Puyallup Tribe of Indians Smolt Trap Report 2008

Puyallup River Juvenile Salmonid Production Assessment
Project 2008
By: Puyallup Tribal Fisheries Department

Andrew Berger Puyallup, WA 98371
Robert Conrad
Justin Paul December 2008
Acknowledgments
Evaluation of juvenile salmonid production requires a tremendous amount of work.

We would like to thank the following people for their time in the field and support
in writing this document: Russ Ladley, Eric Marks, Chris Phinney, Terry
Sebastian, and Blake Smith. Editorial and statistical support was provided by
Robert Conrad from the Northwest Indian Fisheries Commission.
Other individuals and agencies contributed efforts to this project. We would like
to thank the City of Puyallup for the access to the trap site along the levy and the
Pacific Salmon Treaty for funding the project.
TABLE OF CONTENTS
List of Figures……….…………………………..…………………………………………….....iii
List of Tables……………………………………..……………………………………………….v
List of Appendices…………………………………………..……………………………….......vii
Introduction………………………………………………….………………………....………....1
Goals and Objectives…………………………………..………………………………….……....2
Methods…………………………………………………..……………………………………….3
Trapping Gear and Operations……………………………...………...………..……......3
Sampling Procedures…………..……..…………………..……………………..............3
Measuring Flow and Turbidity…………………………..………………………………..4
Capture Efficiency…………………………………………………...................................4
Catch Expansion………………………………………………..…………………………5
Production Estimates…………………………………………..……………………….....6
Results……………….………………………….………………..……………………………….9
Flow and Turbidity…………………………………..…………………………………....9
Temperature………………………………..………………………………………….…10
CHINOOK…...………………………………………..…………………………………....11
Catch…………………………………..……………………………………………..…..11
Size…………………………………………………..…………………………………..11
Capture Efficiency.....................................................................................................…....12
Estimated Production…………………………..………………………………………...21
Migration Timing….………………………………………….……………………........23
Freshwater Survival...….…………………………………..…………………….……....24
COHO………………………………………………………..……………………………….25
Catch………………………………………………………..……………………………25
Size……………………………………………………………….………………….......26
Capture Efficiency…………………………………………..…………………………...27
Estimated Production………………………………..…………………………………...31
Migration Timing….………………………………………..………………………...…31
In-River Mortality....…………………………..…………………………………………32
CHUM………………………………………………….……………………………..............32
Catch………………………………………..……………………………………………32
Size…………………………………………..………………………………………......33
Capture Efficiency……………………………….………………………………………33
Estimated Production….…………………………………..……………………………..39
Migration Timing….………………………………….…………………………………39
PINK………………………………………………….……………………………..............40
Catch………………………………………..……………………………………………40
Size…………………………………………..………………………………………......41
Capture Efficiency……………………………….………………………………………41
Estimated Production….…………………………………..……………………………..43
Migration Timing….………………………………….…………………………………44
i
Puyallup River Juvenile Salmonid Assessment Project 2008
STEELHEAD……………………………………………………………………………….45
Catch……………………………………………..………………………………………45
Size………………………………………………….……...…………………….….…..45
Capture Efficiency......……………………………………….…………..……………....46
Migration Timing………………………………..………………………………………47
ASSUMPTIONS……………………………….……………………………………………..48
Catch…………………………………………….……………………………………….48
Catch Expansion………………………………………………………………………....48
Trap Efficiency…………………………………………………………………..…….48
Chinook………………………………………………………………………………….48
Coho…………………………………………….………………………………………..48
Chum…………………………………………..………………………….……………..49
Pink………….………………………………..………………………….…………...….49
Turbidity, Flow and Temperature……………………….………...….…….…..……....49
DISCUSSION…………………………………………………….…………………………...50
Turbidity and Flow………………….…………………………………………………...50
Temperature……...………………….…………………………………………………...50
Catch and Migration Timing…………………………………………………………….50
Trap Efficiency and Production Estimates…………………….………………………...51
Freshwater Survival………………………………….…………………………………..53
Mortality……………………………………….………………………………………...55
Incidental Catch………………………………………….………………………………55
REFERENCES……………………………………….…………………………….…………56
Literature Citations……………………….……………………………………………...56
Personal Communications…………………………….…………………………………57
ii
LIST OF FIGURES
Figure 1. Secchi depth and mean daily flow for Puyallup River, 2008……...……………...9
Figure 2. Scatterplot of mean daily flow and secchi depth for the Puyallup River,
2008……………………………………………………………………………....10
Figure 3. Mean daily water temperature recorded on the Puyallup River smolt trap,
2008……………………………………………………………………...………10
Figure 4. Mean weekly fork length and size range of unmarked age 0+ Chinook captured in
the screw trap, 2008………………………………………………………………12
Figure 5 Summary of the capture efficiency estimates for daytime and nighttime Chinook
smolt releases conducted in 2004—2008………………………………………....13
Figure 6. Summary of the capture efficiency estimates for glacial and non-glacial Chinook
smolt releases conducted in 2004—2008……………………………….……..14
Figure 7. Comparison of mean capture efficiency estimates for Chinook smolt releases con
ducted in 2004—2008 with 95% confidence intervals……………….………14
Figure 8. Comparison of mean and range of secchi disk depth measurements taken during
Chinook capture efficiency experiments, 2004 – 2008…………………………..15
Figure 9. Comparison of mean and range of flow taken during Chinook capture efficiency
experiments, 2004—2008……………………………………................................16
Figure 10. Plot of capture efficiency versus flow for Chinook releases, 2004—2008.............16
Figure 11. Plot of capture efficiency versus secchi depth for Chinook releases, 2004 -
2008……………………………………………………………………………….17
Figure 12. Plot of capture efficiency versus inverse of secchi depth for daytime Chinook re-
leases, 2004—2008………..………………………………………...…………….17
Figure 13. Plot of capture efficiency versus LN(secchi depth) for nighttime Chinook releases,
2004 – 2008………………………...….…………………………………………18
Figure 14. Plot of capture efficiency versus LN(secchi depth) of daytime and nighttime Chi-
nook releases, 2004 – 2008. Linear regression line represents slope of all data,
but intercept for only 2008 data………………………………………………....20
iii
Figure 15. Fork length of hatchery Chinook used for capture efficiency experiments,
2008………………………………………………………………….………....21
Figure 16. Capture efficiency and mean fork length of of hatchery Chinook used for mark-
recapture tests, 2004—2008. Tests conducted in 2008 indicated by (Δ and ◊).
……………………………………………………………………………………21
Figure 17. Estimated daily migration of unmarked 0+ Chinook smolts with mean daily flow,
2008……………………………….……………………………………….……..23
Figure 18. Percent estimated daily migration of unmarked age 0+ Chinook, 2008………....24
Figure 19. Mean weekly fork length and size range of unmarked, age 1+ coho captured in the
smolt trap, 2008 ……………………...……………………………….……..…..27
Figure 20. Comparison of mean capture efficiency estimates for coho smolt releases con-
ducted in 2004 – 2008 with 95% confidence intervals………………...………..28
Figure 21. Summary of the capture efficiency estimates for coho smolt releases conducted
from 2004—2008.................................................................29
Figure 22. Plot of estimated capture efficiency versus secchi depth for 1+ coho salmon re-
leases, 2004—2008……..…………………………………………………..…....30
Figure 23. Plot of estimated capture efficiency versus flow for unmarked 1+ coho releases,
2004—2008……………………….........................................................30
Figure 24. Estimated daily migration of unmarked 1+ coho with mean daily flows, 2008...31
Figure 25. Percent migration of unmarked age 1+ coho migrants, 2008……………………32
Figure 26. Mean weekly fork length and size range of chum captured in the screw trap,
2008………………………………………………….……………..………...…..33
Figure 27. Summary of capture efficiency estimates for chum fry releases conducted in 2004
– 2008…………………………………………..……………..………...…..34
Figure 28. Comparison of mean capture efficiency estimates for chum fry releases conducted
in 2004—2008 with sample size (n) and 95% confidence intervals…….35
Figure 29. Plot of estimated capture efficiency versus secchi disk depth for chum releases,
2004– 2008………………………………………………………………………36
Figure 30. Plot of estimated capture efficiency versus flow for chum release, 2004–
2008…………………………………………………………………………… 36
iv
Figure 31. Mean capture efficiency and 95% confidence interval for the original three possi-
ble strata defined for chum experiments conducted from 2004– 2008…………..37
Figure 32. Plot of estimated capture efficiency of wild chum salmon versus secchi disk depth
for the Puyallup River smolt trap data, 2004 –2008……………………..………38
Figure 33. Plot of estimated capture efficiency of wild chum salmon versus flow for the
Puyallup River smolt trap data, 2004—2008........................................................39
Figure 34. Daily estimated migration of chum fry with mean daily flows, 2008…………...40
Figure 35. Percent estimated migration of chum fry, 2008………………………………….40
Figure 36. Mean weekly fork length and size range of pink salmon captured in the screw
trap, 2008……………………………………...…………………………………41
Figure 37. Summary of capture efficiency estimates, by statistical week, for wild pink re-
leases conducted in 2004, 2006 and 2008……………………………………….42
Figure 38. Comparison of mean capture efficiency estimates, by statistical week, for wild
pink releases conducted in 2004, 2006 and 2008 with sample size (n=) and 95%
confidence intervals………………………………..…………………………….42
Figure 39. Mean weekly for length and size range of pink fry captured in the screw trap,
2008……………………………………………………………………………...43
Figure 40. Daily estimated migration of pink fry with mean daily flows, 2008…...………..44
Figure 41. Percent daily estimated migration of pink fry, 2008……………….……………44
Figure 42. Total number of unmarked steelhead captured in the Puyallup River screw trap,
2000—2008……………………………………………………………………...45
Figure 43. Mean weekly fork length and size range of unmarked steelhead captured in the
screw trap, 2008………………………………………………………………….46
Figure 44. Daily catch of steelhead migrants with mean daily flows, 2008………………47
Figure 45. Percent in-river mortality and number of Chinook released for migration years,
2004—2008…………………………………………...…………………………53
Figure 46. Correlation of peak incubation flows (Aug.—Feb.) on South Prairie Creek and
freshwater survival estimates on the Puyallup River, migration years 2004—
2008……………………………………………………………………………....54
v
LIST OF TABLES
Table 1. Annual Summary statistics for capture efficiency of Chinook release experiments,
2004-2008………………………………………………………………………15
Table 2. Summary statistics for GLM parameters estimated from capture efficiency experi-
ments, 2004-2008…………………………………………..…………………....19
Table 3. Summary statistics for GLM parameters estimated from capture efficiency experi-
ments, 2004-2007………………….……………………………………..………19
Table 4. Total unmarked Chinook production for pre-glacial and glacial melt periods,
2 0 0 8 …………………………………………………………………………… . 2 2
Table 5. Total unmarked Chinook catch for pre-glacial and glacial melt periods,
2008……………………………………………………………………………....22
Table 6. In-river mortality of marked Chinook from the Puyallup River, 2008
…………………………………………………………………………………....25
Table 7. Freshwater survival of unmarked Chinook from the Puyallup River,

