Data for 2006 annual reportSteelhead in the John Day River Basin
Annual Technical Report
Prepared by:
Terra Lang Schultz, Assistant Project Leader Wayne H. Wilson, Assistant Project Leader
Oregon Department of Fish and Wildlife
John Day, Oregon
Oregon Department of Fish and Wildlife
La Grande, Oregon
Funded by:
Project Number: 1998-016-00
Contract Number: 25467
TABLE OF CONTENTS
Objectives.......................................................................................................................1 Accomplishments and Findings .....................................................................................1 Acknowledgements ........................................................................................................2
LIST OF FIGURES
Figure 1. Map of John Day River basin. Arrows indicate approximate locations of rotary screw traps....................................................................................................................................... 5 Figure 2. Map of the upper mainstem John Day River. Arrows indicate upstream and downstream limits of census spawning ground surveys. ................................................................ 6 Figure 3. Map of the Middle Fork John Day River. ....................................................................... 7 Figure 4. Map of the North Fork John Day River........................................................................... 8 Figure 5. Index and census spawning ground survey counts of spring Chinook salmon redds in the John Day River basin. ............................................................................................... 18 Figure 6. Weekly number of juvenile spring Chinook captured at four rotary screw traps operated on the John Day River basin during autumn 2005 and spring 2006. ............................. 32 Figure 7. Weekly number and catch per unit effort (CPUE, number/seine haul) of spring Chinook smolts captured while seining the John Day River between river kilometers 274 and 296 during spring, 2006. ........................................................................................................ 32 Figure 8. Weekly number of juvenile summer steelhead captured at four rotary screw traps operated on the John Day River basin during autumn 2005 and spring 2006. ............................. 33
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LIST OF TABLES
Table 1. Description, length, date of index, census, and random spawning survey sections in the John Day Basin for 2006..................................................................................................... 10 Table 2. Summary of ELISA optical density value ranges, designated Rs antigen category, and significance of result with respect to adult Chinook salmon.................................................. 12 Table 3. Kilometers surveyed, total number of redds observed, and number of new redds observed during spring Chinook salmon spawning surveys in the John Day River basin, 2006............................................................................................................................................... 16 Table 4. Estimated number of spring Chinook salmon redds and spawners and percentage of redds in each survey area compared to all survey areas in the John Day River basin, 2006. ............................................................................................................................................ 17 Table 5. Number of carcasses sampled during all surveys of spring Chinook salmon spawning surveys in the John Day River basin during 2006. Totals include carcasses of unknown sex. ................................................................................................................................ 19 Table 6. Number of female, male, and unknown carcasses (n) sampled during all surveys of spring Chinook salmon spawning surveys in the John Day River basin during 2006.............. 19 Table 7. Sex ratio of carcasses sampled during all surveys in the John Day River basin, 2006. Number of carcasses (n) in which sex could be determined is also shown. ...................... 20 Table 8. Percent age (y) and sex composition of male (M) and female (F) spring Chinook salmon carcasses sampled in the survey areas of the John Day River basin during 2006.. .......... 20 Table 9. Number examined (n), mean, standard error (SE), and range of middle of eye to posterior scale (MEPS) length (mm) by age (y) and sex (male, M; female, F) of spring Chinook salmon carcasses sampled during spawning ground surveys in the John Day River basin during 2006.......................................................................................................................... 21 Table 10. Number of female spring Chinook salmon assigned to one of five categories based on the percentage of total eggs retained as estimated by dissection of carcasses observed during spawning ground surveys of the John Day River basin, 2006.. ......................... 22 Table 11. Number of adult spring Chinook salmon observed for gill lesions as determined by carcass gill observations in four subbasins (five spawning areas) during spawning ground surveys in the John Day River basin, 2006....................................................................... 22 Table 12. Percent pre-spawning mortality (PSM; 100% egg retention) of female carcasses and percent gill lesion incidence (GL) of all examined carcasses in the Granite Creek System, including significant difference, between 2000–2006 in the John Day Basin.. .............. 23
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Table 13. Sample date, sample identification, stream location, fin clip, sex, medial eye to posterior scale length (MEPS, mm), and hatchery (H) origin and release location as determined by coded wire tag (CWT) information for all fin-clipped spring Chinook salmon sampled during spawning ground surveys of the John Day Basin, 2006.. ....................... 23 Table 14. ELISA readings (OD405) for Renibacterium salmoninarum from kidney samples taken from spring Chinook salmon carcasses July through September in the John Day River basin, 2006.. ........................................................................................................................ 24 Table 15. Number of juvenile spring Chinook and summer steelhead PIT tagged during the fall/winter (8 October 2005 to 31 January 2006) and spring (1 February to 26 June 2006) at three rotary screw traps and while seining in the Mainstem John Day River................ 27 Table 16. Number (n), mean, standard error (SE), and range of fork length (mm), mass (g), and coefficient of condition for spring Chinook migrants captured in four rotary screw traps and while seining on the Mainstem John Day River during the spring (1 February to 26 June 2006). ............................................................................................................................... 27 Table 17. Smolt/redd ratios based on recent and historic estimates of smolt abundance and census redd counts for spring Chinook salmon for the entire John Day River basin.. ................. 28 Table 18. Mainstem John Day River smolt/redd ratios based on estimates of smolt abundance and census redd counts for spring Chinook salmon, 2002–2004 brood years (Wilson et al 2002, 2005, Schultz et al, 2007). ............................................................................. 28 Table 19. Middle Fork John Day River smolt/redd ratios based on estimates of smolt abundance and census redd counts for spring Chinook salmon, 2002–2004 brood years (Wilson et al 2002, 2005, Schultz et al, 2007). ............................................................................. 28 Table 20. North Fork John Day River smolt/redd ratios based on estimates of smolt abundance and census redd counts for spring Chinook salmon, 2002–2004 brood years............ 29 Table 21. Number (n), mean, standard error (SE), and range of fork length (mm), mass (g), and coefficient of condition for steelhead migrants captured in four rotary screw traps and while seining on the Mainstem John Day River during two periods (Fall [8 October, 2005 to 31 January 2006]; Spring [1 February to 26 June 2006]). ........................................................ 29 Table 22. Season, collection period, number captured, percent capture efficiency, and abundance estimates for juvenile spring Chinook migrants captured at four rotary screw trap sites and while seining in the John Day River (rkm 274–296) from 8 October 2005 to 26 June 2006. ................................................................................................................................ 30 Table 23. Season, collection period, number captured, capture efficiency, and abundance estimates for juvenile steelhead migrants captured at four rotary screw trap sites and while seining in the John Day River (rkm (274-296) from 8 October 2005 to 26 June 2006. ............... 30
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Table 24. Number of each fish species captured incidentally at the South Fork (SF), Mainstem (MS), Middle Fork (MF), and North Fork (NF) trap sites, and in the Mainstem seining operation (rkms 274–296, 4/5/06–5/22/06). ..................................................................... 33 Table 25. Number detected (N), first and last detection dates, and mean, standard error (SE) and range of travel time (days) to detection at John Day Dam, Bonneville Dam, and the Columbia River Estuary during 2006 for spring Chinook and summer steelhead smolts PIT tagged during the spring (February 1 to June 26, 2006) in the John Day Basin.................... 34 Table 26. Brood year, migration year, number of smolts PIT tagged, and the number and age of PIT-tagged adult Chinook salmon detected at Bonneville Dam during each return year. Estimated smolt-to-adult survival (SAR) of spring Chinook salmon PIT tagged from 2000–2005 is also shown. ............................................................................................................. 35 Table 27. Detection year and number of PIT tagged adult spring Chinook tagged in the John Day basin and detected at Bonneville, McNary, Ice Harbor, and Lower Granite Dams during 2001–2006. ........................................................................................................................ 35
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LIST OF APPENDICES Appendix A. 2006 Spring Chinook Spawning Survey Data....................................................... 47 Appendix B. 2006 Spring Chinook Salmon Redd Locations ..................................................... 54 Appendix C. Historic Census and Index Redd Counts ............................................................... 70 Appendix D. Location Information for Major Spring Chinook Spawning Survey Sections ...... 77 Appendix E. 2006 Mainstem John Day Seining Sites and Catch Statistics................................ 83
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1. Estimate number and distribution of spring Chinook salmon Oncorhynchus tshawytscha redds and spawners in the John Day River subbasin.
2. Estimate smolt-to-adult survival rates (SAR) and out-migrant abundance for spring Chinook and summer steelhead O. mykiss and life history characteristics of summer steelhead.
Accomplishments and Findings
To estimate spring (stream-type) Chinook Oncorhynchus tshawytscha and summer steelhead O. mykiss smolt-to-adult survival (SAR) we PIT tagged 3,418 juvenile spring Chinook and 2,167 juvenile steelhead during the spring of 2006. We estimated that 101,262 (95% CI, 59,688–179,494) juvenile spring Chinook emigrated from the upper John Day subbasin past our four rotary screw trap sites during the spring. We also estimated that 52,640 (95% CI, 26,320–101,614) juvenile spring Chinook and 58,490 (95% CI, 22,089–90,428) juvenile steelhead migrated past our Mainstem rotary screw trap at river kilometer (rkm) 326 between 10 February and 26 June 2006. We estimated that 18,306 (95% CI, 14,372–23,892) juvenile spring Chinook and 20,720 (95% CI, 14,401– 30,870) steelhead migrated past our Middle Fork trap (rkm 24) between 6 March and 22 June 2006. For the 2004 brood year, we estimated 61 spring Chinook smolts per redd for the entire John Day River basin, 159 smolts per redd for the Mainstem, 65 smolts per redd for the Middle Fork, and 54 smolts per redd for the North Fork. Steelhead emigrant age structure differed among the four trap sites (χ2 = 153.8; P < 0.0005; df = 9). More age-1 juvenile steelhead (17.9%) were captured at our Mainstem trap (χ2 = 86.9; P < 0.0005; df = 1) and fewer age-1 juvenile steelhead (0.1%; χ2 = 51.2; P < 0.0005; df = 1) were captured at our South Fork Trap than at all other traps (6.7%). The age structure of all steelhead emigrants PIT-tagged in the spring was estimated to be 63.1% age 2, 30% age 3, 6.7% age 1, and 0.1% age-4 fish. Spring Chinook SAR for the 2001 brood year was estimated at 2.08% (128 returns of 6,147 PIT tagged smolts). Summer steelhead SAR for the 2004 migration year was estimated at 2.84% (106 returns of 3,732 PIT-tagged migrants).
