wild adult steelhead and chinook salmon …...bonneville power administration (bpa); projects: ......
TRANSCRIPT
WILD ADULT STEELHEAD AND CHINOOK SALMON
ABUNDANCE AND COMPOSITION AT LOWER GRANITE DAM,
SPAWN YEAR 2009
2009 ANNUAL REPORT
Photo: Ron Roberts
Prepared by:
William C. Schrader, Principal Fishery Research Biologist
Timothy Copeland, Senior Fishery Research Biologist Michael W. Ackerman, Fishery Research Biologist
Kristin Ellsworth, Fishery Research Biologist Matthew R. Campbell, Genetics Laboratory Manager
IDFG Report Number 11-24
December 2011
Wild Adult Steelhead and Chinook Salmon Abundance and Composition at Lower Granite Dam, Spawn Year 2009
2009 Annual Report
By
William C. Schrader Timothy Copeland
Michael W. Ackerman Kristin Ellsworth
Matthew R. Campbell
Idaho Department of Fish and Game 600 South Walnut Street
P.O. Box 25 Boise, ID 83707
To
U.S. Department of Energy Bonneville Power Administration
Division of Fish and Wildlife P.O. Box 3621
Portland, OR 97283-3621
Project Numbers #1990-055-00, 1991-073-00, 2010-026-00 Contract Numbers 36150, 40650, 40873, 48347
IDFG Report Number 11-24 December 2011
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ACKNOWLEDGEMENTS
Report Authors: William C. Schrader (IDFG) Timothy Copeland (IDFG) Michael W. Ackerman (IDFG / PSMFC) Kristin Ellsworth (IDFG / PSMFC) Matthew R. Campbell (IDFG) Report Contributors: Data, reviews, and other assistance (alphabetical) IDFG Alan Byrne John Cook Matt Corsi Gary Fitzgerald Sam Hagen Pete Hassemer Lance Hebdon Patrick Kennedy Charlie Petrosky Scott Putnam Lynn Schrader IDFG / PSMFC Miranda Adams Paul Bunn Carlos Camacho Stacey Dauwalter
Casey Frantz Lisa Kautzi Dylan Kovis Jesse McCane Rachel Neuenhoff Laura Redfield Ron Roberts Thea Vanderwey University of Idaho Kirk Steinhorst Columbia River Inter-Tribal Fish Commission Jon Hess Andrew Matala Shawn Narum
NMFS Northwest Fisheries Science Center Vicky Brenner Randy Bunce Shane Collier Jerry Harmon Dan Lyman Jack Lyman Doug Marsh Ken McIntyre Darren Ogden Neil Paasch Ken Thomas Bill VanVogt
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ACKNOWLEDGEMENTS (CONTINUED)
Project Administration: Funding and other assistance (alphabetical) Bonneville Power Administration (BPA); projects:
1990-055-00 Idaho Steelhead Monitoring and Evaluation Studies 1991-073-00 Idaho Natural Production Monitoring and Evaluation Program 2010-026-00 Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
Idaho Office of Species Conservation (IOSC) Pacific States Marine Fisheries Commission (PSMFC) Quantitative Consultants, Inc. (QCI) U. S. Fish and Wildlife Service, Lower Snake River Compensation Program (LSRCP) Suggested citation: Schrader, W. C., T. Copeland, M. W. Ackerman, K. Ellsworth, and M. R. Campbell. 2011. Wild
adult steelhead and Chinook salmon abundance and composition at Lower Granite Dam, spawn year 2009. Idaho Department of Fish and Game Report 11-24. Annual report 2009, BPA Projects 1990-055-00, 1991-073-00, 2010-026-00.
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ABBREVIATIONS AND ACRONYMS
BPA Bonneville Power Administration
BY Brood Year
CI Confidence Interval
COE U. S. Army Corps of Engineers
CWT Coded Wire Tag
DPS Distinct Population Segment
ESA Endangered Species Act
ESU Evolutionarily Significant Unit
F Female
FL Fork Length
GSI Genetic Stock Identification
IA Individual Assignment
ICTRT Interior Columbia Technical Recovery Team
IDFG Idaho Department of Fish and Game
IOSC Idaho Office of Species Conservation
LGD Lower Granite Dam
LSRCP Lower Snake River Compensation Plan
M Male
MCMC Markov Chain Monte Carlo
MM Mixture Modeling
MPG Major Population Group
MSA Mixed Stock Analysis
NMFS National Marine Fisheries Service
PBT Parentage Based Tagging
PIT Passive Integrated Transponder
PSMFC Pacific States Marine Fisheries Commission
QCI Quantitative Consultants, Inc.
SNP Single Nucleotide Polymorphism
SY Spawn Year
TAC Technical Advisory Committee, US v. Oregon
VSP Viable Salmonid Population
WDFW Washington Department of Fish and Wildlife
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TABLE OF CONTENTS Page
ACKNOWLEDGEMENTS .............................................................................................................. i
ACKNOWLEDGEMENTS (continued) .......................................................................................... ii
ABBREVIATIONS AND ACRONYMS ........................................................................................... iii
ABSTRACT ................................................................................................................................... 1
INTRODUCTION .......................................................................................................................... 2
METHODS .................................................................................................................................... 3
Adult Trap Operations at Lower Granite Dam ............................................................................ 3 Valid Sample Selection .............................................................................................................. 4 Scale and Genetics Tissue Processing and Analysis ................................................................ 4 Escapement by Origin, Size, Age, Sex, and Stock .................................................................... 7 Wild Stock Escapement by Sex and Age ................................................................................... 9
RESULTS ..................................................................................................................................... 9
Steelhead Escapement .............................................................................................................. 9 Wild Steelhead Age, Sex, and Stock Composition .................................................................. 10 Chinook Salmon Escapement .................................................................................................. 11 Wild Chinook Salmon Age, Sex, and Stock Composition ........................................................ 12 Age and Stock Validation ......................................................................................................... 13
DISCUSSION .............................................................................................................................. 13
LITERATURE CITED .................................................................................................................. 18
TABLES ...................................................................................................................................... 21
FIGURES .................................................................................................................................... 24
APPENDICES ............................................................................................................................. 39
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LIST OF TABLES Page
Table 1. Major population groups and independent populations within the Snake
River steelhead distinct population segment (DPS) and spring-summer Chinook salmon evolutionary significant unit (ESU; ICTRT 2003, 2005; Ford et al. 2010; NMFS 2011). ............................................................................ 22
Table 2. Status of the fish ladder, the fish counting window and video, and the adult trap sample rate at Lower Granite Dam (LGD), 7/1/2008 to 8/17/2009 (COE 2008; 2009). ............................................................................. 23
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LIST OF FIGURES Page
Figure 1. Daily number of steelhead counted at the Lower Granite Dam (LGD)
window or by video, spawn year 2009. Horizontal bar indicates when the adult trap was open or closed; overall, it was open during 95.0% of the total run (n = 178,870). ........................................................................................ 25
Figure 2. Estimated escapement, by fish size and origin, of steelhead at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Confidence intervals are at 95%. .................. 26
Figure 3. Estimated hatchery and wild steelhead escapement at Lower Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%. ....................... 27
Figure 4. Estimated escapement by age class of wild adult steelhead at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%. ....................................................... 28
Figure 5. Estimated escapement by brood year of wild adult steelhead at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%. ....................................................... 29
Figure 6. Estimated escapement by gender of wild adult steelhead at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%. ....................................................... 30
Figure 7. Estimated escapement by stock of wild adult steelhead at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%. See Appendix Table B-1 for stock abbreviations. ...................................................................................................... 31
Figure 8. Daily number of Chinook salmon counted at the Lower Granite Dam (LGD) window or by video, spawn year 2009. Horizontal bar indicates when the adult trap was open or closed; overall, it was open during 98.3% of the total run (n = 111,580). .............................................................................. 32
Figure 9. Estimated escapement by origin of Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin. Confidence intervals are at 95%. ................................................................... 33
Figure 10. Estimated hatchery and wild Chinook salmon escapement at Lower Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%. .......... 34
Figure 11. Estimated escapement by age class of wild adult Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%. .................................................................................................................... 35
Figure 12. Estimated escapement by brood year of wild adult Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%. .................................................................................................................... 36
Figure 13. Estimated escapement by gender of wild adult Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%. .......... 37
Figure 14. Estimated escapement by stock of wild adult Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%. See Appendix Table B-2 for stock abbreviations. ................................................ 38
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LIST OF APPENDICES Page
Appendix A. Lower Granite Dam trap steelhead sampling protocol, fall 2008. ......... 40
Appendix Table B-1. Reporting groups and baseline collections used for steelhead mixed stock analysis (MSA) at Lower Granite Dam (LGD), spawn year 2009 (Ackerman et al. 2011). MPG = major population group. .................................................................................. 48
Appendix Table B-2. Reporting groups and baseline collections used for Chinook salmon mixed stock analysis (MSA) at Lower Granite Dam (LGD), spawn year 2009 (Ackerman et al. 2011). MPG = major population group. .................................................................................. 49
Appendix Table C-1. Weekly window or video counts and adult valid trap samples of steelhead at Lower Granite Dam (LGD), spawn year 2009. ................. 51
Appendix Table C-2. Number of steelhead captured in the adult trap, by fish size and origin, at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. ......................................................................................................... 52
Appendix Table C-3. Percentage of steelhead captured in the adult trap, by fish size and origin, at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Percentages may not sum to 100.0% due to rounding error. ...................................................................................... 53
Appendix Table C-4. Estimated weekly escapement, by fish size and origin, of steelhead at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. ........................................................................................... 54
Appendix Table C-5. Number of wild adult steelhead scale and genetics samples collected at Lower Granite Dam (LGD) and subsequently aged or genotyped, spawn year 2009. Large and small fish were combined. ............................................................................................. 55
Appendix Table C-6. Weekly age frequencies, by brood year and age class, of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. ................................. 56
Appendix Table C-7. Weekly age percentages, by brood year and age class, of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Percentages may not sum to 100.0% due to rounding error. .................................... 57
Appendix Table C-8. Weekly gender frequencies of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. .............................................................................. 58
Appendix Table C-9. Weekly gender percentages of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Percentages may not sum to 100.0% due to rounding error. ...................................................................................... 59
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List of Appendices, continued. Page
Appendix Table C-10. Frequencies of wild adult steelhead sampled at Lower Granite
Dam (LGD) by gender by age for each stock in spawn year 2009. Large and small fish were combined. Only individual fish whose assignment probability was ≥0.90 are included. See Appendix Table B-1 for stock abbreviations. ........................................ 60
Appendix Table C-11. Percentage of wild adult steelhead sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Large and small fish were combined. Only individual fish whose assignment probability was ≥0.90 are included. Percentages may not sum to 100.0% due to rounding error. See Appendix Table B-1 for stock abbreviations. ........................................ 61
Appendix Table C-12. Estimated escapement of wild adult steelhead sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Large and small fish were combined. Only individual fish whose assignment probability was ≥0.90 are included. Total stock escapement estimates are from Figure 7; see Appendix Table B-1 for stock abbreviations. ........................................................ 62
Appendix Table D-1. Weekly window or video counts and adult valid trap samples of Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. ..................................................................................................... 64
Appendix Table D-2. Number of Chinook salmon captured in the adult trap, by origin, at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin. ......................................................... 65
Appendix Table D-3. Percentage of Chinook salmon captured in the adult trap, by origin, at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin. Percentages may not sum to 100.0% due to rounding error. .......................................................... 66
Appendix Table D-4. Estimated weekly escapement, by origin, of Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin. ......................................................... 67
Appendix Table D-5. Number of wild adult Chinook salmon scale and genetics samples collected at Lower Granite Dam (LGD) and subsequently aged or genotyped, spawn year 2009. ........................... 68
Appendix Table D-6. Weekly age frequencies, by brood year and age class, of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009. ................................................................................. 69
Appendix Table D-7. Weekly age percentages, by brood year and age class, of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009. Percentages may not sum to 100.0% due to rounding error. ...................................................................................... 70
Appendix Table D-8. Weekly gender frequencies of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009. ................... 71
Appendix Table D-9. Weekly gender percentages of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009. Percentages may not sum to 100.0% due to rounding error. ............... 72
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List of Appendices, continued. Page
Appendix Table D-10. Frequencies of wild adult Chinook salmon sampled at Lower
Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Only individual fish whose assignment probability was ≥0.90 are included. See Appendix Table B-2 for stock abbreviations. ....................................................................................... 73
Appendix Table D-11. Percentage of wild adult Chinook salmon sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Only individual fish whose assignment probability was ≥0.90 are included. Percentages may not sum to 100.0% due to rounding error. See Appendix Table B-2 for stock abbreviations. ....................................................................................... 74
Appendix Table D-12. Estimated escapement of wild adult Chinook salmon sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Only individual fish whose assignment probability was ≥0.90 are included. Total stock escapement estimates are from Figure 14; see Appendix Table B-2 for stock abbreviations. ....................................................................................... 75
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ABSTRACT
This report summarizes the abundance and composition of wild adult steelhead and spring-summer Chinook salmon returning to Lower Granite Dam during spawn year 2009. We used a combination of window counts and systematic biological samples from the adult fish trap to decompose each run by origin, body size (steelhead only), age, gender, and genetic stock. For steelhead between July 1, 2008 and June 30, 2009, wild escapement was estimated to be 25,764 fish or 14.4% of the total run. Of these, 130 fish were from brood year (BY) 2006; 5,241 fish from BY2005; 13,465 fish from BY2004; 5,760 fish from BY2003; and 1,168 fish from BY2002. Total age at spawning ranged from three to seven years, with freshwater age ranging from one to five years and saltwater age ranging from one to three years. Using a sex-specific genetic assay, we estimate 17,127 females and 8,637 males returned. The sex ratio was female-biased for the entire run. Stock composition estimates were 6,254 fish for the main Salmon River aggregate; 2,223 fish for the Middle Fork Salmon River; 947 fish for the South Fork Salmon River; 2,844 fish for the upper Clearwater River; 2,746 fish for the South Fork Clearwater River; 1,836 fish for the lower Clearwater River; 1,863 fish for the Imnaha River; 5,936 fish for the Grande Ronde River; and 1,115 fish estimated to originate from below the Dam. The combined wild and hatchery steelhead escapement was 178,870 fish counted at the window by U.S. Army Corps of Engineers. We estimate that 153,106 of these fish were of hatchery origin, of which 13.0% were unclipped. For Chinook salmon between March 2 and August 17, 2009, wild escapement was estimated to be 16,479 fish or 14.8% of the total run. Of these, 3,447 fish were from BY2006; 10,014 fish from BY2005; 2,957 fish from BY2004; and 61 fish from BY2003. Total age at spawning ranged from three to six years, with freshwater age ranging from zero to two years and saltwater age ranging from one to four years. Using a sex-specific genetic assay, we estimate 6,169 females and 10,310 males returned. The sex ratio was nearly equal at the beginning of the run but became increasingly male-biased as the run progressed. Stock composition estimates were 3,723 fish for the upper Salmon River; 2,016 fish for the Middle Fork Salmon River; 4,758 fish for the South Fork Salmon River; 5,634 fish for the Clearwater-Grande Ronde-Imnaha River aggregate; and 111 fish for the Lower Snake (Tucannon) River. In addition, 237 fish or 1.4% of the wild run were identified as fall Chinook salmon based on genetic data. The combined wild and hatchery Chinook salmon escapement was 111,580 fish counted at the window by U.S. Army Corps of Engineers. We estimate that 95,101 of these fish were of hatchery origin, of which 3.7% were unclipped. In the future, estimates of wild adult abundance and composition for these two species will be combined with similar information for smolts from the Lower Granite Dam juvenile facility. This will enable us to estimate productivity and other viable salmonid population parameters.
Authors: William C. Schrader, Principal Fishery Research Biologist Timothy Copeland, Senior Fishery Research Biologist Michael W. Ackerman, Fishery Research Biologist Kristin Ellsworth, Fishery Research Biologist Matthew R. Campbell, Genetics Laboratory Manager
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INTRODUCTION
Populations of steelhead trout Oncorhynchus mykiss and Chinook salmon O. tshawytscha in the Snake River basin declined substantially following the construction of hydroelectric dams in the Snake and Columbia rivers. Raymond (1988) documented a decrease in survival of emigrating steelhead trout and Chinook salmon from the Snake River following the construction of dams on the lower Snake River during the late 1960s and early 1970s. Abundance rebounded slightly in the early 1980s, but then escapements over Lower Granite Dam into the Snake River basin declined again (Busby et al. 1996). In recent years, abundances in the Snake River basin have slightly increased. The increase has been dominated by hatchery fish, while the returns of naturally produced steelhead and Chinook salmon remain critically low. As a result, Snake River steelhead trout (hereafter steelhead) were classified as threatened under the Endangered Species Act (ESA) in 1997. Within the Snake River steelhead distinct population segment (DPS), there are six major population groups: Lower Snake River, Grande Ronde River, Imnaha River, Clearwater River, Salmon River, and Hells Canyon Tributaries (Table 1; ICTRT 2003, 2005; NMFS 2011). However, the Hells Canyon major population group is considered to be extirpated. A total of 24 extant demographically independent populations have been identified. Snake River spring-summer Chinook salmon (hereafter Chinook salmon) were classified as threatened in 1992 under the ESA. Within the Snake River spring-summer Chinook salmon evolutionarily significant unit (ESU), there are five major population groups: Lower Snake River, Grande Ronde/Imnaha Rivers, South Fork Salmon River, Middle Fork Salmon River, and Upper Salmon River. A total of 29 extant demographically independent populations have been identified.