2008………………………………………………………………………….…...25
Table 8. Summary statistics for the mean capture efficiency for all coho salmon releases
experiments conducted in 2004-2008.…………………………………………28
Table 9. Summary statistics comparing the mean capture efficiency for daytime and night-
time experiments for coho salmon releases conducted in 2004—2008………….29
Table 10. Summary statistics for the ordinary least squares linear regression of
secchi depth (X) and capture efficiency (Y)……………………………………...31
Table 11. Summary statistics for the ordinary least squares linear regression of flow (X) and
capture efficiency (Y)...................................................................................…......31
Table 12. In-river mortality of coho 1+ mark groups for the Puyallup River,
2008………………………………………………………………………..……..32
Table 13. Summary statistics comparing the mean capture efficiency for hatchery
daytime, hatchery nighttime, and wild nightt i me expe ri me nt s for
chum salmon releases conducted in 2004-2008……………………………...…..37
Table 14. Summary statistics comparing the mean capture efficiency for hatchery
and wild experiments for chum salmon releases conducted in 2004-
2008……………………………………………………………………………....38
vi
Table 15. Annual summary statistics for the mean capture efficiency for pink salmon release
experiments conducted in 2004, 2006 and 2008 (mean of estimates for statistical
weeks)……………………………………………………………………………43
Table 16. Length data of unmarked and marked steelhead captured in the Puyallup River
screw trap, 2008………………………………………………...…..………….46
Table 17. Capture Percentage of Marked Steelhead from Voights Creek Hatchery,
2004-2008…………………………..…………………………………….……...46
APPENDICES
Figure A1. The Puyallup River Watershed.……………… ………………………………...A1
Figure A2. Diagram of a rotary screw trap.…………………………………………….….A2
Figure A3. Orientation of the screw trap in the lower Puyallup River channel at R.M.
10.6………………………………………………………………………………A3
Table B1. Fork length data for unmarked age 0+ Chinook migrants, 2008………….…….B1
Table B2. Fork length data for unmarked age 1+ coho migrants, 2008……..…………..…B2
Table B3 Fork length data for unmarked chum fry, 2008…………….……….…………..B3
Table B4. Fork length data for pink fry, 2008…………………………..…………….....…B4
Table B5. Fork length data for unmarked steelhead, 2008……………...…………….....…B5
Table C1. Hatchery Chinook mark and recapture data for the Puyallup River,
2004-2008………...………………………………………………………....…...C1
Table C2. Hatchery coho mark and recapture data for the Puyallup River,
2004-2008……………………………………………………….…………….....C2
Table C3. Hatchery and wild chum mark and recapture data for the Puyallup
River, 2004-2008………………………………………………………………...C3
Table C4. Wild pink mark and recapture data for the Puyallup
River, 2004, 2006 and 2008……………………………………………………..C4
vii
INTRODUCTION
The Puyallup River Watershed encompasses 438 square miles and includes three major
tributaries: the Carbon River, Mowich River and South Prairie Creek. The Puyallup River
flows westward more than 54 miles from the southwest slope of Mount Rainier to
Commencement Bay and has an average annual flow of 1,729 cfs near the location of the
smolt trap (USGS, 2006). The Puyallup, Carbon and Mowich Rivers originate from glaciers
located in Mt. Rainer National Park and exhibit the classic features of glacial streams:
frequently shifting braided channels, high turbidity, and low temperatures. South Prairie
Creek, which is a non-glacial tributary of the Carbon River, is fed by groundwater and
seasonal runoff and offers clear water and moderate temperatures. The Puyallup-White River
Watershed is identified as a Water Resource Inventory Area (WRIA) 10 by the Washington
State Department of Ecology.
The watershed supports eight species of anadromous fishes including six species of Pacific
Salmon (Oncorhynchus spp.), coastal Cutthroat trout (Oncorhynchus clarki) and Bull trout
(Salvelinus confluentus). Prior to the construction of the Electron Diversion Dam at river
mile (R.M.) 41.5 in 1904 natural production occurred throughout the entire Puyallup River
Basin. However, the dam eliminated access to 21.5 miles of spawning habitat. In the fall of
2000, the Puyallup Tribe reopened this habitat for fish use by installing a fish ladder at the
Electron Dam.
The State of Washington began hatchery production within the watershed in 1914 at Voights
Creek State Salmon Hatchery. The confluence of Voights Creek enters the Carbon River at
R.M. 4.0 (Appendix A1). Currently, Voights Creek Hatchery rears fall coho, winter
steelhead and fall Chinook. In 1998, the Puyallup Tribe began planting hatchery-reared fall
Chinook and coho into three acclimation ponds in the upper Puyallup watershed. Cowskull
pond drains directly into the Puyallup River at R.M. 45.5. The Rushingwater and Mowich
ponds drain into the Mowich River, which enters the Puyallup at R.M. 42.3. In addition,
surplus Chinook and coho from Voights Creek Hatchery are released above Electron Dam
and allowed to spawn naturally in an attempt to repopulate available habitat.
Puyallup River fall Chinook were classified as a distinct stock by the 1992 State Salmon and
Steelhead Stock Inventory (SASSI) on the basis of geographic distribution. In 1999, the
National Marine Fisheries Service (NMFS) listed Puget Sound Chinook as a threatened
species under the Endangered Species Act (ESA). Also in 1999, the Puyallup Tribe (PTF)
and the Washington State Department of Fish and Wildlife (WDFW) created a joint fall
Chinook recovery plan with a goal of maintaining natural fall Chinook production while
evaluating the production potential of the Puyallup River system and current stock status
(WDFW and PTF, 2000). In addition to Chinook, Puget Sound steelhead were listed as
threatened under the ESA in 2007. Estimating smolt production is a necessary step towards
evaluating trends in stock productivity and production potential of the Puyallup River
system.
In 2000, the Puyallup Tribal Fisheries Department started the Puyallup River Smolt
Production Assessment Project to estimate: (1) juvenile production of native salmonids, with
an emphasis on natural fall Chinook salmon production, and (2) survival of hatchery and
1
Puyallup River Juvenile Salmonid Production Assessment Project 2008
acclimation pond Chinook. Beginning in 2000, an E. G. Solutions 5-ft diameter rotary screw
trap has been operated annually on the lower Puyallup at R.M. 10.6, just upstream of the
confluence with the White River, and has been used to monitor the outmigration of juvenile
salmonids.
As more data become available, juvenile production estimates may provide baseline
information allowing managers to re-evaluate escapement objectives in the watershed, create
a production potential-based management strategy, and accurately forecast future returns of
hatchery and naturally produced adults. In addition, a basin spawner/recruit analysis will
help: (1) indicate stock productivity, (2) determine the overall health of the watershed, and
(3) evaluate the contribution of enhancement projects.
GOALS AND OBJECTIVES
The goals of this project are to estimate the production of juvenile salmonids, characterize
juvenile migration timing, describe the length distribution for all wild salmonid outmigrants,
and fulfill the objectives of the Puyallup River Fall Chinook Recovery Plan.
To achieve these goals, this study will produce population estimates of out-migrating smolts,
estimate species specific migration timing, compare natural versus hatchery production and
run timing, analyze mean fork length of wild smolts and detail species composition of the
sampled population. The objectives of this project are to:
1. Estimate juvenile production for all salmonids in the Puyallup River and
estimate freshwater survival for unmarked juvenile Chinook.
2. Estimate in-river mortality of hatchery and acclimation pond Chinook.
3. Investigate physical factors such as light (day vs. night), river flow, and river
turbidity and their importance to trap capture efficiency.
In this report, all stated objectives will be met for Chinook and coho salmon for the 2008
smolt outmigration season. Non-target species such as chum, pink and steelhead will be
addressed to a lesser extent.
2
METHODS
Trapping Gear and Operations
The rotary screw-trap used in this study consists of a rotary cone suspended within a steel
structure on top of twin, 30-foot pontoons. The opening of the rotary cone is 5 feet in
diameter, and has a sampling depth of approximately 2.5 feet. The cone and live box
assembly are attached to a steel frame that may be raised or lowered by hand winches
located at the front and rear of the assembly (Appendix A2).
Two five-ton, bow-mounted anchor winches with 3/8’’ steel cables are used to secure and
adjust the direction of the trap and keep it in the thalweg (Appendix A3). The cables are
secured to trees on opposite banks. Additional rear cables are secured to trees located on the
banks to further stabilize the trap. Four 55-gallon containers filled with water are secured on
the deck at the rear of the trap to compensate for the generation of force at the front of the
trap during operation.
The 5-ft diameter rotary screw trap was installed in the lower Puyallup River (R.M. 10.6)
just above the confluence with the White River. This year the trap was positioned
approximately 250 meters upstream of its location in 2007, close to where it had been
positioned from 2000 to 2006.
Trap operation began on January 18th and continued, when possible, 24 hours a day, seven
days a week until August 10th. The trap was not fished during some high flow events and
hatchery fish release schedules in order to avoid damage to the screw and stress to fish.
These dates are described in the catch expansion section of the report. The trap was checked
for fish at least twice each day: at dawn and at dusk periods. Civil twilight, and sunrise and
sunset hours, were used to separate catch into day and night periods. During hatchery
releases and high flow events personnel remained onsite throughout the night to clear the
trap of debris and to prevent the fish in the live box from overcrowding.
Revolutions per minute (rpm), secchi depth (cm) and weather conditions were recorded
during each trap check.
Sampling Procedures
Smolts were anesthetized with MS-222 (tricaine methanesulfonate) for handling purposes
and subsequently placed in a recovery bin of river water before release back to the river.
Juveniles were identified as natural or hatchery-origin. All hatchery fish in the Puyallup
system are marked with an adipose fin clip or adipose fin clip plus a coded wire tag.
Therefore, unmarked fish are identified as natural and marked fish are identified as hatchery
origin.
Hatchery-origin fish were identified in two ways: (1) by visual inspection for adipose fin
(Ad) clips, and (2) with a Northwest Marine Technology “wand” detector used for coded
wire tag (CWT) detection. Fork length (mm) was measured and recorded for unmarked fish.
3
When possible, 50 fish were measured per day for each species. Scale and DNA samples
were taken from most wild steelhead smolts.
Species were separated by size/age class. Coho were identified as fry, age 0+ (<70mm) or
smolts, age 1+ (>70mm). In some instances coho were recorded as either 0+ or 1+
depending on morphological characteristics and time of season rather than a rigid measuring
scale. Chinook smolts were recorded as age 0+ (<150mm) or age 1+ (>150mm). All chum
and pinks were identified as age 0+. Trout fry age 0+ (<60mm) were not differentiated to
species.
Measuring Flow, Turbidity and Temperature
Stream flow measurements were obtained from the United States Geological Surveys
(USGS) Alderton gauge, number 12096500 (USGS, 2008), located approximately 1.5 miles
above the screw trap. Mean daily flow, measure in cubic feet per second (cfs), was recorded
throughout the sample season and stream flow was noted during each capture efficiency
experiment.
Turbidity was measured by taking a secchi depth (cm) measurement off the front of the trap
during each trap check. Each secchi measurement was applied to its respective day or night
catch period. In order to expand secchi readings during un-fished intervals, averages were
taken and applied where appropriate, i.e., if fish were migrating and secchi depth was used as
a measure of capture efficiency.
Surface water temperature was measured using an Onset Hobo U22 water temperature data
logger. The logger was placed in a live-box located on the smolt trap. Temperature was
recorded every hour, twenty-four hours a day for the entire migration season. Daily
temperature is the average of the hourly readings for the twenty-four hour period.
Capture Efficiency
For the 2008 trapping season, marked Chinook and coho were released at the same site 650
meters above the smolt trap. Marked chum and pink were released 300 meters above the
trap. One chum test group was released at the same site as Chinook and coho. The time of
release varied for each species and is described below.
Chinook – Chinook reared at Clarks Creek Tribal Hatchery were used for all capture
efficiency experiments in 2008. The first five release groups were not given an additional
clip for identification because of the absence of ad-clipped Chinook in the river. The last
three groups were stained with Bismarck Brown Y Biological stain solution. No MS-222
was used on any Chinook except to measure samples for fork length. After marking, fish
were transferred to one large aerated container and immediately moved upstream and
released. The marked fish were released at either day or night times in order to examine
differences in capture efficiency as a result of daylight. Day and night release groups were
classified as either day or night by the majority of the first 10 hours after release being in
light or dark. Sunrise and sunset times, as well as civil twilight, were used to determine the
4
amount of light for each hour. No control groups were held for releases but all fish were
vigorous at release.
Coho – Coho releases were conducted using hatchery fish reared at Voights Creek State
Hatchery. Fish were anesthetized with MS-222 and clipped with either an upper or lower
caudal clip. The fish were then transferred to an aerated container and immediately moved
and released. All experiments with marked coho occurred at night. No control groups were
held for releases but all fish were vigorous at release.
Chum – Wild chum captured in the screw trap and hatchery chum obtained from Diru Creek
Tribal Hatchery were used to conduct capture efficiency experiments. All fish were marked
with Bismarck Brown Y Biological Stain solution. Fish were placed in an aerated stain
solution of 0.4 grams Bismark Brown per 5 gallons of water and held in the solution for 20-
30 minutes. After marking, hatchery fish were placed in totes and aerated until release.
Wild chum were marked and held in a live-box on the screw trap until release. In 2008, all
marked chum were released at night. All chum were captured, marked, and released within
24 hours to reduce stress.
Pink – Wild pink salmon captured in the screw trap were used for capture efficiency
experiments throughout the migration period. Pink salmon were marked with Bismarck
Brown Y Biological stain solution in the same manner as chum. Groups of 100 or more
were released within 24 hours of capture.
Catch Expansion
Due to high flows, hatchery releases, and screw stoppers, the trap was not fished
continuously throughout the trapping season. There were a total of 10 days out of 207 days
when the trap was not fishing for a 24-hour period. In May, the trap was pulled for four
consecutive days due to high flows and debris, the longest period the trap was out this year.
There were other day or night periods when the trap was not fishing. On these days, the
average catch per day (or night) period was used to estimate the number of missed fish. The
average was calculated by taking the respective catch from the day or night period before
and after the un-fished interval, adding them together and then dividing by the total number
of periods. Because this method incorporates the catch around the un-fished interval it was
used for all un-fished periods throughout the migration season. These dates were: Feb. 9th,
night of March 10th, March 11th, night of March 22nd, May 15th – 18th, night of May 20th,
May 21st, night of May 23rd, 27th, 28th and 30th, June 11th and 12th, night of June 30th. This
year all species were treated the same with the methods described above; however not all
days had fish expansion because there were no fish present on the listed days.
In addition to the dates above, hourly expansion was used during high flows and hatchery
releases. On these days, the trap was fished for a known number of hours, pulled for a
known number of hours, and then fished again. The number of fish per hour was calculated
during the fished interval and applied to the un-fished interval. Hourly expansion was used
on: night of Feb. 10th, May 14th, day of May 19th and 20th, May 22nd and 29th, day of May
5
29th – June 2nd, June 3rd, day of June 7th and 9th, June 10th, night of June 13th and day of June
14th, night of June 28th, June 29th and day of June 30th.
When the trap was fished for a 24-hour period without being checked, catch was split using
the percent day: night catch ratio for actual paired day and night catches. Further, day: night
catch ratios were estimated separately for the two time period strata (pre-glacial and glacial).
On some days, there were large numbers of fish in the trap and net expansion was used to
estimate the total number of fish. In this instance, every other net full was sampled while the
next was passed. This occurred during the peak of pink migration, on the morning of April
18th, 21st, 22nd, 23rd, 24th, 27th, 28th and all day on April 29th.
Production Estimates
Because of differences in the relationship between environmental variables and capture

efficiency for each species, production estimates for each species were calculated using
different methods. Although the methods used to estimate production were different for
each species, estimated capture efficiency was calculated similarly for each experiment.
Capture efficiency (e) of the trap for a species and the total catch by the trap (either for the
season or a defined period of time) was calculated as follows:
ê = r / m
and
N̂ = C / ê
where:
ê = estimated capture efficiency,
r = number of marked fish recaptured,
m = number of marked fish released,
N̂ = total estimated number of migrants passing the trap, and
C = total number of unmarked fish caught in the screw trap.
Since our trap was checked twice in a 24-hour period (once in the morning and once in the
evening) each morning check roughly reflects the number of fish caught during the previous
night and each evening check reflects the number of fish caught during the day. When
calculating the total number of migrants passing the trap (N), the number of unmarked fish
caught in the smolt trap (C) is the number of fish caught during each date’s respective day or
night period and is not the total number of fish counted on the date the trap was checked. In
this report, one day will reflect the total number of fish caught in a combined day and night
period. For some species, the number of unmarked fish caught in the trap (C) is the sum
over some specified amount of time, e.g., a week, season, or glacial turbidity period.
SPSS statistical software was used to analyze data and provide predictive modeling for
capture efficiency experiments for each species (SPSS, 2003).
6
Chinook – The capture efficiency experiment data from 2004 - 2007 indicated that there was
a significant relationship between capture efficiency and secchi depth measured at the time
of release. In 2007, we concluded that two of the strata were not significantly different from
one another, pre-glacial night and glacial day, and therefore all experiments conducted
within those two strata were combined into one. For the 2008 data, we wanted to continue to
examine the differences between day and night capture efficiency and pre-glacial and glacial
period capture efficiency. We also wanted to examine whether it was appropriate to
combine the data from 2008 with data from the previous four years.
Capture efficiency trials were classified as either daytime or nighttime trials and stratified on
a 50 cm threshold, similar to 2007. If tests were conducted with secchi depth readings of 50
cm or less they belonged to the glacial strata, if 51 cm or above they belonged to the pre-
glacial strata. This resulted in similar stratification that was used in previous years.
In order to compare capture efficiency experiments from 2008 to previous year’s several
analyses were conducted. First, graphical representation of annual means and environmental
variables: flow and turbidity, daytime and nighttime and glacial and non-glacial periods,
were used to compare years. One-way analysis of variance (ANOVA) was used to compare
means among years. Standard ANOVA methods were used when Levene’s homogeneity of
variances test did not reject the hypothesis of equal group variances. If Levene’s test was
significant (P ≤ 0.05), the Kruskal-Wallis (KW) test was used to compare the mean ranks of
the groups. The KW test is the non-parametric equivalent of ANOVA. If an ANOVA was
significant (P ≤ 0.05) for an analysis, Bonferroni’s multiple comparison method was used to
determine which years had significantly different means. Bonferroni’s method was selected
because it performs well with unequal group sample sizes (as was the case for these
comparisons) and only a small number of comparisons were being conducted (typically <
10).
Second, based on previous years’ analyses, we focused on the relationship between secchi
depth and capture efficiency. The relationship between secchi depth and capture efficiency
was analyzed separately for daytime and nighttime releases using ordinary least squares
linear regression. Two different secchi depth versus capture efficiency models were
examined: inverse and logarithmic. For the inverse model the independent variable was
1/(secchi disk depth) and for the logarithmic model the independent variable was LN(secchi
disk depth). Separate regression analyses were conducted for daytime sets and nighttime
sets.
Third, a general linear model (GLM) was constructed to examine which factors, including
both categorical and continuous factors and interactions, were significant influences on
Chinook capture efficiency. A GLM analysis provides regression analysis and analysis of
variance for one dependent variable with one or more factors and/or independent variables.
The factor variables divide the population into groups. The GLM procedure was used to test
the null hypotheses about the effects of specific factors (categorical variables) on the mean
capture efficiency of various groupings (day or night experiment and year) and the
interactions between these two factors. In addition, the effects of covariates and covariate
interactions with factors were examined. For the regression part of the GLM analysis, the
independent (predictor) variables used as covariates were secchi depth and flow. Competing
models were evaluated using Akaike’s Information Criterion (AIC) where smaller numbers
7
indicate better model fit. The SPSS GLM Univariate procedure was used to estimate the
parameters values for the models.
Coho – Coho capture efficiency for 2008 was tested using all capture efficiency experiments
performed during the last five years (2004 - 2008). GLM analysis was used to test for the
effects of environmental variables such as time of day, flow and secchi depth on capture
efficiency. Year was not used as a factor due to the insufficient number of experiments
conducted in most years. Ordinary least squares linear regression was also used to examine
the secchi depth and flow versus capture efficiency relationships.
Chum – Chum capture efficiency for 2008 was tested using all capture efficiency
experiments performed during the last five years (2004 – 2008), except the seven
experiments that released less than 100 chum. Three of these experiments were conducted in
2006 and four were conducted in 2007. It was felt that the capture efficiency estimates
provided by these experiments were too imprecise to be useful due to the relatively small
numbers of fish released. Five of these seven experiments resulted in only one recapture and
the remaining two experiments had no recaptures.
GLM analysis was used to test for the effects of wild and hatchery, and environmental
variables such as flow, secchi depth and time of day. Year was not used as a factor due to
the insufficient number of experiments conducted in most years. Ordinary least squares
linear regressions were also used to examine the effects of secchi depth and flow versus
capture efficiency relationships.
Pink – During the 2008 season, twelve separate capture efficiency experiments were
conducted using wild pink salmon. An attempt to conduct two experiments per statistical
week was generally followed. This was the third year of capture efficiency experiments for
pink salmon, as juvenile outmigration only occurs in even years.
Because of the difficulty in capturing and holding sufficient numbers of wild pink salmon
for capture efficiency experiments, the pink salmon data are treated differently than the
other species. Pink salmon capture efficiency experiments often consisted of multiple,
relatively small (less than 200 outmigrants released) releases of marked, wild pink salmon
during a statistical week. Therefore, the release and recapture data during a statistical week
were combined to estimate capture efficiency by statistical week. In 2004, 31 separate CE
experiments resulted in seven estimates by statistical week. In 2006, 14 separate CE
experiments resulted in eight estimates by statistical week. In 2008, 12 separate CE
experiments resulted in eight estimates by statistical week. ANOVA was used to test for
difference in annual mean capture efficiency estimates calculated by statistical week.
Only pink capture efficiency experiments conducted in 2004, 2006, and 2008 that released
more than 100 fish and had more than three re-captures were included in the flow analysis
using the GLM. The relationship between capture efficiency versus time of day and secchi
depth was not examined for pink salmon. Only five daytime experiments had been
conducted during the three years of experiments, and secchi depth, or turbidity, is not a
major factor during pink migration.
8
RESULTS
Flow and Turbidity
During the 2008 trapping season, there were three large peaks in mean daily flow. On
February 10th mean daily flow reached 3,370 cfs, on May 18th it reached 6,280 cfs and on
June 30th it reached 4,000 cfs (Figure 1). This year the trap was put in on January 18th, while
in previous years the trap had not been operational until after February 23rd. The difference
in trap timing prevents any comparison of catch and peak flow patterns before late February
for all previous years. The two peaks in May and June are later and smaller than what was
seen in 2007. As a whole this year’s peak flows lasted longer, and were larger than what has
been experienced during similar time periods in years prior to 2007. The average daily flow
for the trapping season, January 18th to August 10th, was 1,763 cfs.
In 2008, there was a lack of correlation between flow and secchi disk depth, similar to the
previous five-years of flow-secchi disk depth analysis. Although this year’s data shows a
stronger correlation between flow and turbidity, the basic trend of previous years is still
present (Figure 2). The clusters of data points at secchi depths <50 cm heavily influence the
relationship. Without the points at <50 cm the relationship becomes more significant. This
cluster of points belongs to measurements taken from late June and July, which is the period
we have defined as the glacial melt period. It is evident that glacial melt influences the
timing, and degree, of turbidity on the Puyallup River and the large-scale shift in flow
regime during juvenile salmon migration.
7000 350
Mean flow
Mean secchi depth
6000 300
Mean Daily Secchi Depth (cm)

