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

Transcription

1 COMPARATIVE SURVIVAL STUDY (CSS) of PIT-tagged Spring/Summer Chinook and PIT-tagged Summer Steelhead 2005 Annual Report Mark/Recapture Activities and Bootstrap Analysis BPA Contract # Prepared by Fish Passage Center and Comparative Survival Study Oversight Committee: Thomas Berggren, Henry Franzoni, and Larry Basham, Fish Passage Center Paul Wilson and Howard Schaller, U.S. Fish and Wildlife Service Charlie Petrosky, Idaho Department of Fish and Game Kristen Ryding, Washington Department of Fish and Wildlife Earl Weber, Columbia River Inter-Tribal Fish Commission Ron Boyce, Oregon Department of Fish and Wildlife representing the Columbia Basin Fish & Wildlife Agencies and Columbia Basin Tribes Project Leader: Michele DeHart, Fish Passage Center Final Draft 10/10/2005

2 TABLE OF CONTENTS List of Tables... iii List of Figures...viii Acknowledgements... x Executive Summary... xi Chapter 1 Introduction... 1 Chapter 2 Methods...4 Sources of study fish...4 Detection of study fish...7 Holdovers within the hydrosystem below Lower Granite Dam...8 Annual SARs for each study category...9 Annual Overall SAR estimates Annual estimates of D Representation of PIT-tag fish used in CSS aggregates Chapter 3 SARs for wild and hatchery Chinook and Steelhead Wild Chinook Further analysis of wild Chinook SARs and T/C ratios Hatchery Chinook Wild Steelhead Hatchery Steelhead Conclusions Chapter 4 Inter-dam dropout rates for PIT-tagged wild and hatchery Chinook between Bonneville and Lower Granite dams Conclusions Chapter 5 Hatchery-to-hatchery smolt-to-adult survival rates for key upstream Chinook hatcheries adjusted for harvest...60 PIT-tag detections at Lower Granite Dam adult trap and the hatcheries...60 Hatchery-to-hatchery SARs for migration years 1997 to Conclusions Chapter 6 Smolt-to-adult survival rates for lower Columbia River stocks including Carson NFH spring Chinook and John Day River wild Chinook with comparisons to upriver stocks Background...65 Carson NFH Spring Chinook...65 Comparing SARs for Upriver and Downriver Hatchery Spring Chinook stocks Page i

3 John Day River Wild Chinook...71 Comparing SARs for upstream and downstream wild stocks...72 Conclusions...73 Chapter 7 Computer program to created simulated PIT-tag input files for testing robustness of CJS survival estimates...74 Background...74 New features added to the simulator during Literature Cited...76 Appendix A Release sites of PIT-tagged wild Chinook and wild & hatchery steelhead (individual sites are not present for each migration year)...78 Appendix B Estimated number of smolts per study category with associated 90% confidence interval and number of returning adults per study category...84 Appendix C Reach survival estimates with bootstrap 95% confidence intervals...91 ii

4 LIST OF TABLES Table 1. Percentage of PIT-tagged wild steelhead out-migrating in expected migration year that were excluded by minimum length threshold of 130 mm at time of tagging Table 2. Hatchery Chinook PIT-tagged and released specifically for CSS in 1997 to Table 3. 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 Table 4. 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 Table 5. 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 Table 6. Number of PIT-tagged wild and hatchery steelhead detected at one or more dams in the expected migration year that held over an extra year in the hydrosystem and were detected the next year at a downstream dam or trawl site... 8 Table 7. 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 Table 8. Number of PIT-tagged wild Chinook actually transported from each dam and estimate (t i ) of total PIT-tagged wild Chinook that would have been transported if all PIT- tagged fish had been transported at same rate as the untagged run-at-large Table 9. Estimated dam-specific transportation SAR percentages of PIT-tagged wild Chinook in the annual aggregate groups for 1994 to 2003 (with 90% confidence intervals) Table 10. Estimated SAR LGR-to-LGR (%) for PIT-tagged wild Chinook in annual aggregate for each study category from 1994 to 2003 (with 90% confidence intervals) Table 11. Proportion of Lower Granite Dam estimated combined tagged and untagged population of wild Chinook in each study category with associated SAR LGR-to-LGR Table 12. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged wild Chinook for migration years 1994 to 2003 (with 90% confidence intervals) Table 13. Mean, standard deviation, and standard error of mean (%), from beta distributions of SAR(C 0 ), SAR(C 1 ), and SAR(T 0 ), reflecting environmental stochasticity, for wild Snake River Chinook migration years (2003 omitted due to incomplete returns) compared to arithmetic mean of nine migration years with complete adult returns Table 14. Number of returning PIT-tagged hatchery Chinook adults and jacks detected at Lower Granite Dam that migrated as smolts in 1997 to 2003 and percent of total return iii

