “instantaneous differential morality” and “differential mortality.” 20. p. 68 and figure 1 (Page 69.) The report states, “Although the estimated ΔM differ using hatcheries, there is a common arrival pattern among the five upriver hatcheries.” Part of this pattern is due to the use of the same denominator (i.e., SARdownriver) and across all hatcheries, i.e., the covariate… Response: We edited the word “arrival” to “annual”. We agree that part of the commonality in annual patterns is due to the same denominator. Additional downriver hatchery stocks would help determine how common the annual patterns are among Snake and downriver hatcheries generally. The ISAB/ISRP has recommended exploring additional downriver stocks, and the CSS project will modify future proposals to address these recommendations. 21. p. 68 first sentence. Estimation of differential mortality, as proposed in the CSS study, is a function of the ratio SARLGR-BON/SARBON-BON

…There is no reason to expect that ratio to be equal to 1. Instead, interest should focus on whether that ratio of SARs differs appreciably from the smolt survival estimates between Lower Granite and Bonneville… Response: The reviewer’s recommended analysis, although interesting, would not provide estimates of differential mortality, which is the primary objective of this chapter. We are primarily interested in whether the SARs of upriver and downriver stream-type wild and hatchery Chinook differ by a similar magnitude as estimated from spawner recruit data for wild Chinook by Deriso et al. (2001) and updated in Marmorek et al. (2004).

Deriso et al. (2001) estimated differential mortality between Snake River and downriver (wild) stream-type Chinook populations using spawners on the spawning grounds as adults and recruits as returns to the Columbia River mouth. The SAR-based estimates of differential mortality, therefore, index smolts leaving the natal areas (arrivals to the first dam), and returns to Bonneville Dam (assuming the same harvest rate for both groups below Bonneville Dam). Chapter 8

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22. The issue of replicability is labeled a “red herring” by Hurlbert (1984). No two things can be identical, and try as we might, we can never prove they are so. The more important issue is replication. As stated in the 2005 ISAB review, additional downstream hatcheries need to be incorporated into the design. In so doing, the between-replicate, within-category variance can be used to compare treatment conditions. Until that additional downstream replication is incorporated, the upstream-downstream comparison is not useful. Response: Our intention in preparing Chapter 8 was not to prove that upriver and downriver populations are identical, but rather to assess the degree to which they differ in life history characteristics that have been shown to affect survival patterns (e.g., size; Zabel and Williams 2002; Williams et al. 2005; Zabel et al. 2005). While downriver-population replication is one of our goals for the near future, testing for size- and/or life history-based similarities or differences helps assess the potential for confounding in previous upriver-downriver comparison-based inferences. Chapter 9 23. Page 87, second paragraph, last sentence. The report states wild Chinook were the focus of the size-detection probability analysis because “this group exhibits the largest transport vs. inriver SAR difference.” Based on the CSS report, geometric mean T/C ratios were 0.99 for wild Chinook (Table 3, p. 12), 1.46 for hatchery Chinook (Table 10, p. 21), 1.46 for hatchery steelhead (Table 20, p. 38), and 1.72 for wild steelhead (Table 17, p. 31). These data indicate wild Chinook have the most similar SARs for transport and inriver fish, while wild steelhead, the most different SAR values. Using the CSS annual report rationale, this suggest that analysis should focus on wild steelhead, not wild chinook; this needs further explanation. Response: Our decision to focus on wild Chinook salmon over other species in Chapter 9 was based on post-Bonneville SARs (i.e., D = SARBON-LGR(T0)/SARBON-LGR(C0)) rather than SARLGR-

LGR differences (i.e., T:C = SARLGR-LGR(T0)/SARLGR-LGR(C0)). In particular, wild Chinook salmon exhibit the greatest level of post-Bonneville differential delayed mortality among the Snake River-origin anadromous salmonids evaluated as part of the CSS. In response to this comment, we have added language to clarify our justification for future readers. 24. Page 89, second paragraph, Table 4, and Figure 1. A meta-analysis looking at the overall significance of the slope terms for size vs. detection probability should be performed. Multiple annual results in the same direction but not significant may be statistically significant when examined over the multiple-year data set. Response: Using the suggested meta-analysis framework, we computed overall parameter estimates (and CIs) based on the reviewer’s recommendation and updated our report accordingly. While this improved our analysis and reporting, neither the general patterns nor the overall conclusions were affected.

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References cited Berggren, T., H. Franzoni, L. Basham, P. Wilson, H. Schaller, C. Petrosky, K. Ryding, E.

Weber, and R. Boyce. 2005. Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook. 2003/04 Annual Report, Migration Years 1997-2002 Mark/Recapture Activities and Bootstrap Analysis. BPA Contract # 19960200.

Buchanan, R.A., and J.R. Skalski. 2006. Estimating the effects of smolt transportation from different vantage points and management perspectives. North American Journal of Fisheries Management. 26:460-472.

Burnham, K.P., D.R. Anderson, G.C. White, C. Brownie, and K.H. Pollock. 1987. Design and analysis methods for fish survival experiments based on release-recapture. American Fisheries Society Monograph 5, Bethesda, MD, 437 pp.

Deriso, R.B., D.R. Marmorek and I.J. Parnell. 2001. Retrospective patterns of differential mortality and common year-effects experienced by spring and summer Chinook (Oncorhynchus tshawytscha) of the Columbia River. Canadian Journal of Fisheries and Aquatic Sciences 58:2419-2430.

Marmorek, D.R., M. Porter , I.J. Parnell and C. Peters, eds. 2004. Comparative Survival Study Workshop, February 11–13, 2004; Bonneville Hot Springs Resort. Draft Report compiled and edited by ESSA Technologies Ltd., Vancouver, B.C. for Fish Passage Center, Portland, OR and the US Fish and Wildlife Service, Vancouver, WA. 137 pp.

Perez-Comas, J. A, and J. R. Skalski. 2000. Appraisal of system-wide survival estimation of Snake River yearling Chinook salmon using PIT-tags recovered from Caspian tern and double-crested cormorant breeding colonies on Rice Island. Volume XIII in the Design and Analysis of Salmonid Tagging Studies in the Columbia Basin. Bonneville Power Administration, Portland, OR.

Ryding, K. 2006. Comparative Survival Study 2006 Design and Analysis Technical Report. Washington Department of Fish and Wildlife – CSS Oversight Committee Member. BPA Contract # 19960200, Portland OR.

Williams, J.G., S.G. Smith, R.W. Zabel, W.D. Muir, M.D. Scheuerell, B.D. Sandford, D.M. Marsh, R.A. McNatt, and S. Achord. 2005. Effects of the Federal Columbia River Power System on salmonid populations. NOAA Technical Memorandum NMFS-NWFSC-63. (http://www.nwfsc.noaa.gov).

Zabel, R.W., and J.G. Williams. 2002. Selective mortality in Chinook salmon: what is the role of human disturbance? Ecological Applications 12:173-183.

Zabel, R.W., T. Wagner, J.L. Congleton, S.G. Smith, and J.G. Williams. 2005. Survival and selection of migrating salmon from capture-recapture models with individual traits. Ecological Applications 15:1427-1439.

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