5000 250
Mean Daily Flow (cfs)
4000 200
3000 150
2000 100
1000 50
0 0
1/18 2/3 2/19 3/6 3/22 4/7 4/23 5/9 5/25 6/10 6/26 7/12 7/28
Date
Figure 1. Secchi depth and mean daily flow for the Puyallup River, 2008.
9
300
R² = 0.3572
250
Mean Daily Secchi Depth (cm)

200
150
100
50
0
0 1000 2000 3000 4000 5000 6000 7000
Figure 2. Scatter plot of mean daily flow and secchi depth for the Puyallup River, 2008.
Temperature
Mean daily water temperatures are shown from January 24th to August 10th (Figure 3).
Daily surface water temperature never exceeded 16oC, the limit for Washington Department
of Ecology Surface Water Quality Standards for Core Summer Salmonid Habitat (WDOE,
2006). During the 2008 trapping season, temperatures stayed below 10oC until June 16th and
did not reach 12oC until June 27th. Last season surface water temperatures reached 10oC by
April 28th and reached 12oC by May 12th. This year surface water temperatures appeared to
stay much cooler for a longer period of time and did not reach critically high temperatures.
16.00
Temperature (*C)
14.00
12.00
Temperature (C o)
10.00
8.00
6.00
4.00
2.00
0.00
1/24 2/8 2/23 3/9 3/24 4/8 4/23 5/8 5/23 6/7 6/22 7/7 7/22 8/6
Date
Figure 3. Mean daily water temperature recorded on the Puyallup River smolt trap, 2008.
10
CHINOOK
Catch
Unmarked Chinook
A total of 4,760 unmarked Chinook migrants were captured in the screw trap between
January 31st and August 9th. Fifty-three percent (2,517) was actual catch and 47% (2,243)
was expanded catch. This is the highest number of unmarked Chinook captured in the smolt
trap since the beginning of trapping on the Puyallup River in 2000. This year the trap was
installed about one month earlier to investigate the possibility of missed catch in previous
years. Between January 31st and February 15th, 29 Chinook were captured, 0.61% of total
catch.
In general, catch was fairly consistent from the first fish until the last fish except for three
individual peaks: the first peak was the second largest (239) and occurred on March 3rd, the
second peak was the largest peak and occurred on May 14th (365) and the last and smallest
peak occurred on June 29th (148). All peaks coincided with increases in flow. Catch is not
used to describe migration timing of Chinook; instead daily production estimates are used.
Hourly expansion was used to estimate catch for the peaks occurring on May 14th and June
29th peaks. As discussed previously, catch on the days when the trap was not fishing might
not reflect the actual catch had the trap been operating.
Marked Chinook
We captured a total of 20,900 hatchery Chinook migrants between May 13st and August 9th.
The hatchery catches were broken down into 19,018 Ad-clipped Chinook and 1,882
Ad/CWT Chinook. Forty-one percent (7,788) of Ad-clipped Chinook and 50% of Ad/CWT
Chinook were actual catch.
Of the 20,900 hatchery Chinook, 37% (7,695) were captured on the largest peak during a
four- day period from May 20th to May 23rd. Two of these days hourly expansion was used
to assume missed catch. A smaller peak occurred on June 13th, the same day as force release
from Voight’s Creek Hatchery. Table 6 shows the number of Chinook released for each
mark group.
Size
Throughout the trapping season, the mean fork length of unmarked age 0+ Chinook sampled
in the screw trap generally increased and began to vary during stat week 16 (Mid April)
(Figure 4). Other than the increase from 51mm to 68mm seen from the first week in May to
the second week in May mean fork length continued a gradual increase throughout the
trapping season without any drastic increase between stat weeks. Mean daily fork length
peaked at 91 mm during stat week 29 (Mid July) after which it gradually decreased till the
end of the season. This is a typical trend of mean daily fork length, peaking in late July/early
August and then slowly decreasing thereafter.
11
The largest range in length occurred during stat week 27 (early July) where there was a
maximum of 131 mm and a minimum of 50 mm (Appendix B1). In general, the minimum
length of the weekly size range remained small (<45 mm) until stat week 25 (mid June).
Compared to the previous year years, this is the longest period of time the minimum length
has stayed below 50 mm. Furthermore, in 2008 length did not reach above 90 mm until 3
weeks later than previous trapping seasons. This late growth may be due to cold water
temperatures extending into the middle of July.
.
130
120
110
Mean Fork Length (mm)
100
90
80
70
60
50
40
30
20
4 6 8 10 12 14 16 18 20 22 24 26 28 30 32
Statistical Week
Figure 4. Mean weekly fork length and size range of unmarked age 0+ Chinook captured in the
screw trap, 2008.
Capture Efficiency
During the 2008 season, eight capture efficiency experiments using hatchery Chinook
salmon were conducted at the new screw trap location. There were three daytime releases
and five nighttime releases. From 496 to 556 fish were used in each release (Appendix C1).
A total of 4,096 hatchery Chinook were released during the eight experiments.
Because of the change in the location of the screw trap, the 2008 capture efficiency data
were compared to the previous years’ data to see if the relationships observed and
conclusions concerning stratification of the data from previous years (2004 - 2007) had
changed.
All Chinook capture efficiency experiments conducted from 2004 - 2008 were included in
the analyses. We examined capture efficiency as it related to several different parameters.
These included:
• the relationship between capture efficiency and river flow (cfs),
• the relationship between capture efficiency and secchi depth (cm)
measurements made at the trap at the start of each experiment,
• the difference in capture efficiency between daytime and nighttime releases,
and
12
• the difference in capture efficiency between releases made during the pre-
glacial (clear water) and glacial (turbid water) periods.
A total of 45 separate releases of Chinook were made during the five-years (Appendix C1).
Capture efficiency estimates ranged from 0.098% to 7.7%.
Comparison of Capture Efficiency Estimates in 2008 to Previous Years’ Estimates
The range of capture efficiency estimates from the experiments conducted in 2008 was
relatively broad compared to previous years’ estimates (Figure 5 and 6); capture efficiency
estimates in 2008 ranged from 1.2% to 7.7%. The 7.7% capture efficiency was the highest
observed during the five-year study. In 2008, the highest capture efficiency for a daytime
experiment was observed (6.3%, Figure 5), as well as the four highest capture efficiencies
for experiments conducted during non-glacially influenced periods (Figure 6). In general,
the results for the 2008 capture efficiency experiments appear to have more relatively high
estimates (>4%) and fewer low estimates (<2%).
9.00%
8.00% Day Night

Capture Efficiency Percentage
7.00%
6.00%
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 5. Summary of the capture efficiency estimates for daytime and nighttime Chinook smolt
releases conducted in 2004 – 2008.
13
8.00%
Non-glacial
7.00% Glacial

6.00%
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 6. Summary of the capture efficiency estimates for glacial and non-glacial Chinook smolt
releases conducted in 2004 – 2008.
The graph of the mean capture efficiency by year (with 95% confidence intervals) shows
that the mean for the 2008 experiments was more than 2% greater than previous years
(Figure 7). Table 1 summarizes capture efficiency means by year. For the ANOVA
conducted on these data, Levene’s test of the homogeneity of group variances was not
significant (P = 0.251) indicating ANOVA was an appropriate method to compare annual
means. The ANOVA of the annual means was significant (P = 0.021). The Bonferroni
multiple-comparison procedure indicated that 2008 was significantly different than 2004 and
2007 (both P < 0.05), while 2004, 2005, 2006, and 2007 were not significantly different
from each other (all P = 1.00).
8.00%
7.00%
6.00%
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 7. Comparison of mean capture efficiency estimates for Chinook smolt releases conducted in
2004 – 2008 with 95% confidence intervals.
14
Table 1. Annual summary statistics for capture efficiency of Chinook release experiments, 2004 –
2008.
Year Mean N St. Error Median 95% Confidence Interval
2004 2.136% 15 0.5001% 0.832% 1.064% - 3.209%
2005 2.378% 9 0.6389% 2.357% 0.905% - 3.852%
2006 2.472% 6 0.5604% 2.659% 1.031% - 3.912%
2007 1.749% 7 0.3638% 1.569% 0.859% - 2.639%
2008 4.673% 8 0.7946% 5.029% 2.794% - 6.552%
Because previous year’s analyses have demonstrated that capture efficiency can be
influenced by water turbidity (secchi depth) and river flow at the time of the experiment,
Figures 8 and 9 compare secchi depths and river flows for the experiments conducted each
year, respectively. The mean secchi depth for 2008 was the largest observed and continued
the trend of an annual increase in the mean secchi depth for the capture efficiency
experiments. The range of secchi depths for the 2008 experiments was similar to 2006 and
2007. For the ANOVA of mean secchi depths, Levene’s test of the homogeneity of group
variances was significant (P = 0.009) so the KW test was used. The KW test of the
hypothesis of equal group mean ranks for the secchi depth data was not significant (P =
0.071). The range of river flows during 2008 was broader than in previous years although
the mean flow was similar to previous years. For the ANOVA conducted on these data,
Levene’s test of the homogeneity of group variances was not significant (P = 0.091)
indicating ANOVA was an appropriate method to compare annual means. The ANOVA of
the annual means was not significant (P = 0.944).
250
200
Secchi Depth (cm)
150
100
50
0
2003 2004 2005 2006 2007 2008 2009
Year
Figure 8. Comparison of mean and range of secchi disk depth measurements taken during Chinook
capture efficiency experiments, 2004 – 2008.
15
3,000
2,500
Flow (cfs) 2,000
1,500
1,000
500
2003 2004 2005 2006 2007 2008 2009
Year
Figure 9. Comparison of mean and range of flow measurements taken during Chinook capture
efficiency experiments, 2004 – 2008.
Capture Efficiency versus Secchi Depth
Previous year’s analyses have demonstrated that there is a significant (P for the slope
parameter < 0.05) relationship between secchi disk depth and capture efficiency and river
flow and capture efficiency. Figures 10 and 11 show the relationship between capture
efficiency and river flow and secchi depth for the 2008 experiments relative to the previous
years, respectively. Based on previous years’ results, we focused on the relationship
between secchi disk depth and capture efficiency and conducted separate analyses for
daytime and nighttime sets.
9.0%
Day Time Set Night Time Set
8.0%
2008 Day 2008 Night

7.0%
6.0%
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
1,000 1,500 2,000 2,500 3,000
Flow(cfs)
Figure 10. Plot of capture efficiency versus flow for Chinook releases, 2004 – 2008.
16
9.0%
Day Time Set Night Time Set
8.0%
2008 Day 2008 Night

7.0%
6.0%
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 11. Plot of capture efficiency versus secchi depth for Chinook releases, 2004 – 2008.
When all available daytime set data were used in the regression analysis the slope
parameters for both the inverse secchi and LN(secchi) models were not significant, P =
0.433 and P = 0.733, respectively. When the 2008 data were excluded from the analysis the
slope parameters for both models became significant, P = 0.001 and P = 0.002, respectively.
Figure 12 shows the regression line though the origin for the inverse secchi model estimated
using 2004-2007 data and its relationship to the 2008 data.
7.0%
Day Time Set
2008 Day
6.0%
Linear (2004 - 2007)
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
0.000 0.005 0.010 0.015 0.020 0.025 0.030 0.035 0.040
Inverse of Secchi Depth (cm)
Figure 12. Plot of capture efficiency versus inverse of secchi depth for daytime Chinook releases,
2004 – 2008.
When all available nighttime set data were used in the regression analysis, the slope
parameters for the inverse secchi and LN(secchi) models were P = 0.059 and P = 0.032,
respectively. Although the slope was significant for the LN(secchi) model, the adjusted R2
17
for this model was only 0.144. When the 2008 data were excluded from the analysis the
slope parameters for both models became significant, P = 0.006 and P = 0.004, respectively.
The adjusted R2 for the LN(secchi) model improved to 0.358. Figure 13 shows the
regression line for the LN(secchi) model estimated using 2004-2007 data and its relationship
to the 2008 data.
9.0%
Night Time Set
8.0% 2008 Night
Linear (2004 - 2007)

7.0%
6.0%
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
2.00 2.50 3.00 3.50 4.00 4.50 5.00 5.50 6.00
LN Secchi Depth (cm)
Figure 13. Plot of capture efficiency versus LN(secchi depth) for nighttime Chinook releases, 2004
– 2008.
General Linear Model Analysis
The initial GLM analysis of capture efficiency included time of day (day or night) and year
as factors and secchi disk depth and flow as covariates and the time of day|year interaction
term. For this model, flow (P = 0.200) and the interaction term (P = 0.758) were both not
significant while the remaining independent factors were significant (all P ≤ 0.01). The AIC
value for this model was -236.3. The next GLM model omitted the two non-significant
terms and included only time of day (day or night) and year as factors and secchi disk depth
as a covariate. All factors and the covariate were significant (P ≤ 0.006) and the AIC
increased (improved) to -240.9. The last exploratory model was identical to the above
except that LN(secchi) was used as the covariate. Again, all factors and the covariate were
significant (P ≤ 0.001) and the AIC increased (improved) to -247.9. The parameter
estimates for this model are summarized in Table 2. The sign of the coefficients for the
factor variables indicate several interesting things. The sign for the coefficients for each
year is negative relative to the reference year 2008 (the year the other years are contrasted
against) which indicates that the capture efficiency in 2008 was, in general, higher than the
other years even when accounting for differences in time of day and secchi depths. The
negative sign for the coefficient for the day (D or N = D) indicates that, in general, the
capture efficiency for day time sets was less than nighttime sets even when accounting for
differences in years and secchi depths.
18
Table 2. Summary statistics for GLM parameters estimated from capture efficiency experiments,
2004 – 2008.
95% Wald Confidence Interval
Parameter Coefficient Standard Error
Lower / Upper
Intercept 0.109286 0.0141 0.082 / 0.137
Year 2004 -0.032981 0.0062 -0.045 / -0.021
Year 2005 -0.029501 0.0066 -0.042 / -0.017
Year 2006 -0.026077 0.0071 -0.040 / -0.012
Year 2007 -0.032170 0.0067 -0.045 / -0.019
Year 2008 0.000000 - - / -
Day -0.014698 0.0040 -0.023 / -0.007
Night 0.000000 - - / -
LnSecchi -0.011946 0.0028 -0.017 / -0.006
Finally, the 2008 data were removed and the GLM analysis was conducted using the 2004
through 2007 data. For this analysis, year was not a significant factor (P = 0.599) while
time of day and LN(secchi) remained significant (P < 0.001). The results of the GLM
analysis after removing year as a factor from the reduced data set are presented in Table 3.
Table 3. Summary statistics for GLM parameters estimated from capture efficiency experiments,
2004 – 2007.
95% Wald Confidence Interval
Parameter Coefficient Standard Error
Lower / Upper
Intercept 0.079100 0.0107 0.058 / 0.100
Day -0.016281 0.0038 -0.024 / -0.009
Night 0.000000 - - / -
LNSecchi -0.011944 0.0025 -0.017 / -0.007
Capture Efficiency Estimates for Chinook
Based on this year’s analysis there appears to be strong evidence that the relationship
between capture efficiency and secchi disk depth was fundamentally different in 2008
compared to previous years:
• The mean capture efficiency for the experiments conducted in 2008 was the highest
estimated in the past five years and was significantly different than the mean for
2004 and 2007 (Table 1).
19
• The linear regressions examining the relationship between inverse secchi disk depth
and LN(secchi) versus capture efficiency were both improved by omitting the 2008
data from the analyses (Figure 12 and 13).
• The GLM model developed indicated that when the 2008 were included in the
analysis year was a significant factor but when the 2008 data were removed year
was no longer a significant factor.
Based on this, we used the year specific model estimated using a GLM and the combined
2004 – 2008 data (Table 2 and Figure 14). From this, capture efficiency (CE) for 2008 is
estimated as:
1. CE = 0.109286 – 0.014698 + (-0.011944 x LN (secchi disk depth)) for daytime sets

and
2. CE = 0.109286 + (-0.011944 x LN (secchi disk depth)) for nighttime sets.
9.0%
2004 - 2007 Daytime Data
2004 - 2007 Nighttime Data
8.0%
2008 Nighttime Line