Spawning ground surveys for spring (stream-type) Chinook salmon were conducted in four main spawning areas (Mainstem, Middle Fork, North Fork, and Granite Creek System) and seven minor spawning areas (South Fork, Camas Creek, Desolation Creek, Trail Creek, Deardorff Creek, Clear Creek, and Big Creek) in the John Day River basin during August and September of 2006. Census surveys included 299.1 river kilometers (88.2 rkm within index, 198.6 rkm additional within census, and 12.3 rkm within random survey areas) of spawning habitat. We observed 1,044 redds and 598 carcasses including 451 redds in the Mainstem, 199 redds in the Middle Fork, 262 redds in the North Fork, 99 redds in the Granite Creek System, and 33 redds in Desolation Creek. Age composition of carcasses sampled for the entire basin was 1.0% age-2 precocious, 2.6% age-3, 93.5% age
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4, and 2.8% age 5. The sex ratio was 51.4% female and 48.6% male. During 2006, 93.9% of female carcasses sampled had released all of their eggs. Pre-spawn mortality did not significantly differ between subbasins as in the past. Twelve (2.0%) of 598 carcasses were of hatchery origin. Of 394 carcasses examined, 7.9% were positive for the presence of lesions. A significantly higher incidence of gill lesions was found in the Granite Creek System when compared to the rest of the basin. Of 169 kidney samples tested, one (0.6%) had clinical BKD levels. The infected fish was an age-4 male in Desolation Creek, within the North Fork subbasin. All samples tested for IHNV were negative.
Acknowledgements
We would like to acknowledge the assistance and cooperation of many private landowners throughout the John Day River basin who allowed us to survey on their property. The cooperation of private landowners and The Confederated Tribes of the Warm Springs Reservation was essential in meeting our project objectives. Additionally, we would also like to thank Tim Unterwegner and Jeff Neal for providing much needed guidance and advice. We would also like to thank all those who volunteered to assist us with our spawning ground surveys. This project was funded by the U. S. Department of Energy, Bonneville Power Administration, Environment, Fish, and Wildlife. Project Number: 1998-016-00. Contract Number: 25467.
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INTRODUCTION
The John Day River subbasin supports one of the last remaining intact wild populations of spring Chinook salmon and summer steelhead in the Columbia River Basin. These populations, however, remain depressed relative to historic levels. Between the completion of the life history and natural escapement study in 1984 and the start of this project in 1998, spring Chinook spawning surveys did not provide adequate information to assess age structure, progeny-to-parent production values, smolt-to-adult survival (SAR), or natural spawning escapement. Further, only very limited information is available for steelhead life history, escapement, and productivity measures in the John Day subbasin. Numerous habitat protection and rehabilitation projects to improve salmonid freshwater production and survival have also been implemented in the basin and are in need of effectiveness monitoring. While our monitoring efforts outlined here will not specifically measure the effectiveness of any particular project, they will provide much needed background information for developing context for project-specific effectiveness monitoring efforts. To meet the data needs as index stocks, to assess the long-term effectiveness of habitat projects, and to differentiate freshwater and ocean survival, sufficient annual estimates of spawner escapement, age structure, SAR, egg-to-smolt survival, smolt-per-redd ratio, and freshwater habitat use are essential. We have begun to meet this need through spawning ground surveys initiated for spring Chinook salmon in 1998 and smolt PIT-tagging efforts initiated in 1999. Additional sampling and analyses to meet these goals include an estimate of smolt abundance and SAR rates, and an updated measure of the freshwater distribution of critical life stages.
Because Columbia Basin managers have identified the John Day subbasin spring Chinook population as an index population for assessing the effects of alternative future management actions on salmon stocks in the Columbia Basin (Schaller et al. 1999) we continue our ongoing studies. This project is high priority based on the high level of emphasis the NWPPC Fish and Wildlife Program, Subbasin Summaries, NMFS, and the Oregon Plan for Salmon and Watersheds have placed on monitoring and evaluation to provide the real-time data to guide restoration and adaptive management in the region.
By implementing the proposed program we have been able to address many of the goals for population status monitoring, such as defining areas currently used by spring Chinook for holding and spawning habitats and determining range expansion or contraction of summer rearing and spawning populations. The BiOp describes these goals as defining population growth rates (adult monitoring), detecting changes in those growth rates or relative abundance in a reasonable time (adult/juvenile monitoring), estimating juvenile abundance and survival rates (juvenile/smolt monitoring), and identifying stage- specific survival (adult-to-smolt, smolt-to-adult).
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STUDY AREA
The John Day River drains 20,300 km2 of east central Oregon, the third largest drainage area in the state (Figure 1). From its source in the Strawberry Mountains at an elevation near 1,800 m, the John Day River flows 457 km, to an elevation near 90 m, to the Columbia River. It enters the Columbia River at river kilometer (rkm) 351. The basin is bounded by the Columbia River to the south and the Ochoco Mountains to the west.
Spring Chinook salmon primarily spawn in the upper Mainstem John Day River (hereafter called Mainstem) above the mouth of Indian Creek (Figure 2), in the Middle Fork John Day River (hereafter called Middle Fork) above Armstrong Creek (Figure 3), and in the North Fork John Day River (hereafter called North Fork; Figure 4) above the mouth of Camas Creek. Important spawning tributaries of the North Fork include Granite Creek and its tributaries (Clear Creek and Bull Run Creek; hereafter called Granite Creek System) and Desolation Creek. Spawning has also occurred in the South Fork John Day River (hereafter called South Fork), and the North Fork Tributaries Camas Creek, and Trail Creek. Fall Chinook are thought to spawn in the Lower Mainstem downstream of Kimberly, OR (rkm 298) but primarily between Cottonwood Bridge (rkm 64) and Tumwater Falls (rkm 16).
Summer steelhead sampled during this study have a spawning and rearing distribution in the Mainstem, South Fork, Middle Fork, and North Fork channels and tributaries of the John Day River upstream of rkm 298 where the North Fork and Mainstem merge. Summer steelhead also spawn and rear in lower Mainstem tributaries downstream of rkm 298. When juvenile steelhead are referenced in this document, we acknowledge the presence of alternate life-history forms and that some juveniles of all sizes may be resident (redband trout) or anadromous (steelhead) life-history forms. These alternate life-history forms are typically morphologically indistinguishable when examined as immature parr. We therefore refer to all juvenile O. mykiss as juvenile steelhead. Maps of the distribution of both Chinook and steelhead in the John Day River basin can be found at the Streamnet website: http://www.streamnet.org/online-data/map_catalog.html.
Day River
10 0 10 20 30 40 50 60 70 805 Kilometers
Day
Figure 1. Map of John Day River basin. Arrows indicate approximate locations of rotary screw traps.
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Figure 2. Map of the upper mainstem John Day River. Arrows indicate upstream and downstream limits of census spawning ground surveys.
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Figure 3. Map of the Middle Fork John Day River. Arrows indicate upstream and downstream limits of census spawning ground surveys.
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Figure 4. Map of the North Fork John Day River. Survey areas begin at the confluence with Desolation Creek and extend upstream to the confluence with Baldy Creek. Granite creek survey areas extend from the mouth to approximately two kilometers above the confluence with Bull Run Creek, Clear Creek to the confluence with Beaver Creek, and Bull Run Creek upstream to the USFS Boundary guard station. Arrows show limits of census survey area. Not all reaches of stream between arrows were surveyed. Dashed lines denote boundaries of North Fork John Day wilderness.
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METHODS
Spring Chinook Spawning Surveys
Spring Chinook salmon spawning surveys including historic index, census, and random survey sections were conducted during the months of August and September to encompass the spatial and temporal distribution of Chinook spawning in the John Day River basin (Table 1). Index sections were surveyed to provide relative abundance comparisons with historic redd count data collected since 1959. Index counts only encompass redds counted within index reaches, at the index time. New redds observed during post-index surveys are not included in the index count unless spawning is exceptionally late and more live fish than redds are observed during the index. Census survey sections are areas where redds have been previously documented, outside of the index area. Random surveys are conducted outside of the known spawning area to account for range expansion. Collectively, these surveys provide an annual census of spawning spring Chinook salmon and their redds. Index surveys were scheduled to take place near the peak of spawning in each of the four primary spawning areas (Mainstem, Middle Fork, North Fork, and Granite Creek System). Pre- index surveys, one week prior to the index survey, were conducted in the North Fork. Post-index surveys, one week after the index surveys, were conducted in index sections in the Mainstem and Granite Creek System (GCS) to account for temporal variation in spawning. Post-index surveys were not conducted in the Middle Fork and North Fork because spawning was completed and few live fish were left at the time of the index survey.
Census surveys were conducted the same day or within one day as the index and post-index surveys in all four main spawning areas as well as in the South Fork and various tributaries of the North Fork to ensure that all spawning habitat was observed. If many live fish were observed during the initial surveys, we would return one week later to re-survey and make certain that all spawning was complete. Census surveys were conducted twice in the Mainstem and Desolation Creek, and thrice in the North Fork. A pre-census survey was conducted during early August in the upper North Fork (between Trail Crossing and Trout Creek) due to early spawning activity.
Random survey sections, approximately 2 km in length, were drawn from a sampling universe defined as 20 km downstream of our current survey sections or 20 km downstream of the most downstream redd observed in each HUC (4th level HUC; North Fork, Middle Fork, Upper Mainstem), and 4 km upstream of our current survey sections or the most upstream redd observed since 1959. If redds are observed in a random site, that survey section is added to the census survey the following year. Random surveys were conducted when time and personnel allowed.