Anadromous fish management programs in the Snake River basin include large-scale
hatchery programs – intended to mitigate for the impacts of hydroelectric dam construction and operation in the basin – and recovery planning and implementation efforts aimed at recovering ESA-listed wild steelhead and salmon stocks. The Idaho Department of Fish and Game’s long-range goal of its anadromous fish program, consistent with basinwide mitigation and recovery programs, is to preserve Idaho’s salmon and steelhead runs and recover them to provide benefit to all users (IDFG 2007). Management to achieve these goals requires an understanding of how salmonid populations function as well as regular status assessments (McElhany et al. 2000). However, specific data on Snake River steelhead and Chinook salmon populations are lacking, particularly key parameters such as population abundance, age composition, genetic diversity, recruits per spawner, and survival rates (ICTRT 2003). The key metrics to assessing viability of salmonid populations are abundance, productivity, spatial structure and diversity (McElhany et al. 2000).
The aggregate escapement of Snake River steelhead and Chinook salmon is measured
at Lower Granite Dam (LGD), with the exception of the Tucannon River, Washington, population. Some of the wild fish are headed to Washington or Oregon tributaries to spawn, but the majority is destined for Idaho. Age, sex, and stock composition data are important for monitoring recovery of wild fish for both species. Age data collected at LGD are used to assign returning adults to specific brood years, for cohort analysis, and to estimate productivity and survival rates (Copeland et al. 2007; Copeland and Putnam 2009; Copeland et al. 2009). In addition, escapement estimates by cohort are used to forecast run sizes in subsequent years, and these forecasts are the basis for preliminary fisheries management plans in the Columbia River basin.
At Columbia River dams, U.S. Army Corps of Engineers (COE) designates jack Chinook
salmon as fish between 30 and 56 cm (12 and 22 inches) in length, and salmonids under 30 cm
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(12 inches) in length are not identified as to species. Mini-jacks are precocious fish generally under 30 cm in length and thus are not counted (Steve Richards, WDFW, personal communication). Throughout this report, unless otherwise stated, adult Chinook salmon refers to reproductively mature fish returning to spawn, including jacks but excluding mini-jacks less than 30 cm. For Chinook salmon, the run year at LGD is defined to be from March 1 to June 17 for the spring run, and from June 18 to August 17 for the summer run. For steelhead, the run year at LGD is defined to be from July 1 to June 30. The steelhead run year dates were chosen to be consistent with the upriver steelhead run year at Bonneville Dam as defined in the US v. Oregon management agreement.
This report summarizes the abundance and composition of wild adult steelhead and
Chinook salmon returning to LGD during spawn year (SY) 2009. For steelhead, fish passing LGD during the summer and fall of 2008 comprise the bulk of the 2009 spawn year. There are two previous preliminary accountings of the data: Copeland and Putnam (2009) reported on the fall 2008 steelhead samples (see their Appendix for genetic results based on microsatellite markers), and Ackerman et al. (2011) reported initial genetic results for both steelhead and Chinook salmon using single nucleotide polymorphisms (SNPs). Here we develop those analyses further and this report supersedes the earlier work. Because of the collaborative nature of the work at LGD, this report is a product of several Bonneville Power Administration (BPA) projects: Idaho Steelhead Monitoring and Evaluation Studies (1990-055-00), Idaho Natural Production Monitoring and Evaluation Program (1991-073-00), and Chinook and Steelhead Genotyping for Genetic Stock Identification at Lower Granite Dam (2010-026-00).
METHODS
Adult Trap Operations at Lower Granite Dam
Systematic samples of steelhead and Chinook salmon returning to LGD were collected during daily operation of the adult fish trap by National Marine Fisheries Service (NMFS; BPA project 2005-002-00, Lower Granite Dam Adult Trap Operations; Harmon 2003; Harmon 2009; Ogden 2010). The adult trap is located in the LGD fish ladder upstream from the fish counting window. The trap captures a systematic random sample of fish by operating a trap gate according to a predetermined sample rate. The sample rate determines how long the trap gate remains open four times per hour; the trap is operational 24 hours per day. Additional details on the adult trap can be found in Harmon (2003) and Steinhorst et al. (2010). During 2008, the trap sample rate changed four times and ranged from 4% in early July to 20% in late August and early September (Table 2). The trap was closed from August 9 to 23, 2008 due to high water temperatures, and from November 25 to December 31, 2008 due to freezing water temperatures. During 2009, the trap sample rate started at 10% on March 4 and switched to 5% on May 19. The trap was closed from July 21 to August 17, 2009 due to high water temperatures. The adult fish ladder was dewatered from January 6 to March 1, 2009; hence, there was no adult passage during this time period.
Standard methods were used by NMFS or Idaho Department of Fish and Game (IDFG)
staff to process and biologically sample adult fish (Harmon 2003; Harmon 2009; Ogden 2010; Appendix A). All adult fish captured were anesthetized; examined for external marks, tags, and injuries; scanned for an internal coded wire tag (CWT) or passive integrated transponder (PIT) tag; and measured for fork length (FL, nearest cm). All fish were classified by origin (wild or hatchery) and the presence (hereafter unclipped) or absence (hereafter clipped) of the adipose fin. Wild fish have an unclipped adipose fin because they spend their entire lifecycle in the
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natural environment. Although most hatchery origin steelhead and Chinook salmon have a clipped adipose fin, some are released with an unclipped adipose fin for supplementation purposes. For unclipped steelhead, hatchery origin was determined primarily by the presence of dorsal or ventral fin erosion, which is assumed to occur only in hatchery-reared fish (Latremouille 2003). We also used the presence of a CWT to determine if an unclipped fish was of hatchery origin. For unclipped Chinook salmon, hatchery origin was determined solely by the presence of a CWT. Captured fish determined to be wild were subsampled for scales and tissue.
Scale samples were taken from above the lateral line and posterior to the dorsal fin.
Samples were stored in coin envelopes for transport to the IDFG aging laboratory in Nampa, Idaho. Tissue samples were taken from a small clip of the anal fin. Tissues were stored in a vial with 200-proof nondenatured ethyl alcohol for transport to the IDFG genetics laboratory in Eagle, Idaho. Gender was not visually determined at the trap but was assessed using sex-specific genetic assays (Ackerman et al. 2011; Steele et al. 2011).
After processing, all fish were returned to the adult fish ladder to resume their upstream
migration. No trap mortalities for either species were observed during SY2009 (Harmon 2009; Ogden 2010).
Valid Sample Selection
Not all trapped fish were deemed valid for sample selection or analysis. Trapped fish that were missing data entry records for any of the following five fields were considered invalid: date of collection; species; fork length; origin (hatchery or wild); or adipose fin status (clipped or unclipped). Trapped fish less than 30 cm (FL) were considered invalid as they are not identified to species at the COE fish-counting window. Further, the adult trap was not designed to efficiently trap smaller fish (Darren Ogden, NMFS, personal communication); for Chinook salmon this includes all mini-jacks less than 30 cm. Finally, any sort by code PIT-tagged fish that were trapped outside the normal trap sampling timeframe were considered invalid. A computer program written by Doug Marsh (NMFS) was used to make this determination. For SY2009, there were eight trapped steelhead that were considered invalid – one was less than 30 cm (FL), one was sort by code for the Asotin Creek floy tag project (Mayer et al. 2010), and six were missing data entry fields. There were 22 trapped Chinook salmon that were considered invalid by these criteria – six were hatchery mini-jacks and 16 were sort by code for the Lemhi River radio telemetry project (Bowersox and Biggs 2010).
Our goal was to age and genotype approximately 1,000 wild steelhead and 1,000 wild
Chinook salmon. When necessary, trap samples were systematically subsampled to reach this goal. The result was a pool of samples collected systematically across the spawning run of each species and generally in constant proportion to their abundance. Hence, the sample pool can be considered a simple random sample (Kirk Steinhorst, University of Idaho, personal communication).
Scale and Genetics Tissue Processing and Analysis
Technicians processed scale samples in the IDFG aging laboratory. Scales were examined for regeneration and 6-10 nonregenerated scales were cleaned and mounted between two glass microscope slides. Scales were examined on a computer video monitor using a Leica DM4000B microscope and a Leica DC500 digital camera. A technician chose the best scales for aging the fish and saved them as digitized images. The entire scale was imaged
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using 12.5x magnification. In addition, the freshwater portion was imaged using 40x magnification. Two technicians independently viewed each image to assign ages without reference to fish length. If there was no age consensus among the readers, a third reader viewed the image and all readers collectively examined the image to resolve their differences before a final age was assigned. If a consensus age was not attained, the sample was excluded from further analysis.
Freshwater annuli were defined by pinching or cutting-over of circuli within the
freshwater zone in the center of the scale. The criterion for a saltwater annulus was the crowding of circuli after the rapid saltwater growth had begun. We used only visible annuli formed on the scales, excluding time spent overwintering in fresh water prior to spawning. We use the European system to designate ages; freshwater age is separated from saltwater age by a decimal. Brood year, or total age at spawning, is the sum of freshwater and saltwater ages, plus 1. Fish lacking either a freshwater or saltwater determined age were not used for analysis.
Known ocean-age fish that were PIT tagged as juveniles were used for saltwater age
validation. We currently do not have any validation methods for wild fish freshwater ages. Accuracy of age assignments was estimated by percent agreement between saltwater age and known emigration date, determined from juvenile PIT tag detection in the hydrosystem. Known ocean-age hatchery and wild fish were used to compute accuracy rate for Chinook salmon ages; only known ocean-age wild fish were used to compute accuracy rate for steelhead ages. The mean coefficient of variation was used to measure aging precision between primary readers (formula from Chang 1982; see Copeland et al. 2007).
Detailed methods for genomic DNA extraction and amplification and SNPs genotyping
are described in Ackerman et al. (2011). Briefly, genomic DNA was extracted and then “pre-amped” to jumpstart SNP amplification via increased copy number of target DNA regions. For steelhead, all individuals were genotyped at 191 SNPs and a Y-chromosome-specific assay that differentiates gender in O. mykiss. For Chinook salmon, all individuals were genotyped at 95 SNPs and a Y-chromosome-specific assay that differentiates gender in O. tshawytscha. SNP amplification was performed using Fluidigm 96.96 Dynamic Array IFCs (chips). Chips were imaged on a Fluidigm EP1 system and analyzed and scored using the Fluidigm SNP Genotyping Analysis Software. Samples were processed at either IDFG’s genetics laboratory in Eagle, Idaho, or at the Columbia River Inter-Tribal Fish Commission’s genetics laboratory in Hagerman, Idaho (BPA project 2010-026-00).
Two types of genetic classification techniques are generally used for mixed stock
analyses (MSA) and both use allele frequencies from baseline populations as reference information to characterize potentially contributing stocks. Individual assignment (IA) methods assign individual samples to stocks in which the probability of its genotype occurring is the greatest. Stock proportions are then estimated by summing all of the individual assignments. In contrast, mixture modeling (MM) does not assign each individual to one specific stock. Instead, MM uses likelihood or Bayesian modeling methods to fractionally allocate individual samples within the mixture to each stock in proportion to the probability that it belongs to that stock. Mixture modeling methods have been shown to be more accurate for estimating stock composition when all individual assignments cannot be made with high confidence (Manel et al. 2005, Koljonen et al. 2005). Since we are interested in estimating both the stock composition of the wild escapement as a whole, as well as estimating sex and age proportions (using biological data from individuals) of fish returning to individual stocks, we used a combination of both MM and IA techniques for genetic stock reconstruction of adults at Lower Granite Dam. For both MSA procedures, fish were initially sampled from discrete “reference” populations (i.e. Snake
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River spawning aggregations) that potentially contribute to the aggregation of mixed populations (i.e. aggregate wild escapement at LGD) and genotyped to establish a genetic baseline. Fish captured at LGD were then genotyped and assigned wholly (IA) or fractionally (MM) back to their population or reporting group of origin (Pella and Milner 1987, Shaklee et al. 1999). Ackerman et al. (2011) describe the Snake River genetic baselines used for both steelhead and Chinook salmon (also see Appendix B). The reporting groups used for both MM and IA were chosen based on two criteria: 1) the genetic relationship among baseline populations (Ackerman et al. 2011) and 2) delineations of Snake River MPGs for both steelhead and Chinook salmon.
Mixture modeling using multi-locus genotype data was performed to estimate stock
proportions of the wild escapement at LGD. Mixture modeling of individuals genotyped from the LGD adult fish trap was done using the Bayesian version of the program gsi_sim (Anderson et al. 2008, Anderson 2010). The Bayesian version of gsi_sim uses Markov chain Monte Carlo (MCMC) to compute the posterior probabilities of stock membership conditional on the allele frequencies estimated from the baseline. The likelihood that a fish originates from a stock is computed using the compound Dirichlet-multinomial formulation of Rannala and Mountain (1997) conditional on the baseline samples and these likelihoods remain fixed throughout the MCMC simulation. To perform the MCMC, gsi_sim uses a Gibbs sampler in which alternately, 1) the stock assignments of the fish in the mixture are updated as a multinomial draw from their posterior probabilities given the current estimate of the stock proportions and the stock-likelihoods of the fish; and 2) the stock proportions are updated as a draw from a Dirichlet distribution given a unit-information prior and the current values of the stock assignments of all the fish in the mixture. By sampling the current values of the stock proportions as the chain proceeds, a Monte Carlo estimator of the posterior mean and any desired quantiles can be computed. For estimating stock proportions, we ran 300,000 MCMC sweeps with a burn-in of 50,000 sweeps and a thinning interval of 50 to obtain 5,000 Bayesian posterior estimates of stock proportions for each stock. The 5,000 Bayesian posterior estimates of stock proportions were used for subsequent calculation of confidence intervals (CI) for stock abundances. The maximum likelihood estimates of stock proportions were used to calculate stock abundances.
To estimate sex and age proportions within each genetic stock, genotyped individuals
were assigned to their “best-estimate” reporting group-of-origin using the program ONCOR (Kalinowski et al. 2007). The IA option in ONCOR determines the “best-estimate” stock of origin based on the reporting group with the highest probability of assignment for a particular fish. Because the accuracy of assignment declines with decreased assignment probabilities, only individuals with ≥90% probability of assignment to a particular stock were used to calculate stock-by-sex-by-age proportions.
To evaluate the resolution of the Snake River genetic baselines for MM, we performed
100% simulations as implemented in the program ONCOR. An analysis was run for each of the baseline populations in which baseline and mixture genotypes were randomly generated using baseline allele frequencies and the leave-one-out cross validation method (Anderson et al. 2008). The mixture (n = 300) for each analysis contained 100% individuals simulated from the baseline population being tested. The simulated mixture was then proportionally assigned back to the resampled baseline to evaluate the proportion of the mixture that assigned back to the correct reporting group. A population is generally considered to be acceptably identifiable if ≥90% (mean estimate from bootstrap resamples) of individuals assign back to the correct reporting group.
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To evaluate the resolution of the Snake River genetic baselines for IA, we conducted “leave-one-out” tests using the program ONCOR. In leave-one-out tests, each individual from the baseline is removed (one-at-a-time) and their reporting group of origin is estimated. For each baseline collection, we calculated the proportion of individuals that correctly assigned back to their reporting group of origin and the proportion of individuals that assigned back to each of the incorrect reporting groups.
In the future, we will estimate the accuracy of both MM and IA using fish that were either
PIT tagged as wild juveniles or detected as adults at tributary PIT antenna arrays that represent “known stock” mixtures. However, too few wild known origin fish were detected in SY2009 to accurately make this assessment.
The sex of each individual was determined using modified Y-chromosome specific
assays for steelhead and Chinook salmon (Ackerman et al. 2011, Steele et al. 2011). Individuals that amplify only at the autosomal control region are determined to be females. Individuals that amplify at both the autosomal control region and the Y-chromosome region are determined to be males.
Escapement by Origin, Size, Age, Sex, and Stock
The COE daily window counts, which occur in the fish ladder downstream of the adult trap, were assumed to be the daily aggregate escapement to LGD for each species. Video counts were used by COE in lieu of window counts in November, December, and March (Table 2). Window count times were 0400-2000, whereas video count times were 0600-1600 Pacific Time. Count data were downloaded from the COE website (http://www.nwp.usace.army.mil/environment/fishdata.asp). Additional daily window and video operation information was obtained from COE annual fish passage reports (COE 2008; 2009). For Chinook salmon, the adult count was combined with the jack count to derive the total count on a daily basis.
To estimate escapement by origin or size, the daily window or video counts were
combined with adult trap sample data on a statistical week basis to account for changes in the trapping rate and run characteristics through time. Statistical weeks started on Monday and ended on Sunday. If necessary, weeks were grouped to try to provide a minimum sample size of 100 trapped fish. In some time strata, we opted not to combine if adjacent strata were above the minimum or if there was a gap in sampling (e.g., spring sampling for steelhead). For steelhead, weekly proportions of wild, clipped hatchery, and unclipped hatchery fish were estimated for large fish (≥78 cm, FL) and small fish (<78 cm, FL) using the trap data. These size criteria are used to inform management processes. For Chinook salmon, weekly proportions were estimated for wild, clipped hatchery, and unclipped hatchery fish irrespective of size. For both species, weekly escapement was estimated by multiplying the weekly window or video counts by the weekly trap proportions; the sum of the weekly escapement estimates was the total escapement to LGD by origin or size. In essence, the weekly proportions for origin (and size) are weighted by weekly run size of all fish as counted at the window or by video.