2008 Nighttime Data
7.0%
2008 Daytime Data
2008 Daytime Line
6.0%
5.0%
4.0%
3.0%
2.0%
1.0%
0.0%
2.00 2.50 3.00 3.50 4.00 4.50 5.00 5.50 6.00
LN Secchi Depth (cm)
Figure 14. Plot of capture efficiency versus LN(secchi depth) of daytime and nighttime Chinook
releases, 2004 – 2008. Linear regression line represents slope of all data, but intercept
for only 2008 data.
Hatchery Chinook Length used for Capture Efficiency Experiments
Fork length data were collected for all mark-recapture tests conducted in 2008. Average fork
length of the hatchery Chinook used for mark-recapture tests increased over the course of the
testing period (Figure 15). In previous years, we found a weak positive correlation between
capture efficiency and fork length at the time of release. With the addition of this years’ data
there was no apparent relationship (Figure 16), however there continues to be a significant
difference between the mean lengths of hatchery Chinook released during glacial and pre-
glacial periods (P = .012).
20
120
100
Mean Fork length (mm)

80
60
40
20
0
2/2 2/22 3/13 4/2 4/22 5/12 6/1 6/21 7/11
Date
Figure 15. Fork length of hatchery Chinook used in capture efficiency experiments, 2008.
9.0%
Glacial Night
8.0% Glacial Day
Estimated Capture Efficiency
Non-Glacial Night
7.0%
Non-Glacial Day
6.0% 2008 Glacial Night
2008 Glacial Day

5.0%
2008 Non-Glacial Night
4.0% 2008 Non-Glacial Day
3.0%
2.0%
1.0%
0.0%
0 20 40 60 80 100 120 140
Fork Length (mm)
Figure 16. Capture efficiency and mean fork length of hatchery Chinook used for mark-recapture
tests, 2004 - 2008. Tests conducted in 2008 indicated by (Δ and ◊).
Estimated Production
Using daytime and nighttime models generated from GLM analysis, an estimated total of
89,536 unmarked Chinook passed the screw trap between January 31th and August 9th. This
is the largest production estimate within the last five years of assessment.
Glacial and Non-Glacial Catch/Production
Glacial melting and its relevance to migration timing and capture efficiency are an important
aspect of catch and production estimates in the Puyallup River. Tables 4 and 5 show the
21
total catch and production of Chinook for the pre-glacial melt period (< June 27th) and the
glacial melt period (≥ June 27th). The glacial period here is defined as the date at which
secchi depth measurements were less than 51 cm for the remainder of the trapping season. A
majority of unmarked Chinook, 79% of total catch and 83% of total outmigration migrated
past the trap during the pre-glacial melt period. This migration pattern is evident in all
previous years’ analyses.
Although a majority of Chinook migrated before the glacial period there were days when
glacial like conditions occurred during the pre-glacial period, signifying the importance of
monitoring turbidity and its relevance to capture efficiency.
Day and Night Catch/Production
Day and night migration is an important aspect of juvenile migration patterns and has been
an important component of smolt trap operation in the Puget Sound region. On the Skagit
River, daytime migration rates of age 0+ Chinook were found to be affected by turbidity
(Seiler et al., 2004). This year, and in previous years, we were able to establish a
relationship between turbidity and its effects on capture efficiency in daytime and nighttime
conditions, where the trap is less efficient at capturing Chinook during daytime conditions
and most efficient at catching Chinook during nighttime conditions. Capture efficiency
results from this year generally followed the same pattern (Figures 5 and 11).
In contrast to the previous three years, where day catch accounted for less than half of total
catch but made up more than half of production, day catch and production in 2008 accounted
for both a majority of fish captured and estimated (Tables 4 and 5). This is the first year of
this observation.
On the Green River, Seiler et al. (2004) found a wide range of day/night catch ratios for
similar months as our pre-glacial period (February to June). They reported a day/night catch
ratio range of 25% (January to March-fry period) to 46% (May to June-smolt period). For
these same periods, we found a ratio of 1.32 and 1.30, respectively. For our pre-glacial and
glacial period strata, D:N ratios were 1.38 and .63 respectively. This is in sharp contrast to
2006 and 2007 where night catches, regardless of strata, were always more than half of day
catches.
Table 4. Total unmarked Chinook production for pre-glacial and glacial melt period, 2008.
Date Day Night Total
Pre-Glacial 48,020 26,499 74,519 (83%)
Glacial 6,663 8,354 15,017 (17%)
Total 54,683 (52%) 34,853 (48%) 89,536 (100%)
Table 5. Total unmarked Chinook catch for pre-glacial and glacial melt period, 2008.
Date Day Night Total
Pre-Glacial 2,189 1,592 3,781 (79%)
Glacial 379 600 979 (21%)
Total 2,568 (54%) 2,192 (46%) 4,760 (100%)
22
Migration Timing
Unmarked 0+ Chinook
The migration timing in 2008 had a similar pattern as 2007, with two distinct peaks in daily
estimated migration during early March and the second during mid-May or early June
(Figure 17). However, in 2008 a third peak occurred at the end of June which is not typical
timing for Chinook migrants. The largest peak occurred earlier than normal on March 1st
with 6,183 migrants passing the trap, but the largest numbers of Chinook migration (23%)
occurred in the five-days around the middle peak (May 14th –18th). All peaks occurred
around increases in flow.
The migration pattern this year was different than any other previous year. In 2005, there
were three peaks of relatively equal amounts of migrating Chinook a couple weeks apart, in
2006 there was one large peak and in 2007 there were only two peaks with the first being the
smaller of the two; however, for all four years, the largest percentage of migration always
occurred during mid-May/early June and around peaks in flow.
7000 7000
"'Unmarked Chinook
(n=89,536)"
6000 6000
Estimated Number of Migrants

Flow (cfs)
5000 5000
4000 4000
3000 3000
2000 2000
1000 1000
0 0
1/18 2/7 2/27 3/18 4/7 4/27 5/17 6/6 6/26 7/16 8/5
Date
Figure 17. Estimated daily migration of unmarked age 0+ Chinook smolts with mean daily flow,
2008.
Based upon our production estimates, the first 25% of unmarked Chinook migrated by April
14th, 50% by May 18th, just after the large peak and 75% by June 4th. The last fish was
captured on August 9th. Percent daily migration was very similar to 2005 with only 25% of
the estimated number of Chinook migrating 11 days earlier than in 2005 and the other days +
or – 3 days. The 75% migration mark was similar for the previous four years + or – 5 days
(Figure 18).
23
100%
June 4th
75%
Percent Migration
May 18th
50%
April 14th
25%
0%
1/18 2/2 2/17 3/3 3/18 4/2 4/17 5/2 5/17 6/1 6/16 7/1 7/16 7/31
Date
Figure 18. Percent estimated daily migration of unmarked age 0+ Chinook, 2008.
Freshwater Survival
In-River Mortality of Hatchery Releases
All hatchery-origin Chinook were marked with either an Ad-clip or Ad/CWT, which enabled
us to estimate in-river mortality between Voights Creek Hatchery and the screw trap.
Relating overall production estimates of hatchery Chinook to the known number of hatchery
fish released into the system gives us an estimate of in-river mortality.
A total of 1,792,000 marked fall Chinook were released into the Puyallup River in 2008,
1,695,500 Chinook were released from Voights Creek Hatchery (R.M. 21.9), and a total of
96,500 Chinook were released from Cowskull acclimation pond (R.M. 44.75). A total of
382,772 marked Chinook were estimated to have passed the smolt trap. Production
estimates and in-river mortality are provided for each release group (Table 6).
In 2008, total in-river mortality for all hatchery Chinook combined was 79%. The Ad/CWT
mark group belonging to Voight’s Creek Hatchery and Cowskull acclimation pond had
greater mortality than did the group belonging to Voight’s Creek Hatchery only, and
exhibited the highest mortality rate on any tag group since observation of in-river mortality
in 2004.
24
Table 6. In-river mortality of marked Chinook from the Puyallup River, 2008.
Date Capture Estimated In-River

Number Number Percentage for Production for Mortality for
Mark Type
Released Captured Each Release Each Release Each Release
Start End Group Group Group
AD/CWT
22-May 29-May 96,500
(Cowskull)
1,882 0.62% 35,513 88.2%
AD/CWT
13-June 13-June 205,000
(Voights)*
AD (Voights)* 13-June 13-June 1,490,500 19,018 1.27% 347,259 76.7%

* = Personal communication, WDFW
Freshwater Survival of Wild Smolts
Relating our total unmarked Chinook outmigration estimate to our potential egg deposition
gives us freshwater survival estimate to the screw trap (Table 7). This estimate does not
include mortality that may occur after fish pass the screw trap.
The number of females used to calculate the smolt-to-female ratio and egg production is
based on the estimated total number of fish that spawned in the Puyallup River using a
live/redd count based methodology (Scharpf, Pers. Comm.). The number of females was
calculated from the male-to-female ratio from South Prairie Creek and fecundity from
Voights Creek hatchery fall Chinook was used to estimate total egg production. A fecundity
of 3,900 eggs/female was used for the 2007 brood (Davis, Pers. Comm.). Maximum and
minimum flows are from South Prairie Creek.
Table 7. Freshwater survival of unmarked Chinook from the Puyallup River, 2008.
Total Total Potential Maximum and Percent Freshwater
Smolt /
Run Year Outmigration Number of Egg Minimum Flows Survival
Female
Estimate Females Deposition Aug.-Feb.* (#smolts / #eggs)
2007-2008 89,536 906 3,533,400 99 921 27 2.53%
*
= Data gathered from USGS Water Resource Division
Survival rate for this year’s brood was about average compared to the previous four years
and is the same survival rate as 2006, 2.53%. Annual survival rates in conjunction with
maximum/minimum flows are provided in the discussion.
COHO
Catch
Unmarked 1+ Coho
We captured a total of 1,321 unmarked coho in the 2008 trapping season. Fifty-one percent
(674) of coho were expanded and 49% (647) were actual. This is the greatest number of coho
captured in the trap in the past five years. This year the trap was installed about one month
25
earlier to investigate the possibility of missed catch in previous years. Between January 31st
and February 15th 30 fish were captured, 2.2% of total catch.
The first coho migrant was caught on January 18th and the last on July 13th. Although catch
rates varied from day to day, overall catch followed a fairly regular progression and peaked
on May 25th. Thirty-three percent (435) of all coho were captured in one week from May
19th to May 25th when flows were high.
Marked 1+ Coho
A total of 11,451 hatchery coho were captured in the screw trap in 2008. Catch by mark
type is provided in Table 12. For all mark groups combined, fifty-two percent (5,988) of
catch was actual and 48% (5,463) was expanded.
The first marked coho was captured on January 18th and the last on June 20th. This suggests
that hatchery coho are escaping prior to the Voight's Creek Hatchery release; however, the
peak in catch occurred on April 29th, the force date from Voight’s Creek Hatchery. Eighty-
eight percent of the hatchery coho were caught between April 18th and May 2nd. The
majority of hatchery coho moved quickly past the smolt trap, although some coho were
captured nearly a month later than their wild counterpart.
Size
Unmarked age 1+ coho averaged from 71 mm to 136 mm throughout the sampling season.
There was not a continuous trend in increased mean weekly fork length throughout the
season, instead there were two peaks in mean fork length, stat week 17 (late April) and stat
week 25 (early June) (Figure 19). Similar to previous years, the majority of coho migrants
between 100 mm and 120 mm moved past the trap between stat week 14 and 24. Migrants
measuring 80 mm or less were captured at the beginning of the season as well as near the
end (Appendix B2).
26
190
170
Mean Fork Length (mm)

150
130
110
90
70
50
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30
Statistical Week
Figure 19. Mean weekly fork length and size range of unmarked, age 1+ coho captured
in the screw trap, 2008.
Capture Efficiency
During the 2008 season, two capture efficiency experiments using hatchery coho from
Voights Creek were conducted at the new screw trap location (Appendix C2). Both releases
occurred at night.
Because of the change in the location of the screw trap, the 2008 capture efficiency data
changed due to the new location.
All coho capture efficiency experiments conducted from 2004 - 2008 were included in the
analysis. The relationships between capture efficiency and several different parameters
were examined as follows:
• capture efficiency for day-time and night-time releases,

• capture efficiency and secchi depth measurements made at the trap at the start of
each experiment, and
• capture efficiency and river flow measured in cubic feet per second.
A total of 15 separate releases of coho have been made during the five-years of the study.
Capture efficiency estimates have ranged from 0.8% to 2.9%.
With only two experiments in 2008, it is not possible to conduct rigorous statistical tests to
determine if the capture efficiencies at the new trap location are significantly different from
previous years. However, there appears to be a slight difference between years (Figure 20).
27
The capture efficiency estimated for one of the experiments conducted in 2008 was the
highest estimate observed (2.9%) during the five-years of the study. Further, the 2008 mean
capture efficiency was 1.24% higher than the mean capture efficiency for 2007, and 2007
had the lowest capture efficiency during the five years of the study (Table 8). Although
there are not enough experiments to test for significance, there appears to be a minor
difference in capture efficiency that corresponds to the trap locations in 2007 and 2008;
however the difference between years for coho is minimal when compared to the differences
between years for Chinook.
Table 8. Summary statistics for the mean capture efficiency for all Coho salmon release
experiments conducted in 2004-2008.
Release Number Number
Mean N
Date Released Recaptured
2004-2006 1.54% 5010 77 11

2007 1.06% 1415 15 2
2008 2.30% 1612 37 2
10.00%
7.50%
5.00%
2.50%
0.00%
-2.50%
-5.00%
2003 2004 2005 2006 2007 2008 2009
Date
Figure 20. Comparison of mean capture efficiency estimates for coho smolt releases conducted in
2004 – 2008 with 95% confidence intervals.
Comparison of Capture Efficiency Estimates for Daytime versus Nighttime Releases
There was less than a 0.4% difference between the mean daytime and nighttime capture
efficiency estimates (Table 9). The difference between the two means is not significant
(t-test equal variances assumed, P = 0.912). There is no apparent influence of daytime or
nighttime on capture efficiency. Figure 21 shows that the range of capture efficiency
percentage between day and night is similar. Also in 2006 there was a release during the day
and the night which saw no affect on capture efficiency by time of day.
28
3.0%
2004
2005

2.5%
2006
2007
2.0%
2008
1.5%
1.0%
0.5%
0.0%
0 1 2 3
Day (1) or Night (2) experiment
Figure 21. Summary of the capture efficiency estimates for coho smolt releases conducted from
2004 - 2008.
Table 9. Summary statistics comparing the mean capture efficiency for daytime and nighttime
experiments for coho salmon releases conducted in 2004-2008.
Release Mean N St. Error Median 95% Confidence Interval
Daytime 1.56% 6 0.2155% 1.66% 1.008% - 2.116%
Nighttime 1.59% 9 0.1880% 1.44% 1.161% - 2.028%
All 1.58 15 0.1370% 1.442% 1.287% - 1.875%
Capture Efficiency versus Secchi Depth and Flow
Figure 22 plots the estimated capture efficiency for an experiment versus the secchi depth at
the time of the release. Figure 23 plots the estimated capture efficiency for an experiment
versus the river flow. The GLM analysis of capture efficiency included time of day (day or
night) as a factor and secchi disk depth and flow as covariates. Year could not be used as a
factor because there were an insufficient number of observations in most years. For this
model, secchi disk depth (P = 0.988), flow (P = 0.496), and the time of day factor (P =
0.932) were all not significant.
29
3.0%
2004 to 2007 Day
2004 to 2007 Night