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Table 1. Description, length, date of index, census, and random spawning survey sections in the John Day Basin for 2006. Sections are listed in upstream order for Mainstem and Middle Fork subbasins, and downstream order for South Fork and North Fork subbasins. Distance
Stream Survey
Census Census Index Index Index Census Index Index Census
Canyon Creek: Mouth of Berry Creek to 2.1 km downstream of Vance Creek Indian Creek to PWP Lower Boundary PWP Lower Boundary to Dad’s Creek Dad’s Creek to Field Lower Fence Field Lower Fence to Jacobs Upper Fencea Jacobs Upper Fence to Road 13 Bridge Mouth of Deardorff Creek to 2.3 km upstream Road 13 Bridge to Reynolds Upper Fenceb Reynolds Upper Fence to Ricco Upper Fence Ricco Upper Fence to Call Creek
1.9
1.2
4.4 3.1 2.1 5.5 1.2 1.4 1.4 2.8 2.0
Sep 21 Access Denied Sep 5, 13 Access Denied Sep 5, 13 Access Denied Sep 5 Sep 5, 13 Access Denied Sep 5
South Fork Census Census Census Random
Izee Falls to Cougar Gulch Cougar Gulch to Rock Pile Ranch Bridge Rock Pile Ranch Bridge to Murderer’s Creek Road 42 Bridge to 0.2 km upstream of Deadman Gulch
5.2 4.5 5.5 1.9
3.2 2.8 3.4 1.2
Middle Fork Random Random Census Index Census
0.8 km downstream of Hwy 395 Bridge to 1.0 km downstream of Willow Creek 1.0 km downstream of Elliot Creek to Bullrun Creek Armstrong Creek to Beaver Creek Beaver Creek to Highway 7 Culvert Highway 7 Culvert to Phipps Meadow
1.9
Sep 27 Sep 27 Sep 20 Sep 19 Sep 19
Clear Creekc
Census Census
Mouth to Highway 26 Bridge Highway 26 Bridge to 1.6 km upstream
2.1 1.6
1.3 1.0
Sep 19 Sep 19
North Fork Random Census Census Census Index Census Index Census Random
Mouth of Crane Creek to 1.0 km upstream North Fork Trail Crossing to Cunningham Creek Cunningham Creek to Trout Creek Trout Creek to Granite Creek Granite Creek to Cougar Creek Cougar Creek to Big Creek Big Creek to Nye Creek Nye Creek to Camas Creek 0.8 km downstream of Deerhorn Creek to 0.9 km upstream of Jericho Creek
1.0 3.5
10.3 1.1
Aug 31 Aug 28, Sep 22 Aug 4, 14, 28, Sep 12 Sep 12, 13 Sep 6, 7, 14, 15 Sep 15 Sep 8, 15 Sep 15 Sep 25
Big Creek Census Mouth to Winom Creek 2.6 1.6 Sep 8 Trail Creek Census Mouth to confluence of North and South Forks 3.1 1.9 Aug 29, Sep 12 Granite Creek
Index Census
Road 73 Culvert to Buck Creek Buck Creek to mouth
9.5 7.9
5.9 4.9
Clear Creekd
Census Census Census
Ruby Creek Trailhead to Alamo Road Alamo Road to Smith Lower Boundary Smith Lower Boundary to Beaver Creek
1.8 1.3 1.4
1.1 0.8 0.9
Census Index
Beaver Creek to Old Road Crossing Old Road Crossing to Mouth
1.6 4.8
1.0 3.0
Bull Run Creek
2.4 5.0
1.5 3.1
Camas Creek
Census Random
0.4 km upstream to 0.4 km downstream of Fivemile Creek Bridge Creek to 1.9 km upstream near Fivemile Creek
0.8 1.9
0.5 1.2
Desolation Creek
Census Impassable Waterfalls on South Fork to Mouth 46.0 28.5 Sep 11, 18
a Includes mileage of North Channel and South Channel b Reynolds Upper Fence was previously listed as Klondike Lower Fence c Tributary of the Middle Fork d Tributary of Granite Creek in the North Fork subbasin
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Spawning surveys were conducted by walking in an upstream direction on the Mainstem, Middle Fork, South Fork, Big Creek, Trail Creek, and Clear Creek, and in a downstream direction on the North Fork, Camas Creek, Desolation Creek, Granite Creek, and Bull Run Creek. Where we were denied access to one side of the river on the Mainstem, the crew only walked on the permissible side. Survey sections ranged in length between 0.2 and 9.7 rkm depending on accessibility and difficulty. Start and stop GPS coordinates were determined using Maptech software (2004) and are listed in Appendix Tables D-1 through D-9. Typically teams of two would walk stream sections for safety reasons and to ensure accuracy when distinguishing redds. In each section, surveyors recorded the number of new redds, number of live adult fish (on/near and off dig), and number of carcasses. On reaches surveyed more than once (i.e. index and census), the first team of surveyors marked redds with numbered colored flagging placed near each redd or group of redds. During subsequent surveys, surveyors re-visited flagged redds and recorded any new redds. During the last survey of each reach, surveyors marked geographic, UTM coordinates (NAD 27 conus datum) of each redd or group of redds with a GPS receiver and topographic map. Flagging was removed during the final surveys.
Each observed carcass was examined and sampled in each subbasin (except the North Fork below Trout Creek) due to typically smaller numbers of fish and the need for disease surveillance. Every other carcass was sampled in the North Fork in order to be time efficient. However, each carcass encountered throughout the basin was recorded as a hash mark according to sex (male, female, jack or 3-year old, or 2-year old precocious) and origin (hatchery or wild). Sampled carcasses were measured for fork length (FL, mm) and medial eye to posterior scale length (MEPS, mm), and dissected to verify sex. Females were checked for egg retention and retained eggs were estimated to the nearest 25%. Trained surveyors recorded gill lesion presence or absence on fresh carcasses. The location of each lesioned fish was marked using a hand-held GPS receiver and later transferred to Maptech for spatial pattern analysis. Differences in the proportions of incompletely spawned females and prevalence of gill lesions on carcasses among survey areas were tested using the z-test (SigmaStat 2004). Genetic samples (consisting of a small piece of rayed fin or skeletal muscle tissue on fresh carcasses) were collected and placed in vials containing 100% denatured ethanol at the request of the National Oceanic and Atmospheric Administration (NOAA) Fisheries Department.
Kidney samples were collected from fresh spring Chinook carcasses in each of the main spawning areas to determine concentration and prevalence of Renibacterium salmoninarum (Rs) antigen, the causative agent of bacterial kidney disease (BKD), in the spawning population. Trained surveyors selected carcasses with intact organs and membranes and non-glazed eyes, indicative of recent mortality. Wooden craft sticks and plastic spoons were used to scrape a 1–2 gram sample of kidney from each carcass. Samples were placed in sterile 1-oz whirl-pack bags and stored in a cooler with ice until transported to a freezer. The enzyme-linked immunosorbent assay (ELISA) was used to obtain optical density (OD) values according to methodology adapted from Pascho and Mulcahy (1987). The Rs antigen level is an indication of bacterial infection load of R. salmoninarum. Table (2) summarizes the optical density value ranges and standard infection level categories used for BKD. Some samples were also examined for the presence of infectious hematopoietic necrosis virus (IHNV) by standard cell culture techniques using a portion of the collected kidney tissue. Viral samples were plated on Epithelioma papillosum cyprini and Chinook salmon embryo cell lines and incubated 10 to 14 days respectively.
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Table 2. Summary of ELISA optical density value ranges, designated Rs antigen category, and significance of result with respect to adult Chinook salmon.
Optical density value (OD405) range
Rs antigen category
≤ 0.100 Negative or Very Low
Infection not detected by ELISA.
0.100–0.299 Low Positive Low level of Rs antigen detected, not a factor in death, did not have BKD. 0.300–0.699 Moderate
Positive Moderate level of Rs antigen detected, beginning of significant infection with Rs in this range, signs of disease absent, rarely factor in death.
0.700–0.999 High Positive Infection with Rs at high level, gross signs rare, could be factor in death. ≥ 1.000 Clinicala Grossly infected with Rs, signs of disease usually, death probable, fish had
BKD. a By the ELISA, an optical density (OD) equal to or greater than 1.000 is considered to be clinical BKD b Generally the significance to the maternal progeny is that there is a greater probability of vertical transmission (female parent to progeny) of Rs (BKD) from females with higher ELISA values
Trained surveyors on Granite Creek (1.6 km above Clear Creek to Buck Creek) individually cultured potential lesion areas on gills using disposable sterile loops. Samples were then immediately plated onto cytophaga agar in the field. Inoculated plates were incubated in the lab at 37ºC and examined five days later. Plates were scrutinized for colony and wet mount morphology, gram status and oxidase reactivity.
The seven-day moving average of daily maximum and minimum temperatures from the GCS was calculated by computing the sum of the first seven daily maximum or minimum temperatures divided by seven. The calculated average was then plotted on the date of the seventh day of measurement for that period. Then, starting with the second day, the next seven days were averaged and the calculated value was plotted on the eight day of measurement and so forth. This process was completed for temperatures from July through September to see if any correlations existed between temperature and lesion incidence. Some temperature data was also obtained from the USFS and DART. Results were compared to data from previous years. Stream flow in each subbasin was accessed using the USGS website http://waterdata.usgs.gov.
Due to time constraints, we sub-sampled carcasses. Surveyors collected scale samples from wild and hatchery carcasses encountered with a MEPS length of ≤ 550 mm (likely age-3 adults) and ≥ 650 mm (likely age-5 adults). Carcasses from 551 to 649 mm were assumed to be 4-year old fish, based on the size-at-age distribution of carcasses examined during previous years. Scales were mounted on gummed cards, impressions were made in acetate and viewed using a microfiche reader, and annuli were counted to determine age, by two different readers. We calculated age structure for spawning populations separately for the Mainstem, Middle Fork, North Fork, GCS, and Desolation Creek. Tails were removed from all carcasses to prevent re- sampling. Carcasses were then returned near their original position in the stream.
Carcasses of hatchery fish were identified by an adipose fin clip and subsequently had their snout removed to detect the presence of a coded wire tag (CWT). Snouts were bagged with a numbered identification card and frozen. Later in the lab, snouts were halved and scanned for a CWT using a v-box tag detector. Any CWTs found were cleaned and examined for a tag code (binary or numerical) using a microscope. Tag codes were entered into the CWT database for ODFW and hatchery of origin was queried using the Pacific States Marine Fish Commission Regional Mark Information System database.
All spring Chinook redds in the basin were visually counted with the exception of areas in the Mainstem where landowners denied access. Where we were denied access, we multiplied the number of index kilometers not surveyed (11.9) by the redds/kilometer ratio (8.45) of index sections that were surveyed. Where we were denied access to a Mainstem census survey section, we multiplied the number of denied census kilometers (7.1) by the ratio of known redds/kilometer (4.4) of those census sections surveyed in 2006. If we were denied access to a random survey section, we drew the next random site.
A lack of weir counts in the basin prevents basin-specific fish/redd estimates. We therefore estimated spawner escapement conservatively by multiplying the number of redds counted by the standard ratio of three fish/redd. We also estimated spawner escapement by multiplying the number of redds by 5.9 fish/redd estimated above the Warm Springs River weir (Deschutes River basin) and 2.31 fish/redd from above the Catherine Creek weir in the Grande Ronde River basin in 2006 (Lisa Hewlett, CTWSR, unpublished data; Fred Monzyk, ODFW, unpublished data).