To estimate wild escapement by age, sex, or stock, the total wild escapement estimate
was multiplied by the overall age, sex, or stock proportions from the trap biological samples of wild fish. Stock proportions were estimated based on MM using multi-locus genotype data. Because we systematically subsampled all wild fish trapped at LGD, and because this sample pool can be considered a simple random sample selected in proportion to abundance, time
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stratification was not necessary for the age, sex, or stock abundance point estimates (Kirk Steinhorst, University of Idaho, personal communication).
Confidence intervals for all point estimates were computed using a bootstrapping
algorithm (Manly 1997). There are two sources of sampling error in the decomposed escapement estimates: variance in the estimated number of wild fish and variance in estimates of age, gender, and stock proportions. To account for these sources of variability when estimating abundance by age and by sex, both the trap origin data and the trap biological sample data (age and sex) for wild fish were resampled simultaneously with replacement 5,000 times. For each iteration the number of wild fish and the numbers of wild fish of various ages or sex were computed. The one-at-a-time bootstrap intervals were found by finding the 2.6th and 97.5th percentiles of the 5,000 ordered bootstrap values for each group. Simultaneous confidence intervals for the number of wild fish of different ages or sex were found by expanding the hypercube formed from the one-at-a-time bootstrap confidence intervals 0.5% in each dimension until 95% of all the bootstrap points were within the expanded hypercube. The algorithm was written and implemented in the R programming environment (R Development Core Team 2008) by Kirk Steinhorst (University of Idaho).
Variance in the wild fish escapement estimate was incorporated into variance in the
genetic stock proportion estimates using a combination of bootstrapping (variance in wild fish escapement) and Monte Carlo methods (variance in stock proportions). The bootstrapping algorithm outlined above was used to create a vector of 5,000 bootstrap estimates of total wild escapement. The MCMC method implemented in gsi_sim was used to generate a vector of 5,000 Bayesian posterior estimates of stock proportion for each genetic stock. The bootstrap estimates of total wild escapement were then multiplied through the Bayesian posterior estimates of stock proportions for each genetic stock to obtain a vector of stock abundance. The one-at-a-time bootstrap intervals of stock abundance were found via the 2.6th and 97.5th percentiles of the 5,000 ordered “bootstrap” values for each group. Similar to age and sex calculations, simultaneous CIs for each genetic stock’s abundance were found by expanding the hypercube formed from the one-at-a-time bootstrap CIs 0.5% in each dimension until 95% of all the bootstrap points were within the expanded hypercube.
Nine wild steelhead reporting groups were used during MM and IA analyses (Appendix
Table B-1). The reporting groups include: 1) SALMON: an aggregate composed of the upper and lower Salmon River; 2) MFSALM: Middle Fork Salmon River (including Bargamin Creek); 3) SFSALM: South Fork Salmon River; 4) UPCLWR: upper Clearwater River (Lochsa and Selway rivers); 5) SFCLWR: South Fork Clearwater River (including Clear Creek); 6) LOCLWR: lower Clearwater River; 7) IMNAHA: Imnaha River; 8) GRROND: Grande Ronde River (including Asotin Creek); and 9) BLWLGD: Below LGD. Results from some reporting groups are aggregated to report by Snake River steelhead MPGs (Table 1). Two reporting groups proposed in Ackerman et al. (2011) – the upper Salmon River and lower Salmon River – were combined to increase the resolution of MSA and to increase the probability of assignment of individuals to the aggregate reporting group. The BLWLGD reporting group was based on samples from the Tucannon and Touchet rivers but excluded Asotin Creek; they were intended to represent fish that might ascend LGD and stray upriver to spawn or fall back and spawn downriver.
Six wild Chinook salmon reporting groups were used during MM and IA analyses
(Appendix Table B-2). The reporting groups include: 1) UPSALM: upper Salmon River; 2) MFSALM: Middle Fork Salmon River (including Chamberlain Creek); 3) SFSALM: South Fork Salmon River; 4) CLWRGR: an aggregate reporting group that includes the Clearwater, Grande Ronde, and Imnaha rivers; 5) TUCANO: the Lower Snake (Tucannon) River, and 6) FALL:
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Snake River fall Chinook salmon. Except for fall Chinook salmon, these reporting groups correspond to Snake River spring-summer Chinook salmon individual or combined MPGs (Table 1). The Lower Snake (Tucannon) River reporting group was included in the baseline to represent fish that might ascend LGD and stray upriver to spawn or fall back and spawn downriver. Two collections of Snake River fall Chinook salmon from the Nez Perce Tribal Hatchery and the Clearwater River were added to the baseline presented in Ackerman et al. (2011); our purpose was to genetically distinguish fall Chinook salmon from spring-summer Chinook salmon trapped prior to August 17.
Wild Stock Escapement by Sex and Age
After estimating the wild escapements by stock using MM, we used results from IA analyses to decompose the stock escapements by sex and age. As the accuracy of assignment declines with decreased assignment probabilities, only individuals that assigned with ≥90% probability to a particular stock were used to calculate stock-by-sex-by-age proportions. Calculated proportions from fish that assigned with ≥90% probability were then applied to the estimated stock escapements to obtain abundance for stock-by-sex-by-age.
RESULTS
Steelhead Escapement
For SY2009 – from July 1, 2008 to June 30, 2009 – a total of 178,870 wild and hatchery steelhead were counted at the LGD window or by video (Figure 1; Appendix Table C-1). The first fish was counted on July 1, 2008, and the last fish was counted on June 30, 2009. Of the total escapement, there were 6,907 fish or 3.9% of the run that passed during the August 9-23, 2008 trap closure. Another 2,056 fish or 1.1% of the run passed during the November 26, 2008 to March 3, 2009 trap closure. The trap was operational during 95.0% of the run.
At the adult trap, a total of 20,883 wild and hatchery steelhead were captured and
considered valid (Appendix Table C-1). Of these, 19,514 fish or 93.4% were trapped during fall 2008, and 1,369 fish or 6.6% were trapped during spring 2009. The adult trap sampled 11.7% of the window count overall (weekly range 1.5-20.2%).
Of the steelhead trapped, there were 654 large (≥78 cm, FL) wild fish; 4,613 large
hatchery clipped fish; 784 large hatchery unclipped fish; 2,140 small (<78 cm, FL) wild fish; 11,155 small hatchery clipped fish; and 1,537 small hatchery unclipped fish (Appendix Table C-2). Combining large and small fish, a total of 5,115 unclipped and 15,768 clipped fish were trapped.
We estimate that 3.2% of the run was large wild; 22.3% was large hatchery clipped;
3.9% was large hatchery unclipped; 11.2% was small wild; 52.2% was small hatchery clipped; and 7.2% was small hatchery unclipped (Appendix Table C-3). About 43.5% of all unclipped fish were of hatchery origin based on visual identification at the trap. About 13.0% of all returning hatchery fish were unclipped. We estimate that 10.9% of all large fish were wild compared to 15.9% of all small fish. Overall, 14.4% of the run was wild and 85.6% was of hatchery origin. However, the percentage that was wild was not constant throughout the run. Roughly a third of the trapped fish were wild at the start of the run in July and August 2008. That percentage declined through the fall to as low as 10%, then began climbing as winter approached. The lowest percentage was 2-3% in early March 2009.
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Of the total steelhead escapement to LGD, we estimate that 5,729 fish (95% CI 3,958-
7,760) were large wild; 39,887 fish (95% CI 36,120-43,727) were large hatchery clipped; 6,933 fish (95% CI 5,067-9,039) were large hatchery unclipped; 20,035 fish (95% CI 16,343-23,913) were small wild; 93,380 fish (95% CI 88,007-98,939) were small hatchery clipped; and 12,906 fish (95% CI 10,105-15,977) were small hatchery unclipped (Figure 2; Appendix Table C-4). Overall, 25,764 wild (95% CI 20,301-31,673) and 153,106 hatchery (95% CI 139,299-167,682) steelhead returned to LGD after combining large, small, clipped, and unclipped fish (Figure 3). Our total estimate of 45,603 unclipped fish, wild and hatchery combined, is 102.2% of the COE reported window count of 44,614 unclipped fish.
Wild Steelhead Age, Sex, and Stock Composition
Of the 1,592 wild steelhead scale and genetics samples collected at the trap, we systematically subsampled 1,083 for aging and genotyping (Appendix Table C-5). The first sample was collected on August 24, 2008, and the last was collected on May 11, 2009. We were able to assign total age to 993 samples or 3.9% of the estimated run size (weekly range 1.5-5.3%). We were able to assign gender to 1,041 samples or 4.0% of the run size (weekly range 1.5-5.8%). We were able to obtain complete genotype data (≥90% of SNPs amplify successfully) for 1,057 samples or 4.1% of the run size (weekly range 1.5-5.8%).
We observed 11 different age classes from the 993 fish that we were able to assign a
total age (Appendix Table C-6). Total age at spawning ranged from three to seven years, with freshwater age ranging from one to five years and saltwater age ranging from one to three years. We estimate that 0.5% of the wild return was from brood year (BY) 2006; 20.3% from BY2005; 52.3% from BY2004; 22.3% from BY2003; and 4.5% from BY2002 (Appendix Table C-7).
Estimated escapement to LGD by age class was 130 fish for age 1.1 (95% CI 21-320);
78 fish for age 1.2 (95% CI 0-226); 5,163 fish for age 2.1 (95% CI 3,561-7,340); 7,861 fish for age 2.2 (95% CI 5,609-10,928); 5,604 fish for age 3.1 (95% CI 3,908-7,964); 519 fish for age 2.3 (95% CI 245-962); 4,463 fish for age 3.2 (95% CI 3,059-6,432); 778 fish for age 4.1 (95% CI 411-1,333); 493 fish for age 3.3 (95% CI 230-908); 649 fish for age 4.2 (95% CI 322-1,143); and 26 fish for age 5.1 (95% CI 0-102; Figure 4). Estimated escapement to LGD by saltwater age was 11,701 one-saltwater fish (95% CI 7,901-17,059); 13,051 two-saltwater fish (95% CI 8,990-18,729); and 1,012 three-saltwater fish (95% CI 475-1,870). Estimated escapement to LGD by total age at spawning was 130 fish from BY2006 (95% CI 24-276); 5,241 fish from BY2005 (95% CI 4,290-6,305); 13,465 fish from BY2004 (95% CI 11,721-15,410); 5,760 fish from BY2003 (95% CI 4,750-6,915); and 1,168 fish from BY2002 (95% CI 788-1,618; Figure 5).
Of the 1,041 fish that gender was successfully determined using the sex-specific assay,
692 were female and 349 were male (Appendix Table C-8). The gender percentages for the entire run were 66.5% female and 33.5% male (Appendix Table C-9). The sex ratio was female-biased for the entire run and ranged from 56.8 to 73.9%. Expanding the overall percentages to the wild run gives 17,127 females (95% CI 15,776-18,549) and 8,637 males (95% CI 7,674-9,663; Figure 6). We estimate that 36.9% of the females and 62.2% of the males were one-saltwater.
Based on MM results using the 1,057 fish with complete genotypes, we estimate that
24.3% of the wild return was from the main Salmon River aggregate; 8.6% from the Middle Fork Salmon River; 3.7% from the South Fork Salmon River; 11.0% from the upper Clearwater River; 10.7% from the South Fork Clearwater River; 7.1% from the lower Clearwater River; 7.2% from
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the Imnaha River; 23.0% from the Grande Ronde River; and 4.3% estimated to originate from below LGD. Aggregating by MPG, 36.6% of the wild return was from the Salmon River; 28.8% from the Clearwater River; 7.2% from the Imnaha River; 23.0% from the Grande Ronde River (including Asotin Creek); and 4.3% was from the Lower Snake River (excluding Asotin Creek).
Based on MM results, estimated escapement to LGD by stock was 6,254 fish for the
main Salmon River aggregate (95% CI 4,776-8,252); 2,223 fish for the Middle Fork Salmon River (95% CI 1,549-3,102); 947 fish for the South Fork Salmon River (95% CI 567-1,461); 2,844 fish for the upper Clearwater River (95% CI 2,077-3,882); 2,746 fish for the South Fork Clearwater River (95% CI 1,934-3,671); 1,836 fish for the lower Clearwater River (95% CI 1,098-2,618); 1,863 fish for the Imnaha River (95% CI 1,107-2,622); 5,936 fish for the Grande Ronde River (including Asotin Creek; 95% CI 4,622-8,051); and 1,115 fish estimated to originate from below LGD (95% CI 551-1,770; Figure 7). Aggregating by MPG, estimated escapement was 9,424 fish for the Salmon River (95% CI 7,810-11,372); 7,426 for the Clearwater River (95% CI 6,052-8,820); 1,863 fish for the Imnaha River (95% CI 1,107-2,622); 5,936 fish for the Grande Ronde River (including Asotin Creek; 95% CI 4,622-8,051); and 1,115 fish for the Lower Snake River (excluding Asotin Creek; 95% CI 551-1,770).
Of the 1,057 fish with complete genotypes, 434 fish or 41.1% assigned to a stock with
≥90% probability (Appendix Table C-10). Percentages of sex by age were calculated for each stock (Appendix Table C-11) and then applied to SY2009 stock escapement estimates (Appendix Table C-12).
Chinook Salmon Escapement
For SY2009 – from March 2 to August 17, 2009 – a total of 111,580 wild and hatchery Chinook salmon were counted at the LGD window or by video (Figure 8; Appendix Table D-1). This total combines adult and jack counts. The first fish was counted on April 12 and the last fish was counted on August 17. Of the total escapement, there were 1,886 fish or 1.7% of the run that passed during the July 21 to August 17, 2009, trap closure. The trap was operational during 98.3% of the run.
At the adult trap, a total of 6,812 wild and hatchery Chinook salmon were captured and
considered valid (Appendix Table D-1). The adult trap sampled 6.1% of the window count overall (weekly range 3.1-10.0%).
Of the Chinook salmon trapped, there were 981 wild fish, 5,615 hatchery clipped fish,
and 216 hatchery unclipped fish (Appendix Table D-2). A total of 1,197 unclipped and 5,615 clipped fish were trapped.
We estimate that 14.8% of the run was wild, 82.1% was hatchery clipped, and 3.1% was
hatchery unclipped (Appendix Table D-3). About 17.5% of all unclipped fish were of hatchery origin, which is a minimum estimate based on CWT. About 3.7% of all returning hatchery fish were unclipped. Overall, 14.8% of the run was wild and 85.2% was of hatchery origin. However, the percentage that was wild was not constant throughout the run and ranged from 8.8% in mid-May to 23.2% in mid-June 2009.
Of the total Chinook salmon escapement to LGD, we estimate that 16,479 fish (95% CI
13,445-19,697) were wild; 91,610 fish (95% CI 88,122-94,950) were hatchery clipped; and 3,491 fish (95% CI 2,147-5,045) were hatchery unclipped (Figure 9; Appendix Table D-4). The hatchery unclipped estimate is a minimum because unclipped hatchery fish without a CWT
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could not be identified. Overall, 16,479 wild (95% CI 13,445-19,697) and 95,101 hatchery (95% CI 90,269-99,995) Chinook salmon returned to LGD after combining clipped and unclipped fish (Figure 10). Our total estimate of 19,970 unclipped fish, wild and hatchery combined, is 88.2% of the COE unreported window count of 22,651 unclipped fish (John Dalen, COE, personal communication).
Wild Chinook Salmon Age, Sex, and Stock Composition
Of the 981 wild Chinook salmon scale and genetics samples collected at the trap, we systematically subsampled 843 for aging and genotyping (Appendix Table D-5). The first sample was collected on April 26 and the last was collected on July 20. We were able to assign total age to 808 samples or 4.9% of the estimated run size (weekly range 4.5-5.3%). We were able to assign gender to 796 samples or 4.8% of the run size (weekly range 4.5-5.1%). We were able to obtain complete genotype data (≥90% of SNPs amplify successfully) for 834 samples or 5.1% of the run size (weekly range 4.5-5.5%).
We observed eight different age classes from the 808 fish that we were able to assign a
total age (Appendix Table D-6). Total age at spawning ranged from three to six years, with freshwater age ranging from zero to two years and saltwater age ranging from one to four years. We estimate that 20.9% of the wild return was from BY2006; 60.7% from BY2005; 17.9% from BY2004; and 0.3% from BY2003 (Appendix Table D-7).
Estimated escapement to LGD by age class was 61 fish for age 0.2 (95% CI 0-171);
3,386 fish for age 1.1 (95% CI 2,413-4,707); 9,912 fish for age 1.2 (95% CI 7,580-12,911); 102 fish for age 2.1 (95% CI 17-241); 2,916 fish for age 1.3 (95% CI 2,052-4,081); 41 fish for age 2.2 (95% CI 0-125); 20 fish for age 1.4 (95% CI 0-77); and 41 fish for age 2.3 (95% CI 0-125; Figure 11). Estimated escapement to LGD by saltwater age was 3,488 one-saltwater fish (95% CI 2,430-4,948); 10,014 two-saltwater fish (95% CI 7,580-13,207); 2,957 three-saltwater fish (95% CI 2,052-4,206); and 20 four-saltwater fish (95% CI 0-77). Estimated escapement to LGD by total age at spawning was 3,447 fish from BY2006 (95% CI 2,826-4,161); 10,014 fish from BY2005 (95% CI 8,824-11,341); 2,957 fish from BY2004 (95% CI 2,395-3,586); and 61 fish from BY2003 (95% CI 0-146; Figure 12).
Of the 796 fish that were genotyped for gender, 298 were female and 498 were male
(Appendix Table D-8). The gender percentages for the entire run were 37.4% female and 62.6% male (Appendix Table D-9). The sex ratio was nearly equal at the beginning of the run but became increasingly male-biased as the run progressed; males ranged from 49.6 to 75.0%. Expanding the overall percentages to the wild run gives 6,169 females (95% CI 5,412-6,981) and 10,310 males (95% CI 9,341-11,390; Figure 13). We estimate that 0.3% of the females were one-saltwater jills and 34.7% of the males were one-saltwater jacks.