2008 Night
2.5%
2.0%
1.5%
1.0%
0.5%
0.0%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 22. Plot of estimated capture efficiency versus secchi disk depth for 1+ coho salmon
releases, 2004 - 2008.
3.0%
2004 to 2007 Day
2004-2007 Night
2.5% 2008 Night
2.0%
1.5%
1.0%
0.5%
0.0%
0 500 1000 1500 2000 2500 3000
Flow (cfs)
Figure 23. Plot of estimated capture efficiency versus flow for 1+ coho salmon releases, 2004 –
2008.
Using all data, separate ordinary least squares (OLS) linear regressions were conducted to
further examine the secchi disk depth and flow versus capture efficiency relationships.
These analyses confirmed the results of the GLM. The results of the OLS regressions are
summarized in Tables 10 and 11. The estimated slopes for these relationships were not
significant: P = 0.898 and P = 0.524 for secchi depth and flow, respectively. The R2 values
for the linear regression models were only 0.1% for secchi depth and 3.2% for flow. There
is no evident relationship between capture efficiency and either secchi depth or flow.
30
Table 10. Summary statistics for the ordinary least squares linear regression of secchi depth (X)
and capture efficiency (Y).
Estimated Coefficients 95% Confidence Interval for B
Model t Signifi-
Parameter statistic cance
B Std. Error Lower Bound Upper Bound
Constant 0.016506 0.005499 3.001 0.010 0.004625 0.028386

Secchi Depth -0.0000045 0.0000344 -0.130 0.898 -0.0000788 0.0000698
Table 11. Summary statistics for the ordinary least squares linear regression of flow (X) and
capture efficiency (Y).
Estimated Coefficients 95% Confidence Interval for B
Model t Signifi-
Parameter statistic cance
B Std. Error Lower Bound Upper Bound
Constant 0.013314 0.004069 3.272 0.006 0.004523 0.022106

Flow 0.0000017 0.0000026 0.654 0.524 -0.0000039 0.000073
Using the mean capture efficiency estimate based upon all available data from 2004 – 2008
we estimate that 83,608 unmarked 1+ coho passed the trap from January 18th to July 13th.
This estimate is higher than all estimates from 2004 - 2007.
Migration Timing
Coho migration followed a regular, unimodal progression, with a peak migration day on
May 25th coinciding with a peak flow (Figure 24). Based on these production estimates, 25%
of migration occurred between January 18th and May 15th, 50% by May 20th, 75% by May
25th, and the remaining migrants moved out between May 26th and July 13th (Figure 25).
6,000 Estimated Migrants 6,000

Captured (n=83,608)
Flow (cfs)
Estimated Number of 1+ Coho
5,000 5,000
Mean Flow (cfs)
4,000 4,000
Migrants
3,000 3,000
2,000 2,000
1,000 1,000
0 0
1/19 2/3 2/18 3/4 3/19 4/3 4/18 5/3 5/18 6/2 6/17 7/2
Date
Figure 24. Estimated daily migration of unmarked age 1+ coho with mean daily flows, 2008.
31
100%
May 25th
75%
Percent Migration
May 20th
50%
May 15th
25%
0%
1/18 2/2 2/17 3/3 3/18 4/2 4/17 5/2 5/17 6/1 6/16 7/1
Date
Figure 25. Percent migration of unmarked age 1+ coho migrants, 2008.
In-River Mortality
Table 12 shows the estimated production and in-river mortality for each mark group in 2008.
Comparing the total estimated production for all mark groups combined with the total
number of marked coho released, we estimate a total in-river mortality of 19%. This is the
lowest mortality estimate in the past four years. In-river mortality of the Ad/CWT group
was more than twice as high as any other group.
Table 12. In-river mortality of coho 1+ mark groups for the Puyallup River, 2008.
Date In River
Estimated
Mortality Total Total
Number Number Production for
Mark Type for Each Number Estimated
Start End Released Captured Each Release
Release Captured Production
Group
Group
CWT 25- 29-
45,300 551 34,873 23%
(Voights)* Apr Apr
25- 29-
AD (Voights)* 708,500 9,909 627,152 11%
Apr Apr
AD + CWT 11,451 724,747
3-
(Lake 3-Mar 93,000
Mar
Kapowsin) 991 62,722 55%
AD + CWT 25- 29-
45,300
(Voights)* Apr Apr
CHUM
Catch
A total of 13,305 juvenile chum migrants were captured in the screw trap in 2008, the most
caught in the past five years. Forty-eight percent (6,407) of these fish were expanded for
32
periods when the trap was not fishing. The first chum migrant was caught on February 12th
and the last was caught on June 13th. Two peaks of similar magnitude occurred on April 29th
and May 14th.
Size
There was little difference in mean fork length of chum between sample weeks, but an
increase in the size range until stat week 19 (Figure 26). The greatest range occurred on stat
week 19 with a maximum of 77 mm and a minimum of 31 mm. Minimum length remained
similar throughout the sampling season (Appendix B3). This year average fork length did not
increase toward the end of the migration as in previous years, and fork length remained
below 45 mm for the entire year except for one week.
80
75
70
65
60
Forkl Length (mm)
55
50
45
40
35
30
25
20
6 8 10 12 14 16 18 20 22 24 26
Statistical Week
Figure 26. Mean weekly fork length and size range of chum captured in the screw trap,
2008.
Capture Efficiency
During the 2008 season, five capture efficiency experiments using chum fry were conducted
at the new screw trap site. All five releases occurred during the night time, two of the
releases used hatchery fish and three used wild chum captured in the smolt trap (Appendix
C3).
Because of the change in the location of the smolt trap, the 2008 capture efficiency data
changed.
All experiments from 2004 - 2008 were used for analysis, except the seven experiments with
releases of less than 100 fish. Of the seven, three experiments were conducted in 2006 and
33
four were conducted in 2007. Five of these seven experiments resulted in no recaptures and
for the remaining two experiments only one chum was recaptured. It was felt that the seven
capture efficiency estimates provided by these experiments were too imprecise to be useful
due to the relatively small numbers of chum released. Further, it was not possible to
conduct rigorous analysis for all years’ data because in some years not all factors were
accounted for (limited releases of wild chum and no daytime releases in some years).
A total of 33 separate releases of chum were made during the five years (Appendix C3).
Capture efficiency estimates ranged from 0.6% to 5.2%.
The relationships between capture efficiency and several different parameters were
examined, these include:
• capture efficiency for releases of hatchery chum compared to releases of
wild chum,
• capture efficiency for day-time and night-time releases,
• capture efficiency and secchi depth measurements made at the trap at the
start of each experiment, and
• capture efficiency and river flow.
With only five experiments in 2008 split between hatchery and wild releases, it is not
possible to conduct rigorous statistical tests to determine if the capture efficiencies at the
new trap location are comparable to previous years. However, the capture efficiency
estimates in 2008 fall within the range of previous estimates observed during the five years
of the study (Figure 27).
6.00%
Wild - Nighttime
Hatchery - Nighttime
5.00%
Hatchery - Daytime
4.00%
3.00%
2.00%
1.00%
0.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 27. Summary of the capture efficiency estimates for chum fry releases, 2004 – 2008.
34
The graph of the mean capture efficiency by year (with 95% confidence intervals) shows
that the mean capture efficiencies for the 2008 experiments are similar to the means for
previous years (Figure 28). However, small samples sizes in all years except 2004 and 2005
prevent any meaningful statistical analysis examining year as an effect.
12.50%
Hatchery
Wild
10.00%
7.50%
5.00%
2.50% n=1
n=7
n=6 n=8 n=1
0.00%
n=3
n=3
-2.50% n=2
n=2
-5.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 28. Comparison of mean capture efficiency estimates for chum fry releases conducted in
2004 - 2008 with sample size (n) and 95% confidence intervals.
GLM analysis Capture Efficiency versus Secchi Depth and Flow
Figure 29 shows the relationship between capture efficiency and secchi depth, while figure
30 shows the relationship with river flow, for the 2008 experiments relative to the previous
years. Since mean capture efficiencies are similar for all years the data from 2008 are treated
as being similar to the previous years and combined with that data for analysis.
The GLM analysis of capture efficiency included time of day (day or night) and hatchery or
wild as factors and secchi disk depth and flow as covariates. Year could not be used as a
factor because there were an insufficient number of observations in most years. For this
model, secchi disk depth (P = 0.155) and the time of day factor (P = 0.381) were not
significant. The next GLM analysis of capture efficiency included only hatchery or wild as
factors and flow as the covariate. Both the hatchery or wild factor and the flow covariate
were significant (P = 0.022 and P = 0.013, respectively).
A visual examination of this relationship (Figure 30) indicates that the point in the lower
right hand portion of the graph may be very influential in determining the CE versus flow
relationship (flow of 4,480 and CE = 0.56%). In fact, if this observation is omitted from the
previous analysis the coefficient estimated for the flow covariate becomes non-significant (P
= 0.118). For both analyses, however, the hatchery or wild factor is significant. The
estimated coefficient for this factor is 0.011 indicating that the trap is, on average, about
1.1% more efficient in capturing hatchery chum smolts than wild chum smolts under the
same flow conditions.
35
6.00%
Hatchery - Daytime
Hatchery - Nighttime

5.00% Wild - Nighttime
2008 Hatchery - Nighttime
2008 Wild - Nighttime
4.00%
3.00%
2.00%
1.00%
0.00%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 29. Plot of estimated capture efficiency versus secchi disk depth for chum releases, 2004 –
2008.
6.00%
5.00%
4.00%
Hatchery - Daytime
3.00% Hatchery - Nighttime
Wild - Nighttime
2.00% 2008 Hatchery - Nighttime
2008 Wild - Nighttime

1.00%
0.00%
0 1000 2000 3000 4000 5000
Flow(cfs)
Figure 30. Plot of estimated capture efficiency versus flow for chum releases, 2004 – 2008.
Comparison of Capture Efficiency Estimates for Daytime versus Nighttime Releases
There was about a 0.7% difference between the mean daytime and nighttime capture
efficiency estimates for the hatchery releases (Table 13) while the wild release experiments
had the lowest mean capture efficiency (Figure 31). The differences between the three
means are not significant (one-way ANOVA, P = 0.202).
36
Table 13. Summary statistics comparing the mean capture efficiency for hatchery daytime,
hatchery nighttime, and wild nighttime experiments for chum salmon releases conducted
in 2004 - 2008.
Release Mean N St. Error Median 95% Confidence Interval
Hatchery Daytime 3.48% 7 0.5505% 4.08% 2.137% - 4.831%
Hatchery Nighttime 2.80% 15 0.4035% 2.92% 1.939% - 3.700%
Wild Nighttime 2.24% 11 0.3362% 2.00% 1.491% - 2.990%
5.00%
4.00%
3.00%
2.00%
n=7
n=15
n=11
1.00%
0.00%
0 1
Daytime Hatchery 2
Nighttime Hatchery 3 Wild
Nighttime 4
Group
Figure 31. Mean capture efficiency and 95% confidence interval for the original three
possible strata defined for chum experiments conducted from 2004-2008.
Conclusion of Capture Efficiency Experiments for Chum
The GLM analyses indicate that there is a difference between trap capture efficiency for
hatchery compared to wild chum fry. Even though the mean capture efficiency for hatchery
chum experiments is not significantly different from the mean capture efficiency for wild
chum experiments (two sample t-test equal variances assumed, P = .0144), this may reflect
the imprecision of the estimates of the mean which both have a coefficient of variation of
about 50% (Table 14). A power analysis indicated that the data could only detect mean
differences the size of those observed (about 0.8%) with only about 30% power. To detect
differences in means with power of 80% or more would require mean differences in the
range of 1.2% to 1.4%.
37
Table 14. Summary statistics comparing the mean capture efficiency for hatchery and wild
experiments for chum salmon releases conducted in 2004-2008.
Release Mean N St. Dev. Coef. Var. 95% Confidence Interval
All Hatchery 3.021% 22 1.529% 50.6% 2.343% - 3.699%
Wild Nighttime 2.240% 11 1.115% 49.8% 1.491% - 2.990%
Using only the data from the wild chum experiments, separate ordinary least squares (OLS)
linear regressions were conducted to further examine the secchi disk depth and flow versus
capture efficiency relationships. These analyses confirmed the results of the GLM. The
estimated slopes for these relationships were not significant: P = 0.935 and P = 0.607 for
secchi depth and flow, respectively. The R2 values for the linear regression models were
only 2.8% for secchi depth and 17.5% for flow. There is no evident relationship between
capture efficiency and either secchi depth (Figure 32) or flow (Figure 33) for the wild chum
release experiments.
Our interest is primarily estimating the outmigration of wild chum smolts, therefore, we
limit our focus to those data. There is no apparent relationship between capture efficiency
and either secchi disk depth or flow for the wild chum experiments, and whether a set occurs
during the daytime or nighttime does not appear to influence the results of the capture
efficiency experiment; therefore data was not stratified and a single mean estimate of
capture efficiency (2.24%) based upon all available wild chum data was used for the
production estimate. Tables 13 and 14 present the summary statistics for the 11 wild chum
experiments.
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
0 50 100 150 200 250
Secchi Depth (cm)
Figure 32. Plot of estimated capture efficiency of wild chum salmon versus secchi disk depth
for Puyallup River smolt trap data 2004-2008.
38
5.00%

4.00%
3.00%
2.00%
1.00%
0.00%
0 500 1000 1500 2000 2500
Flow (cfs)
Figure 33. Plot of estimated capture efficiency of wild chum salmon versus flow for Puyallup
River smolt trap data 2004-2008.
Using a single mean estimate from all available wild chum experiments, we estimate that
593,973 chum passed the trap in 2008. The estimated production this year is the highest
since chum estimation began in 2004.
Migration Timing
Using production estimates, the peak of the migration occurred on April 29th when 81,563,
14% of the total run passed the trap (Figure 34). Throughout the season migration increased
and decreased progressively. Fifty percent of the migration occurred by May 9th (Figure 35),
near the end of the expected migration range.
39
7,500 90,000
Chum Migrants (n = 593,973)
Estimated Number of Chum Migrants

Mean Flow (cfs)
6,250 75,000
5,000 60,000
Mean Flow (cfs)
3,750 45,000
2,500 30,000
1,250 15,000
0 0
2/11 2/21 3/2 3/12 3/22 4/1 4/11 4/21 5/1 5/11 5/21 5/31 6/10
Date
Figure 34. Daily estimated migration of chum fry with mean daily flows, 2008.
100%
May 16th
75%
Percent Migration
May 9th
50%
April 29th
25%
0%
Date
Figure 35. Percent estimated migration of chum fry, 2008.
Pink
Catch
This year we captured a total of 251,373 pink migrants in the smolt trap. The first pink was
captured on January 31st and the last on May 29th, the largest range in catch for all years. This
year the trap was installed about one month earlier to investigate the possibility of missed
catch in previous years. Between January 31st and February 15th we captured 186 pink, 0.07%
of the total catch.
40
Size
The pink migrants sampled exhibited little difference in mean length between statistical weeks,
however there was a gradual increase in the minimum length (Figure 36). The largest pink
measured was 42 mm in stat week 10 and the smallest was 25 mm in stat week 6 (Appendix
B4).
46
44
42
40
Fork Length (mm)
38
36
34
32
30
28
26
24
4 6 8 10 12 14 16 18 20 22 24
Statistical Weeks
Figure 36. Mean weekly fork length and size range of pink fry captured in the screw trap, 2008.
Capture Efficiency
We completed 12 capture efficiency experiments over eight statistical weeks in 2008. A total
of 6,501 pink were released during mark-recapture experiments. The number of individuals
used in each experiment ranged from 161 to 751. Capture efficiency for each individual
experiment ranged from 0.13% to 3.45% (Appendix C4).
The range of combined weekly capture efficiency experiments conducted in 2008 are
generally intermediate to those from 2004 and 2006 (Figure 37), and the annual mean capture
efficiency for 2008 is between 2004 and 2006 estimates (Figure 38). For the ANOVA
conducted on these data, Levene’s test of the homogeneity of group variances was significant
(P = 0.006) so the KW test was used. The KW test of the hypothesis of equal group mean
ranks for the CE data was significant (P = 0.004). A multiple, pair-wise comparison
procedure based on the KW test (Conover, 1980) was used to compare the years. The mean
rank of the capture efficiency estimates for 2004 was significantly different from 2006 and
2008 (both P ≤ 0.05) but 2006 and 2008 were not significantly different from each other (P >
0.05).
41
4.00%
3.50%