Smolt Capture and Tagging
During the 2006 migration, juvenile spring Chinook and summer steelhead migrants were captured at four rotary screw trap sites in the John Day River basin and while seining in the Mainstem John Day River to estimate abundance, smolt-to-adult survival (SAR), and to study life history characteristics of summer steelhead in the John Day River basin. Two rotary screw traps were located in the Upper Mainstem fourth level HUC and are hereafter referred to as the Mainstem trap at rkm 326 of the Mainstem John Day River and the South Fork trap located at rkm 10 of the South Fork John Day River. The Mainstem trap was located downstream of the confluence of the South Fork and Mainstem rivers. A third rotary screw trap was operated in the Middle Fork John Day River at rkm 24 and is hereafter referred to as the Middle Fork trap. The fourth trap is located at rkm 26 on the North Fork John Day River and is hereafter referred to as the North Fork trap. The Mainstem seining operation was located downstream of three of the four fourth level HUC’s in the John Day River basin including the Upper Mainstem, Middle Fork, and North Fork.
The Mainstem trap, North Fork trap, and Mainstem seining operation are located downstream of all known spring Chinook summer rearing habitat. The Middle Fork trap is upstream of four fish bearing tributaries entering the Middle Fork including Six-mile Creek, Three-mile Creek, Long Creek, and Eight-mile Creek. The North Fork trap is upstream of one North Fork tributary, Rudio Creek. The South Fork trap was operated to supplement steelhead PIT tagging efforts for SAR estimates. All rotary screw traps were equipped with live boxes, which safely hold juvenile fish over a 24 to 72 h time interval. At the Mainstem and North Fork trap sites (rkm 326, and rkm 26, respectively) we fished 2.44 meter diameter rotary screw traps. Smaller 1.52 meter diameter rotary screw traps were fished at the South Fork (rkm 10) and Middle Fork (rkm 24) trap sites. Traps were either removed or stopped during times of ice-up and during high water events.
Traps were typically fished four days per week starting on Mondays and ending on Fridays. Traps were checked daily during this weekly period. We assumed that all fish captured were migrants. Non-target fish species were enumerated and removed from the traps. Captured juvenile spring Chinook and steelhead migrants were anesthetized with tricane methane
13
sulfonate (MS-222), interrogated for passive integrated transponder tags (PIT tags) or pan jet paint marks, enumerated, weighed to the nearest 0.1 g, and measured (fork length, FL) to the nearest millimeter (mm). We followed PTAGIS marking procedures while PIT tagging (PTAGIS 1999), and standard techniques when pan jet marking juvenile migrants (, Keefe et al. 1995, Hart and Pitcher 1969).
When traps were not operational due to high water events, Chinook and steelhead smolts were captured by beach and boat seining in the Mainstem John Day River between rkm 274 and 296 from April 2 to May 24, 2006. Eddies, riffles, and river margins were sampled with a seine constructed of 12.7 mm mesh netting that measured 30.5 m long by 2.4 m deep with a 1.2 x 1.2 m bag constructed of 9.5 mm mesh netting in the middle. Locations for sampling within our study reach varied on a daily basis depending on discharge and success during previous sampling days (see Appendix Table F-1 for a list of sample sites). Captured fish were handled similarly as at the rotary screw trap sites except all PIT-tagged emigrants were released at Mainstem rkm 298, 2 km upstream of our most upstream seining site. Recaptured smolts were released 7 km downstream of Spray, OR at rkm 267. Mean weekly catch-per-seine estimates were determined to assess smolt migration timing through the lower Mainstem (rkm 268–296) during the months of April and May. PIT-tag information was submitted to the PIT tag Information System (PTAGIS).
Trapping efficiency was estimated separately for each fish species at individual rotary screw trap sites by releasing previously marked fish upstream of the trap and then counting the number of marked fish recaptured (Thedinga et al. 1994). Fish were marked with either a pan jet paint mark below the surface of the fish’s skin at the insertion of the anal fin (Hart and Pitcher 1969, Keefe et al, 1998) or by PIT tagging. Up to 20 fish of each species (spring Chinook and summer steelhead) were released daily upstream of the trap sites. Trap efficiency (TE) fish were released 4 km upstream of Mainstem trap and all other fish were released 550 m downstream. At the South Fork trap TE fish were released 4.8 km upstream and all other fish were released 100 meters downstream. At the Middle Fork trap site TE fish were released 2.5 km upstream and all other fish were released 100 m downstream. At the North Fork trap site TE fish were released 4 km upstream and all other fish were released 18.5 km downstream. Trap efficiency intervals were one week or until 10 fish of each species were recaptured (Keefe et al, 1998). Trap efficiency was estimated from the equation:
TE = R/M (1)
where TE is the estimated trap efficiency, R is the number of marked fish released upstream and R is the number of marked fish recaptured. A stratified trap efficiency method, utilizing the Bailey estimator, was use to estimate migrant abundance (Steinhorst et al. 2004) for each species. A bootstrapping procedure was then used to estimate 95% confidence intervals for migrants during both the fall/winter and springtime periods. A similar mark-recapture and bootstrapping method was used to estimate capture efficiency (CE) for our seining efforts. Linear interpolation was used to estimate catch during time periods when traps or seines did not operate.
Additional information was collected from captured fish. Scale samples were taken from a subsample of steelhead migrants at all four traps and in the seining operation. Scales were collected from the key scale area and annuli were counted to determine age at capture (Nicholas and Van Dyke, 1982). At each trapping site, scales were taken from the first 25 fish captured in
14
each of four FL intervals, 65–90 mm, 91–120 mm, 121–200 mm, and ≥ 201 mm. This information provided an age structure of all steelhead migrating past our trapping sites. The presence of trematode cysts (black spot disease; Neascus spp.) on captured smolts was noted. We identified fin clips on captured adult steelhead and spring Chinook to determine if they were of hatchery origin. Sex, MEPS length, fork length, and scale samples were taken when steelhead carcasses were observed. Snouts of captured steelhead with adipose and left ventral fin clips were collected for coded wire tag identification.
Mean, standard error, and range of fork length (L; mm), weight (W; g), and coefficient of condition (K) were reported for both fall/winter (September, 2004 to January, 2005) and spring (February 1 to June 24, 2005) migrating juvenile spring Chinook and steelhead. Coefficient of condition was calculated as:
K = 100 W/Lb (2) Where b = 3—the ratio of specific growth rates for length (L) and weight (W) (Saltzman 1977).
Travel times for fall/winter and spring tagged emigrants to reach John Day and Bonneville Dams from the release sites were summarized for each tagging location. In addition, the first and last detection dates and mean, standard error, and range of travel time to John Day Dam, Bonneville Dam, and the Columbia Estuary were estimated. Detection rates for each seasonal tag group were calculated by dividing the number of first time detections at dams by the number PIT tagged and released. Detection rates represent a minimum survival rate because they are not adjusted to account for fish that pass undetected through the hydrosystem.
Smolt-to-adult survival rate (SAR; marine survival) was estimated by the ratio of smolts PIT tagged in our trapping and seining efforts to the number of returning PIT-tagged adults detected at dams as they ascended the Columbia River. Spring Chinook adults return at three ages (ages 3–5) so return rate of any cohort requires three years of adult data detection. Summer steelhead typically spend 1-2 years in the ocean requiring two years of adult data detection for a single smolt cohort. We also estimated stray rates of adult spring Chinook and summer steelhead from PIT tag detections at Columbia River dams upstream of McNary Dam. Freshwater survival (smolt-per-redd estimates) for the 2004 brood year of spring Chinook was also estimated using the number of smolts estimated to pass individual trap sites (Mainstem, Middle Fork) and the seining reach (representing the entire basin) during 2006 by the number of redds estimated during 2004.
RESULTS
Spring Chinook Salmon Redds and Escapement
During the 2006 census spawning survey, we observed 1,044 spring Chinook salmon redds while surveying 299.1 rkm of the John Day River basin (88.2 rkm within index areas, 198.6 rkm within census survey areas, and 12.3 rkm within random survey areas (Table 3; Appendix Tables A-1 to C-2). The Mainstem composed 43.2% of all redds observed (451 of 1,044 including estimated redds), while 25.1% (262) were observed in the North Fork, 19.0% (199) in the Middle
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Fork, 9.5% (99) in the GCS, and 3.2% (33) in Desolation Creek (Tables 3 and 4; Appendix Table C-1). The overall basin redd count was similar to that observed in 2005, however, percentage of redds recorded in each subbasin had changed. The Mainstem contained the highest proportion of redds and second highest redd count observed since 2002. The North Fork declined from a redd count of 497 in 2005 to 262 redds observed in 2006.
Table 3. Kilometers surveyed, total number of redds observed, and number of new redds observed during spring Chinook salmon spawning surveys in the John Day River basin, 2006.
Kilometers surveyed New redds observed Stream
Index
Census
Random
Mainstem and Tributary
Mainstem 19.0a 15.2b 1.9 450 -- 150 186a 114b 0 Deardorff Creek -- 2.3 -- 1 -- -- -- 1 -- South Fork -- 15.2 1.9 0 -- -- -- 0 0 Middle Fork 21.4 34.3 3.8 199c -- 153 -- 46 0 North Fork and Tributaries
North Fork 28.5 62.7 2.8d 262 144 16 -- 102 0 Desolation Cr. -- 46.0 -- 33 -- -- -- 33 -- Trail Creek -- 3.1 -- 0 -- -- -- 0 -- Big Creek -- 2.6 -- 0 -- -- -- 0 -- Camas Creek -- 0.8 1.9 0 -- -- -- 0 0 Granite Creek System
Granite Creek 9.5 7.9 -- 55 -- 32 10 13 -- Clear Creek 4.8 6.1 -- 30e -- 22 0 8e -- Bull Run Creek 5.0 2.4 -- 14 -- 9 5 0 -- Entire Basin 88.2 198.6 12.3 1,044 144 382 201 317 0 a Only 9.2 index kilometers were surveyed. We counted 150 index redds and added an estimate of the redds in the survey sections that we did not have landowner permission to survey. We estimated 160 redds for 9.8 index kilometers that were not surveyed (9.8 index kilometers · 16.3 redds/index kilometer). Twenty-six redds were observed during the post-index surveys b Landowner denied access to 7.1 kilometers of the lower census survey sections. We counted 45 redds within 4.9 kilometers and estimated 65 redds for 7.1 kilometers that were not surveyed (7.1 · 9.2 redds/census kilometer). This was added to 4 redds seen in upper census reaches c Includes 3 redds found in Clear Creek d Includes 1.0 kilometer surveyed in Crane Creek
e Landowner denied access to 1.3 kilometers of census survey. We counted 6 redds within 4.8 kilometers above and below the property and estimated 2 redds (1.3 denied kilometers · 1.3 redds/census kilometer)
Spawning densities within census survey reaches (combined index and census sites) were 3.5 redds/km for the John Day River basin, 11.7 redds/km in the Mainstem (including Deardorff Creek), 2.6 redds/km in the North Fork, 3.3 redds/km in the Middle Fork, 2.8 redds/km in the GCS, and 0.7 redds/km in Desolation Creek (Appendix Table C-3). We did not observe any redds in the South Fork or any of the selected random sites in 2006.