Based on MM results using the 834 fish with complete genotypes, we estimate that
22.6% of the wild return was from the upper Salmon River; 12.2% was from the Middle Fork Salmon River; 28.9% was from the South Fork Salmon River; 34.2% was from the Clearwater-Grande Ronde-Imnaha aggregate; and 0.7% was from the Lower Snake (Tucannon) River. In addition, 1.4% of the wild return was genetically identified as fall Chinook salmon.
Based on MM results, estimated escapement to LGD by stock (and MPG) was 3,723 fish
for the upper Salmon River (95% CI 2,509-5,025); 2,016 fish for the Middle Fork Salmon River (95% CI 1,176-2,891); 4,758 fish for the South Fork Salmon River (95% CI 3,573-6,722); 5,634 fish for the Clearwater-Grande Ronde-Imnaha River aggregate (95% CI 4,257-7,511); and 111
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fish for the Lower Snake (Tucannon) River (95% CI 17-291; Figure 14). In addition, an estimated 237 fish were identified as fall Chinook salmon based on genetic data (95% CI 106-446).
Of the 834 fish with complete genotypes, 238 fish or 28.5% assigned to a stock with
≥90% probability (Appendix Table D-10). Percentages of sex by age were calculated for each stock (Appendix Table D-11) and then applied to SY2009 stock escapement estimates (Appendix Table D-12).
Age and Stock Validation
Readers accurately determined the ocean-age of 97% of the scale samples (n = 29) from known ocean-age PIT-tagged wild steelhead. The known ocean-age sample was approximately 31% one-saltwater, 66% two-saltwater, and 3% three-saltwater adults. There were no four-saltwater adults in the known ocean-age sample. Mean coefficient of variation between primary readers for wild fish analysis was 8.5% for freshwater age and 5.5% for saltwater age.
Readers accurately determined the ocean-age of 97% of the scale samples (n = 154)
from known ocean-age PIT-tagged wild and hatchery Chinook salmon. The known ocean-age sample was approximately 49% one-saltwater, 40% two-saltwater, and 11% three-saltwater adults. There were no four-saltwater adults in the known ocean-age sample. Mean coefficient of variation between primary readers for wild fish analysis was 1.3% for freshwater age and 2.1% for saltwater age.
Based on 100% simulations performed in the program ONCOR to test the resolution of
MM, 40 of the 49 steelhead collections in the current Snake River baseline are considered acceptably identifiable. Across all steelhead collections (1,000 bootstrap resamples per collection), 95.0% of the aggregate mixtures simulated from baseline collections assigned to the correct reporting group. Of the 33 Chinook salmon collections in the current Snake River baseline, 32 are considered acceptably identifiable. Across all spring-summer Chinook salmon collections (1,000 bootstrap resamples per collections), 97.6% of the aggregate mixtures simulated from baseline collections assigned to the correct reporting group. Further, 100.0% of the aggregate mixtures simulated from the fall Chinook salmon collections assigned to the correct reporting group.
Leave-one-out tests were performed in ONCOR to test the resolution of the current
Snake River baselines to perform IA. For the steelhead baseline, 75.4% and 82.7% of baseline individuals assigned back to the correct reporting group and MPG of origin, respectively. For the Chinook salmon baseline, 75.6% of individuals assigned back to the correct reporting group of origin. Further, for both fall Chinook salmon collections in the baseline, 100% of baseline individuals assigned back to the fall Chinook reporting group. Ackerman et al. (2011) describes in further detail the resolution of the Snake River baselines to perform IA.
DISCUSSION
This report is the first attempt at a complete stock assessment for wild Snake River steelhead, exclusive of the Tucannon River, using genetic stock identification and run decomposition. Previous comprehensive stock assessments were done on the aggregate A-run and B-run at LGD (e.g., Busby et al. 1996, Good et al. 2005; Ford et al. 2010). This is also the first attempt at a complete stock assessment for wild Snake River spring-summer Chinook
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salmon, exclusive of the Tucannon River, before they arrive at their spawning grounds. Previous stock assessments were done using data collected from spawning ground surveys or from the aggregate at LGD (e.g., Good et al. 2005; Ford et al. 2010). Further, our overall wild escapement estimates for both species at LGD is more refined than those done previously because we attempt to account for unclipped hatchery fish. This is possible because we use morphological data (for steelhead) and tagging data (for steelhead and Chinook salmon) from fish that are handled at the adult trap. Previous estimates used window counts that are unadjusted for unclipped hatchery fish. Beginning in SY2012, we anticipate further refinement to our wild escapement estimates by using parentage based tagging (PBT), which has been shown to be near 100% accurate identifying unclipped hatchery fish (Steele et al. 2011). For both species, SY2012 will be the first year that two-ocean hatchery fish will return from hatchery baseline collections that started in SY2008.
Ideally, the entire run at LGD would be counted accurately at the window or by video,
and the entire run would be sampled in a completely systematic random manner at the adult trap. All passage would be through the fish ladder, and all fish passing once through the ladder would continue migrating upstream to spawn. It is well documented that this ideal scenario is not the case (e.g., Boggs et al. 2004; Steinhorst et al. 2010). However, despite the imperfections, we discuss why our estimates are reasonably accurate (unbiased) and relatively precise. Our hope is to make the reader aware of some issues related to counting and sampling fish at LGD in order to aid interpretation of our results, as well as to identify areas where improvement to the sampling design and statistical analysis may be needed.
Our wild (and hatchery) escapement estimates are based on unadjusted window counts;
i.e. we treat the counts as a complete census. However, fish may ascend the ladder, be counted, fall back, and reascend the ladder to be counted again, in which case the window count is an overcount. Fish may fall back and die or go elsewhere downriver to spawn (undercount). Fish may pass through the navigation lock or at night and not be counted at all (undercount). Boggs et al. (2004) describe these issues in detail and they used radio telemetry to observe the fate of fish passing LGD during 1996-2001. Overall, they found that the LGD window counts were slightly and positively biased – of the window counts, 91.2-96.6% (n = 4 yr) of steelhead and 95.0-99.5% (n = 5 yr) of spring-summer Chinook salmon continued upriver presumably to spawn. Hydrosystem management currently includes more spill than during the Boggs et al. (2004) study, so these percentages are likely different today. There are no radio telemetry studies similar to Boggs et al. (2004) currently being conducted at LGD to estimate fish-count adjustment factors on a yearly basis.
It is tempting to use PIT tags to: 1) adjust for the overestimation caused by double
counting from fallback and reascension, or 2) adjust for the underestimation caused by after-hours passage. However, it is not possible to completely quantify alternate routes of passage or fallback and non-reascension using PIT tags due to incomplete coverage of PIT tag antennas at LGD and throughout the Columbia River basin. As many as 22.2% of radio-tagged steelhead and 28.6% of radio-tagged spring-summer Chinook salmon that fell back at LGD later entered tributaries or hatcheries downstream of LGD (Boggs et al. 2004). Further, not all spawning areas below LGD are currently monitored by PIT antenna arrays. Unfortunately, Boggs et al. (2004) do not report navigation lock passage at LGD, but it was documented to occur at lower Columbia River dams. There are no PIT antenna arrays on navigation locks or spillway bays. At the present time, any accounting of escapement using PIT tag detections will be biased and incomplete to some unknown degree.
15
Another issue that may potentially bias our wild escapement and composition estimates is the separation by code process. There are two sampling processes or events that occur at the adult fish trap: systematic random sampling and sort by code. For the latter, the computer guiding the adult trap gate is programmed with a series of predetermined PIT tag codes. In SY2009, this included Asotin Creek steelhead, Lemhi River Chinook salmon, and Snake River fall Chinook salmon that were tagged as juveniles. If one of these tags is detected in the ladder, the computer opens the trap gate and shunts the tagged fish into the trap. A potential problem arises because fish frequently migrate in groups; therefore, untagged “by-catch” fish may accompany the tagged individual. One result is that the percent of the run actually trapped is often higher than the desired trap rate (Appendix Tables C-1 and D-1). The problem is most pernicious for estimates based on trap expansions (e.g., Steinhorst et al. 2010) and leads to overestimation. To address this issue, our wild (and hatchery) escapement estimate is stratified over time (statistical weeks) and partitions the trap data into time groups along with the window counts. We assume that these extra by-catch fish are random and do not differ from the systematic sample in terms of origin or size. If true, the only effect of the sort by code by-catch is to increase the sample size for any particular time stratum. Until the various issues affecting the true trapping rate can be fully addressed, our escapement estimates based on window counts should be more accurate than estimates based on trap expansions.
The wild steelhead and Chinook salmon abundance estimates at LGD and other dams in
the hydrosystem are used to plan fishing seasons. It is possible that our wild escapement estimates at LGD are slightly positively biased. However, they are still more accurate than estimates based solely on window counts due to our accounting for and removal of unclipped hatchery fish from wild fish estimates. This ensures for risk-averse planning in regards to harvest impacts on ESA-listed populations. Given greater scrutiny on steelhead in the Columbia River basin, our estimate will allow for a fishing season planning process similar to that for Chinook salmon. We note that IDFG managers have used our method of estimating wild escapement at LGD for several decades, and these estimates have been used in US vs. Oregon TAC and other management forums.
For our composition estimates, because we systematically subsampled all wild fish
trapped at LGD, and because this sample pool can be considered a simple random sample selected in proportion to abundance, time stratification was not necessary (Kirk Steinhorst, University of Idaho, personal communication). The effective result was that the percent of the run actually aged or genotyped for gender or stock was approximately constant over time (Appendix Tables C-5 and D-5). It was not exactly constant over time because scale and tissue samples of wild fish were not taken from some portions of the run. This was due to trap closure, extra sort by code “by-catch” fish, and perhaps other unknown reasons. The trap typically closes in late summer due to high water temperatures and in early winter due to freezing water temperatures. We recommend that COE in conjunction with NMFS explore fixing the high water temperature issue, which is caused by the surface location of the ladder water intake. This would also likely result in more attractive fish ladder entrance water temperatures. In the meantime, adequate sampling prior to and after closure should allow valid interpolation of the data.
Abundance and stock composition estimation for spring-summer Chinook salmon at
LGD could potentially be confounded by the short period of overlap in migration timing with fall-run Chinook salmon. Of the 16,479 wild Chinook salmon returning to LGD between March 2 and August 17, 2009, we estimate that 237 fish or 1.4% of the escapement during this period were actually fall Chinook salmon, with the remaining 16,242 fish being spring-summer Chinook salmon. Genetic assignment testing of known origin samples indicates 100% accuracy in differentiating spring-summer Chinook salmon from fall-run Chinook salmon (IDFG, unpublished
16
data). In addition to fall Chinook salmon identified within the spring-summer Chinook salmon escapement time period, it is also likely that some summer Chinook salmon arrive at LGD after the August 17 cutoff date. Several summer Chinook salmon individuals, based on phenotypic characteristics, were recorded by the trap crew after this date (Darren Ogden, NMFS, personal communication). In the future, we will use IA methodologies to assess the accuracy of these phenotypic characteristics to discriminate between the two run types.
In this report we provide genetic stock reconstruction of steelhead and Chinook salmon
adults at Lower Granite Dam. The construction and testing of these initial Snake River genetic baselines using SNPs clearly support the long-term management use of MSA methodologies in the basin. However, there will still be a number of opportunities to improve the accuracy and precision of MM and IA over the next several years. During 100% simulations to evaluate MM, 40 of the 49 steelhead populations and 32 of the 33 Chinook salmon populations currently represented in the baselines were considered acceptably identifiable for MM analyses. During IA analyses, 41.1% of steelhead and 28.5% of Chinook salmon individuals were able to be assigned with ≥90.0% probability. Ideally, all populations represented would be acceptably identifiable during MM and a greater proportion of individuals would be assigned to stock or MPG with certainty. Currently, we are undergoing measures to improve the resolution of the Snake River baselines including:
Increasing the sample size of baseline collections to better estimate allele
frequencies of the wild populations represented. Conducting temporal sampling to better estimate allele frequencies of wild
populations represented. Increasing the number of wild populations represented to better estimate the
allele frequencies of stocks (or MPGs). In the future we will implement further measures to increase the accuracy and precision
of MSA for steelhead and Chinook salmon in the Snake River including:
Remove certain populations from the baseline that based on either field or genetic data do not appear to be contributing to escapement to reduce “noise” in our characterization of wild Snake River stocks.
Conduct additional testing on the accuracy of MM and IA using known-origin
individuals. These could be individuals sampled from populations or stocks that are not included in the baseline or individuals that were PIT-tagged as adults or juveniles.
Investigate new methodologies and procedures for stock characterization and
MSA.
With proper management of the genetic baselines, MSA will be a powerful tool for managers. Stock composition estimates obtained from MM will become more accurate and precise over time. Further, our estimation of biological parameters such as gender and age for each stock (or MPG) will become more accurate and precise as we are able to assign a higher proportion of genotyped individuals with greater certainty, effectively increasing sample size.
17
The wild escapement and composition estimates reported here will be used to evaluate the status of wild populations relative to three viable salmonid population (VSP) criteria: abundance, productivity, and diversity. We directly estimate adult abundance at LGD as well as elements of diversity such as sex ratio, life history variations, and run timing. We estimate abundance by brood year through use of age data, and these estimates are necessary for productivity analyses. Productivity is the generational replacement rate, defined as the number of progeny per parent. In the future, estimates of wild adult abundance and composition will be combined with similar information for smolts from the LGD juvenile facility. This will enable us to estimate adult-to-adult, adult-to-juvenile, and juvenile-to-adult productivity. The data necessary to compute productivity accumulate over time. In general, it will take 4-5 years before the first productivity data are complete.
18
LITERATURE CITED
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Anderson, E. C., R. S. Waples, and S. T. Kalinowski. 2008. An improved method for predicting
the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 65:1475-1486.
Anderson, E. C. 2010. Assessing the power of informative subsets of loci for population
assignment: standard methods are upwardly biased. Molecular Ecology Resources 10(4):701-710.
Boggs, C. T., M. L. Keefer, C. A. Peery, T. C. Bjornn, and L. C. Stuehrenberg. 2004. Fallback,
reascension, and adjusted fishway escapement estimates for adult Chinook salmon and steelhead at Columbia and Snake River dams. Transactions of the American Fisheries Society 133:932-949.
Bowersox, B., and M. Biggs. 2010. Monitoring state restoration of salmon habitat in the
Columbia Basin. Semi-Annual Progress Report for the Pacific States Marine Fisheries Commission, Contract 08-103. Idaho Department of Fish and Game, Boise.
Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, R. S. Waples, F. W. Wauneta, and
I. V. Lagomarsino. 1996. Status review of West Coast steelhead from Washington, Idaho, Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-27.
Chang, W. Y. B. 1982. A statistical method for evaluating the reproducibility of age
determination. Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. COE (U. S. Army Corps of Engineers). 2008. Annual fish passage report. U. S. Army Engineer
Districts, Portland and Walla Walla. COE (U. S. Army Corps of Engineers). 2009. Annual fish passage report. U. S. Army Engineer
Districts, Portland and Walla Walla. Copeland, T., M. W. Hyatt, and J. Johnson. 2007. Comparison of methods used to age
spring/summer Chinook salmon in Idaho: validation and simulated effects on estimated age composition. North American Journal of Fisheries Management 27:1393-1401.
Copeland, T., J. Johnson, K. Apperson, J. Flinders, and R. Hand. 2009. Idaho natural
production monitoring and evaluation. Idaho Department of Fish and Game Report 09-06. Annual report 2008, BPA Project 1991-073-00.
Copeland T., and S. Putnam. 2009. Idaho steelhead monitoring and evaluation studies. Idaho
Department of Fish and Game Report 09-05. Annual report 2008, BPA Project 1990-055-00.
Ford, M. J. (Ed.), T. Cooney, P. McElhany, N. Sands, L. Weitkamp, J. Hard, M. McClure, R.
Kope, J. Myers, A. Albaugh, K. Barnas, D. Teel, P. Moran, and J. Cowen. 2010. Status
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review update for Pacific salmon and steelhead listed under the Endangered Species Act: Northwest. Draft US Department of Commerce, NOAA Technical Memorandum NOAA-TM-NWFSC-XX.
Good, T.P., R. S. Waples, and P. Adams. 2005. Updated status of federally listed ESUs of West
Coast salmon and steelhead. US Department of Commerce NOAA Technical Memorandum NOAA-TM-NWFSC-66.
Harmon, J. R. 2003. A trap for handling adult anadromous salmonids at Lower Granite Dam on
the Snake River, Washington. North American Journal of Fisheries Management 23:989-992.
Harmon, J. R. 2009. Operation of the Lower Granite Dam adult trap. National Marine Fisheries
Service. Annual report 2008, BPA project 2005-002-00. ICTRT (Interior Columbia Technical Recovery Team). 2003. Independent populations of
Chinook, steelhead, and sockeye for listed evolutionarily significant units within the interior Columbia River domain. Working Draft, July 2003.
ICTRT (Interior Columbia Technical Recovery Team). 2005. Updated population delineation in
the interior Columbia Basin. Memo to NMFS Northwest Regional Office May 11, 2005. IDFG (Idaho Department of Fish and Game). 2007. Fisheries management plan 2007-2012.
IDFG, Boise. Kalinowski, S. T., K. R. Manlove, and M. L. Taper. 2007. ONCOR: software for genetic stock
identification. Montana State University, Bozeman. Available at: www.montana.edu/kalinowski/Software/ONCOR.htm.