3.00%
2.50%
2.00%
1.50%
1.00%
0.50%
0.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 37. Summary of capture efficiency estimates, by statistical week, for wild pink releases
conducted in 2004, 2006 and 2008.
4.00%
3.50%
3.00%
2.50%
2.00% n=7
1.50%
1.00%
n=8
0.50%
n=8
0.00%
2003 2004 2005 2006 2007 2008 2009
Year
Figure 38. Comparison of mean capture efficiency estimates, by statistical week, for wild pink
releases conducted in 2004, 2006 and 2008 with sample size (n=) and 95% confidence
intervals.
Capture Efficiency versus Flow
To examine the flow versus capture efficiency relationship only those experiments that
released more than 100 wild pink salmon, and in addition those experiments with more than
three re-captures were used in the analysis. This resulted in using data from 16 experiments
in 2004, six experiments in 2006 and ten experiments in 2008 (Figure 39). For the analyses,
the capture efficiency data from 2008 are treated as being similar to the previous years and
combined with that data for analysis.
42
7.00%
2004
6.00% 2006

2008
5.00%
4.00%
3.00%
2.00%
1.00%
0.00%
500 1,000 1,500 2,000 2,500
Flow (cfs)
Figure 39. Mean weekly fork length and size range of pink fry captured in the screw trap, 2008.
GLM analysis of capture efficiency included year as a factor and flow as a covariate. For this
model, year was a significant factor (P < 0.001) but the flow covariate was not significant (P =
0.110).
Conclusion of Capture Efficiency Experiments for Pink
Because of the significant year factor from the GLM analysis, we did not combine all years’
data and used the mean estimate of capture efficiency (1.683%) from all combined stat weeks
in 2008 for the production estimate. Table 15 presents the annual summary statistics for the
three years of pink experiments.
Table 15. Annual summary statistics for the mean capture efficiency for pink salmon release
experiments conducted in 2004, 2006 and 2008 (mean of estimates for statistical weeks).
Year Mean N St. Error Median 95% Confidence Interval
2004 2.712% 7 0.2325% 2.614% 2.143% - 3.281%
2006 0.989% 8 0.1447% 1.075% 0.647% - 1.331%
2008 1.683% 8 0.3104% 1.766% 0.949% - 2.417%
We estimate that 14,936,007 pink migrants passed the trap from January 31st to May 29th.
The estimated production this year is the highest since pink estimation began, 1.9 million
(2004) and 7.0 million (2006).
43
Migration Timing
The first pink was captured on January 31st and the last on May 29th (Figure 40). The peak in
pink migration occurred on April 28th when 1.8 million pink, 12 % of the total estimate
passed the trap. Like previous years, migration was uni-modal with one large distinct peak;
however unlike previous years the peak occurred nearly one month later than in 2004 and
2006. Fifty percent of pink migrated in 18 days, between April 11th and April 28th (Figure
41).
7,000 1.93E+06
Pink Migrants (n = 14,936,007)
Flow (cfs)
6,000 1.65E+06
Estimated Number of Pink

5,000 1.38E+06
4,000 1.10E+06
Flow (cfs)
3,000 8.25E+05
2,000 5.50E+05
1,000 2.75E+05
0 0.00E+00
1/26 2/10 2/25 3/11 3/26 4/10 4/25 5/10 5/25
Date
Figure 40. Daily estimated migration of pink fry with mean daily flows, 2008.
100%
April 28th
75%
Percent Migration
April 20th
50%
April 11th
25%
0%
1/26 2/10 2/25 3/11 3/26 4/10 4/25 5/10 5/25
Date
Figure 41. Percent daily estimated migration of pink fry, 2008.
44
STEELHEAD
Catch
One-hundred and eighty-nine (189) unmarked and 679 marked steelhead were captured in the
smolt trap during the 2008 trapping season, the highest catch of unmarked steelhead in the
past six years (Figure 42). This ended the trend of less than 100 unmarked steelhead
captured in the smolt trap over the past five consecutive years. Seventy percent (130) of
unmarked catch was actual and 30% (59) was expanded. For marked steelhead, 84% (569)
was actual catch and 16% (110) was expanded.
The trap was installed about one month earlier to investigate the possibility of missed catch.
Twelve unmarked steelhead (6%) were captured between January 18th and February 15th. If
this number is subtracted from the total number of steelhead captured this year is still greater
than the 8-year average of 152.
600
539
Unmarked Steelhead Captured
500
400
300
250
189
200 156
100 74 77
54
39 25
0
2000 2001 2002 2003 2004 2005 2006 2007 2008
Year
Figure 42. Total number of unmarked steelhead captured in the Puyallup River screw trap, 2000-
2008.
Size
There does not appear to be a trend of positive growth during the 23 weeks of migration;
however beginning statistical week 19 (early May) larger steelhead were captured (Figure 43).
Maximum and minimum fork length was variable for each statistical week with a wide range
occurring in all months (Appendix B5).
For all unmarked and marked steelhead sampled throughout the migration period, marked
steelhead on average were larger than unmarked steelhead, but there was a larger range and
standard deviation for unmarked wild steelhead (Table 16).
45
240
220
200
Mean Length (mm) 180
160
140
120
100
80
2 4 6 8 10 12 14 16 18 20 22 24 26
Statistical Week
Figure 43. Mean weekly fork length and size range of unmarked steelhead captured
in the screw trap, 2008.
Table 16. Length data of unmarked and marked steelhead captured in the Puyallup River
screw trap, 2008.
Steelhead
Attribute Count Mean Min. Max St. dev.
Type
Unmarked Length 130 167 90 242 25.98
Marked Length 79 201 146 238 20.28
Capture Efficiency
No capture efficiency tests were completed this year, or in any previous year for steelhead
due to the difficulty of obtaining and marking steelhead and error associated with tests of
large mobile fish. Capture percentage from Voight’s Creek Hatchery is supplied for 2004-
2008 (Table 17). In 2008, capture efficiency from Voight’s Creek Hatchery was the highest
among the previous five-years but remained below 1% for all years. The combined average
capture efficiency for all years is 0.18%.
Table 17. Capture Percentage of Marked Steelhead from Voights Creek Hatchery, 2004-2008.
Date Number
Mark Type Number Captured Capture Percentage
Start End Released
AD (Voights)* (2008) 1-May 6-May 161,975 679 0.41%
AD (Voights)* (2007) 13-Apr 16-Apr 128,100 105 0.08%
AD (Voights)**(2004) 4-Apr 30-Apr 231,859 191 0.08%
* = Data gathered from Voights Creek Hatchery
** = Data gathered from Pacific States Marine Fisheries Commission
46
Migration Timing
The first steelhead was caught on January 18th and the last on June 18th, the largest catch
range in any of the previous nine years (Figure 44). There was a large single peak that
occurred on June 3rd, the latest peak date in the previous nine years. May is typically the
peak month, followed by April and then June. Similar to previous years, a majority of the
migrants were caught on periods of high flows between April 15th and May 31st: 77% in
2005, 88% in 2006 and 52% in 2008. However, unlike these years, the peak migration
occurred outside of this time period.
7,000 35
Migrants Captured (n=187)
Flow (cfs)
6,000 30
Steelhead Migrants Captured

5,000 25
Flow (cfs)
4,000 20
3,000 15
2,000 10
1,000 5
0 0
1/18 2/2 2/17 3/3 3/18 4/2 4/17 5/2 5/17 6/1 6/16
Date
Figure 44. Daily catch of steelhead migrants with mean daily flows, 2008.
47
ASSUMPTIONS
Catch
Catch recorded during morning and evening trap checks is the actual number of fish that
outmigrated during the night and day periods, respectively.
Catch Expansion
Our data represents actual and observed samples, except during certain instances when the trap
could not be fished due to any number of reasons: high flows, high volumes of hatchery fish,
trap maintenance or screw stoppers. During these un-fished intervals, average daily catch and
hourly sub-sampling was used to expand for the missed catch. Catch data for these un-fished
periods is assumed to be what would have been captured had the trap been operating.
For most species, we expanded a significant amount of fish during times when the trap was not
fishing. The percent expanded is provided for each species in their respective sections. We
feel that expanding for times when the trap is not fishing is better than assuming no catch at
all. We will continue to monitor the actual and expanded percentages of fish captured in the
trap.
• The entire outmigration season for all species was sampled (January 18th to August
10th). Complete migration curves were generated for Chinook, coho, pink, chum and
steelhead.
• The trap was fished twenty-four hours a day, seven days a week with the exception of
the periods noted above. During these periods catch numbers were extrapolated to
adequately reflect the catch that was missed.
Trap Efficiency
• All marked fish are identified and recorded.
• The number of marked fish passing the trap is known. Survival from release site to
trap is 100%.
• Release strata are contained within the measured period (i.e., marked fish pass the trap
within a week and have no chance of being counted in the following week’s release
group).
• All fish in a release group have an equal chance of being captured.
Chinook
• Marked hatchery Chinook are captured at the same rate as wild Chinook.
• Chinook capture efficiency is a function of daylight and water clarity.
• There was a difference in capture efficiency between this year and the previous four
years, and the GLM analysis used reflects the difference in capture efficiency between
years.
Coho
• Marked hatchery coho are captured at the same rate as wild coho.
• Coho capture rate is not a function of mean daily flow or water clarity.
48
• Using all available capture efficiency experiments from 2004 – 2008 to generate a
single average capture efficiency accurately reflects the capture efficiency in 2008.
Chum
• Marked hatchery chum and marked wild chum are not captured at the same rate.
Only wild chum mark-recapture tests were used to estimate trap efficiency.
• Environmental conditions (i.e., flow and turbidity) were not significant factors
influencing trap efficiency during the chum migration period.
• There was no significant difference between individual wild chum mark-recapture
trials conducted from 2004 – 2008.
Pink
• Wild pink used for mark-recapture experiments migrate similar to unmarked wild pink.
• Environmental conditions, i.e. flow and turbidity, were not significant factors
influencing trap efficiency during the pink migration period.
Turbidity, Flow and Temperature