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Table 4. Estimated number of spring Chinook salmon redds and spawners and percentage of redds in each survey area in the John Day River basin, 2006. To estimate the number of spawners, we multiplied the number of redds counted in each spawning area by 5.9 fish/redd (fish/redd ratio for Warm Springs River above Warm Springs River Weir (Lisa Hewlett, CTWSR, unpublished data), 2.31 fish/redd (from Catherine Creek in the Grande Ronde Basin; Fred Monzyk, ODFW, unpublished data), and by 3.0 fish/redd.
Number of spawners estimated Stream
Number of redds 2.31 fish/redd 3.0 fish/redd 5.9 fish/redd
Percentage of total basin
Mainstem 451 1,042 1,353 2, 661 43.2 South Fork 0 0 0 0 0 Middle Fork 199 460 597 1,174 19.0 North Fork 262 605 786 1,546 25.1 Desolation Creek 33 76 99 195 3.2 Granite Creek 55 127 165 324 5.3 Clear Creek 30 69 90 177 2.9 Bull Run Creek 14 32 42 83 1.3 Entire basin 1,044 2,411 3,132 6,160
Within the historic index spawning survey area, redd density for the basin in 2006 was 7.8 redds/km; an increase from 2005 observations but still below what was observed in 2000–2004. The index redd count (686) and spawning density (7.8 redds/km) for the basin was the second lowest observed since 1999 (Appendix Tables C-4, C-5, Figure 5). Within the four main historic index spawning survey reaches for 2006, redd density was 16.3 redds/km in the Mainstem, 7.1 redds/km in the Middle Fork, 5.6 redds/km in the North Fork, and 3.3 redds/km in the GCS (Appendix Table C-5). Since 2000, when census counts were initiated, index counts have averaged 71% of total (census) redd counts in the basin. Over these seven years, this percentage has varied from 65–77%. Percentage of redds found in particular census areas has increased in each subbasin (Appendix Table C-6).
We estimated that between 2,411 and 6,160 spring Chinook adults escaped to the John Day Basin this year (Table 4). This escapement estimate is based on our observation of 1,044 redds and three independent fish per redd ratios calculated in 2006: 2.31 fish/redd observed above the Catherine Creek weir in the Grande Ronde River basin, three fish/redd as the standard conservative estimate, and 5.9 fish/redd observed above the Warm Springs River weir (Fred Monzyk, ODFW, unpublished data; Lisa Hewlett, CTWSR, unpublished data).
Characteristics of Spring Chinook Spawners
There were several reports of adult Chinook pre-spawn mortalities by ODFW and other co- managers in the John Day River basin before our spawning ground surveys were initiated. Twelve adult Chinook were found dead in July, in the Mainstem near Dayville, OR, just below a landowner’s rock dam (Jeff Neal, ODFW, personal communication). There are several other barriers that probably strand a few salmon each year, especially if the stream flow is low. One major barrier near Clyde Holliday State Park will be breached in the summer of 2007,
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N um
Census
Figure 5. Index and census spawning ground survey counts of spring Chinook salmon redds in the John Day River basin. A linear regression fit to the index redd counts (P = 0.002) is also shown. to allow easier passage for salmonids. The ODFW John Day Screen Shop brought us four carcasses that were found dead on a ditch diversion fish screen on Reynolds Creek in the Mainstem, rkm 440.76, in July. These carcasses had no external markings and were all age-4 fish, two males and two females. The females contained 100% of their eggs. Eggs collected from the female carcasses (MEPS length 545 mm and 616 mm) revealed fecundity estimates of 2402.6 ± 42.1 eggs and 4,234.4 ± 21.9 eggs, respectively. Another age-4 carcass was found on the Mainstem Forrest Conservation Area by the Confederated Tribes of the Warm Springs Reservation (CTWSR) in early August. This was an unmarked female pre-spawn mortality (MEPS length 587 mm) with a fecundity estimate of 4,032.2 ± 145.5 eggs. ODFW biologists observed and collected data from one adult female Chinook carcass near The Nature Conservancy lower property boundary in late July. This fish (MEPS length 590 mm) had a fecundity estimate of 3,464 ± 57.5 eggs. Live fish (six adult Chinook) were also observed holding in three pools on TNC property during the same time period. The pre-spawn mortalities
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noted above are not included in data tables unless indicated. Any pre-spawn mortalities discovered while on spawning surveys however, are included in the data set.
We observed 598 carcasses during spawning surveys, representing between 9.7%, 19.1%, and 24.8% of the estimated escapement of 6,160, 3,132, and 2,411 adult spring Chinook respectively (Table 5). We were able to sex 551 carcasses; female and male carcasses were evenly distributed in all subbasins (Table 6). A 51.4% female and 48.6% male composition was observed throughout the John Day River basin (Table 7).
Table 5. Number of carcasses sampled during all surveys of spring Chinook salmon spawning surveys in the John Day River basin during 2006. Totals include carcasses of unknown sex.
Number of carcasses Stream Total Pre-index Index Post-index Census Random
Mainstem 128 -- 35 41 52 -- South Fork 0 -- -- -- 0 0 Middle Fork 170 -- 136 -- 34 -- North Fork and tributaries North Fork 141 53 54 -- 34 0 Big Creek 0 -- -- -- 0 -- Trail Creek 0 -- -- -- 0 -- Desolation Creek 58 -- -- -- 58 -- Camas Creek 0 -- -- -- 0 0 Granite Creek System 101 -- 42 47 12 -- Basin total 598 53 267 88 190 0
Table 6. Number of female, male, and unknown carcasses (n) sampled during all surveys of spring Chinook salmon spawning surveys in the John Day River basin during 2006.
Number of carcasses Stream n Female Male Unknown
Mainstem 128 62 51 15 South Fork 0 -- -- -- Middle Fork 170 80 75 15 North Fork 141 66 65 10 Desolation Creek 58 29 29 0 Granite Creek System 101 46 48 7 Basin total 598 283 268 47
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Table 7. Sex ratio of carcasses sampled during all surveys in the John Day River basin, 2006. Number of carcasses (n) in which sex could be determined is also shown.
Survey type n % Female % Male Pre-index 52 53.8 46.2 Index 251 50.2 49.8 Post-index 78 57.7 42.3 Census 170 49.4 50.6 Random 0 -- -- All surveys 551 51.4 48.6
Table 8. Percent age (y) and sex composition of male (M) and female (F) spring Chinook salmon carcasses sampled in the survey areas of the John Day River basin during 2006. Number of carcasses (n) where both age and sex could be determined is also shown.
Age (y) 2 3 4 5
Stream
n M F M F M F M Mainstem 93 1.1 0.0 3.2 53.8 41.9 0.0 0.0 Middle Fork 155 0.0 0.6 2.6 51.0 45.2 0.0 0.6 North Fork 97 0.0 0.0 1.0 37.1 52.6 6.2 3.1 Desolation Creek 58 0.0 0.0 1.7 50.0 48.3 0.0 0.0 Granite Creek System 90 4.4 0.0 3.3 47.8 40.0 1.1 3.3 Basin total 493 1.0 0.2 2.4 48.1 45.4 1.4 1.4
We determined the MEPS length, age, and gender of 493 carcasses. Age-4 adults composed
the majority, 93.5%, of the carcasses aged with age-5 adults accounting for 2.8%, age-3 adults 2.6%, and age-2 precocious adults 1.0% (Table 8). Five of 493 carcasses (1.0%) in the basin consisted of age-2 precocious males. Twelve of 493 were age-3 males (jacks). One of 493 (0.2%) was an age-3 female (Table 9).
We estimated the percentage of eggs retained by 245 individual female carcasses sampled during spawning surveys (Table 10). Of those sampled, 93.9% (230) spawned completely, 4.5% (11) were incompletely spawned, and 1.6% (4) were pre-spawn mortalities (i.e. 100% egg retention). All pre-spawn mortalities were observed in the North Fork in early to mid-August. The GCS exhibited no pre-spawning mortality, as opposed to 2005 observations when 54.5% of female carcasses revealed egg retention greater than 0%.
Of 394 carcasses examined for gill lesions during spawning ground surveys, 7.9% (31) were positive for the presence of lesions (Table 11). Gill lesion frequency differed among spawning areas of the John Day Basin. Proportion of gill lesions in the GCS was significantly greater (23 of 80 or 28.8%; P < 0.001) compared to the rest of the basin. Twenty-one infected fish (twelve males and nine females) were observed in Granite Creek, one male was observed in Clear Creek, and one female was observed in Bull Run Creek (all within the GCS). There were significantly more lesions observed in Granite Creek than Clear Creek (P < 0.001). Lesion presence in this system was 10.6% higher than what was recorded in 2005 (Wilson et al. 2007; Table 12). Results from 14 lesion cultures were inconclusive. No culture had identifiable Flavobacterium columnaris bacteria present, but they did exhibit similar growth appearances. All cultures were a mixture of many different bacteria and ranged from low to high growth
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levels. Six completely spawned fish with gill lesions were also observed in the North Fork mainstem. An infected carcass was observed both on the Middle Fork and Desolation Creek as well. No lesions were observed on Chinook in the Mainstem. Temperatures recorded at the mouth of Granite Creek in 2006 were not significantly different from 2005 during July- September (Kristy Groves, USFS, personal communication). Granite Creek had slightly cooler temperatures in August 2006 versus 2005. However, for one week in June and two weeks in July of 2006, temperatures were near or at the lethal limit for adult Chinook. Table 9. Number examined (n), mean, standard error (SE), and range of middle of eye to posterior scale (MEPS) length (mm) by age (y) and sex (male, M; female, F) of spring Chinook salmon carcasses sampled during spawning ground surveys in the John Day River basin during 2006.