5 Table 15. Number of PIT-tagged hatchery Chinook actually transported from each dam and estimate (t i ) 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 Table 16. Estimated dam-specific transportation SAR percentages of PIT-tagged hatchery spring/summer Chinook that outmigrated in 1997 to 2003 (with 90% confidence intervals) Table 17. Estimated SAR LGR-to-LGR (%) for PIT-tagged spring Chinook from Rapid River Hatchery for each study category from 1997 to 2003 (with 90% confidence intervals) Table 18. Estimated SAR LGR-to-LGR (%) for PIT-tagged spring Chinook from Dworshak Hatchery for each study category from 1997 to 2003 (with 90% confidence intervals) Table 19. Estimated SAR LGR-to-LGR (%) for PIT-tagged spring Chinook from Catherine Creek AP for each study category from 2001 to 2003 (with 90% confidence intervals) Table 20. Estimated SAR LGR-to-LGR (%) for PIT-tagged summer Chinook from McCall Hatchery for each study category from 1997 to 2003 (with 90% confidence intervals) Table 21. Estimated SAR LGR-to-LGR (%) for PIT-tagged summer Chinook from Imnaha River AP for each study category from 1997 to 2003 (with 90% confidence intervals) Table 22. Proportion of Lower Granite Dam estimated combined tagged and untagged population of each hatchery group in each study category with associated LGR-to-LGR SAR (returning adults age 4 and 5 in all years) Table 23. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged Rapid River Hatchery spring Chinook for 1997 to 2003 (with 90% confidence intervals) Table 24. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged Dworshak Hatchery spring Chinook for 1997 to 2003 (with 90% confidence intervals) Table 25. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged Catherine Creek AP spring Chinook for 1994 to 2003 (with 90% confidence intervals) Table 26. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged McCall Hatchery summer Chinook for 1997 to 2003 (with 90% confidence intervals) Table 27. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged Imnaha AP summer Chinook for 1997 to 2003 (with 90% confidence intervals) Table 28. 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 Table 29. 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 iv

6 Table 30. Number of PIT-tagged wild steelhead actually transported from each dam and estimate (t i ) 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 Table 31. Estimated dam-specific transportation SAR percentages of PIT-tagged wild steelhead in the annual aggregate groups for 1997 to 2002 (with 90% confidence intervals) Table 32. Estimated SAR LGR-to-LGR (%) for PIT-tagged wild steelhead in annual aggregate for each study category from 1997 to 2002 (with 90% confidence intervals) Table 33. Proportion of Lower Granite Dam estimated combined tagged and untagged population of wild steelhead in each study category with associated SAR LGR-to-LGR Table 34. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged wild steelhead for migration years 1997 to 2002 (with 90% confidence intervals) Table 35. Age composition of returning PIT-tagged hatchery steelhead adults detected at Lower Granite Dam that migrated as smolts in 1997 to Table 36. 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 Table 37. Number of PIT-tagged hatchery steelhead actually transported from each dam and estimate (t i ) of total PIT-tagged hatchery steelhead that would have been transported if all PITtagged fish had been transported at same rate as the untagged run-at-large Table 38. Estimated dam-specific transportation SAR percentages of PIT-tagged hatchery steelhead in the annual aggregate groups for 1997 to 2002 (with 90% confidence intervals) Table 39. Estimated SAR LGR-to-LGR (%) for PIT-tagged hatchery steelhead in annual aggregate for each study category from 1997 to 2002 (with 90% confidence intervals) Table 40. Proportion of Lower Granite Dam estimated combined tagged and untagged population of hatchery steelhead in each study category with associated SAR LGR-to-LGR Table 41. Estimated inriver survival LGR to BON (V C ), T/C ratio, and D of PIT-tagged hatchery steelhead for migration years 1997 to 2002 (with 90% confidence intervals) Table 42. PIT-tag detections of returning jack (1-salt) and adult (2- and 3-salt) Chinook at Bonneville (BON), McNary (MCN), Ice Harbor (ICH), and Lower Granite (LGR) dams for CSS hatchery and wild Chinook returns from smolts that outmigrated in 2001 to Table 43. Dropout rate of jack and adult wild and hatchery Chinook between dams with adult PIT-tag monitors (percentage relative to fish first detected at BON) returns from smolts that outmigrated in 2001 to Table 44. Number of PIT-tagged wild and hatchery Chinook adults (combined 2- and 3-salt) detected at Bonneville (BON), McNary (MCN), Ice Harbor (ICH), and Lower Granite (LGR) dams from smolts that outmigrated by transport (T) or inriver (C) in 2001 to v