• Ambient light at each secchi measurement remained similar throughout the sampling
period, regardless of the time of day.
• Secchi measurements taken in day and night time actually reflect the clarity of water
during the entirety of that time period strata.
• Flows obtained from USGS website are actual and true flows that are represented at the
trap site.
• Water temperature recorded in the livebox at the screw trap site is the true river water
temperature.
49
DISCUSSION
Turbidity and Flow
Although there is no strong evidence that flow effects turbidity, a large-scale shift in turbidity
and flow exists during the juvenile migration period of salmonids. During this event, flow
generally increases as secchi depth decreases (increase in turbidity), and then after some period
both flow and secchi depth steadily decrease. This large-scale shift is a seasonal phenomenon
on the Puyallup River and is attributed to the degree of glacial melting at higher elevations.
Turbidity should continue to be measured by secchi depth at each trap check and each capture
efficiency test.
The importance of other environmental factors such as, air temperature, snow pack and
freezing levels at glacial elevations are being monitored since these factors may dictate the
timing of migration and ultimately the life history patterns of juvenile salmonids.
Temperature
In 2008 average surface water temperatures were 2o (F) colder than 2007, for the months from
March till late July. As a result, most species exhibited either a delay in migration timing or
reduced growth until later in the year compared to previous years. For example, it took three
weeks longer for 0+ Chinook to reach an average fork length of 90 mm compared to the
previous three years, but migration timing remained similar. For chum and pink, a delay in
peak migration was evident along with a smaller average fork length for chum, while steelhead
only exhibited a slight delay in peak migration. There seemed to be no apparent affect of fork
length or delayed migration for 1+ coho.
Temperature is the dominate factor for embryonic development and alevin emergence. It can
take up to an additional month for Chinook fry to emerge from the gravel when temperatures
are 8o (C) compared to 11o (C) (Quinn, 2005). Reliable surface water temperature data was
only collected in 2007 and 2008, so comparison of the affect of temperature on development
and growth in other years is difficult; however temperature data is collected at other sites in the
Puyallup River and future work will explore the affects of temperature on migration timing
and growth.
Catch and Migration Timing
Using smolt trap catches to monitor migration timing does not take into account the influence
of a dynamic river system on the capture efficiency of the screw trap. We found differences
between the migration timing of juvenile Chinook and coho using screw trap catches as
opposed to daily production estimates. Due to the increase in capture efficiency of the screw
trap in turbid environments and at night for Chinook, we believe the best way to quantify
migration is to use daily estimated production because it attempts to normalize all catch days.
Evaluation of migration timing using estimated daily production will continue in future years.
50
This year we began fishing the trap in mid-January, about one month earlier than our normal
start date. We did not catch a large percentage of any species (<7%) during that time.
Although we do not feel we are missing a significant portion of fish due to the sampling period
in previous years, we will continue to sample the early run timing of outmigrants.
Trap Efficiency and Production Estimates
Chinook
Using the availability of five years worth of capture efficiency data we were able to generate a
relationship between the capture efficiency of the screw trap and night/day strata in 2008. In
previous years, we defined capture efficiency into three or four separate strata, e.g. day/pre-
glacial, day/glacial, night/pre-glacial and night/glacial. This year’s GLM analysis showed a
difference in capture efficiency experiments conducted in 2008 compared to previous years.
This was attributed to the new location of the screw trap in 2008. Because of the difference in
capture efficiency, this year’s data were not separated into pre-glacial or glacial strata, instead
it was stratified by day and night only and combined with previous year’s data to generate a
linear relationship based on all available data, which accounted for the difference between
2008 and previous years.
The D:N catch and production ratios from 2005 – 2007 indicate that a majority of fish are
captured during the night, but a majority of production is generated from the day; except in
2008 where there was both more catch and production during the day. In 2004, catch during
the day was greater than night, but production during the day was less than night. Whether or
not there is actually more fish migrating during the daytime hours than nighttime hours could
be a function of low capture efficiency estimates applied to daytime catches, however we
noticed that during the morning hours, just after light, a number of Chinook are captured in the
trap. This would be counted as day catch. It is likely that juvenile Chinook are migrating
aggressively during the night only to reach the trap’s location in the early morning, which
would explain the large D:N ratios in the Puyallup trap.
We would have expected to observe a negative correlation between mean length of Chinook
used for mark-recapture tests and estimated capture efficiency, similar to other projects
(Conrad et. al, 2000). It is likely that during the glacial period, when Chinook are normally
larger at release, the positive affect of turbidity on capture efficiency negates any relationship
between the size of Chinook and capture efficiency.
Coho
Coho mark-recapture tests completed in 2004 - 2006 revealed a relationship between capture
efficiency and flow, where capture efficiency increased with increased flow. With the
inclusion of the 2007 and 2008 data the relationship between flow and capture efficiency
became less evident. In both years, the screw trap was fished at different sites due to changes
in bathymetry at the old sites. Although capture efficiency for the previous five-years was
lowest in 2007 and highest in 2008, the difference in capture efficiency between all years was
only 2.1%, therefore we combined all years’ data for a single average capture efficiency in
2008. GLM analysis concluded no relationship between flow and secchi depth for all years;
51
however there were not enough tests completed to test for difference between years. Capture
efficiency tests should continue to further clarify the relationship between capture efficiency of
the trap and flow as a predictor of overall production.
No mark-recapture tests were completed for sub-yearling coho captured in the screw trap.
There were 278 0+ age coho captured this year, there is evidence that this age component may
be an important aspect of the life history strategy for coho salmon and may be an indication of
factors contributing to the survival of coho salmon (Miller et. al., 2003). The numbers of 0+
age coho will continue to be monitored on the Puyallup River.
Chum
Using GLM analysis for all available data from 2004 – 2008, we were able to find a significant
difference between the capture efficiency of wild and hatchery chum using all mark-recapture
experiments. Although GLM analysis concluded difference, the two sample t-test concluded
no difference; however the power to detect a difference in the t-test was low and we concluded
there was in fact a difference between the average capture efficiency for wild and hatchery
chum. Volkhardt et. al. (2006) reported similar data between wild and hatchery Chinook,
where there was no detectable difference (α = .05) between groups and a lower capture
efficiency for wild fish than for hatchery fish. In addition, GLM analysis concluded there was
no relationship between capture efficiency and flow for wild chum.
For all data from 2004 – 2008, we found the average capture efficiency for hatchery chum was
0.8% higher than the average trap capture efficiency for wild chum. If this finding is true for
other species of salmonids, our reported capture efficiencies using hatchery Chinook and coho
are likely biased high. Since chum are the only species where large numbers of both hatchery
and wild fish are available for testing, future analysis of the relationship between the efficiency
of the trap in capturing wild and hatchery chum should be completed.
Pink
For all available data (2004, 2006 and 2008), GLM analysis concluded year was a significant
factor, while flow was not, so data from 2008 was not combined with previous years’ results.
In previous years, production was estimated using combined capture efficiency experiments
completed within each stat week. This year it was felt that a mean capture efficiency based on
all combined statistical weeks would better suit the production estimate.
Steelhead
This year unmarked steelhead catch in the screw trap was greater than in any of the past six
years. Whether or not this is an actual trend in population abundance or an artifact of annual
variation of trap efficiency remains to be seen. From 2004 – 2008 capture efficiency of
hatchery steelhead from Voight’s Creek Hatchery ranged from .08% to .41%. If these capture
efficiency results are applied to their respective years unmarked steelhead catch the trend in
the total number of steelhead differs between catch and the abundance estimate. Trends in
both the catch and abundance of natural steelhead smolt are continually being monitored to
investigate these differences.
52
Freshwater Survival
Hatchery In-River Mortality
Chinook
The total estimated mortality rate for 2008 is the highest in the previous five years. Previous
mortality rates ranged from 67% in 2006 to 20% in 2005 (Figure 45). Like 2006 and 2007,
mortality rate in 2008 was greater than 50% of the migrating fall Chinook. On the Skagit
River, Vokhardt et. al. (2006) reported the average mortality over the past several years at
around 50%. Over the past four years, mortality rates in the Puyallup River have been higher,
around 60%, except for 2005 where mortality was low. There appears to be a positive
relationship between the total number of hatchery Chinook released and in-river mortality;
however the one point in 2005 heavily influences the relationship, and in fact, without the
2005 data point the relationship would not exist.
90%
R² = 0.8367 2008
80%
70%
2006
% In-river Mortality
60%
2007
50%
40%
2004
30%
2005
20%
10%
0%
500,000 1,000,000 1,500,000 2,000,000
Total Number of Marked Chinook Released
Figure 45. Percent in-river mortality and number of marked Chinook released for migration years
2004 - 2008.
In 2004, 2005, 2007 and 2008, acclimation pond Chinook were released in the upper
watershed above Puget Sound Energy’s Electron diversion facility. For all years except 2007,
the mark group belonging to the upper Puyallup River exhibited a higher mortality rate than
the mark group belonging exclusively to Voight’s Creek hatchery.
No distinct external mark group exists for acclimation pond Chinook, however a distinct CWT
number does exist, so a thorough evaluation of mortality associated with releases from the
upper watershed is difficult without CWT sacrifice at the screw trap. Increased mortality of
hatchery mark groups including acclimation pond Chinook could be a reflection of the longer
migration route, including the passage through Puget Sound Energy’s Electron diversion
facility, but without a unique identification mark on acclimation pond fish we cannot
accurately compare mortality between mark groups.
53
Coho
In-river mortality for the Ad/CWT group was more than twice that of any other group of coho
released in 2008. This is probably because a large percentage of this group was planted in
Lake Kapowsin rather than released in the upper Puyallup River, as in previous years. It’s
likely that a large percentage of coho were preyed upon or took residence within the lake.
This year there was a large decrease in the total estimated mortality relative to all other years:
2007 (90%), 2006 (75%) and 2005 (65%). This was also the greatest number of hatchery coho
captured compared to previous years: 8,010 (2005), 4,182 (2006) and 847 (2007). From this
data it appears as if there is a negative relationship between the number of coho captured and
the survival of migrating hatchery coho.
Production estimates used to generate in-river mortality from 2005 - 2008 were produced by
two different methods: a single capture efficiency estimate in 2007 and 2008, and a flow-
capture efficiency model in 2005 and 2006. When a single capture efficiency percentage is
used to estimate production, catch and production directly reflect one another, but when a flow
model is used capture efficiency fluctuates on a daily basis. This association makes
comparison of data difficult. In the future, trends in in-river mortality will continue to be
monitored to investigate the degree of survival.
Freshwater Survival of Wild 0+ Age Chinook
The 2008 estimate of freshwater survival for 0+ Chinook is near the four-year average of
2.01%. Survival rates appear to be influenced by peak incubation flows on South Prairie
Creek, the major spawning tributary on the Puyallup River (Figure 46). The low survival rate
in 2007 is attributed to record flows on the Puyallup River in November 2006. Low survival
rates are also explained by high flows on the Skagit River (Volkhardt et. al. 2006).
4.50%
R² = 0.8789
4.00%
Freshwater Survival Estimate
3.50%
2004
3.00%
2008 2006
2.50%
2.00%
2005
1.50%
1.00%
0.50%
2007
0.00%
0 1,000 2,000 3,000 4,000 5,000 6,000 7,000
Peak incubation flow (cfs) on South Prairie Creek
Figure 46. Correlation between peak incubation flows (Aug. – Feb.) on South Prairie Creek and
freshwater survival estimates on the Puyallup River, migration years 2004 – 2008.
54
The range of freshwater survival estimates on the Puyallup River appear to be on the lower end
when compared to other watersheds in Washington. Studies completed in several watersheds
by the WDFW show a wide range of freshwater survival rates for Chinook salmon: 1.7% to
5.0% on Bear Creek, a tributary to Lake Washington (Volkhardt et. al., 2006), 5.3% to 7.3%
on the Green River (Seiler et. al., 2004), and 1.2% to 16.7% on the Skagit River (Volkhardt et.
al., 2006). Maximum and minimum flows in conjunction with freshwater survival will
continue to be monitored on the Puyallup River to better understand the influence of flow
regimes on the survival of juvenile Chinook salmon.
Mortality
No mortalities were recorded on wild or hatchery steelhead or cutthroat trout. However, screw
trap mortalities did include: 24 unmarked 0+ Chinook (0.5%), 351 Ad-marked Chinook, 8
Ad/CWT Chinook, 5 unmarked 1+ coho (0.4%), 3 Ad 1+ coho, 4 unmarked 0+ coho (1.4%),
115 wild chum (0.9%) and 12,337 wild pink (4.9%).
Measures were taken to reduce predation on chum and pink fry by coho and steelhead smolts
through the inclusion of artificial, protective habitat structures in the live box. We found the
inclusion of black plastic Bio-Rings® strung together in the water column was the most
effective in reducing mortality and predation.
Incidental Catch
In addition to the focus species, we also caught 6 cutthroat trout and 278 wild coho (0+) fry.
Non-salmonid species caught in the screw trap included brook lamprey, pacific lamprey,
sculpin, long-nose dace, sticklebacks, and sunfish.
55
REFERENCES
Literature Citations
Conover, W. J. 1980. Practical Nonparametric Statistics, Second Edition. John Wiley and
Sons, New York. 493 p.
Conrad, R.and M. T. MacKay. 2000. Use of a Rotary Screwtrap to monitor the Out-migration
of Chinook Salmon Smolts from the Nooksack River:1994-1998. Northwest
Fishery Resource Bulletin. Proj. Report Series No. 10. NWIFC. Olympia,
Washington.
Miller, B.A., S. Sadro. 2003. Residence Time and Seasonal Movements of Juvenile Coho
Salmon in the Ecotone and Lower Eustuary of Winchester Creek, South Slough,
Oregon. Transactions of the American Fisheries Society Volume 132:546-559.
Pacific States Marine Fisheries Commission. 2007. Regional Mark Information System.
www.rmis.org
Quinn, Thomas P. 2005. The Behavior and Ecology Of Pacific Salmon And Trout. University
of Washington Press, Canada.
Region 6-Fish Management Division and Puyallup Tribe of Indians. 2000. Puyallup River
Fall Chinook Baseline Report. Washington Department of Fish and Wildlife,
Olympia, Washington.
Seber, G.A.F. 1982. The Estimation of Animal Abundance, Second Edition. MacMillan
Publishing Co. New York: 654.
Seiler, D., G, Volkhardt, P. Topping and L. Kishimoto. 2004. Green River Juvenile
Salmonid Production Evaluation. WA Department of Fish and Wildlife Annual
Report, Fish Program, Science Division. Olympia, Washington
SPSS. 2003. SPSS version 12.0 for windows. SPSS Inc.
USGS Surface-Water Annual Statistics for Washington, USGS 12096500 Puyallup River at
Alderton. 2006. United States Geological Survey. December 2006.
<http://waterdata.usgs.gov/wa/nwis/uv/?site_no=12096500&PARAmeter_cd=000
60,00065>
Washington State Department of Ecology. 2006. Water Quality Standards for the Surface
Waters of the State of Washington Chapter 173-201A WAC. Publication number
06-10-091 November 2006.
56
Volkhardt G., D. Seiler, S. Neuhauser, L. Kishimoto and C. Kinsel. 2006. 2005 Skagit River
0+ Chinook Production Evaluation. Washington Department of Fish and Wildlife,
Fish Program, Science Division. Olympia, WA.
Volkhardt G., D. Seiler, L. Fleischer, and K. Kiyohara.. 2006. Evaluation of Downstream

Migrant Salmon Production in 2005 from the Cedar River and Bear Creek.
Washington Department of Fish and Wildlife, Fish Program, Science Division.
Olympia, WA.
Personal Communications
Davis, S. WDFW Voights Creek Hatchery. August 2008
Sharpf, M. Fisheries Biologist. WDFW Region 6. August 2008.
Clemens, John. United States Geological Survey. Media Contact USGS. USGS
Washington Water Science Center. August 2008.
57
Appendix A
Puyallup River Screw Trap Location, Design and Position

Figure A1. The Puyallup River Watershed, the red dot depicts screw trap location at R.M. 10.6 and the
black dot depicts Voight’s Creek State Salmon Hatchery at RM 4.0.

A1
Figure A2. Diagram of a rotary screwtrap.
A2
Figure A1. Position of the screw trap in the lower Puyallup River at R.M. 10.6
A3
Appendix B
Mean Weekly Fork Length Data for Unmarked Chinook, Coho, Chum,
Pink and Steelhead, Puyallup River Screw Trap 2008
Table B1. Fork length data of unmarked age 0+ Chinook migrants, 2008.
Average
Fork Standard
Dates Stat Week Max Min N
Length Deviation
(mm)
1/28-2/3 5 39.50 40 39 0.71 2
2/4-2/10 6 38.31 45 32 2.98 32
2/11-2/17 7 38.66 45 32 3.57 51
2/18-2/24 8 40.81 45 35 2.80 42
2/25-3/2 9 39.76 44 34 2.18 110
3/3-3/9 10 39.80 45 33 2.50 60
3/10-3/16 11 40.01 50 30 2.52 147
3/17-3/23 12 39.53 45 35 2.23 45
3/24-3/30 13 40.80 52 38 3.51 15
3/31-4/6 14 40.35 56 33 5.36 23

4/7-4/13 15 41.72 69 36 6.08 43
4/14-4/20 16 45.92 68 37 8.47 50
4/21-4/27 17 52.50 60 42 7.40 6
4/28-5/4 18 51.79 67 38 8.56 42
5/5-5/11 19 68.27 76 43 9.79 11
5/12-5/18 20 60.58 76 40 8.78 45
5/19-5/25 21 59.98 87 39 10.71 280
5/26-6/1 22 64.61 88 41 9.96 215
6/2-6/8 23 65.71 91 45 10.07 126
6/9-6/15 24 68.15 92 41 11.96 54
6/16-6/22 25 73.97 92 55 10.05 39
6/23-6/29 26 80.26 100 46 10.11 186
6/30 - 7/6 27 84.12 131 50 9.30 205
7/7 - 7/13 28 87.78 105 60 8.92 95
7/14 - 7/20 29 91.26 118 60 9.97 7
7/21 - 7/27 30 88.54 110 62 11.82 63
7/28 - 8/3 31 85.29 106 60 12.74 28

8/4 - 8/10 32 82.00 110 67 14.84 14
B1
Table B2. Fork length data of unmarked age 1+ coho migrants, 2008.
Average
Standard
Dates Stat Week Fork Length Max Min N
Deviation
(mm)
1/14-1/20 3 88 100 75 17.68 2

1/21-1/27 4 97 122 80 12.58 11
1/28-2/3 5 92 105 80 7.78 9
2/4-2/10 6 110 110 110 - 1
2/11-2/17 7 95 107 65 11.79 11

2/18-2/24 8 102 123 87 18.58 3
2/25-3/2 9 71 71 71 - 1
3/3-3/9 10 89 105 72 23.33 2
3/10-3/16 11 90 92 88 1.63 4
3/17-3/23 12 97 97 96 0.71 2
3/24-3/30 13 136 136 136 - 1
3/31-4/6 14 108 129 73 30.29 3

4/7-4/13 15 111 112 110 1.41 2
4/14-4/20 16 122 122 122 - 1
4/21-4/27 17 125 127 123 2.83 2
4/28-5/4 18 112 185 75 23.06 23

5/5-5/11 19 109 142 72 11.38 87
5/12-5/18 20 110 138 82 10.47 51
5/19-5/25 21 109 176 69 12.98 236

5/26-6/1 22 107 147 88 10.60 94
6/2-6/8 23 119 136 96 10.68 51
6/9-6/15 24 123 136 109 7.63 16
6/16-6/22 25 130 136 127 3.35 6
6/23 - 6-29 26 107 116 102 6.08 4
6/30 - 7/6 27 94 106 86 6.77 6
7/7 - 7/13 28 97 100 95 2.65 3
B2
Table B3. Fork length data for wild chum migrants, 2008.
Average
Standard
Deviation
(mm)
2/11-2/17 7 35.00 35 35 - 1
2/18-2/24 8 - - - - -
2/25-3/2 9 - - - - -
3/3-3/9 10 - - - - -
3/10-3/16 11 37.33 40 34 3.06 3
3/17-3/23 12 38.15 42 34 1.93 26
3/24-3/30 13 38.88 48 33 2.20 143
3/31-4/6 14 37.95 51 31 1.95 262
4/7-4/13 15 38.97 48 32 2.04 328
4/14-4/20 16 39.31 55 33 2.95 518
4/21-4/27 17 39.03 51 31 2.56 246
4/28-4/4 18 39.42 58 30 3.00 337
5/5-5/11 19 40.18 77 31 4.81 318
5/12-5/18 20 41.23 62 34 5.88 60
5/19-5/25 21 39.91 64 34 5.84 85
5/26-6/1 22 39.25 43 36 2.99 4
6/2-6/8 23 37.44 40 35 1.59 9
6/9-6/15 24 53.00 56 50 4.24 2
B3
Table B4. Fork length data of pink fry, 2008.
Average
Standard
Deviation
(mm)
1/28-2/3 5 35.33 40 30 5.03 3

2/4-2/10 6 31.36 36 25 2.07 44
2/11-2/17 7 31.90 40 28 2.00 80
2/18-2/24 8 31.95 37 29 1.55 175
2/25-3/2 9 32.09 36 29 1.44 337
3/3-3/9 10 32.82 42 27 1.76 354
3/10-3/16 11 33.63 39 30 1.49 322
3/17-3/23 12 33.84 38 30 1.51 425
3/24-3/30 13 34.47 39 29 1.43 770
3/31-4/6 14 34.70 39 28 1.47 573
4/7-4/13 15 34.20 39 30 1.46 540
4/14-4/20 16 34.71 38 29 1.34 640
4/21-4/27 17 34.48 40 29 1.45 479
4/28-5/4 18 34.80 39 31 1.35 381
5/5-5/11 19 34.95 41 30 1.52 350
5/12-5/18 20 33.98 40 31 1.90 50
5/19-5/25 21 33.17 35 31 1.47 12
5/26-6/1 22 37.00 37 37 - 1
B4
Table B5. Fork length data of unmarked steelhead migrants, 2008.
Average Fork Standard