MEPS length Survey area Age Sex n Mean SE Range
Mainstem 2 M 1 113.0 –– –– 3 M 3 393.3 10.1 375–410 4 M 39 590.9 7.6 484–735 4 F 50 600.3 4.9 520–714 Middle Fork 3 M 4 382.5 17.9 335–420 3 F 1 445.0 –– –– 4 M 70 588.1 7.1 434–745 4 F 79 582.6 1.0 435–700 5 M 1 760.0 –– –– North Forka 3 M 1 530.0 –– –– 4 M 51 615.3 8.5 480–745 4 F 36 617.9 8.7 505–770 5 M 3 755.7 26.9 719–808 5 F 6 733.8 20.3 700–833 Granite Creek System 2 M 4 101.8 4.6 90–112 3 M 3 423.3 13.3 410–450 4 M 36 585.6 10.4 460–785 4 F 43 587.1 7.5 505–745 5 M 3 726.7 18.6 690–750 5 F 1 710.0 –– –– Desolation Creek 3 M 1 445.0 –– –– 4 M 28 597.7 10.2 435–680 4 F 29 587.5 5.3 530–640 Entire basin 2 M 5 104.0 4.2 90–113 3 M 12 412.9 13.9 335–530 3 F 1 445.0 –– –– 4 M 224 595.6 3.9 434–785 4 F 237 593.1 2.8 435–770 5 M 7 743.9 13.8 690–808 5 F 7 730.4 17.5 700–833
aIncludes three fish sampled by our steelhead EMAP crew in August
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Stream flow recorded at Bonneville Dam and the Dalles Dam in 2006 was significantly higher during April through June as adult Chinook migrated upriver, compared to previous years (DART). Stream flow at Service Creek, OR in the Mainstem and at Monument, OR in the North Fork was higher during August–September (> 100 cfs) 2006 compared to 2005 (USGS).
Hatchery carcasses composed 2% (12 of 598) of all carcasses examined for adipose fin clips and were observed in the Mainstem, Middle Fork, North Fork, and Desolation Creek (Appendix Table A-1). Three of eleven snouts (27.3%) collected contained CWTs (Table 13). Table 10. Number of female spring Chinook salmon assigned to one of five categories based on the percentage of total eggs retained as estimated by dissection of carcasses observed during spawning ground surveys of the John Day River basin, 2006. Each female was examined separately and placed into one of five categories shown. Number of female carcasses examined in each survey section (n) is also shown.
Survey Area n 0% 25% 50% 75% 100% Mainstem 54 51 2 1 0 0 Middle Fork 77 74 3 0 0 0 North Fork 43 37 2 0 0 4 Desolation Creek 28 25 2 1 0 0 Granite Creek 24 24 0 0 0 0 Clear Creek 11 11 0 0 0 0 Bull Run Creek 8 8 0 0 0 0 Granite Creek System 43 43 0 0 0 0 Entire basin 245 230 9 2 0 4
Table 11. Number of adult spring Chinook salmon observed for gill lesions as determined by carcass gill observations in four subbasins (five spawning areas) during spawning ground surveys in the John Day River basin, 2006. Each carcass was examined separately and placed into one of two categories shown. Number of carcasses examined for lesions in each survey section (n) is also shown.
Survey Area n Gill lesions No gill lesions Mainstem 87 0 87 Middle Fork 115 1 114 North Fork 81 6 75 Desolation Creek 31 1 30 Granite Creek System 80 23 57 Entire basin 394 31 363
One hundred sixty-nine total kidney samples were taken from fresh spring Chinook salmon carcasses and analyzed for Rs antigen by the ELISA method. Of 169 samples, one (0.6%) had clinical ELISA values above 1.0 (2.053 OD units), indicating the presence of BKD (Tables 2 and 14). The infected fish was a 4-year old male sampled between Peep Creek and Road 1003 Bridge in Desolation Creek, in the North Fork Subbasin. The other 168 samples had negative or low positive values of ≤ 0.279. All incompletely spawned females or pre-spawn mortalities had negative or low positive levels of Rs antigen. Of 169 kidney samples, 71 (42%) were tested for IHNV and found to be negative.
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Table 12. Percent pre-spawning mortality (PSM; 100% egg retention) of female carcasses and percent gill lesion incidence (GL) of all examined carcasses in the Granite Creek System, including significant difference, between 2000–2006 in the John Day Basin. Significance (P- value) of z-tests to determine differences in PSM and GL incidence between the GCS and the remainder of the basin are also shown. Carcasses were not examined for gill lesions until 2003.
John Day Basina GCS P-value Year % PSM % GL % PSM % GL PSM GL 2006 2.0 2.5 0.0 28.8 P = 0.789 P < 0.001 2005 2.6 1.6 36.4 18.2 P < 0.001 P < 0.001 2004 1.4 2.6 0.0 19.6 P = 0.969 P < 0.001 2003 5.0 20.5 0.0 59.0 P = 0.254 P < 0.001 2002 1.7 -- 6.0 -- P = 0.049 -- 2001 4.4 -- 16.7 -- P < 0.001 -- 2000 0.5 -- 0.9 -- P = 0.867 --
a Values may differ from previous annual reports due to data revisions and error corrections
Table 13. Sample date, sample identification, stream location, fin clip, sex, medial eye to posterior scale length (MEPS, mm), and hatchery (H) origin and release location as determined by coded wire tag (CWT) information for all fin-clipped spring Chinook salmon sampled during spawning ground surveys of the John Day Basin, 2006. Fin clips were adipose (Ad).
Date Sample
CWT record of hatchery origin and release
8/14/06 06E 2730 North Fork Ad M 610 McCall H., SFK Salmon River at Knox Bridge, ID 9/08/06 06E 2690 North Fork Ad F 610 No CWT 9/13/06 06E 2775 North Fork Ad F 610 No CWT 9/05/06 06E 2770 Mainstem Ad M 395 No CWT 9/13/06 06E 2600 Mainstem Ad M 565 No CWT 9/13/06 06E 2601 Mainstem Ad F 694 No CWT 9/13/06 No ID # Mainstem Ad F 568 No snout taken 9/19/06 06E 2738 Middle Fork Ad M 335 No CWT 9/19/06 06E 2739 Middle Fork Ad F 620 McCall H., SFK Salmon River at Knox Bridge, ID 9/19/06 06E 2750 Middle Fork Ad M 380 No CWT 9/19/06 06E 4611 Middle Fork Ad M 510 No CWT 9/18/06 06E 4610 Desolation Cr. Ad F 610 Lookingglass H., Grande Ronde River, OR
Surveyors recovered two passive integrated transponder (PIT) tags from adult male
Chinook during spawning surveys. One fish measured 591 mm MEPS and 723 mm FL, and was recovered from the Middle Fork on 20 September between Coyote Creek and TNC upper boundary. This Chinook was initially captured via rotary screw trap in the Middle Fork and implanted with a PIT tag as a juvenile on 14 April 2004. It was observed and detected as an adult at Bonneville Dam on 20 May 2006. The second fish measured 630 mm MEPS and 770 mm FL, and was recovered from the North Fork on 8 September between Oriental Creek and Sulphur Creek. It was first captured via beach seine in the Mainstem and implanted with a PIT tag on 12 April 2004. Both fish were classified as age-4 based on scale pattern analysis.
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Table 14. ELISA readings (OD405) for Renibacterium salmoninarum from kidney samples taken from spring Chinook salmon carcasses July through September in the John Day River basin, 2006.
Granite Creek System North Fork Mainstem Middle Fork Desolation
Creek Sample OD405 Sample OD405 Sample OD405 Sample OD405 Sample OD405
26 0.105 4d 0.063 1f 0.098 9 0.076 8a 0.131 31 0.104 5d 0.074 2f 0.084 30 0.076 42 0.162 37 0.146 11 0.084 3f 0.098 33 0.142 61 0.115
39a 0.108 12d 0.070 6 0.071 34 0.244 62 0.194 43a 0.099 13 0.068 7 0.077 71 0.103 87e 0.097 48a 0.075 14 0.064 10 0.070 75 0.150 92 0.148
2.053 59 0.110 15 0.074 27 0.102 118 0.090 99h 72a 0.092 16a 0.198 28 0.096 133 0.160 102 0.143 73a 0.085 17 0.063 35 0.088 138 0.110 104 0.103 77 0.127 18 0.073 36 0.133 153 0.125 122 0.097
88a ,b 0.116 19 0.075 38 0.127 154g 0.117 129 0.148 94 0.139 20e 0.061 40 0.086 155 0.145 139 0.116
95a 0.075 21a 0.063 41 0.087 156 0.095 142 0.089 96a 0.088 22 0.059 44 0.103 158 0.113 143 0.090
97 a, c 0.135 23 0.066 46 0.103 159 0.112 144 0.082 101a 0.129 24 0.080 49 0.093 160 0.118 105 0.074 25a 0.088 51 0.104 161 0.114 107a 0.104 29 0.069 52 0.132 162 0.161 108 0.096 32 0.085 57 0.075 164 0.100 109 0.163 45 0.076 60 0.077 165 0.120 111 0.085 50 0.076 63 0.119 166 0.093 112 0.098 56 0.072 64 0.067 167 0.153 113 0.085 58 0.078 65 0.133 168 0.134 115 0.121 68 0.081 66 0.074 170 0.134 116 0.096 80 0.075 67 0.068 171 0.092 117 a 0.101 84 0.095 69 0.090 172 0.078 119 0.135 86 0.088 70 0.087 173 0.182 120 0.279 89 0.070 74 0.091 174 0.145 121 0.121 91 0.066 76 0.095 175 0.130 123 0.146 98 0.070 78 0.088 176 0.109 124 0.105 103 0.077 81 0.116 178 0.150 125 0.115 106 0.111 83 0.074 179 0.135 126 0.138 131 0.091 85 0.074 180 0.092 127 0.082 137 0.087 90 0.081 181 0.076 128 0.148 93 0.104 182 0.148 136 0.240 100 0.136 184 0.082 149 0.063 132 0.086
135 0.117 140 0.109 141e 0.126 145 0.110 146 e 0.211 147 0.059 148 0.080 150 0.103 151 0.098 152 0.093
a Gill lesions observed b Sample contained Yersinia ruckeri, or enteric red mouth disease (ERM) c Sample contained Aeromonas/Pseudomonas species of bacteria d Female pre-spawn mortality, 100% egg retention, collected during the 4-Aug pre-census survey e Adipose-clipped (presumably non-native, i.e. hatchery) fish f Pre-spawn mortalities found in July before spawning surveys began g Female incompletely spawned, 25% egg retention; scoliosis observed h Fish had clinical BKD
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Juvenile Spring Chinook Capture and Tagging
We PIT tagged 3,418 juvenile spring Chinook at our four trap sites and in the
Mainstem seining operation during the 2006 spring migration from 1 February to 26 June 2006 (Table 15). High water prevented trapping at the Mainstem and North Fork trap sites during most of the month of April when peak movement usually occurs (Figure 6). However, peak movements were recorded during the months of April, May and June at all trap sites. Mean FL at capture for spring migrants from all trapping sites was 102 mm (± 0.2 SE, range 65–150 mm; Table 16). Of the 3,418 juvenile spring Chinook examined for Neascus spp. infestation, 59 (1.7%) showed visible signs of black spot. Based on adult spring Chinook redd counts and juvenile abundance estimates from our seining operation in the Mainstem between Kimberly and Spray we estimated freshwater production at 61 smolts per redd (95% CL’s 36, 108) for the 2004 brood year (Table 17).