Koljonen, M. L., J. J. Pella, and M. Masuda. 2005. Classical individual assignments versus
mixture modeling to estimate stock proportions in Atlantic salmon Salmo salar catches from DNA microsatellite data. Canadian Journal of Fisheries and Aquatic Sciences 62(9):2413-2158.
Latremouille, D. N. 2003. Fin erosion in aquaculture and natural environments. Reviews in
Fisheries Science 11:315-335. Manel, S., O. E. Gaggiotti, and R. S. Waples. 2005. Assignment methods: matching biological
questions with the appropriate techniques. Trends in Ecology & Evolution 20(3):136-142. Manly, B. F. J. 1997. Randomization, bootstrap, and Monte Carlo methods in biology, 2nd
edition. Chapman and Hall, New York. Mayer, K., M. Schuck, and P. Iverson. 2010. Assess salmonids in the Asotin Creek watershed.
Washington Department of Wildlife. Annual report 2009, BPA project 2002-053-00. McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, and E. P. Bjorkstedt. 2000.
Viable salmonids populations and the recovery of evolutionarily significant units. National Oceanic and Atmospheric Administration Technical Memorandum NMFS-NWFSC-42.
20
NMFS (National Marine Fisheries Service). 2011. Five-year review: summary and evaluation of Snake River sockeye, Snake River spring-summer Chinook, Snake River fall-run Chinook, Snake River basin steelhead. NMFS, Northwest Region.
Ogden, D. A. 2010. Operation of the Lower Granite Dam adult trap. National Marine Fisheries
Service. Annual report 2009, BPA project 2005-002-00. Pella, J. J., and G. B. Milner. 1987. Use of genetic marks in stock composition analysis. Pages
274-276 in N. Ryman and F. Utter, editors. Population genetics and fisheries management. University of Washington Press, Seattle.
R Development Core Team. 2008. R: A language and environment for statistical computing. R
Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.
Rannala, B., and J. L. Mountain. 1997. Detecting immigration by using multilocus genotypes.
Proceedings of the National Academy of Sciences of the United States of American 94(17):9197-9201.
Raymond, H. L. 1988. Effects of hydroelectric development and fisheries enhancement on
spring and summer Chinook salmon and steelhead in the Columba River basin. North American Journal of Fisheries Management 8:1-24.
Shaklee, J. B., T. D. Beacham, L. Seeb, and B. A. White. 1999. Managing fisheries using
genetic data: case studies from four species of Pacific salmon. Fisheries Research 43:45-78.
Steele, C., M. Ackerman, J. McCane, M. Campbell, M. Hess, N. Campbell, and S. Narum. 2011.
Parentage based tagging of Snake River hatchery steelhead and Chinook salmon. Idaho Department of Fish and Game Report 11-111. Annual report 2010, BPA Project 2010-031-00.
Steinhorst, K., D. Milks, G. P. Naughton, M. Schuck, and B. Arnsberg. 2010. Use of statistical
bootstrapping to calculate confidence intervals for the fall Chinook salmon run reconstruction to Lower Granite Dam. Transactions of the American Fisheries Society 139:1792-1801.
21
TABLES
22
Table 1. Major population groups and independent populations within the Snake River steelhead distinct population segment (DPS) and spring-summer Chinook salmon evolutionary significant unit (ESU; ICTRT 2003, 2005; Ford et al. 2010; NMFS 2011).
Snake River steelhead DPS Snake River spring-summer Chinook salmon
ESU Major population
group Population name Major population
group Population name Lower Snake
River 1. Tucannon River Lower Snake
River 1. Tucannon River
2. Asotin Creek 2. Asotin Creek (extirpated)
Grande Ronde River
3. Lower Grande Ronde River
Grande Ronde/Imnaha
Rivers
3. Wenaha River 4. Joseph Creek 4. Lostine River 5. Wallowa River 5. Minam River 6. Upper Grande Ronde River 6. Catherine Creek
Imnaha River 7. Imnaha River 7. Upper Grande Ronde River
Clearwater River
8. Lower Clearwater River 8. Imnaha River 9. North Fork Clearwater River (extirpated)
9. Big Sheep Creek (extirpated)
10. Lolo Creek 10. Lookinglass Creek 11. Lochsa River
South Fork Salmon River
11. Little Salmon River 12. Selway River 12. South Fork Salmon River 13. South Fork Clearwater River 13. Sesesh River
Salmon River
14. Little Salmon and Rapid Rivers
14. East Fork South Fork Salmon River
15. Chamberlain Creek
Middle Fork Salmon River
15. Chamberlain Creek
16. South Fork Salmon River 16. Lower Middle Fork Salmon River
17. Secesh River 17. Big Creek 18. Panther Creek 18. Camas Creek 19. Lower Middle Fork Salmon River 19. Loon Creek 20. Upper Middle Fork Salmon River
20. Upper Middle Fork Salmon River
21. North Fork Salmon River 21. Sulphur Creek 22. Lemhi River 22. Bear Valley Creek 23. Pahsimeroi River 23. Marsh Creek 24. East Fork Salmon River
Upper Salmon River
24. North Fork Salmon River 25. Upper Salmon River 25. Lemhi River
Hells Canyon Tributaries (extirpated)
26. Upper Salmon River Lower Mainstem 27. Pahsimeroi River 28. East Fork Salmon River 29. Yankee Fork Salmon River 30. Valley Creek 31. Upper Salmon River Upper Mainstem 32. Panther Creek (extirpated)
23
Table 2. Status of the fish ladder, the fish counting window and video, and the adult trap sample rate at Lower Granite Dam (LGD), 7/1/2008 to 8/17/2009 (COE 2008; 2009).
Sampling period Statistical Ladder Window Video Adult trap 2008-09 week open? count? count? sample rate 7/1-7/6 27
Yes, Start 7/1/08, End
1/5/09
Yes, 0400-2000, Start 7/1/08, End
10/31/08
Yes, 0200-0400, Start 7/1/08, End 8/31/08 (not used
for reported counts)
0.04 Rate, Start 7/1/08, End 8/8/08
7/7-7/13 28 7/14-7/20 29 7/21-7/27 30 7/28-8/3 31 8/4-8/10 32 Trap Closed, Start 8/9/08,
End 8/23/08 8/11-8/17 33 8/18-8/24 34
0.20 Rate, Start 8/24/08, End 9/12/08
8/25-8/31 35 9/1-9/7 36
No, Start 9/1/08, End 10/31/08
9/8-9/14 37 0.12 Rate, Start 9/13/08, End 9/26/08 9/15-9/21 38
9/22-9/28 39
0.10 Rate, Start 9/27/08, End 11/25/08
9/29-10/5 40 10/6-10/12 41
10/13-10/19 42 10/20-10/26 43 10/27-11/2 44
No, Start 11/1/08, End 3/31/09
Yes, 0600-1600, Start 11/1/08, End 12/31/08
11/3-11/9 45 11/10-11/16 46 11/17-11/23 47 11/24-11/30 48
Trap Closed, Start 11/26/08, End 3/3/09
12/1-12/7 49 12/8-12/14 50
12/15-12/21 51 12/22-12/28 52
12/29-1/4 53-1
No, Start 1/1/09, End 3/1/09
1/5-1/11 2
No, Start 1/6/09, End
3/1/09
1/12-1/18 3 1/19-1/25 4 1/26-2/1 5 2/2-2/8 6
2/9-2/15 7 2/16-2/22 8 2/23-3/1 9 3/2-3/8 10
Yes, Start 3/2/09, End
8/17/09
Yes, 0600-1600, Start 3/2/09, End
3/31/09
0.10 Rate, Start 3/4/09, End 5/18/09
3/9-3/15 11 3/16-3/22 12 3/23-3/29 13 3/30-4/5 14
Yes, 0400-2000, Start 4/1/09, End
8/17/09
No, Start 4/1/09, End 6/14/09
4/6-4/12 15 4/13-4/19 16 4/20-4/26 17 4/27-5/3 18 5/4-5/10 19
5/11-5/17 20 5/18-5/24 21
0.05 Rate, Start 5/19/09, End 7/20/09
5/25-5/31 22 6/1-6/7 23
6/8-6/14 24 6/15-6/21 25
Yes, 0200-0400, Start 6/15/09,
End 8/17/09 (not used for reported
counts)
6/22-6/28 26 6/29-7/5 27 7/6-7/12 28
7/13-7/19 29 7/20-7/26 30
Trap Closed, Start 7/21/09, End 8/17/09
7/27-8/2 31 8/3-8/9 32
8/10-8/16 33 8/17 34
24
FIGURES
25
Figure 1. Daily number of steelhead counted at the Lower Granite Dam (LGD) window or
by video, spawn year 2009. Horizontal bar indicates when the adult trap was open or closed; overall, it was open during 95.0% of the total run (n = 178,870).
0
1,000
2,000
3,000
4,000
5,000
6,000Number of steelhead
Date
Daily steelhead escapement
Trap open
Trap closed
26
Figure 2. Estimated escapement, by fish size and origin, of steelhead at Lower Granite
Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Confidence intervals are at 95%.
0
50,000
100,000
150,000
200,000
Large wild Large hatcheryclipped
Large hatcheryunclipped
Small wild Small hatcheryclipped
Small hatcheryunclipped
Number of steelhead
Size and origin
27
Figure 3. Estimated hatchery and wild steelhead escapement at Lower Granite Dam
(LGD), spawn year 2009. Confidence intervals are at 95%.
0
50,000
100,000
150,000
200,000
Hatchery Wild
Number of steelhead
Origin
28
Figure 4. Estimated escapement by age class of wild adult steelhead at Lower Granite
Dam (LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%.
0
3,000
6,000
9,000
12,000
1.1 1.2 2.1 2.2 3.1 2.3 3.2 4.1 3.3 4.2 5.1
Number of steelhead
Age class
29
Figure 5. Estimated escapement by brood year of wild adult steelhead at Lower Granite
Dam (LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%.
0
4,000
8,000
12,000
16,000
2006 2005 2004 2003 2002
Number of steelhead
Brood year
30
Figure 6. Estimated escapement by gender of wild adult steelhead at Lower Granite Dam
(LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%.
0
5,000
10,000
15,000
20,000
25,000
Female Male
Number of steelhead
Gender
31
Figure 7. Estimated escapement by stock of wild adult steelhead at Lower Granite Dam
(LGD), spawn year 2009. Large and small fish were combined. Confidence intervals are at 95%. See Appendix Table B-1 for stock abbreviations.
0
3,000
6,000
9,000
SALMON MFSALM SFSALM UPCLWR SFCLWR LOCLWR IMNAHA GRROND BLWLGD
Number of steelhead
Stock
32
Figure 8. Daily number of Chinook salmon counted at the Lower Granite Dam (LGD)
window or by video, spawn year 2009. Horizontal bar indicates when the adult trap was open or closed; overall, it was open during 98.3% of the total run (n = 111,580).
0
500
1000
1500
2000
2500
3000
3500
4000Number of Chinook salm
on
Date
Daily Chinook salmon escapement
Trap open
Trap closed
33
Figure 9. Estimated escapement by origin of Chinook salmon at Lower Granite Dam
(LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin. Confidence intervals are at 95%.
0
20,000
40,000
60,000
80,000
100,000
Wild Hatchery clipped Hatchery unclipped
Number of Chinook salm
on
Origin
34
Figure 10. Estimated hatchery and wild Chinook salmon escapement at Lower Granite Dam
(LGD), spawn year 2009. Confidence intervals are at 95%.
0
20,000
40,000
60,000
80,000
100,000
Hatchery Wild
Number of Chinook salm
on
Origin
35
Figure 11. Estimated escapement by age class of wild adult Chinook salmon at Lower
Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%.
0
3,500
7,000
10,500
14,000
0.2 1.1 1.2 2.1 1.3 2.2 1.4 2.3
Number of Chinook salm
on
Age class
36
Figure 12. Estimated escapement by brood year of wild adult Chinook salmon at Lower
Granite Dam (LGD), spawn year 2009. Confidence intervals are at 95%.
0
3,000
6,000
9,000
12,000
2006 2005 2004 2003
Number of Chinook salm
on
Brood year
37
Figure 13. Estimated escapement by gender of wild adult Chinook salmon at Lower Granite
Dam (LGD), spawn year 2009. Confidence intervals are at 95%.
0
3,000
6,000
9,000
12,000
Female Male
Number of Chinook salm
on
Gender
38
Figure 14. Estimated escapement by stock of wild adult Chinook salmon at Lower Granite
Dam (LGD), spawn year 2009. Confidence intervals are at 95%. See Appendix Table B-2 for stock abbreviations.
0
2,000
4,000
6,000
8,000
UPSALM MFSALM SFSALM CLWRGR TUCANO FALL
Number of Chinook salm
on
Stock
39
APPENDICES
40
Appendix A. Lower Granite Dam trap steelhead sampling protocol, fall 2008.
2008 Lower Granite Dam Steelhead Field Sampling Protocol
Background IDFG has annually requested biological sampling of steelhead at Lower Granite Dam to collect data for estimating: 1) the proportion of adipose fin clipped and unclipped fish; 2) the proportion of non-adipose fin clipped fish that are unmarked fish of hatchery origin (as evidenced by fin erosion associated with raceway rearing, i.e. “stubbies”) and the proportion that are of natural origin; 3) the length frequencies of adipose fin clipped hatchery fish, stubbies, and natural fish; 4) the age composition of hatchery and natural origin fish and; 5) the stock composition of hatchery and natural origin fish. Steelhead at Lower Granite Dam in the fall are captured during the collection of fall Chinook broodstock, generally beginning August 18 unless the trap is shut down due to high water temperatures (>70°F). Sample rates among steelhead are dependent upon the permitted trapping rate for fall Chinook salmon. On August 29, 2007, NOAA Fisheries approved a revised trapping rate of 20% for fall Chinook at Lower Granite Dam. We will assume a similar rate for 2008. IDFG has modified the proposed sampling rates among trapped steelhead at Lower Granite Dam to be consistent with the new trapping rates and to provide sample sizes consistent with our aforementioned monitoring objectives. Sampling Sampling will be primarily directed towards natural origin fish although we also intend to collect a valid sample of hatchery fish. All trapped steelhead will be classified as adipose fin clipped hatchery fish, unclipped hatchery fish (“stubbies”), or unclipped natural origin fish. Clipped and unclipped hatchery fish will be lumped together for sampling purposes. Subsequent sampling rates will differ between hatchery and natural origin fish. All information will be generated from fish chosen for scale sampling. We may wish to post-stratify the population into early and late time strata, so the desired sample size is 1020 natural and 1020 hatchery samples. NOAAF and IDFG personnel will subsample the number of fish collected at the trap. For unclipped natural fish, we recommend a sample rate of 40%, which is 2 of every 5 natural fish collected at the Lower Granite Dam trap. Proposed numbers of listed Snake River natural origin fish handled are within the take limits in Permit 1533. For hatchery origin fish (clipped and unclipped), a sample rate of 4% is required, which is every twenty-fifth fish at the trap.
Unclipped Natural 2:5 Clipped and Unclipped Hatchery 1:25 All trapped fish will be visually scanned for the presence or absence of an adipose fin, and all unclipped fish will be visually scanned for the presence of fin erosion that typifies stubbies. All trapped fish will be examined for marks, tags, and scars. They will be measured to the nearest centimeter (fork length). For all sampled fish, five to six scales will be removed from the preferred area on both right and left sides of the fish, for a total of ten to twelve scales per sample. Scales should be left un-cleaned and stored in paper envelopes. Care should be taken to store envelopes in such a manner that they can dry quickly. Lastly, for all unclipped natural origin fish that are sampled, a tissue sample should be taken from one of the fins and stored in a closed vial with 100% ethanol for future genetics analysis.
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Scale Sample Collection Collection of scale samples requires following only a few simple steps. The two most important things to remember are to guard against cross contamination of samples and to make sure that all information is filled out on the sample envelopes. At every step of the collection process, care must be taken to keep individual samples separate. Collection Packets 2 ½” x 4 ¼” (6.4 x 10.8 cm) Coin envelopes (as many as needed) 2” x 8” strips of paper (same # as coin envelopes) 2” x 4” Mailing labels (Avery 5163) (same # as coin envelopes)
1. Species, life stage (Adult), sample number, and location will be filled out for you. 2. The date requested is the day you are taking the sample. 3. Circle the sex of the fish from which you are collecting the sample, if you are able to tell; if not,
circle unknown. If you are just guessing, please circle unknown. 4. Make sure to circle one of the options for markings. If the fish is not marked circle none. AD =
adipose fin clip. LV = left ventral fin clip. RV = right ventral fin clip. OP = Operculum Punch (this can be on either side of the fish and usually is a “hole punch” taken out of this area).
5. Measure fork length in centimeters. MEHP length is not recorded at LGD.
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6. Scan the fish with a PIT tag detector. If one is present, circle PIT on the collection packet. 7. If the fish has a PIT tag, write down the number that the PIT tag detector gives you. MAKE SURE
you have the number written down correctly. If the fish does not have a tag, put a dash on the Tag Number line.
8. In the comment line, put anything you feel may be of interest; for example, scars or deformities on the fish.
9. Print your full name on the collector line so that you may be contacted if necessary.
Make sure EVERY section is filled out. Double check envelopes! If information is missing, the sample will be useless!!
Scale Sample Collection Method Supplies: Knife Rags or paper towels Collection packet
1. Take any measurements requested (instructions for filling out the collection packet are above). 2. Clear away dirt from the area located on both sides of the fish, within six scales on either side of
an imaginary line running from the posterior base of the dorsal fin to the anterior base of the anal fin and two to three scale rows above the lateral line.