7 Table 45. Dropout rate of adult (2-and 3-salt) wild and hatchery Chinook between dams with adult PIT-tag monitors (percentage relative to fish first detected at BON) grouped by whether the fish outmigated in 2001 to 2003 as a transported or inriver migrant Table 46. Number of returning PIT-tagged hatchery Chinook adults and jacks detected at Lower Granite Dam (LGR) and the hatchery racks (HAT) from smolts migrating in 2001 and 2002 (includes all returns of CSS fish regardless of final category assignment) Table 47. Dworshak Hatchery rack count, harvest, and total adult return (ages 2- and 3-salt) of run-at-large and PIT-tagged fish for migration years 1997 to Table 48. Rapid River Hatchery rack count, harvest, and total adult return (ages 2- and 3-salt) of run-at-large and PIT-tagged fish for migration years 1997 to Table 49. McCall Hatchery rack count, harvest, and total adult return (ages 2- and 3-salt) of run-at-large and PIT-tagged fish for migration years 1997 to Table 50. Estimated harvest-adjusted survival of PIT-tagged adults from Lower Granite Dam to hatchery rack (LGR to HAT) for hatchery spring/summer Chinook that outmigrated in 1997 to Table 51. Partition of hatchery-to-hatchery SAR rate into three components from hatchery release to LGR (smolts), LGR (smolts) to LGR (adults), and LGR to hatchery (adults) based on PIT-tagged hatchery sp/su Chinook that outmigrated in 1997 to Table 52. Carson NFH release statistics and numbers of PIT-tagged Chinook released for CSS in 1997 to Table 53. Estimated Chinook survival from Carson NFH to Bonneville Dam tailrace based on the trawl and bird colonies being the final downstream PIT-tag detection sites for migration years 1998 to Table 54. Age composition of returning PIT-tagged Carson Hatchery Chinook jacks and adults detected at Bonneville Dam for fish that outmigrated in 1997 to Table 55. 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 Table 56. Estimated number of PIT-tagged Carson Hatchery Chinook smolts passing BON in migration years 1998 to 2003 and returning adults (ages 2- and 3 salt) to BON with associated estimated SAR BON-to-BON Table 57. Estimates of SAR from first dam encountered as smolts to BON as adults for upriver hatchery spring Chinook stocks (Dworshak; Rapid River) that migrated inriver and the downriver Carson Hatchery spring Chinook stock for migration years 2000 to Table 58. Estimates of SAR from first dam encountered as smolts to BON as adults for upriver hatchery spring Chinook stocks (Dworshak; Rapid River) that were transported and the downriver Carson Hatchery spring Chinook stock for migration years 2000 to vi

8 Table 59. Estimated Chinook survival from the aggregate of release sites in John Day River to John Day Dam (JDA) tailrace based on BON and the trawl being the final downstream PIT-tag detection sites for migration years 2000 to Table 60. 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 Table 61. Estimated number of PIT-tagged John Day River wild Chinook smolts passing JDA in migration years 2000 to 2003 and returning adults (ages 2- and 3 salt) to BON with associated estimated SAR JDA-to-BON Table 62. Estimates of SAR from first dam encountered as smolts to BON as adults for the upriver PIT-tagged wild Chinook aggregate and the downriver PIT-tagged John Day River wild Chinook that outmigrated in 2000 to 2002, grouped by study category vii

