Escapement and Productivity of Spring Chinook Salmon and
91
Escapement and Productivity of Spring Chinook Salmon and Summer Steelhead in the John Day River Basin Annual Technical Report December 1, 2005–November 30, 2006 Prepared by: Terra Lang Schultz, Assistant Project Leader Wayne H. Wilson, Assistant Project Leader Oregon Department of Fish and Wildlife John Day, Oregon and James R. Ruzycki, Project Leader Richard Carmichael, Program Leader Oregon Department of Fish and Wildlife La Grande, Oregon and Jaym'e Schricker, Project Assistant Oregon Department of Fish and Wildlife John Day, Oregon Funded by: U. S. Department of Energy Bonneville Power Administration Division of Fish and Wildlife Portland, OR 97208-3621 Project Number: 1998-016-00 Contract Number: 25467
Escapement and Productivity of Spring Chinook Salmon and
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
ii
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
iii
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
iv
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
v
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
vi
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
1
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.
2
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).
3
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.
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. Arrows indicate
upstream and downstream limits of census spawning ground
surveys.
7
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.
8
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.
9
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
10
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.
11
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
15
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.
16
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,
17
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
18
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
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.
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
20
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
21
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.
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.
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.
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.
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
24
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
25
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)
26
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
27
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
28
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
29
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).
31
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.
32
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