3. Inspect for and remove from the knife any scales from the previous sample collected. 4. With the point of the knife gently scrape with the grain. Five to six scales will be removed from the
preferred area. 5. Wipe scales off of the knife onto one side of the folded strip of paper found in the collection
packet. 6. Repeat steps 2 through 5 on the opposite side of the fish until there are at least 10 scales on the
paper. 7. Refold the strip of paper over the scales and place the strip of paper directly into the collection
packet it was removed from. 8. Make sure that all information requested is filled out on the collection packet. 9. Seal the collection packet. 10. Wipe the knife with rag or paper towel and inspect for any scales remaining. If necessary rinse
with water. 11. Place the collection packets on the drying rack at the end of your shift. Provide adequate space
between the packets to promote air flow.
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Genetic Sample Collection Method Supplies: Labeled sample vials filled with 100% ethyl alcohol 100% ethyl alcohol (for cleaning scissors) Paper towels Scissors
1. Clean the scissors with alcohol and paper towel to prevent cross contamination. 2. Clip a small tissue sample, about the size of your small fingernail, from one of the fins. Do not
remove too mush tissue. Too much tissue will overwhelm the sample vial alcohol.
3. Place the tissue sample in an alcohol-filled vial. Record the vial number on the data sheet. 4. Replace the alcohol in each sample vial at the end of the field season.
Mounting Scales Supplies: Scale packets Bowl Forceps Blue shop towels (lint free) Frosted end microscope slides (2x as many samples as need to be mounted) Scotch tape Empty coin envelopes (as many as scale packets that need to be mounted) Labels (1”x 2 5/8” Avery 5160) Fine point Sharpie pen Sample tracking worksheet 1. Print sufficient mounted sample envelope labels. These labels consist only of a sample number and
the location where the sample was taken. 2. Place the printed labels onto the empty coin envelopes, making sure that they are kept in numerical
order. 3. Fill the bowl with water. 4. Lay a sheet of blue paper towel down on a clean, clear surface. 5. Lay out two of the frosted end microscope slides and write the sample number on the end of each
with the fine point sharpie.
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6. Select the eight best scales from the sample packet (Figures 1 and 2). Tape the sample packet closed again after removing the eight scales in order to prevent the remaining scales from falling out of the envelope.
7. Put the selected scales into the water in the bowl. 8. Remove one scale at a time and rub it between your fingers, removing any dirt and/or dried mucus. 9. When you are satisfied that the scale is clean, lay it on the blue paper towel to dry. 10. When all of the selected scales are clean, pat them dry with the paper towel. 11. Place the dried scales on one of the frosted end microscope slide. Orient the scales in the same
direction, either all posterior fields up or all posterior fields down.
12. Lay the other frosted end microscope slide down on top of the slide with scales on it, with the frosted
end on the opposite end.
13. Place a piece of tape around each end to bind the slides together. 14. Place the mounted sample slides into the empty envelope that is labeled with the corresponding
sample number. 15. Wipe the area clean making sure to dispose of ANY scales that you cannot positively attribute to a
specific sample. 16. Keeping the envelopes containing the mounted samples in numerical order, place them into labeled
containers. 17. Record the date each sample is mounted on the Sample Tracking Worksheet.
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Figure 1. Good Scale – the focus of the scale is not regenerated (you can see the circuli in the center of the scale).
Figure 2. Bad Scale (Regenerated Scale) – because it is regenerated you cannot see the circuli
near the center of the scale. This is bad because we cannot age it if it is missing this area. If all you have is regenerated scales, try to pick out the least regenerated ones (the ones with the smallest regenerated area).
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Appendix B: Snake River genetic baselines used for stock identification at Lower Granite Dam, spawn year 2009.
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Appendix Table B-1. Reporting groups and baseline collections used for steelhead mixed stock analysis (MSA) at Lower Granite Dam (LGD), spawn year 2009 (Ackerman et al. 2011). MPG = major population group.
Reporting Group / Collection Name Latitude Longitude MPG SALMON (Main Salmon River)
1 Sawtooth Weir 44.15058 -114.88509 Salmon 2 West Fork Yankee Fork Salmon River 44.35142 -114.72965 Salmon 3 Morgan Creek 44.61346 -114.16408 Salmon 4 Pahsimeroi River Weir 44.68225 -114.03958 Salmon 5 North Fork Salmon River 45.40936 -113.99184 Salmon 6 Boulder Creek 45.20194 -116.31138 Salmon 7 Hazard Creek 45.18360 -116.29953 Salmon 8 Rapid River 45.37194 -116.35564 Salmon 9 Slate Creek 45.63804 -116.28278 Salmon
10 Whitebird Creek 45.75229 -116.31976 Salmon MFSALM (Middle Fork Salmon River) 11 Marsh Creek 44.44930 -115.23011 Salmon 12 Rapid River (MF) 44.67901 -115.14903 Salmon 13 Pistol Creek 44.72175 -115.14885 Salmon 14 Camas Creek 44.89180 -114.72220 Salmon 15 Big Creek - Upper 45.15064 -115.29674 Salmon 16 Big Creek - Lower 45.09249 -114.72967 Salmon 17 Loon Creek 44.59762 -114.81230 Salmon 18 Bargamin Creek 45.57164 -115.19185 Salmon
SFSALM (South Fork Salmon River) 19 East Fork South Fork Salmon River 45.01274 -115.71285 Salmon 20 Secesh River 45.02682 -115.70824 Salmon 21 Stolle Meadows 44.60701 -115.68098 Salmon
UPCLWR (Upper Clearwater River) 22 Storm Creek 46.46072 -114.54670 Clearwater 23 Crooked Fork Lochsa River 46.52513 -114.67865 Clearwater 24 Canyon Creek 46.21614 -115.55587 Clearwater 25 Bear Creek 46.01911 -114.83784 Clearwater 26 North Fork Moose Creek 46.16732 -114.89984 Clearwater 27 Gedney Creek 46.05833 -115.31408 Clearwater 28 O'Hara Creek 46.08095 -115.51791 Clearwater
SFCLWR (South Fork Clearwater River) 29 Crooked River 45.82113 -115.52722 Clearwater 30 Tenmile Creek 45.80569 -115.68334 Clearwater 31 John's Creek 45.82244 -115.88865 Clearwater 32 Clear Creek 46.04859 -115.78140 Clearwater
LOCLWR (Lower Clearwater River) 33 East Fork Potlatch River 46.79851 -116.42349 Clearwater 34 Big Bear Creek 46.63358 -116.65451 Clearwater 35 Little Bear Creek 46.62911 -116.66120 Clearwater 36 Mission Creek 46.36529 -116.73538 Clearwater
IMNAHA (Imnaha River) 37 Big Sheep Creek 45.55741 -116.83446 Imnaha 38 Camp Creek 45.55721 -116.83517 Imnaha 39 Cow Creek 45.76814 -116.74956 Imnaha 40 Lightning Creek 45.65537 -116.72653 Imnaha
GRROND (Grande Ronde River) 41 Crooked Creek 45.97700 -117.55500 Grande Ronde 42 Elk Creek 45.70533 -117.15291 Grande Ronde 43 Little Minam River 45.72548 -117.78539 Grande Ronde 44 Lostine River 45.55206 -117.48979 Grande Ronde 45 Menatchee Creek 46.00747 -117.36507 Grande Ronde 46 Wenaha River 45.94535 -117.45130 Grande Ronde 47 Asotin Creek 46.34423 -117.05510 Lower Snake R.
BLWLGD (Lower Snake River Below LGD) 48 Tucannon River 46.20460 -117.70600 Lower Snake R. 49 Touchet River 46.03399 -118.68363 -
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Appendix Table B-2. Reporting groups and baseline collections used for Chinook salmon mixed stock analysis (MSA) at Lower Granite Dam (LGD), spawn year 2009 (Ackerman et al. 2011). MPG = major population group.
Reporting Group / Collection Name Latitude Longitude MPG UPSALM (Upper Salmon River)
1 Sawtooth Weir 44.15056 -114.88509 Upper Salmon 2 West Fork Yankee Fork Salmon River 44.34900 -114.72700 Upper Salmon 3 East Fork Salmon River 44.11542 -114.42998 Upper Salmon 4 Pahsimeroi River Weir 44.68212 -114.03923 Upper Salmon 5 Hayden Creek (Lemhi) 44.86160 -113.63188 Upper Salmon 6 L3A Trap (Lemhi) 45.15296 -113.81357 Upper Salmon 7 Lower Lemhi Trap 44.86917 -113.62510 Upper Salmon
MFSALM (Middle Fork Salmon River) 8 Marsh Creek 44.38108 -115.15266 Middle Fork Salmon 9 Capehorn Creek 44.38810 -115.17420 Middle Fork Salmon
10 Elk Creek 44.44171 -115.45377 Middle Fork Salmon 11 Bear Valley Creek 44.42739 -115.32805 Middle Fork Salmon 12 Sulphur Creek 44.54261 -115.32938 Middle Fork Salmon 13 Camas Creek 44.89180 -114.72110 Middle Fork Salmon 14 Big Creek 45.13800 -115.03800 Middle Fork Salmon 15 Chamberlain Creek 45.45400 -114.93300 Middle Fork Salmon
SFSALM (South Fork Salmon River) 16 Lake Creek (Secesh) 45.27881 -115.92169 South Fork Salmon 17 Secesh River (Lower) 45.03300 -115.72200 South Fork Salmon 18 Secesh River (Upper) 45.21706 -115.80837 South Fork Salmon 19 Johnson Creek 44.89900 -115.49200 South Fork Salmon 20 South Fork Salmon River Weir 44.66676 -115.70292 South Fork Salmon
CLWRGR (Clearwater / Grande Ronde / Imnaha aggregate) 21 Powell Weir 46.50561 -114.68718 NA 22 Red River Weir 45.70979 -115.34389 NA 23 Crooked River Weir 45.81744 -115.52668 NA 24 Newsome Creek 45.83100 -115.60800 NA 25 Lolo Creek 46.27900 -115.77500 NA 26 Imnaha River 45.56100 -116.83400 Grande Ronde / Imnaha 27 Catherine Creek 45.15800 -117.77900 Grande Ronde / Imnaha 28 Lostine River Weir 45.53500 -117.45100 Grande Ronde / Imnaha 29 Minam River 45.60000 -117.72900 Grande Ronde / Imnaha 30 Wenaha River 45.95600 -117.72800 Grande Ronde / Imnaha
TUCANO (Lower Snake River) 31 Tucannon River 46.52600 -118.14200 Lower Snake
FALL (Fall Chinook) 32 Nez Perce Tribal Hatchery 46.51900 -116.66500 NA 33 Clearwater River 46.52000 -116.61000 NA
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Appendix C: Wild adult steelhead at Lower Granite Dam, spawn year 2009.
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Appendix Table C-1. Weekly window or video counts and adult valid trap samples of steelhead at Lower Granite Dam (LGD), spawn year 2009.
LGD LGD
Sampling LGD adult adult Percent Statistical period Number window valid trap trap sample of run week(a) 2008-09 of days count(b) sample(c) rate (%) trapped
Fall 2008 27-30(d) 7/1-7/27 27 2,672 108 4 4.0 31 7/28-8/3 7 2,978 109 4 3.7 32-34(e) 8/4-8/24 21 9,207 135 0-20 1.5 35 8/25-8/31 7 3,040 576 20 18.9 36 9/1-9/7 7 6,314 1,278 20 20.2 37 9/8-9/14 7 15,653 2,674 12-20 17.1 38 9/15-9/21 7 21,132 2,728 12 12.9 39 9/22-9/28 7 31,094 3,882 10-12 12.5 40 9/29-10/5 7 26,334 2,826 10 10.7 41 10/6-10/12 7 18,614 2,196 10 11.8 42 10/13-10/19 7 10,367 1,203 10 11.6 43 10/20-10/26 7 6,857 625 10 9.1 44 10/27-11/2 7 4,832 450 10 9.3 45 11/3-11/9 7 2,069 182 10 8.8 46 11/10-11/16 7 2,349 264 10 11.2 47-53(d,f) 11/17-12/31 45 4,091 278 0-10 6.8 Fall total: 184 167,603 19,514 0-20 11.6
Spring 2009 1-9(g) 1/1-3/1 60 ND(h) ND ND ND 10(d) 3/2-3/8 7 661 80 0-10 12.1 11 3/9-3/15 7 591 111 10 18.8 12 3/16-3/22 7 1,063 105 10 9.9 13 3/23-3/29 7 1,483 205 10 13.8 14 3/30-4/5 7 1,974 250 10 12.7 15 4/6-4/12 7 1,825 227 10 12.4 16 4/13-4/19 7 1,385 177 10 12.8 17 4/20-4/26 7 1,023 117 10 11.4 18-27(d) 4/27-6/30 65 1,262 97 0-10 7.7 Spring total: 181 11,267 1,369 0-10 12.2
Run total: 365 178,870 20,883 0-20 11.7 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) From COE link. (c) From Darren Ogden (NMFS, personal communication). (d) Includes partial beginning or ending week. (e) The trap was closed 8/9 to 8/23 due to high water temperatures. (f) The trap was closed 11/26 to 12/31 due to freezing water temperatures. (g) The fish ladder, window, and trap were closed 1/1 to 3/1; fish passage only by navigation lock. (h) ND = no data.
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Appendix Table C-2. Number of steelhead captured in the adult trap, by fish size and origin, at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin.
LGD Number of trapped fish that were(c):
Sample adult Large Large Small Small Statistical period valid trap Large hatchery hatchery Small hatchery hatchery Total Total week(a) ending(b) sample(c) wild clipped unclipped wild clipped unclipped hatchery wild
Fall 2008 27-30 7/27 108 2 2 1 35 59 9 71 37 31 8/3 109 2 0 1 37 64 5 70 39 32-34 8/24 135 2 0 0 37 87 9 96 39 35 8/31 576 9 6 1 102 399 59 465 111 36 9/7 1,278 14 35 2 231 904 92 1,033 245 37 9/14 2,674 57 211 13 314 1,866 213 2,303 371 38 9/21 2,728 71 409 51 292 1,727 178 2,365 363 39 9/28 3,882 156 887 122 322 2,099 296 3,404 478 40 10/5 2,826 87 716 121 196 1,490 216 2,543 283 41 10/12 2,196 73 712 104 159 988 160 1,964 232 42 10/19 1,203 44 361 76 108 541 73 1,051 152 43 10/26 625 37 219 46 62 225 36 526 99 44 11/2 450 22 176 38 35 150 29 393 57 45 11/9 182 12 69 16 18 62 5 152 30 46 11/16 264 14 118 17 24 78 13 226 38 47-53 12/31 278 14 105 21 26 95 17 238 40 Fall total: 19,514 616 4,026 630 1,998 10,834 1,410 16,900 2,614
Spring 2009 1-9 3/1 ND(d) ND ND ND ND ND ND ND ND 10 3/8 80 1 36 14 1 22 6 78 2 11 3/15 111 1 53 26 2 20 9 108 3 12 3/22 105 2 56 14 0 25 8 103 2 13 3/29 205 6 102 18 21 48 10 178 27 14 4/5 250 5 132 32 16 44 21 229 21 15 4/12 227 4 95 21 17 57 33 206 21 16 4/19 177 11 75 14 23 33 21 143 34 17 4/26 117 4 32 13 25 31 12 88 29 18-27 6/30 97 4 6 2 37 41 7 56 41 Spring total: 1,369 38 587 154 142 321 127 1,189 180
Run total: 20,883 654 4,613 784 2,140 11,155 1,537 18,089 2,794
(a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) See Appendix Table C-1 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) From Darren Ogden (NMFS, personal communication). (d) ND = no data.
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Appendix Table C-3. Percentage of steelhead captured in the adult trap, by fish size and origin, at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Percentages may not sum to 100.0% due to rounding error.