9 LIST OF FIGURES Figure 1. Salmonid life cycle in the Snake River and lower Columbia River basins (source: Marmorek et al. 2004) Figure 2. Estimated SAR LGR-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 2003) Figure 3. Trend in estimated annual SAR (with 90% confidence intervals for ) 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 2003 (only 2-salt adult returns for 2003) Figure 4. Ratio of SAR 2 (T 0 )/SAR(C 0 ) for PIT-tagged wild Chinook aggregate from migration years 1994 to 2003 with associated 90% confidence intervals and required T/C of 2 for non-differential delayed mortality of transported fish over inriver migrants below BON. Point estimate of T/C ratio is annotated for Figure 5. Estimate of D for PIT-tagged wild Chinook aggregate from migration years 1994 to 2003 with associated 90% confidence intervals. Upper limit of 90% confidence interval is annotated for Figure 6. Probability distributions of SAR(C 0 ) and SAR(T 0 ) for wild Chinook, reflecting only intercohort environmental variance. Utilizes means and standard deviations from Table 13. Target minimum overall SAR shown Figure 7. Probability density, and cumulative density, of T/C for Snake River wild Chinook, migration years , reflection only inter-cohort environmental variance Figure 8. Trend in estimated transport and inriver SARs for Rapid River Hatchery spring Chinook for migration years 1997 to 2003 (only 2-salt adult returns for 2003) Figure 9. Estimated transport and inriver SARs for PIT-tagged Dworshak Hatchery spring Chinook for migration years 1997 to 2003 (only 2-salt adult returns for 2003) Figure 10. Estimated transport and inriver SARs for PIT-tagged Catherine Creek Acclimation Pond spring Chinook for migration years 2001 to 2003 (only 2-salt adult returns for 2003) Figure 11. Estimated transport and inriver SARs for PIT-tagged McCall Hatchery summer Chinook for migration years 1997 to 2003 (only 2-salt adult returns for 2003) Figure 12. Estimated transport and inriver SARs for PIT-tagged Imnaha River Acclimation Pond summer Chinook for migration years 1997 to 2003 (only 2-salt adult returns for 2003) Figure 13. Trend in estimated annual SAR LGR-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 1997 to 2003 (only 2-salt adult returns for 2003) viii

10 Figure 14. Trend in ratio of SAR 2 (T 0 )/SAR(C 0 ) for PIT-tagged hatchery Chinook from migration years 1997 to 2003 (excluding 2001) with 90% confidence intervals and required T/C of 2 for non-differential delayed mortality of transported fish over inriver migrants below BON Figure 15. Trend in estimate of D for PIT-tagged hatchery Chinook from migration years 1997 to 2003 (excluding 2001) with associated 90% confidence intervals Figure 16. Estimated transport and inriver SARs for PIT-tagged wild steelhead aggregate for migration years 1997 to 2002 (incomplete returns for 2002) Figure 17. Estimated annual SAR for wild steelhead 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 2002 (incomplete returns for 2002) Figure 18. Ratio of SAR 2 (T 0 )/SAR(C 0 ) for PIT-tagged wild steelhead from migration years 1997 to 2002 with associated 90% confidence intervals and required T/C of 2 for non-differential delayed mortality of transported fish over inriver migrants below BON. Point estimate is annotated for 2001 (lower limit of 90% confidence interval is 11.6) Figure 19. Estimate of D for PIT-tagged wild steelhead from migration years 1997 to 2002 with associated 90% confidence intervals. Upper limit of 90% confidence interval is annotated for Figure 20. Estimated transport and inriver SARs for PIT-tagged hatchery steelhead aggregate for migration years 1997 to 2002 (incomplete returns for 2002) Figure 21. Comparison of SAR(C 1 )/SAR(C 0 ) ratio for wild and hatchery PIT-tagged steelhead bypassed (C 1 ) or undetected (C 0 ) at Snake River collector dams in migration years 1997 to 2002 (not estimable for 2001) Figure 22. Estimated annual SAR for wild steelhead 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 2002 (incomplete returns for 2002) Figure 23. Trend in estimated annual SAR for hatchery steelhead (HS) and wild (WS) steelhead 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 2002 (incomplete returns for 2002) Figure 24. Ratio of SAR 2 (T 0 )/SAR(C 0 ) for PIT-tagged hatchery steelhead from migration years 1997 to 2002 with associated 90% confidence intervals and required T/C of 2.5 for non-differential delayed mortality of transported fish over inriver migrants below BON. Point estimate is annotated for 2001 (lower limit of 90% confidence interval is zero) Figure 25. Estimate of D for PIT-tagged wild steelhead from migration years 1997 to 2002 with associated 90% confidence intervals. Upper limit of 90% confidence interval is annotated for ix