Dates Stat Week Max Min N
Length (mm) Deviation
1/14- 1/20 3 120 120 120 - 1

1/21-1/27 4 147 193 100 65.76 2
1/28-2/3 5 164 182 135 25.36 3
2/4-2/10 6 - - - - -
2/11-2/17 7 146 186 102 30.63 5
2/18-2/24 8 150 167 133 24 2
2/25-3/2 9 185 185 185 - 1
3/3-3/9 10 0 0 0 0.00 0
3/10-3/16 11 143 143 143 - 1
3/17-3/23 12 - - - - -
3/24-3/30 13 - - - - -
3/31-4/6 14 - - - - -
4/7-4/13 15 139 164 95 37.98 3
4/14-4/20 16 153 166 139 19.09 2
4/21-4/27 17 115 115 115 - 1
4/28-4/4 18 127 160 90 35.12 3
5/5-5/11 19 177 213 148 20.95 9
5/12-5/18 20 178 242 145 37.94 6
5/19-5/25 21 183 240 147 27.77 27
5/26-6/1 22 167 197 152 12.28 20
6/2-6/8 23 168 211 135 16.76 34

6/9-6/15 24 168 178 158 7.55 7
6/16-6/22 25 142 158 117 22.14 3
B5
Appendix C
Mark Recapture Data for Chinook, Coho, Pink and Chum,

Puyallup River Screw Trap, 2004 - 2008
Table C1. Capture efficiency results for hatchery Chinook, 2004 - 2008.
Release Release Day or Glacial Number Number Capture Secchi Flow
Year
Date Time Night Period* Released Recaptured Efficiency Depth (cm) (cfs)
5/19/2004 2004 1500 D 1 800 5 0.00625 104 1,480

5/25/2004 2004 1530 D 1 601 5 0.00832 150 1,110
6/1/2004 2004 1600 D 1 628 5 0.00796 65 2,740
6/4/2004 2004 1550 D 1 609 5 0.00821 82 1,980
6/7/2004 2004 1615 D 1 610 5 0.00820 66 2,370
6/10/2004 2004 2015 N 1 613 2 0.00326 94 2,050
6/15/2004 2004 2200 N 1 610 9 0.01475 113 1,750
6/17/2004 2004 2230 N 1 595 3 0.00504 130 1,610
6/22/2004 2004 1630 D 2 604 5 0.00828 34 1,640
6/23/2004 2004 2200 N 2 610 20 0.03279 13 1,880
7/1/2004 2004 2115 N 2 608 36 0.05921 28 1,390
7/6/2004 2004 1730 D 2 602 15 0.02492 32 1,370
7/7/2004 2004 2200 N 2 615 30 0.04878 30 1,310
7/12/2004 2004 1745 D 2 609 18 0.02956 30 1,070
7/13/2004 2004 2145 N 2 419 23 0.05489 18 1,270
5/2/2005 2005 2107 N 1 1,011 26 0.02572 139 1,700
5/3/2005 2005 1115 D 1 1,017 1 0.00098 163 1,810
5/17/2005 2005 2130 N 1 855 17 0.01988 72 2,440
5/18/2005 2005 1145 D 1 1,025 7 0.00683 84 2,310
6/7/2005 2005 2115 N 1 806 19 0.02357 144 1,380
6/22/2005 2005 2045 N 2 804 27 0.03358 33 1,750
6/23/2005 2005 1115 D 2 804 5 0.00622 29 1,740
7/12/2005 2005 1145 D 2 812 27 0.03325 29 1,340
7/12/2005 2005 2045 N 2 828 53 0.06401 28 1,210
4/18/2006 2006 2052 N 1 512 17 0.03320 206 1,630
4/28/2006 2006 1000 D 1 556 1 0.00180 175 1,530
5/15/2006 2006 2145 N 1 801 16 0.01998 100 1,476
5/25/2006 2006 2105 N 1 810 28 0.03457 79 1,879
6/13/2006 2006 2130 N 2 591 23 0.03892 40 2,172
6/14/2006 2006 945 D 2 605 12 0.01983 43 2,333
3/8/2007 2007 1830 N 1 503 11 0.02187 200 2,420
4/10/2007 2007 2004 N 1 522 16 0.03065 180 1,890
5/8/2007 2007 2130 N 1 510 8 0.01569 135 1,480
5/11/2007 2007 1400 D 1 507 4 0.00789 200 1,430
6/6/2007 2007 1120 D 2 493 14 0.02840 34 1,850
6/7/2007 2007 2130 N 1 265 2 0.00755 61 1,290
6/11/2007 2007 2145 N 1 384 4 0.01042 63 1,610
2/11/2008 2008 2115 N 1 520 24 0.04615 78 2,870
3/5/2008 2008 1115 D 1 500 13 0.02600 229 1,170
3/19/2008 2008 1415 D 1 509 32 0.06287 219 1,360
3/21/2008 2008 2030 N 1 509 6 0.01179 220 1,200
3/25/2008 2008 2230 N 1 496 27 0.05444 211 1,090
5/24/2008 2008 2200 N 2 556 43 0.07734 48 2,610
6/2/2008 2008 2145 N 1 505 33 0.06535 99 2,120
6/27/2008 2008 1330 D 2 501 15 0.02994 45 2,030
* 1 = non-glacial period, 2 = glacial period
C1
Table C2. Capture efficiency results for hatchery coho, 2004 - 2008.
Time of Number Number Secchi Flow Capture
Date Year Release Released Recaptured Depth (cm) (cfs) Efficiency
4/14/2004 2004 1930 208 3 150 1,010 0.01440
5/3/2004 2004 2030 211 4 92 1,230 0.01900
3/21/2005 2005 1715 502 4 138 759 0.00800
3/23/2005 2005 1145 513 6 138 704 0.01170
3/29/2005 2005 1330 516 10 79 2,470 0.01940
3/31/2005 2005 1711 513 11 155 1,590 0.02140
4/13/2005 2005 1915 511 9 162 1,240 0.01760
4/14/2005 2005 1215 516 10 195 1,260 0.01940
4/17/2006 2006 1700 506 7 206 1,790 0.01380
4/27/2006 2006 2045 520 7 188 1,400 0.01350
5/15/2006 2006 2145 494 6 100 1,476 0.01210
3/21/2007 2007 1945 804 9 133 2,730 0.01119
4/12/07 2007 2030 611 6 203 1,480 0.00982
4/9/2008 2008 2130 805 14 219 1,150 0.01739
4/14/2008 2008 2130 807 23 159 1,670 0.02850
C2
Table C3. Capture efficiency results for hatchery and wild chum, 2004 - 2008.
Time of Day or Hatchery Number Number Secchi Flow Capture
Date Year
Release Night or Wild Released Recaptured Depth (cm) (cfs) Efficiency
3/31/2004 2004 800 D H 534 20 150 1340 0.03745

4/1/2004 2004 1900 N H 539 26 150 1230 0.04824
4/6/2004 2004 2010 N H 518 24 150 832 0.04633
4/7/2004 2004 900 D H 461 20 150 832 0.04338
4/9/2004 2004 1900 N W 156 2 150 817 0.01282
4/15/2004 2004 850 D H 519 23 150 964 0.04432
4/16/2004 2004 2000 N H 514 15 150 840 0.02918
4/19/2004 2004 1945 N W 233 6 150 683 0.02575
4/28/2004 2004 2010 N W 200 4 150 940 0.02000
5/10/2004 2004 2000 N W 157 7 150 1000 0.04459
5/18/2004 2004 1945 N W 564 15 150 940 0.02660
5/25/2004 2004 1745 N W 151 1 150 1100 0.00662
6/1/2004 2004 1945 N H 518 7 65 2570 0.01351
3/16/2005 2005 1733 N H 540 19 138 704 0.03519
3/19/2005 2005 1030 D H 525 26 138 677 0.04952
3/27/2005 2005 1710 N H 531 3 23 4480 0.00565
3/28/2005 2005 915 D H 515 21 40 3750 0.04102
4/19/2005 2005 1115 D H 525 7 192 1810 0.01333
4/20/2005 2005 1830 N H 525 20 192 1550 0.03810
5/11/2005 2005 2040 N W 526 6 132 2080 0.01154
5/13/2005 2005 917 D H 530 8 165 1810 0.01518
5/19/2005 2005 2050 N H 535 5 124 2400 0.00943
4/12/2006 2006 2030 N H 119 3 201 1410 0.02521
4/19/2006 2006 2035 N H 492 17 198 1378 0.03455
4/24/2006 2006 2130 N H 518 4 195 1450 0.00772
5/1/2006 2006 2130 N W 58 0 198 1537 0.00000
5/10/2006 2006 2100 N W 51 1 190 1378 0.01961
5/24/2006 2006 2030 N W 51 1 79 2136 0.01961
4/2/2007 2007 1945 N H 506 21 154 1940 0.04150
4/4/2007 2007 1945 N W 27 0 180 1650 0.00000
4/8/2007 2007 2030 N W 53 0 130 1960 0.00000
4/13/2007 2007 2100 N W 48 0 200 1430 0.00000
4/16/2007 2007 2000 N H 523 27 210 1350 0.05163
4/25/2007 2007 2300 N W 114 4 192 1180 0.03509
5/18/2007 2007 2100 N W 60 0 200 1270 0.00000
2/25/2008 2008 1845 N H 516 7 220 1150 0.01357
3/25/2008 2008 2215 N H 525 11 211 1090 0.02095
4/16/2008 2008 2115 N W 379 6 219 1330 0.01583
4/24/2008 2008 2200 N W 630 12 203 908 0.01905
5/6/2008 2008 2225 N W 662 19 148 1700 0.02870
C3
Table C4. Capture efficiency results for wild pink, 2004, 2006 and 2008.
Time of Number Number Flow Capture
Date Year
release Released Recaptured (cfs) Efficiency
3/4/2004 2004 1800 19 0 1409 0.00000
3/5/2004 2004 1745 47 1 1310 0.02128
3/6/2004 2004 2000 41 1 1260 0.02439
3/7/2004 2004 1815 58 1 1250 0.01724
3/8/2004 2004 1830 96 0 1400 0.00000
3/9/2004 2004 1815 99 3 1700 0.03030
3/10/2004 2004 1800 92 1 1670 0.01087
3/11/2004 2004 1800 69 2 1450 0.02899
3/12/2004 2004 1830 80 3 1360 0.03750
3/13/2004 2004 1745 104 4 1250 0.03846
3/14/2004 2004 1800 72 3 1150 0.04167
3/15/2004 2004 1815 172 7 1110 0.04070
3/16/2004 2004 1815 155 4 1060 0.02581
3/17/2004 2004 1800 105 1 1010 0.00952
3/18/204 2004 1830 100 2 1100 0.02000
3/19/2004 2004 1800 110 2 1090 0.01818
3/20/2004 2004 1800 143 4 1030 0.02797
3/21/2004 2004 1830 99 2 1010 0.02020
3/22/2004 2004 1830 106 7 1130 0.06604
3/23/2004 2004 1845 105 2 1270 0.01905
3/25/2004 2004 800 200 6 1370 0.03000
3/25/2004 2004 1900 200 4 1260 0.02000
3/28/2004 2004 1900 506 18 1270 0.03557
3/31/2004 2004 800 510 21 1340 0.04118
4/1/2004 2004 1900 522 14 1230 0.02682
4/3/2004 2004 1830 514 7 885 0.01362
4/5/2004 2004 1945 612 13 870 0.02124
4/6/2004 2004 2015 510 8 825 0.01569
4/7/2004 2004 900 425 23 832 0.05412
4/9/2004 2004 1900 530 5 817 0.00943
4/12/2004 2004 1900 517 19 1120 0.03675
3/3/2006 2006 1645 178 2 1620 0.01124
3/8/2006 2006 1800 123 0 1410 0.00000
3/12/2006 2006 1900 180 4 1270 0.02222
3/15/2006 2006 1900 237 3 1220 0.01266
3/18/2006 2006 1915 251 2 1310 0.00797
3/21/2006 2006 1900 198 1 1200 0.00505
3/23/2006 2006 1900 299 0 1190 0.00000
3/27/2006 2006 2000 294 4 1180 0.01361
3/31/2006 2006 1915 211 0 1209 0.00000
4/3/2006 2006 2100 307 2 1350 0.00651
4/7/2006 2006 2030 522 4 1270 0.00766
4/11/2006 2006 2100 226 0 1339 0.00000
4/16/2006 2006 2115 261 6 2124 0.02299
4/26/2006 2006 1830 201 3 1445 0.01493
3/4/2008 2008 1345 290 10 1310 0.03448
3/8/2008 2008 1915 161 1 1030 0.00621
3/13/2008 2008 2200 493 6 1750 0.01217
3/15/2008 2008 2030 741 1 1640 0.00135
3/17/2008 2008 2100 257 5 1500 0.01946
3/18/2008 2008 2030 625 17 1480 0.02720
3/25/2008 2008 2300 751 18 1090 0.02397
3/30/2008 2008 1730 531 16 1050 0.03013
3/31/2008 2008 2045 729 7 996 0.00960
4/7/2008 2008 2130 509 12 1190 0.02358
4/20/2008 2008 1930 682 8 1020 0.01173
4/24/2008 2008 2200 732 6 908 0.00820
C4

Puyallup Tribe of Indians Smolt Trap Report 2008

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Puyallup Tribe of Indians Smolt Trap Report 2008

Uploaded by

Copyright:

Available Formats

Puyallup River Juvenile Salmonid Production Assessment

By: Puyallup Tribal Fisheries Department

Evaluation of juvenile salmonid production requires a tremendous amount of work.

Figure 25. Percent migration of unmarked age 1+ coho migrants, 2008……………………32

Figure 35. Percent estimated migration of chum fry, 2008………………………………….40

Figure 41. Percent daily estimated migration of pink fry, 2008……………….……………44

Table 7. Freshwater survival of unmarked Chinook from the Puyallup River,

Figure A1. The Puyallup River Watershed.……………… ………………………………...A1

Figure A2. Diagram of a rotary screw trap.…………………………………………….….A2

Table B3 Fork length data for unmarked chum fry, 2008…………….……….…………..B3

Table B4. Fork length data for pink fry, 2008…………………………..…………….....…B4

Table B5. Fork length data for unmarked steelhead, 2008……………...…………….....…B5

GOALS AND OBJECTIVES

2. Estimate in-river mortality of hatchery and acclimation pond Chinook.

Measuring Flow, Turbidity and Temperature

Because of differences in the relationship between environmental variables and capture

Mean Daily Secchi Depth (cm)

Mean Daily Secchi Depth (cm)

Comparison of Capture Efficiency Estimates in 2008 to Previous Years’ Estimates

8.00% Day Night

Capture Efficiency Percentage

2004 2.136% 15 0.5001% 0.832% 1.064% - 3.209%

2005 2.378% 9 0.6389% 2.357% 0.905% - 3.852%

2006 2.472% 6 0.5604% 2.659% 1.031% - 3.912%

2007 1.749% 7 0.3638% 1.569% 0.859% - 2.639%

2008 4.673% 8 0.7946% 5.029% 2.794% - 6.552%

Flow (cfs) 2,000

Capture Efficiency versus Secchi Depth

2008 Day 2008 Night

Capture Efficiency Percentage

Linear (2004 - 2007)

Linear (2004 - 2007)

General Linear Model Analysis

Intercept 0.109286 0.0141 0.082 / 0.137

Year 2004 -0.032981 0.0062 -0.045 / -0.021

Year 2005 -0.029501 0.0066 -0.042 / -0.017

Year 2006 -0.026077 0.0071 -0.040 / -0.012

Year 2007 -0.032170 0.0067 -0.045 / -0.019

Year 2008 0.000000 - - / -

Day -0.014698 0.0040 -0.023 / -0.007

LnSecchi -0.011946 0.0028 -0.017 / -0.006

Intercept 0.079100 0.0107 0.058 / 0.100

Day -0.016281 0.0038 -0.024 / -0.009

LNSecchi -0.011944 0.0025 -0.017 / -0.007

Capture Efficiency Estimates for Chinook

1. CE = 0.109286 – 0.014698 + (-0.011944 x LN (secchi disk depth)) for daytime sets

2008 Nighttime Line

Hatchery Chinook Length used for Capture Efficiency Experiments

Mean Fork length (mm)

2008 Glacial Day

Glacial and Non-Glacial Catch/Production

Day and Night Catch/Production

Estimated Number of Migrants

In-River Mortality of Hatchery Releases

Date Capture Estimated In-River

AD (Voights)* 13-June 13-June 1,490,500 19,018 1.27% 347,259 76.7%

Freshwater Survival of Wild Smolts

Mean Fork Length (mm)

• capture efficiency for day-time and night-time releases,

Comparison of Capture Efficiency Estimates in 2008 to Previous Years’ Estimates

2004-2006 1.54% 5010 77 11

Comparison of Capture Efficiency Estimates for Daytime versus Nighttime Releases

Capture Efficiency Percentage

Daytime 1.56% 6 0.2155% 1.66% 1.008% - 2.116%