LGD Percentage of trapped fish that were:
Sample adult Large Large Small Small Statistical period valid trap Large hatchery hatchery Small hatchery hatchery Total Total week(a) ending(b) sample(c) wild clipped unclipped wild clipped unclipped hatchery wild
Fall 2008 27-30 7/27 108 1.9 1.9 0.9 32.4 54.6 8.3 65.7 34.3 31 8/3 109 1.8 0.0 0.9 33.9 58.7 4.6 64.2 35.8 32-34 8/24 135 1.5 0.0 0.0 27.4 64.4 6.7 71.1 28.9 35 8/31 576 1.6 1.0 0.2 17.7 69.3 10.2 80.7 19.3 36 9/7 1,278 1.1 2.7 0.2 18.1 70.7 7.2 80.8 19.2 37 9/14 2,674 2.1 7.9 0.5 11.7 69.8 8.0 86.1 13.9 38 9/21 2,728 2.6 15.0 1.9 10.7 63.3 6.5 86.7 13.3 39 9/28 3,882 4.0 22.8 3.1 8.3 54.1 7.6 87.7 12.3 40 10/5 2,826 3.1 25.3 4.3 6.9 52.7 7.6 90.0 10.0 41 10/12 2,196 3.3 32.4 4.7 7.2 45.0 7.3 89.4 10.6 42 10/19 1,203 3.7 30.0 6.3 9.0 45.0 6.1 87.4 12.6 43 10/26 625 5.9 35.0 7.4 9.9 36.0 5.8 84.2 15.8 44 11/2 450 4.9 39.1 8.4 7.8 33.3 6.4 87.3 12.7 45 11/9 182 6.6 37.9 8.8 9.9 34.1 2.7 83.5 16.5 46 11/16 264 5.3 44.7 6.4 9.1 29.5 4.9 85.6 14.4 47-53 12/31 278 5.0 37.8 7.6 9.4 34.2 6.1 85.6 14.4 Fall total(d): 19,514 3.2 21.0 3.4 11.2 54.1 7.1 85.6 14.4
Spring 2009 1-9 3/1 ND(e) ND ND ND ND ND ND ND ND 10 3/8 80 1.3 45.0 17.5 1.3 27.5 7.5 97.5 2.5 11 3/15 111 0.9 47.7 23.4 1.8 18.0 8.1 97.3 2.7 12 3/22 105 1.9 53.3 13.3 0.0 23.8 7.6 98.1 1.9 13 3/29 205 2.9 49.8 8.8 10.2 23.4 4.9 86.8 13.2 14 4/5 250 2.0 52.8 12.8 6.4 17.6 8.4 91.6 8.4 15 4/12 227 1.8 41.9 9.3 7.5 25.1 14.5 90.7 9.3 16 4/19 177 6.2 42.4 7.9 13.0 18.6 11.9 80.8 19.2 17 4/26 117 3.4 27.4 11.1 21.4 26.5 10.3 75.2 24.8 18-27 6/30 97 4.1 6.2 2.1 38.1 42.3 7.2 57.7 42.3 Spring total(d): 1,369 2.8 41.1 10.6 11.7 24.5 9.2 85.5 14.5
Run total(d): 20,883 3.2 22.3 3.9 11.2 52.2 7.2 85.6 14.4
(a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) See Appendix Table C-1 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) From Darren Ogden (NMFS, personal communication). (d) Run total percentages for each fish size and origin class were calculated from escapement estimates in Appendix Table C-4. (e) ND = no data.
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Appendix Table C-4. Estimated weekly escapement, by fish size and origin, of steelhead at Lower Granite Dam (LGD), spawn year 2009. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin.
Estimated number of steelhead at LGD that were:
Sample LGD Large Large Small Small Statistical period window Large hatchery hatchery Small hatchery hatchery Total Total week(a) ending(b) count(c) wild clipped unclipped wild clipped unclipped hatchery wild
Fall 2008 27-30 7/27 2,672 49 49 25 866 1,460 223 1,757 915 31 8/3 2,978 55 0 27 1,011 1,748 137 1,912 1,066 32-34 8/24 9,207 136 0 0 2,523 5,934 614 6,548 2,659 35 8/31 3,040 48 32 5 538 2,106 311 2,454 586 36 9/7 6,314 69 173 10 1,141 4,466 455 5,104 1,210 37 9/14 15,653 334 1,235 76 1,838 10,923 1,247 13,481 2,172 38 9/21 21,132 550 3,168 395 2,262 13,378 1,379 18,320 2,812 39 9/28 31,094 1,250 7,105 977 2,579 16,812 2,371 27,265 3,829 40 10/5 26,334 811 6,672 1,128 1,826 13,884 2,013 23,697 2,637 41 10/12 18,614 619 6,035 882 1,348 8,374 1,356 16,647 1,967 42 10/19 10,367 379 3,111 655 931 4,662 629 9,057 1,310 43 10/26 6,857 406 2,403 505 680 2,468 395 5,771 1,086 44 11/2 4,832 236 1,890 408 376 1,611 311 4,220 612 45 11/9 2,069 136 784 182 205 705 57 1,728 341 46 11/16 2,349 125 1,050 151 214 693 116 2,010 339 47-53 12/31 4,091 206 1,545 309 383 1,398 250 3,502 589 Fall total: 167,603 5,409 35,252 5,735 18,721 90,622 11,864 143,473 24,130
Spring 2009 1-9 3/1 ND(d) ND ND ND ND ND ND ND ND 10 3/8 661 8 297 116 8 182 50 645 16 11 3/15 591 5 282 138 11 107 48 575 16 12 3/22 1,063 20 567 142 0 253 81 1,043 20 13 3/29 1,483 43 738 130 152 348 72 1,288 195 14 4/5 1,974 39 1,042 253 126 348 166 1,809 165 15 4/12 1,825 32 764 169 137 458 265 1,656 169 16 4/19 1,385 86 587 110 180 258 164 1,119 266 17 4/26 1,023 35 280 114 219 270 105 769 254 18-27 6/30 1,262 52 78 26 481 534 91 729 533 Spring total: 11,267 320 4,635 1,198 1,314 2,758 1,042 9,633 1,634
Run total: 178,870 5,729 39,887 6,933 20,035 93,380 12,906 153,106 25,764 95% CI: (3,958- (36,120- (5,067- (16,343- (88,007- (10,105- (139,299- (20,301- 7,760) 43,727) 9,039) 23,913) 98,939) 15,977) 167,682) 31,673)
(a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) See Appendix Table C-1 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) From COE link. (d) ND = no data.
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Appendix Table C-5. Number of wild adult steelhead scale and genetics samples collected at Lower Granite Dam (LGD) and subsequently aged or genotyped, spawn year 2009. Large and small fish were combined.
Number of Number of Scale samples: Genetics samples:
scale and scale and Number Percent Number Percent Sampling Wild genetics genetics Number Percent of samples of run of samples of run
Statistical period Number run samples systematic of samples of run genotyped genotyped genotyped genotypedweek(a) 2008-09 of days size(b) collected subsamples aged(c) aged for gender(c) for gender for stock(c) for stock
Fall 2008 27-36(d,e) 7/1-9/7 69 6,436 150 100 94 1.5 94 1.5 96 1.5 37 9/8-9/14 7 2,172 144 109 96 4.4 105 4.8 106 4.9 38 9/15-9/21 7 2,812 142 142 138 4.9 139 4.9 139 4.9 39 9/22-9/28 7 3,829 241 198 184 4.8 184 4.8 191 5.0 40 9/29-10/5 7 2,637 280 140 131 5.0 133 5.0 135 5.1 41 10/6-10/12 7 1,967 231 117 105 5.3 115 5.8 115 5.8 42-43 10/13-10/26 14 2,396 211 128 119 5.0 125 5.2 127 5.3 44-53(d,f) 10/27-12/31 66 1,881 132 88 72 3.8 86 4.6 88 4.7 Fall total: 184 24,130 1,531 1,022 939 3.9 981 4.1 997 4.1
Spring 2009 1-9(g) 1/1-3/1 60 ND(h) ND ND ND ND ND ND ND ND 10-27(d) 3/2-6/30 121 1,634 61 61 54 3.3 60 3.7 60 3.7 Spring total: 181 1,634 61 61 54 3.3 60 3.7 60 3.7
Run total: 365 25,764 1,592 1,083 993 3.9 1,041 4.0 1,057 4.1
(a) Statistical weeks were grouped to try to provide a minimum sample size of 100 aged or genotyped fish. (b) From Appendix Table C-4. (c) Some valid samples were not aged or genotyped due to missing scales or fin clips; other valid samples were not able to be aged (freshwater and saltwater) or successfully genotyped; neither are included here. (d) Includes partial beginning or ending week. (e) The trap was closed 8/9 to 8/23 due to high water temperatures. (f) The trap was closed 11/26 to 12/31 due to freezing water temperatures. (g) The fish ladder, window, and trap were closed 1/1 to 3/1; fish passage only by navigation lock. (h) ND = no data.
56
Appendix Table C-6. Weekly age frequencies, by brood year and age class, of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined.
Sample Number Brood year and age class (frequency):
Statistical period of samples 2006 2005 2005 2004 2004 2003 2003 2003 2002 2002 2002week(a) ending(b) aged 1.1 1.2 2.1 2.2 3.1 2.3 3.2 4.1 3.3 4.2 5.1
Fall 2008 27-36 9/7 94 1 - 20 29 23 - 14 6 - - 1 37 9/14 96 - - 20 24 27 - 18 5 - 2 - 38 9/21 138 1 - 15 39 37 4 26 9 4 3 - 39 9/28 184 - - 39 54 33 5 35 3 5 10 - 40 10/5 131 - - 25 47 27 2 22 2 3 3 - 41 10/12 105 - 1 25 34 22 1 16 1 - 5 - 42-43 10/26 119 3 1 22 35 25 6 20 2 4 1 - 44-53 12/31 72 - - 16 24 15 2 10 1 3 1 - Fall total: 939 5 2 182 286 209 20 161 29 19 25 1
Spring 2009 1-9 3/1 ND(c) ND ND ND ND ND ND ND ND ND ND ND 10-27 6/30 54 - 1 17 17 7 - 11 1 - - - Spring total: 54 0 1 17 17 7 0 11 1 0 0 0
Run total: 993 5 3 199 303 216 20 172 30 19 25 1 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 aged fish. (b) See Appendix Table C-5 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) ND = no data.
57
Appendix Table C-7. Weekly age percentages, by brood year and age class, of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Percentages may not sum to 100.0% due to rounding error.
Sample Number Brood year and age class (percent):
Statistical period of samples 2006 2005 2005 2004 2004 2003 2003 2003 2002 2002 2002week(a) ending(b) aged 1.1 1.2 2.1 2.2 3.1 2.3 3.2 4.1 3.3 4.2 5.1
Fall 2008 27-36 9/7 94 1.1 - 21.3 30.9 24.5 - 14.9 6.4 - - 1.137 9/14 96 - - 20.8 25.0 28.1 - 18.8 5.2 - 2.1 - 38 9/21 138 0.7 - 10.9 28.3 26.8 2.9 18.8 6.5 2.9 2.2 - 39 9/28 184 - - 21.2 29.3 17.9 2.7 19.0 1.6 2.7 5.4 - 40 10/5 131 - - 19.1 35.9 20.6 1.5 16.8 1.5 2.3 2.3 - 41 10/12 105 - 1.0 23.8 32.4 21.0 1.0 15.2 1.0 - 4.8 - 42-43 10/26 119 2.5 0.8 18.5 29.4 21.0 5.0 16.8 1.7 3.4 0.8 - 44-53 12/31 72 - - 22.2 33.3 20.8 2.8 13.9 1.4 4.2 1.4 - Fall total: 939 0.5 0.2 19.4 30.5 22.3 2.1 17.1 3.1 2.0 2.7 0.1
Spring 2009 1-9 3/1 ND(c) ND ND ND ND ND ND ND ND ND ND ND 10-27 6/30 54 - 1.9 31.5 31.5 13.0 - 20.4 1.9 - - - Spring total: 54 0.0 1.9 31.5 31.5 13.0 0.0 20.4 1.9 0.0 0.0 0.0
Run total: 993 0.5 0.3 20.0 30.5 21.8 2.0 17.3 3.0 1.9 2.5 0.1 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 aged fish. (b) See Appendix Table C-5 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) ND = no data.
58
Appendix Table C-8. Weekly gender frequencies of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined.
Number
Sample of samples Statistical period genotyped Gender (frequency): week(a) ending(b) for gender Female Male
Fall 2008 27-36 9/7 94 69 25 37 9/14 105 68 37 38 9/21 139 93 46 39 9/28 184 136 48 40 10/5 133 91 42 41 10/12 115 70 45 42-43 10/26 125 71 54 44-53 12/31 86 50 36 Fall total: 981 648 333
Spring 2009 1-9 3/1 ND(c) ND ND 10-27 6/30 60 44 16 Spring total: 60 44 16
Run total: 1,041 692 349 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 genotyped fish. (b) See Appendix Table C-5 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) ND = no data.
59
Appendix Table C-9. Weekly gender percentages of wild adult steelhead sampled at Lower Granite Dam (LGD), spawn year 2009. Large and small fish were combined. Percentages may not sum to 100.0% due to rounding error.
Number
Sample of samples Statistical period genotyped Gender (percent): week(a) ending(b) for gender Female Male
Fall 2008 27-36 9/7 94 73.4 26.6 37 9/14 105 64.8 35.2 38 9/21 139 66.9 33.1 39 9/28 184 73.9 26.1 40 10/5 133 68.4 31.6 41 10/12 115 60.9 39.1 42-43 10/26 125 56.8 43.2 44-53 12/31 86 58.1 41.9 Fall total: 981 66.1 33.9
Spring 2009 1-9 3/1 ND(c) ND ND 10-27 6/30 60 73.3 26.7 Spring total: 60 73.3 26.7
Run total: 1,041 66.5 33.5 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 genotyped fish. (b) See Appendix Table C-5 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) ND = no data.
60
Appendix Table C-10. Frequencies of wild adult steelhead sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Large and small fish were combined. Only individual fish whose assignment probability was ≥0.90 are included. See Appendix Table B-1 for stock abbreviations.
Brood year and age class (frequency):
2006 2005 2005 2004 2004 2003 2003 2003 2002 2002 2002 Stock Gender 1.1 1.2 2.1 2.2 3.1 2.3 3.2 4.1 3.3 4.2 5.1 Total
SALMON F - - 10 19 11 - 5 - - 2 - 47 M - - 7 7 8 - 1 1 - 1 - 25
Total 0 0 17 26 19 0 6 1 0 3 0 72
MFSALM F - - 1 8 13 1 12 4 3 5 - 47 M - - 1 1 4 - 3 1 - 3 - 13
Total 0 0 2 9 17 1 15 5 3 8 0 60
SFSALM F - - - 2 - 1 8 - 2 - - 13 M - - - - - - 2 - - 1 - 3
Total 0 0 0 2 0 1 10 0 2 1 0 16
UPCLWR F 2 1 3 26 4 1 18 - 2 1 - 58 M 1 - 2 3 5 2 7 - - - - 20
Total 3 1 5 29 9 3 25 0 2 1 0 78
SFCLWR F - - 1 32 1 3 11 1 1 - - 50 M - - 5 7 7 1 2 - 1 1 - 24
Total 0 0 6 39 8 4 13 1 2 1 0 74
LOCLWR F - - 2 4 3 - 4 1 - - - 14 M - - - 2 2 1 - - - - - 5
Total 0 0 2 6 5 1 4 1 0 0 0 19
IMNAHA F - - 4 5 4 - 1 2 - - - 16 M - - 4 - 4 - 2 1 - - - 11
Total 0 0 8 5 8 0 3 3 0 0 0 27
GRROND F - - 15 16 11 1 4 1 - - - 48 M - - 13 7 13 1 1 - 1 - - 36
Total 0 0 28 23 24 2 5 1 1 0 0 84
BLWLGD F - - - 1 - - 1 - - - - 2 M - - 1 1 - - - - - - - 2
Total 0 0 1 2 0 0 1 0 0 0 0 4
Grand total: 3 1 69 141 90 12 82 12 10 14 0 434
61
Appendix Table C-11. Percentage of wild adult steelhead sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Large and small fish were combined. Only individual fish whose assignment probability was ≥0.90 are included. Percentages may not sum to 100.0% due to rounding error. See Appendix Table B-1 for stock abbreviations.
Brood year and age class (percent):
2006 2005 2005 2004 2004 2003 2003 2003 2002 2002 2002 Stock Gender 1.1 1.2 2.1 2.2 3.1 2.3 3.2 4.1 3.3 4.2 5.1 Total
SALMON F - - 13.9 26.4 15.3 - 6.9 - - 2.8 - 65.3 M - - 9.7 9.7 11.1 - 1.4 1.4 - 1.4 - 34.7
Total 0.0 0.0 23.6 36.1 26.4 0.0 8.3 1.4 0.0 4.2 0.0 100.0
MFSALM F - - 1.7 13.3 21.7 1.7 20.0 6.7 5.0 8.3 - 78.3 M - - 1.7 1.7 6.7 - 5.0 1.7 - 5.0 - 21.7
Total 0.0 0.0 3.3 15.0 28.3 1.7 25.0 8.3 5.0 13.3 0.0 100.0
SFSALM F - - - 12.5 - 6.3 50.0 - 12.5 - - 81.3 M - - - - - - 12.5 - - 6.3 - 18.8
Total 0.0 0.0 0.0 12.5 0.0 6.3 62.5 0.0 12.5 6.3 0.0 100.0
UPCLWR F 2.6 1.3 3.8 33.3 5.1 1.3 23.1 - 2.6 1.3 - 74.4 M 1.3 - 2.6 3.8 6.4 2.6 9.0 - - - - 25.6
Total 3.8 1.3 6.4 37.2 11.5 3.8 32.1 0.0 2.6 1.3 0.0 100.0
SFCLWR F - - 1.4 43.2 1.4 4.1 14.9 1.4 1.4 - - 67.6 M - - 6.8 9.5 9.5 1.4 2.7 - 1.4 1.4 - 32.4
Total 0.0 0.0 8.1 52.7 10.8 5.4 17.6 1.4 2.7 1.4 0.0 100.0
LOCLWR F - - 10.5 21.1 15.8 - 21.1 5.3 - - - 73.7 M - - - 10.5 10.5 5.3 - - - - - 26.3
Total 0.0 0.0 10.5 31.6 26.3 5.3 21.1 5.3 0.0 0.0 0.0 100.0
IMNAHA F - - 14.8 18.5 14.8 - 3.7 7.4 - - - 59.3 M - - 14.8 - 14.8 - 7.4 3.7 - - - 40.7
Total 0.0 0.0 29.6 18.5 29.6 0.0 11.1 11.1 0.0 0.0 0.0 100.0
GRROND F - - 17.9 19.0 13.1 1.2 4.8 1.2 - - - 57.1 M - - 15.5 8.3 15.5 1.2 1.2 - 1.2 - - 42.9
Total 0.0 0.0 33.3 27.4 28.6 2.4 6.0 1.2 1.2 0.0 0.0 100.0
BLWLGD F - - - 25.0 - - 25.0 - - - - 50.0 M - - 25.0 25.0 - - - - - - - 50.0
Total 0.0 0.0 25.0 50.0 0.0 0.0 25.0 0.0 0.0 0.0 0.0 100.0
62
Appendix Table C-12. Estimated escapement of wild adult steelhead sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Large and small fish were combined. Only individual fish whose assignment probability was ≥0.90 are included. Total stock escapement estimates are from Figure 7; see Appendix Table B-1 for stock abbreviations.