11 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 realtime 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 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, Jerry McCann, Sergie Rassk, and Dona Watson also provided a valuable contribution to the success of this program. A special thanks goes to coauthors Henry Franzoni, who programmed the bootstrap and simulator routines and to Paul Wilson, who contributed to the planning and development of both the simulator and bootstrap programs. We are also grateful to Nick Bouwes (EcoLogic, Logan UT) valuable assistance early in the planning and development of the bootstrap program. Bonneville Power Administration (BPA Project Number ) 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. x

12 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. New this year is the computation of 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 passage of individual fish is determined from its PIT-tag detection history through the xi

13 hydrosystem. The inriver study groups include smolts that were never collected or bypassed at Snake River collector dams (Category C 0 ) and smolts that were collected and bypassed at one or more Snake River collector dams (Category C 1 ). The transport study group (Category T 0 ) 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 (Chapter 3). Another focus of this annual report (Chapter 5) is showing the partition of PIT-tagged generated hatchery-to-hatchery SARs into components of survival of smolts from hatchery release site to Lower Granite Dam, survival through the hydrosystem and back to Lower Granite Dam as adults, and finally survival rate (including harvest) back to the hatchery. 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 (Chapter 6). Finally, the CSS looks at 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 (Chapter 4). The following summarize key findings to date: Chapter 3 Findings: SARs for wild Snake River spring/summer Chinook, from smolts at Lower Granite Dam (LGR) to LGR adult return, ranged from less than 0.5% to 2.4% during the migration years. SARs for migration year 2003 will likely be less than 0.5% based on 2- ocean returns. Migrants in 1999 were the only year class to experience an overall SAR greater than the minimum 2% SAR 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). For the nine migration years (i.e., 1994 to 2002) with completed adult returns for PITtagged wild Chinook, average SAR for transported fish (Category T 0 ) was lower than the average SAR for inriver migrants (Category C 0 ), based on both a 9-year arithmetic mean of the yearly SARs and the mean of the multiyear beta distribution of SARs for fish in categories T 0 and C 0. Transportation provided little or no benefit to wild spring/summer Chinook during the conditions experienced in most years during , except during the severe drought year The 9-year geometric mean (excluding 2001) SAR ratio transported to inriver migrants (T/C) was 0.99, while in 2001, the T/C was approximately 9-fold higher. The T/C ratio was significantly greater than 1.0 in only one year (2001) out of 10. xii

14 Delayed mortality of transported wild spring/summer Chinook smolts was substantial most years relative to that of inriver migrants, based on estimated values of D. The 9-yr geometric mean D estimate (excluding 2001) was 0.48, 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. The estimated inriver survival of wild spring/summer Chinook from LGR tailrace to Bonneville Dam (BON) tailrace averaged 0.47 (geometric mean) for (excluding 2001, when estimated survival was 0.23). During the 10-yr period 1994 to 2003, SAR(C 1 ) averaged approximately 25% lower than SAR(C 0 ) for wild spring/summer Chinook. SARs (LGR to LGR) for hatchery Snake River spring/summer Chinook have shown similar patterns as wild Chinook during , 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 In general, transportation provided some benefits most years to Snake River hatchery spring/summer Chinook , however benefits varied among hatcheries and between run timing. For migration years (excluding 2001), point estimates of T/C were between 1.0 and 2.0 in all but one case (1998 Dworshak, T/C = 0.7). In 2001, T/C exceeded 5.0 for all hatcheries. Omitting 2001, the 6-year geometric mean T/C ranged from 1.1 at Dworshak, 1.4 at Rapid River, 1.5 at Imnaha and 1.6 at McCall hatcheries, indicating a higher return rate for the transported Chinook from these latter three hatcheries. 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 D values exceeded 1.0, the other six years produced geometric mean D values of 0.62 at Dworshak, 0.79 at Imnaha, 0.80 at Rapid River, and 0.92 at McCall hatcheries. D values in 2001 ranged from 2.16 to The 6-yr geometric mean of the estimated inriver reach survival rate of hatchery spring and summer Chinook from LGR tailrace to BON tailrace ranged from 0.51 to 0.56 across hatcheries for migration years 1997 to 2003 (excluding 2001, when estimated reach survival rate ranged from 0.27 to 0.37 across hatcheries). During the 7-yr period 1997 to 2003, SAR(C 1 ) has remained lower than SAR(C 0 ) for Chinook from Rapid River, Dworshak, Imnaha, and McCall hatcheries. xiii