At our Mainstem trap (rkm 326) we captured 985 and PIT tagged 836 juvenile spring Chinook during the migration from 10 February to 26 June 2006 (Tables 16). Trapping efficiency (TE) was 11.7% during the spring (Table 22). High water prevented Mainstem trap operations during April. However, peaks in juvenile spring Chinook migration timing past the Mainstem trap were recorded during May and June (Figure 9). We estimated that 30,316 (95% CI, 18,996–53,988) juveniles migrated past the Mainstem trap site during our trapping period (Table 22). Mean FL during the spring migration was 98 mm (± 0.5 SE, range 69–146 mm FL; Table 16). Of 836 juvenile spring Chinook examined for Neascus sp. infestation, seven (0.8%) showed visible signs of black spot. Based on adult spring Chinook redd counts and abundance estimates from our Mainstem trap we estimated freshwater production in the upper Mainstem at 159 smolts per redd (95% CI, 60–246) for the 2004 brood year (Table 18).
At our South Fork trap we captured 161 juvenile spring Chinook between 8 October 2005 and 23 June 2006. We estimated that 248 (95% CI, 212–293) juveniles migrated past the South Fork trap site during our Fall trapping period. Only eight spring Chinook were PIT tagged during the spring tag group (Table 12), precluding estimates for this period. Mean FL of spring migrants was 111 mm (± 3.5 SE, range 97–124 mm).
At our Middle Fork trap we captured 1,343 and PIT tagged 1,154 juvenile spring Chinook during the migration from 6 March to 22 June 2006 (Table 15). Trapping efficiency for Chinook was 15.7% during the spring (Table 22) and we estimate that 18,306 (95% CI, 14,372–23,892) juvenile spring Chinook migrated past the Middle Fork trap site during our trapping period. Mean FL was 101 mm (± 0.3 SE, range 65–150 mm). Of 1,154 juvenile spring Chinook examined for Neascus sp. infestation, 32 (2.8%) showed visible signs of black spot. Based on adult spring Chinook redd counts and abundance estimates from our Middle Fork trap, we estimate freshwater production in the Middle Fork to be 65 smolts per redd (95% CI, 45–97) for the 2004 brood year (Table 19).
At our North Fork trap we captured 525 and PIT tagged 494 juvenile spring Chinook during the migration from 6 February to 15 June 2006 (Table 15). Trapping efficiency for Chinook was 1.9% during the spring (Table 22). We estimated that 52,640 (95% CI, 26,320–101,614) juvenile spring Chinook migrated past the North Fork trap site during our trapping period. Mean FL was 102 mm (± 0.5 SE, range 71–138 mm). Of 494 juvenile spring Chinook examined for Neascus sp. infestation, 7 (1.4%) showed visible signs of black spot. Based on adult spring Chinook redd counts and abundance estimates from our
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North Fork trap we estimated freshwater production in the North Fork to be 54 smolts per redd (95% CI, 27–105) for the 2004 brood year (Table 20).
We PIT tagged 926 of the 944 juvenile spring Chinook captured in 167 seine hauls in the Mainstem John Day River between rkm 274–296 from 2 April to 24 May 2006 (Table 15). Nine juveniles were recaptured during our mark-recapture efforts indicating a capture efficiency of 1.1% (Table 22). Catch-per-seine haul peaked higher during April and May (Figure 7). We estimated that 80,536 (95% CI, 55,360–116,525) juveniles migrated past the seining area during our seining period (Table 22). Mean fork length was 106 mm (± 0.3 SE, range, 86–142mm; Table 21). Of 926 smolts examined for Neascus sp. infestation in our Mainstem seining operation, 10 (1.1%) showed visible signs of black spots.
Juvenile Steelhead capture and Tagging
Of the 3,215 juvenile steelhead PIT tagged during the 2006 migration, 1,048 were tagged during the fall and winter (fall/winter tag group) at the South Fork trap site and 2,167 were tagged during the spring (spring tag group) at our four rotary screw traps and while seining between Kimberly and Spray in the Mainstem (Table 15). Migration timing peaked during the month of May at all four trapping sites. However, the Mainstem and North Fork traps were inoperable due to high water during most of the month of April. Mean fork length of migrants captured during the spring period was 164 mm (± 0.5 SE, range, 64–273 mm). Of 3,215 juvenile steelhead examined for Neascus sp. infestation, 27 (0.8%) showed visible signs of black spot.
At our Mainstem trap, we captured 482 and PIT tagged 425 juvenile steelhead during the spring period (Table 15). Trapping efficiency (TE) for steelhead was 1.4% (Table 23). Juvenile steelhead migration peaked during the second week of May however, high water prevented trap operations during April (Figure 8). We estimated that 58,490 (95% CI, 22,089–90,428) juvenile steelhead migrated past the Mainstem trap site during our spring trapping period (Table 23). Mean FL of spring migrants was 153 mm (± 1.7 SE, range, 64–273 mm). Of 425 juvenile steelhead examined for Neascus sp. infestation at the Mainstem trap, 8 (1.9%) showed visible signs of black spot.
At our South Fork trap, we captured 1,735 and PIT tagged 1,704 juvenile steelhead during the 2006 migration from 8 October 2005 to 23 June 2006 (Table 15). Of those PIT tagged, 1,048 were tagged for the fall/winter tag group and 656 were tagged for the spring tag group. Trapping efficiency varied seasonally from 25.8% during the fall/winter to 7.4% during the spring (Table 23). Juvenile steelhead migration peaked during the first week of November, 2005 and second week of May, 2006 (Figure 8). We estimated that 13,185 (95% CI, 9,778–16,942) juveniles migrated past the trap site during our trapping period. Mean FL of fall/winter migrants was 140 mm (± 0.8 SE, range 82–227 mm FL; Table 21). Mean FL of spring migrants was 168 mm (± 0.6 SE, range 98–230 mm). Of 1,704 juvenile steelhead examined for Neascus sp. infestation at the South Fork trap, 6 (0.4%) showed visible signs of black spot.
At our Middle Fork trap we captured 806 and PIT tagged 779 juvenile steelhead from 6 March to 22 June 2006 (Table 15). Trapping efficiency for steelhead during the spring was 7.7% (Table 23). Juvenile steelhead migration peaked during the third week of April and second week of May (Figure 8). We estimated that 20,720 (95% CI, 14,401–30,870)
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juvenile steelhead migrated past the Middle Fork trap site during our spring trapping period (Table 23). Mean FL for spring migrants was 166 mm (± 0.9 SE, range 73–240 mm; Table 21). Of 779 juvenile steelhead examined for Neascus sp. infestation at the Middle Fork trap, four (0.5%) showed visible signs of black spot.
At our North Fork trap we captured 268 and PIT tagged 265 juvenile steelhead from February 6 to June 15, 2006 (Table 15). The North Fork trap did not recapture enough migrants to calculate an abundance estimate. Juvenile steelhead migration peaked during the second week of May (Figure 8). Spring migrant mean fork length was 163 mm (± 1.1 SE, range, 84–231 mm; Table 21). Of 265 emigrants examined for Neascus sp. infestation at the, seven (2.6%) showed visible signs of black spot.
We captured 44 and PIT tagged 42 juvenile steelhead seined in the Mainstem John Day River between rkm 274–296 from April 2 to May 24, 2006. We were unable to estimate an abundance for steelhead past our seining reach because we did not recapture any of our PIT tagged steelhead during our mark-recapture efforts. Mean FL was 170.3 mm (± 3.5 SE, range, 127–229 mm; Table 21). Of the 42 emigrants examined for Neascus sp. infestation, two (4.8%) showed visible signs of black spot. Table 14. Number of juvenile spring Chinook and summer steelhead PIT tagged during the fall/winter (8 October 2005 to 31 January 2006) and spring (1 February to 26 June 2006) at three rotary screw traps and while seining in the Mainstem John Day River.