Brood year and age class (estimated number):
2006 2005 2005 2004 2004 2003 2003 2003 2002 2002 2002 Stock Gender 1.1 1.2 2.1 2.2 3.1 2.3 3.2 4.1 3.3 4.2 5.1 Total
SALMON F - - 869 1,650 955 - 434 - - 174 - 4,082 M - - 608 608 695 - 87 87 - 87 - 2,172
Total 0 0 1,477 2,258 1,650 0 521 87 0 261 0 6,254
MFSALM F - - 37 296 483 37 445 148 111 185 - 1,742 M - - 37 37 148 - 111 37 - 111 - 481
Total 0 0 74 333 631 37 556 185 111 296 0 2,223
SFSALM F - - - 118 - 59 475 - 118 - - 770 M - - - - - - 118 - - 59 - 177
Total 0 0 0 118 0 59 593 0 118 59 0 947
UPCLWR F 73 36 109 949 146 36 657 - 73 36 - 2,115 M 36 - 73 109 182 73 256 - - - - 729
Total 109 36 182 1,058 328 109 913 0 73 36 0 2,844
SFCLWR F - - 37 1,188 37 111 408 37 37 - - 1,855 M - - 186 260 260 37 74 - 37 37 - 891
Total 0 0 223 1,448 297 148 482 37 74 37 0 2,746
LOCLWR F - - 193 386 290 - 387 97 - - - 1,353 M - - - 193 193 97 - - - - - 483
Total 0 0 193 579 483 97 387 97 0 0 0 1,836
IMNAHA F - - 276 345 276 - 69 138 - - - 1,104 M - - 276 - 276 - 138 69 - - - 759
Total 0 0 552 345 552 0 207 207 0 0 0 1,863
GRROND F - - 1,059 1,130 777 71 283 71 - - - 3,391 M - - 919 495 918 71 71 - 71 - - 2,545
Total 0 0 1,978 1,625 1,695 142 354 71 71 0 0 5,936
BLWLGD F - - - 279 - - 278 - - - - 557 M - - 279 279 - - - - - - - 558
Total 0 0 279 558 0 0 278 0 0 0 0 1,115
63
Appendix D: Wild adult Chinook salmon at Lower Granite Dam, spawn year 2009
64
Appendix Table D-1. Weekly window or video counts and adult valid trap samples of Chinook salmon at Lower Granite Dam (LGD), spawn year 2009.
LGD LGD
Sampling LGD adult adult Percent Statistical period Number window valid trap trap sample of run week(a) 2009 of days count(b) sample(c) rate (%) trapped
10-19 3/2-5/10 70 3,975 368 0-10 9.3 20 5/11-5/17 7 15,049 1,502 10 10.0 21 5/18-5/24 7 19,696 1,125 5-10 5.7 22 5/25-5/31 7 13,989 801 5 5.7 23 6/1-6/7 7 12,574 698 5 5.6 24 6/8-6/14 7 11,039 583 5 5.3 25 6/15-6/21 7 10,938 585 5 5.3 26 6/22-6/28 7 9,315 439 5 4.7 27 6/29-7/5 7 5,544 298 5 5.4 28 7/6-7/12 7 5,272 282 5 5.3 29-34(d) 7/13-8/17 36 4,189 131 0-5 3.1
Run total: 169 111,580 6,812 0-10 6.1 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) From COE link. (c) From Darren Ogden (NMFS, personal communication). (d) Includes partial beginning or ending week.
65
Appendix Table D-2. Number of Chinook salmon captured in the adult trap, by origin, at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin.
LGD Number of trapped fish that were(c):
Sample adult Statistical period valid trap Hatchery Hatchery Total Total week(a) ending(b) sample(c) Wild clipped unclipped hatchery wild
10-19 5/10 368 63 285 20 305 6320 5/17 1,502 183 1,273 46 1,319 18321 5/24 1,125 99 980 46 1,026 9922 5/31 801 87 688 26 714 8723 6/7 698 120 560 18 578 12024 6/14 583 135 440 8 448 13525 6/21 585 112 458 15 473 11226 6/28 439 78 344 17 361 7827 7/5 298 47 237 14 251 4728 7/12 282 34 247 1 248 3429-34 8/17 131 23 103 5 108 23
Run total: 6,812 981 5,615 216 5,831 981 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) See Appendix Table D-1 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) From Darren Ogden (NMFS, personal communication).
66
Appendix Table D-3. Percentage of Chinook salmon captured in the adult trap, by origin, at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin. Percentages may not sum to 100.0% due to rounding error.
LGD Percentage of trapped fish that were:
Sample adult Statistical period valid trap Hatchery Hatchery Total Total week(a) ending(b) sample(c) Wild clipped unclipped hatchery wild
10-19 5/10 368 17.1 77.4 5.4 82.9 17.120 5/17 1,502 12.2 84.8 3.1 87.8 12.221 5/24 1,125 8.8 87.1 4.1 91.2 8.822 5/31 801 10.9 85.9 3.2 89.1 10.923 6/7 698 17.2 80.2 2.6 82.8 17.224 6/14 583 23.2 75.5 1.4 76.8 23.225 6/21 585 19.1 78.3 2.6 80.9 19.126 6/28 439 17.8 78.4 3.9 82.2 17.827 7/5 298 15.8 79.5 4.7 84.2 15.828 7/12 282 12.1 87.6 0.4 87.9 12.129-34 8/17 131 17.6 78.6 3.8 82.4 17.6
Run total(d): 6,812 14.8 82.1 3.1 85.2 14.8 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) See Appendix Table D-1 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) From Darren Ogden (NMFS, personal communication). (d) Run total percentages for each origin class were calculated from escapement estimates in Appendix Table D-4.
67
Appendix Table D-4. Estimated weekly escapement, by origin, of Chinook salmon at Lower Granite Dam (LGD), spawn year 2009. Clipped and unclipped refer to the adipose fin.
Sample LGD Estimated number of Chinook salmon at LGD that were:
Statistical period window Hatchery Hatchery Total Total week(a) ending(b) count(c) Wild clipped unclipped hatchery wild
10-19 5/10 3,975 681 3,078 216 3,294 681 20 5/17 15,049 1,834 12,754 461 13,215 1,834 21 5/24 19,696 1,733 17,158 805 17,963 1,733 22 5/31 13,989 1,519 12,016 454 12,470 1,519 23 6/7 12,574 2,162 10,088 324 10,412 2,162 24 6/14 11,039 2,556 8,332 151 8,483 2,556 25 6/21 10,938 2,094 8,564 280 8,844 2,094 26 6/28 9,315 1,655 7,299 361 7,660 1,655 27 7/5 5,544 874 4,410 260 4,670 874 28 7/12 5,272 636 4,617 19 4,636 636 29-34 8/17 4,189 735 3,294 160 3,454 735
Run total: 111,580 16,479 91,610 3,491 95,101 16,479 95% CI: (13,445- (88,122- (2,147- (90,269- (13,445- 19,697) 94,950) 5,045) 99,995) 19,697) (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 trapped fish. (b) See Appendix Table D-1 for inclusive dates and other notes regarding statistical weeks and LGD operations. (c) From COE link.
68
Appendix Table D-5. Number of wild adult Chinook salmon scale and genetics samples collected at Lower Granite Dam (LGD) and subsequently aged or genotyped, spawn year 2009.
Number of Number of Scale samples: Genetics samples:
scale and scale and Number Percent Number Percent Sampling Wild genetics genetics Number Percent of samples of run of samples of run
Statistical period Number run samples systematic of samples of run genotyped genotyped genotyped genotypedweek(a) 2009 of days size(b) collected subsamples aged(c) aged for gender(c) for gender for stock(c) for stock
10-20 3/2-5/17 77 2,515 246 123 112 4.5 121 4.8 122 4.9 21 5/18-5/24 7 1,733 99 86 85 4.9 82 4.7 84 4.8 22 5/25-5/31 7 1,519 87 87 81 5.3 78 5.1 84 5.5 23 6/1-6/7 7 2,162 120 118 112 5.2 109 5.0 118 5.5 24 6/8-6/14 7 2,556 135 135 132 5.2 126 4.9 134 5.2 25 6/15-6/21 7 2,094 112 112 109 5.2 103 4.9 112 5.3 26 6/22-6/28 7 1,655 78 78 76 4.6 77 4.7 78 4.7 27-34(d) 6/29-8/17 50 2,245 104 104 101 4.5 100 4.5 102 4.5
Run total: 169 16,479 981 843 808 4.9 796 4.8 834 5.1 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 aged or genotyped fish. (b) From Appendix Table D-4. (c) Some valid samples were not aged or genotyped due to missing scales or fin clips; other valid samples were not able to be aged (freshwater and saltwater) or successfully genotyped; neither are included here. (d) Includes partial beginning or ending week.
69
Appendix Table D-6. Weekly age frequencies, by brood year and age class, of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009.
Sample Number Brood year and age class (frequency):
Statistical period of samples 2006 2006 2005 2005 2004 2004 2003 2003 week(a) ending(b) aged 0.2 1.1 1.2 2.1 1.3 2.2 1.4 2.3
10-20 5/17 112 - 2 83 1 25 - - 1 21 5/24 85 - 16 53 1 14 - 1 - 22 5/31 81 - 17 44 1 19 - - - 23 6/7 112 - 20 72 - 20 - - - 24 6/14 132 - 26 83 - 23 - - - 25 6/21 109 - 15 68 - 25 1 - - 26 6/28 76 1 25 41 1 8 - - - 27-34 8/17 101 2 45 42 1 9 1 - 1
Run total: 808 3 166 486 5 143 2 1 2 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 aged fish. (b) See Appendix Table D-5 for inclusive dates and other notes regarding statistical weeks and LGD operations.
70
Appendix Table D-7. Weekly age percentages, by brood year and age class, of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009. Percentages may not sum to 100.0% due to rounding error.
Sample Number Brood year and age class (percent):
Statistical period of samples 2006 2006 2005 2005 2004 2004 2003 2003 week(a) ending(b) aged 0.2 1.1 1.2 2.1 1.3 2.2 1.4 2.3
10-20 5/17 112 - 1.8 74.1 0.9 22.3 - - 0.9 21 5/24 85 - 18.8 62.4 1.2 16.5 - 1.2 - 22 5/31 81 - 21.0 54.3 1.2 23.5 - - - 23 6/7 112 - 17.9 64.3 - 17.9 - - - 24 6/14 132 - 19.7 62.9 - 17.4 - - - 25 6/21 109 - 13.8 62.4 - 22.9 0.9 - - 26 6/28 76 1.3 32.9 53.9 1.3 10.5 - - - 27-34 8/17 101 2.0 44.6 41.6 1.0 8.9 1.0 - 1.0
Run total: 808 0.4 20.5 60.1 0.6 17.7 0.2 0.1 0.2 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 aged fish. (b) See Appendix Table D-5 for inclusive dates and other notes regarding statistical weeks and LGD operations.
71
Appendix Table D-8. Weekly gender frequencies of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009.
Number
Gender (frequency):
Sample of samples Statistical period genotyped week(a) ending(b) for gender Female Male
10-20 5/17 121 61 60 21 5/24 82 34 48 22 5/31 78 37 41 23 6/7 109 45 64 24 6/14 126 43 83 25 6/21 103 26 77 26 6/28 77 27 50 27-34 8/17 100 25 75
Run total: 796 298 498 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 genotyped fish. (b) See Appendix Table D-5 for inclusive dates and other notes regarding statistical weeks and LGD operations.
72
Appendix Table D-9. Weekly gender percentages of wild adult Chinook salmon sampled at Lower Granite Dam (LGD), spawn year 2009. Percentages may not sum to 100.0% due to rounding error.
Number
Sample of samples Statistical period genotyped Gender (percent): week(a) ending(b) for gender Female Male
10-20 5/17 121 50.4 49.6 21 5/24 82 41.5 58.5 22 5/31 78 47.4 52.6 23 6/7 109 41.3 58.7 24 6/14 126 34.1 65.9 25 6/21 103 25.2 74.8 26 6/28 77 35.1 64.9 27-34 8/17 100 25.0 75.0
Run total: 796 37.4 62.6 (a) Statistical weeks were grouped to try to provide a minimum sample size of 100 genotyped fish. (b) See Appendix Table D-5 for inclusive dates and other notes regarding statistical weeks and LGD operations.
73
Appendix Table D-10. Frequencies of wild adult Chinook salmon sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Only individual fish whose assignment probability was ≥0.90 are included. See Appendix Table B-2 for stock abbreviations.
Brood year and age class (frequency):
2006 2006 2005 2005 2004 2004 2003 2003 Stock Gender 0.2 1.1 1.2 2.1 1.3 2.2 1.4 2.3 Total
UPSALM F - - 11 - 2 - - - 13 M - 5 16 1 1 - - - 23
Total 0 5 27 1 3 0 0 0 36
MFSALM F - - 5 - 1 - - - 6 M - 6 5 - - - - - 11
Total 0 6 10 0 1 0 0 0 17
SFSALM F - - 10 - 3 1 - - 14 M - 12 16 - 2 - - - 30
Total 0 12 26 0 5 1 0 0 44
CLWRGR F - - 38 - 17 - - 1 56 M - 17 47 1 6 - - - 71
Total 0 17 85 1 23 0 0 1 127
TUCANO F - - - - - - - - M - 1 1 - - - - - 2
Total 0 1 1 0 0 0 0 0 2
FALL F - - - - 2 - - - 2 M 3 1 1 1 3 1 - - 10
Total 3 1 1 1 5 1 0 0 12
Grand total: 3 42 150 3 37 2 0 1 238
74
Appendix Table D-11. Percentage of wild adult Chinook salmon sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Only individual fish whose assignment probability was ≥0.90 are included. Percentages may not sum to 100.0% due to rounding error. See Appendix Table B-2 for stock abbreviations.
Brood year and age class (percent):
2006 2006 2005 2005 2004 2004 2003 2003 Stock Gender 0.2 1.1 1.2 2.1 1.3 2.2 1.4 2.3 Total
UPSALM F - - 30.6 - 5.6 - - - 36.1M - 13.9 44.4 2.8 2.8 - - - 63.9
Total 0.0 13.9 75.0 2.8 8.3 0.0 0.0 0.0 100.0
MFSALM F - - 29.4 - 5.9 - - - 35.3M - 35.3 29.4 - - - - - 64.7
Total 0.0 35.3 58.8 0.0 5.9 0.0 0.0 0.0 100.0
SFSALM F - - 22.7 - 6.8 2.3 - - 31.8M - 27.3 36.4 - 4.5 - - - 68.2
Total 0.0 27.3 59.1 0.0 11.4 2.3 0.0 0.0 100.0
CLWRGR F - - 29.9 - 13.4 - - 0.8 44.1M - 13.4 37.0 0.8 4.7 - - - 55.9
Total 0.0 13.4 66.9 0.8 18.1 0.0 0.0 0.8 100.0
TUCANO F - - - - - - - - 0.0M - 50.0 50.0 - - - - - 100.0
Total 0.0 50.0 50.0 0.0 0.0 0.0 0.0 0.0 100.0
FALL F - - - - 16.7 - - - 16.7M 25.0 8.3 8.3 8.3 25.0 8.3 - - 83.3
Total 25.0 8.3 8.3 8.3 41.7 8.3 0.0 0.0 100.0
75
Appendix Table D-12. Estimated escapement of wild adult Chinook salmon sampled at Lower Granite Dam (LGD) by gender by age for each stock in spawn year 2009. Only individual fish whose assignment probability was ≥0.90 are included. Total stock escapement estimates are from Figure 14; see Appendix Table B-2 for stock abbreviations.
Brood year and age class (estimated number):
2006 2006 2005 2005 2004 2004 2003 2003 Stock Gender 0.2 1.1 1.2 2.1 1.3 2.2 1.4 2.3 Total
UPSALM F - - 1,138 - 207 - - - 1,345M - 517 1,655 103 103 - - - 2,378
Total 0 517 2,793 103 310 0 0 0 3,723
MFSALM F - - 593 - 119 - - - 712M - 712 592 - - - - - 1,304
Total 0 712 1,185 0 119 0 0 0 2,016
SFSALM F - - 1,081 - 324 108 - - 1,513M - 1,298 1,731 - 216 - - - 3,245
Total 0 1,298 2,812 0 540 108 0 0 4,758
CLWRGR F - - 1,686 - 754 - - 44 2,484M - 754 2,086 44 266 - - - 3,150
Total 0 754 3,772 44 1,020 0 0 44 5,634
TUCANO F - - - - - - - - 0M - 56 55 - - - - - 111
Total 0 56 55 0 0 0 0 0 111
FALL F - - - - 40 - - - 40M 59 20 19 20 59 20 - - 197
Total 59 20 19 20 99 20 0 0 237
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Prepared by: Approved by: IDAHO DEPARTMENT OF FISH AND GAME William C. Schrader Peter F. Hassemer Principal Fishery Research Biologist Anadromous Fisheries Manager Timothy Copeland Edward B. Schriever, Chief Senior Fishery Research Biologist Bureau of Fisheries Michael W. Ackerman Fishery Research Biologist Kristin Ellsworth Fishery Research Biologist Matthew R. Campbell Genetics Laboratory Manager