15 Hatchery spring/summer Chinook are not a reliable surrogate for wild Chinook performance in terms of T/C ratios and D values, however, the patterns of SAR, inriver survival, and transportation metrics (T/C and D) appear to generally track those of wild fish. SARs for wild Snake River steelhead (LGR-LGR) averaged about 2% in migration years ; however confidence intervals were quite wide due to small sample sizes. Transportation might provide some benefit to wild Snake River steelhead; the geometric mean T/C ratio was 1.44 for , excluding the low flow year 2001 when the T/C ratio was However, confidence intervals were very wide due to small sample size. Delayed mortality of transported wild steelhead relative to inriver migrants was evident based on estimated values of D. The geometric mean D for (excluding 2001) was 0.67 indicating transported steelhead died at 1.5 times the rate of inriver migrants. In 2001 the estimated D was Confidence intervals were wide due to small sample size. Snake River hatchery steelhead SARs (LGR-LGR) appeared to be lower than those of wild steelhead. None of the study categories had an SAR close to 2%, except for the transport category in Geometric means of hatchery steelhead T/C ratios and D values were 1.30 and 0.52 for (excluding 2001), lower than those for wild steelhead (but also with wide confidence intervals). In 2001, the point estimate of the T/C ratio was 59.7 and D was 2.3, although confidence intervals for both were very wide and contained 0. 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. CSS proposals to tag Snake River hatchery steelhead have not yet been funded. Chapter 4 Findings: Inter-dam dropout rates (combination of harvest, straying, and mortality) for returning PIT-tagged wild and hatchery Chinook adults from the smolt migrations of 2001 to 2003 were higher between BON and MCN than between MCN and LGR, an expected result given greater harvest effort in the Columbia River reach. Dropout rates (combination of harvest, straying, and mortality) of adult Chinook between BON and MCN were generally higher for the returns of fish that were transported as smolts than those that migrated inriver in migration years 2001 to This was the case in all three years for PIT-tagged hatchery Chinook, but only in the first two years for PIT-tagged wild Chinook. xiv

16 Chapter 5 Findings: The PIT-tag SAR hatchery-to-hatchery estimates were higher for the summer Chinook stock from McCall Hatchery than the spring Chinook stocks from Dworshak, Catherine Creek, and Rapid River hatcheries. For migration years, 1997 to 2002, the 6-yr geometric mean of SAR HAT-to-HAT was 0.31%, 0.45%, and 0.72% for Dworshak, Rapid River, and McCall hatcheries, respectively. Chapter 6 Findings: SARs of PIT-tagged downriver hatchery and wild spring Chinook stocks passing one and three dams, respectively, always had higher SARs than PIT-tagged upriver hatchery spring Chinook and wild sp/su Chinook stocks passing eight dams inriver. The SAR LGR-to-BON estimates of transported spring Chinook from Dworshak and Rapid River hatcheries were lower than the downriver Carson Hatchery spring Chinook s SAR BON-to-BON estimate indicating that transportation did not mitigate the mortality associated with passage through the hydrosystem for migration years 2000, 2001, and The SAR JDA-to-BON for PIT-tagged wild spring Chinook from John Day River was generally 2- to 4½- fold higher than the SAR LGR-to-BON estimates of transported wild Chinook of upriver stocks for migration years 2000 to Transportation of upriver wild Chinook stocks did not mitigate the mortality associated with passage through the hydrosystem in these migration years. xv

17 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 2003) and hatchery (1997 to 2003) origin. New this year is coverage of PIT-tagged wild and hatchery summer steelhead (1997 to 2002). 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. arvest Management H R/S Hatchery Wild S/S SAR T:C Eggs Lower Granite Little Goose Lower Monumental Ice Harbor McNary John Day The Dalles Bonneville Estuary D = λ t / λ n Direct survival through dams Freshwater Smolts/ spawner Direct survival of transported fish Ocean Mainstem Spawning / Rearing Habitat Actions Hydrosystem Actions Estuary Habitat Actions Figure 1. Salmonid life cycle in the Snake River and lower Columbia River basins (source: Marmorek et al. 2004). 1