Spring Chinook Steelhead Trap site Spring Fall/Winter Spring
South Fork 8 1,048 656 Mainstem 836 425 Middle Fork 1,154 779 Mainstem Seining 926 42 North Fork 494 265 Total 3,418 1,048 2,167
Table 15. Number (n), mean, standard error (SE), and range of fork length (mm), mass (g), and coefficient of condition for spring Chinook migrants captured in four rotary screw traps and while seining on the Mainstem John Day River during the spring (1 February to 26 June 2006). Fork Length (mm) Weight (g) Coefficient of condition Location n Mean SE Range n Mean SE Range n Mean SE Range South Fork Trap 8 111 3.5 97–124 8 17.4 1.7
10.7– 25.2 8 1.25 0.04 1.1–1.4
Mainstem Trap 836 98 0.5 69–146 829 12.2 0.2 4.0–36.0 829 1.23 0.005 0.7–2.0 Middle Fork Trap 1,154 101 0.3 65–150 1,097 12.6 0.1 3.7–40.8 1,097 1.16 0.004 0.5–1.8 North Fork Trap 493 102 0.5 71–138 469 13.4 0.2 3.2–31.8 469 1.20 0.006 0.6–1.9 Seining 924 106 0.3 86–142 851 14.4 0.1 7–35.4 850 1.19 0.004 0.8–1.9 All sites 3,415 102 0.2 65–150 3,254 13.0 0.1 3.2–40.8 3,253 1.19 0.04 1.1–2.0
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Table 16. Smolt/redd ratios based on recent and historic estimates of smolt abundance and census redd counts for spring Chinook salmon for the entire John Day River basin. Historic estimates from the 1978–1982 brood years are from Lindsay et al. (1986). Estimates for the 1999–2004 brood years are from Ruzycki et al 2002; Carmichael et al 2002; Wilson et al 2002 and 2005; Schultz et al, 2007; Wilson et al 2006). Brood
year
Number
Smolts/redd
95% CI 1978 611 1980 169,000 80,000–257,000 277 131–421 1979 641 1981 83,000 52,000–113,000 129 81–176 1980 306 1982 94,000 1,000–211,000 307 3–690 1981 401 1983 64,000 40,000–89,000 160 100–222 1982 498 1984 78,000 64,000–93,000 157 129–187
1999 478 2001 92,922 79,258–111,228 194 166–233 2000 1,869 2002 103,097 90,280–119,774 55 48–64 2001 1,863 2003 83,394 76,739–91,734 45 41–49 2002 1,959 2004 91,372 76,507–113,027 47 39–58 2003 1,417 2005 130,144 97,133–168,409 92 69–119 2004 1,656 2006 101,262 59,688–179,494 61 36–108
a includes all redds counted from spawning surveys in the John Day Basin for individual brood years. Table 17. Mainstem John Day River smolt/redd ratios based on estimates of smolt abundance and census redd counts for spring Chinook salmon, 2002–2004 brood years (Wilson et al 2002, 2005, Schultz et al, 2007). Brood Year
Number of redds
95% CI
2002 549 2004 10/23/03–6/24/04 23,589 18,310–30,833 43 33–56 2003 323 2005 10/4/04–7/6/05 32,601 29,651–36,264 101 92–112 2004 368 2006 2/10/06–6/26/06 58,490 22,089–90,428 159 60–246 Table 18. Middle Fork John Day River smolt/redd ratios based on estimates of smolt abundance and census redd counts for spring Chinook salmon, 2002–2004 brood years (Wilson et al 2002, 2005, Schultz et al, 2007). Brood Year
Number of redds
95% CI
2002 389 2004 10/29/03–6/23/04 9,744 7,918–12,257 25 20– 32
2003 236 2005 10/6/04–6/17/05 20,193 17,699–22,983 86 75–97 2004 319 2006 3/6/06–6/22/06 20,720 14,401–30,870 65 45–97
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Table 19. North Fork John Day River smolt/redd ratios based on estimates of smolt abundance and census redd counts for spring Chinook salmon, 2002–2004 brood years. Brood Year
Number of redds
95% CI
2002 1,021 2004 58,039 a 50,279–69,937 57 49–68 2003 858 2005 77,350 a 49,783–
109,162 90 58–
101,614 54 27–
105 a Estimated by subtracting Mainstem Trap and Middle Fork Trap estimates from the Mainstem seining estimate. Table 20. Number (n), mean, standard error (SE), and range of fork length (mm), mass (g), and coefficient of condition for steelhead migrants captured in four rotary screw traps and while seining on the Mainstem John Day River during two periods (Fall [8 October, 2005 to 31 January 2006]; Spring [1 February to 26 June 2006]). Fork Length (mm) Weight (g) Coefficient of condition Location Period n Mean SE Range n Mean SE Range n Mean SE Range South Fork Trap
Fall 1,048 140 0.8 82– 227
906 31.5 0.6 7.2– 114.5
906 1.0 0.002 0.8– 1.5
South Fork Trap
635 50.0 0.6 7.9– 121.9
635 1.0 0.004 0.5– 1.7
Mainstem Trap
400 43.0 1.2 3.2– 237.7
400 1.0 0.005 0.6– 1.6
Middle Fork Trap
744 50.6 0.7 4.9– 158
744 1.0 0.003 0.5– 1.8
North Fork Trap
238 47.1 1.0 6.8– 121.8
238 1.0 0.006 0.8– 1.7
Mainstem Seining
35 53.4 3.9 20.4– 121.6
35 1.0 0.01 0.9– 1.4
All sites Spring 2,167 164 0.5 64– 273
2,052 48.6 0.4 3.2– 237.7
2,052 1.0 0.004 0.5– 1.7
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Table 21. Season, collection period, number captured, percent capture efficiency, and abundance estimates for juvenile spring Chinook migrants captured at four rotary screw trap sites and while seining in the John Day River (rkm 274–296) from 8 October 2005 to 26 June 2006.
Trap location
Middle Fork Spring 3/6/06–6/22/06 1,343 15.7 18,306 14,372–23,892
North Fork Spring 2/6/06–6/15/06 525 1.9 52,640 26,320–101,614 Mainstem Seining Spring 4/2/06–5/24/06 944 1.1 80,536 55,360–116,525 South Fork Fall
Spring Total
212–293
212–293 Table 22. Season, collection period, number captured, capture efficiency, and abundance estimates for juvenile steelhead migrants captured at four rotary screw trap sites and while seining in the John Day River (rkm (274-296) from 8 October 2005 to 26 June 2006.
Trap location
1,040 35
660 1,735
25.9 15.0
6,260–12,499 9,778–16,942
Mainstem Spring 2/10/06–6/26/06 482 1.4 58,490 22,089–90,428 Middle Fork
Spring
14,401–30,870
North Fork Spring 2/6/06–6/15/06 268 0.4 Seining Spring 42 0.0
Incidental Catch and Observations
We captured 14 non-target species of fish in our seining and trapping efforts during the 2006 migration (Table 24). Fifteen adult summer steelhead were captured during our trapping and seining efforts. Of these, 33.3% (five observations) were of hatchery origin (adipose fin clips), and 66.6% (10 observations) were unmarked. We captured one bull trout Salvelinus confluentus (200 mm FL) in the Mainstem Trap on 23 February 2006 and one in the Mainstem seining operation (250 mm FL) on 5 April 2006. One Adult Pacific lamprey Lampetra tridentata was captured alive at our Middle Fork trap on 8 June 2006. Juvenile Pacific lamprey of three morphological types; silver with visible eyes, brown with eyes, and brown with no eyes were captured at all three rotary screw trap sites. The brown with no eyes morph type composed the majority of juvenile Pacific lamprey observed. We also captured one sockeye smolt Oncorhynchus nerka at our North Fork trap on 13 June
30
2006. This smolt may have originated from a resident kokanee population in Olive Lake (Jeff Neal, ODFW, personal communication).
PIT-Tag Detections of Juveniles at FCRPS Facilities
Of 3,418 juvenile spring Chinook migrants captured, PIT tagged, and released at our trapping and seining sites between February 1, 2005 and June 26, 2006 (spring tag group), 24.3% (831) were detected at John Day Dam, 9.9% (339) were detected at Bonneville Dam, and 0.6% (20) were detected in the Columbia estuary. Detections at John Day Dam occurred between April 18 and June 23, 2005 and 50% of these were recorded by May 13 (Table 25). Mean travel time from all release sites to John Day Dam was 20 days (± 0.6 days SE, range 3–85 days). Detections at Bonneville dam occurred between April 28 and June 27, 2006 and 50% of these occurred by May 17. Mean travel time to Bonneville Dam was 21 days (± 0.8 days SE, range 4–84 days). Detections in the Columbia River estuary occurred between May 3 and June 5, 2006 and mean travel time was 19 days (± 2.7 days SE, range 6–56 days).
Of 1,048 juvenile steelhead migrants captured, PIT tagged, and released at our South Fork trap between October 8, 2005 and January 31, 2005 (fall/winter tag group), 13.3% (139) were detected at John Day Dam, 1.8% (19) at Bonneville Dam, and 0.09% (1) was detected in the Columbia River Estuary (Table 25). Detections at John Day Dam occurred between April 11 and June 12, 2006 and 50% occurred by May 2, 2006. Mean travel time from all release sites to John Day Dam was 183 days (± 1.6 range 106–226 days). Detections at Bonneville Dam occurred between April 20 and May 24, 2006 with 50% occurring by May 19. Mean travel time to Bonneville Dam was 188 days (± 2.1 days SE, range 169–206 days). A single detection occurred in the Columbia River estuary on May 5, 2006.
Of 2,167 juvenile steelhead migrants captured, PIT tagged, and released at our trapping and seining sites between February 1, 2005 and June 26, 2006 (spring tag group), 33% (715) were detected at John Day Dam, 7.3% (159) at Bonneville Dam, and 1.8% (40) were detected in the Columbia River Estuary (Table 25). Detections at John Day Dam occurred between April 16 and June 24, 2006 with 50% occurring by May 5, 2006. Mean travel time from all release sites to John Day Dam was 10.5 days (± 0.4 days SE, range 3– 93 days). Detections at Bonneville Dam occurred between April 24 and June 22, 2006 and 50% occurred by May 22, 2006. Mean travel time to Bonneville Dam was 11.1 days (± 0.6 days SE, range 4–67 days). Detections in the Columbia River estuary occurred between May 3 and June 15, 2006 and mean travel time was 10.1 days (± 0.6 days SE, range 6–21 days).
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Date
N um
South Fork Mainstem Middle Fork North Fork
Figure 5. Weekly number of juvenile spring Chinook captured at four rotary screw traps operated on the John Day River basin during autumn 2005 and spring 2006.
Date
N um
10Number CPUE
Figure 6. Weekly number and catch per unit effort (CPUE, number/seine haul) of spring Chinook smolts captured while seining the John Day River between river kilometers 274 and 296 during spring, 2006.
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Date
N um
South Fork Mainstem Middle Fork North Fork
Figure 7. Weekly number of juvenile summer steelhead captured at four rotary screw traps operated on the John Day River basin during autumn 2005 and spring 2006.
Adult Chinook and Steelhead Detection at FCRPS Facilities
There were 120 detections of returning of adult summer steelhead PIT tagged in the John Day Basin at Bonneville (118 fish) and McNary Dams (two fish) from June 29 to September 15, 2006. Two adults passed Bonneville Dam without being detected and were instead detected at McNary Dam. Of the 118 fish detected at Bonneville Dam 1.7% (2) were detected in June, 54.2% (64) in July, 40.7% (48) in August, and 3.4% (4) in September. Of the 120 returning adult summer steelhead, 104 were part of our effort to estimate summer steelhead SAR and 16 were from Oregon State University’s tagging efforts. Estimated SAR for summer steelhead from the 2004 juvenile migration year was 0.78% for the Fall/winter tag group and 2.84% for the spring tag group (Table 28). Of the 113 adult summer steelhead that returned during 2005 and 2006, 58% (66 fish) returned as one-ocean fish and 42% (47 fish) returned as two-ocean fish (Table 26).
There were 89 detections of returning adult spring Chinook salmon at Bonneville Dam between April 22 and June 24, 2006 (Table 27). Seventy-five (84.3%) of these