18 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., SAR LGR-to-LGR ) or Bonneville Dam (BON) back to LGR (i.e., SAR BON-to-LGR ) for fish transported around dams and those migrating inriver; (iii) the ratio of SAR LGR-to-LGR of transported fish to SAR LGR-to-LGR of inriver migrants (T/Cs); and, (iv) the ratio of SAR BON-to-LGR of transported fish to SAR BO N-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 will be valuable in diagnosing the salmonid population response to management actions undertaken in the face of changing climatic and oceanic conditions. The 2005 CSS Annual Report is organized into seven chapters, the first being this introduction. Chapter 2 provides the methodology and general information of groups of 2

19 PIT-tagged salmonids used in the CSS. Chapter 3 presents estimates of inriver survivals, SARs, T/C ratios, and Ds. Because of the complexity of these parameters, computing estimates of their theoretical variance is extremely difficult. An alternative approach is to bootstrap the estimation procedure to produce appropriate confidence intervals of these parameters directly. Non-parametric 90% confidence intervals are reported. The longterm time series of SARs with associated bootstrap confidence intervals in this report will be useful to fishery managers when investigating the relationship between survival rates and hydro system experiences in the regional long-term monitoring and evaluation. Chapter 4 presents PIT-tag Chinook adult dropout rates from Bonneville Dam to McNary Dam to Ice Harbor Dam to Lower Granite Dam for adults that outmigrated in 2001 to Chapter 5 presents PIT-tag estimates of hatchery-to-hatchery SARs (includes expansions for sport and tribal fisheries on returning adults prior to arriving at the hatcheries). Chapter 6 presents upstream-downstream comparisons for hatchery and wild Chinook. Yearly trends in SARs for Carson Hatchery Chinook are compared to the upstream hatcheries of Rapid River, Dworshak, Imnaha, and McCall. Yearly trends in SARs of PIT-tagged wild Chinook from John Day River are compared with the upstream aggregate PIT-tagged wild Chinook from the Snake River. Lastly, Chapter 7 presents the progress made this year on the simulation program developed cooperatively between FPC and USFWS staff. The simulator program is designed to evaluate the robustness of the Cormack- Jolly- Seber (CJS) methodology utilized in the CSS, by creating simulated datasets with user controlled input parameters of reach survival, collection efficiency, travel time and other passage parameters. 3

20 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 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 fish to be PIT-tagged should be as representative of the untagged cohorts as possible. In the wild, collection and tagging of fish occurred over lengthy time periods from parr stages to smolt stages for each migration year. 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. 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. 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. Table 1 shows that the minimum 130-mm threshold excluded relatively few PITtagged wild steelhead from the migratory year of interest. 4

21 Table 1. Percentage of PIT-tagged wild steelhead out-migrating in expected migration year that were excluded by minimum length threshold of 130 mm at time of tagging. Expected Percent wild steelhead <130 mm Mig. Year Clearwater R. Grande Ronde R. Imnaha R. Salmon R. Snake R trap Hatchery spring/summer Chinook Yearling 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. Both spring and summer stocks were included. 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 2). 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 on-site releases. Table 2. Hatchery Chinook PIT-tagged and released specifically for CSS in 1997 to Hatchery Rapid River H (RAPH) Dworshak H (DWOR) Catherine Ck AP (CATH) McCall H (MCCA) Migration Year Hatchery Release 85, ,170 2,847,283 2,462, ,601 2,669,476 2,330,557 53, ,400 1,044,511 1,017, ,120 1,000,561 1,033, , , , , ,872 1,143,083 1,039,930 1,076,846 1,022,550 1,053,660 Fish # / lb Median Length at Tagging (mm) 100 A A 115 A 123 A PIT Tags Released 40,452 48,336 47,812 47,747 55,085 54,908 54,763 14,080 47,703 47,845 47,743 55,139 54,725 54,708 20,915 20,796 20,628 52,652 47,340 47,985 47,705 55,124 54,734 74,317 PIT Tag Proportion