puyallup tribe of indians smolt trap report 2008

Puyallup River Juvenile Salmonid Production Assessment Project 2008

By: Andrew Berger Robert Conrad Justin Paul

Puyallup Tribal Fisheries Department Puyallup, WA 98371

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.

Puyallup River Juvenile Salmonid Assessment Project 2008

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

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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

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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

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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 f rom 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

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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

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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,

2008…………………………………………………………………………….22 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 dayt ime, hatchery night t ime, and wild nightt ime experiments 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

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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 Puyal lup River ,

2004-2008……………………………………………………….…………….....C2 Table C3. Hatchery and wild chum mark and recapture data for the Puyallup River, 2004-2008………………………………………………………………...C3 Table C4. W i l d p i n k m a r k a n d r e c a p t u r e d a t a f o r t h e P u y a l l u p River, 2004, 2006 and 2008……………………………………………………..C4

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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


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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.


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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.


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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


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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

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:

e = r / m

and N = C / e

where: e = estimated capture efficiency,

r = number of marked fish recaptured,

m = number of marked fish released, N = 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).


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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


8

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.

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.

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Figure 1. Secchi depth and mean daily flow for the Puyallup River, 2008.


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R² = 0.3572

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Figure 3. Mean daily water temperature recorded on the Puyallup River smolt trap, 2008.


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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.

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. .

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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


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• 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%).

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Figure 5. Summary of the capture efficiency estimates for daytime and nighttime Chinook smolt releases conducted in 2004 – 2008.


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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).

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Figure 7. Comparison of mean capture efficiency estimates for Chinook smolt releases conducted in 2004 – 2008 with 95% confidence intervals.


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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).

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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.

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Figure 10. Plot of capture efficiency versus flow for Chinook releases, 2004 – 2008.


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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.

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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


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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.

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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.


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Table 2. Summary statistics for GLM parameters estimated from capture efficiency experiments, 2004 – 2008.

Parameter Coefficient Standard Error 95% Wald Confidence Interval 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.

Parameter Coefficient Standard Error 95% Wald Confidence Interval 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).

• 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.

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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).


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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


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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%)

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.

0

1000

2000

3000

4000

5000

6000

7000

1/18 2/7 2/27 3/18 4/7 4/27 5/17 6/6 6/26 7/16 8/50

1000

2000

3000

4000

5000

6000

7000

Mea

n D

aily

Flo

w (c

fs)

Date

Estim

ated

Num

ber o

f Mig

rant

s

"'Unmarked Chinook (n=89,536)"

Flow (cfs)

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

0%

25%

50%

75%

100%

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

Perc

ent M

igra

tion

Date

April 14th

May 18th

June 4th

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


25

Table 6. In-river mortality of marked Chinook from the Puyallup River, 2008.

Mark Type Date

Number Released

Number Captured

Capture Percentage for Each Release

Group

Estimated Production for Each Release

Group

In-River Mortality for Each Release

Group Start End

AD/CWT (Cowskull) 22-May 29-May 96,500

1,882 0.62% 35,513 88.2% AD/CWT (Voights)* 13-June 13-June 205,000

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.

Run Year Total

Outmigration Estimate

Total Number of

Females

Potential Egg

Deposition

Smolt / Female

Maximum and Minimum Flows

Aug.-Feb.*

Percent Freshwater Survival

(#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


26

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).

50

70

90

110

130

150

170

190

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30

Mea

n Fo

rk L

engt

h (m

m)

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 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 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%.

Comparison of Capture Efficiency Estimates in 2008 to Previous Years’ Estimates 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 Date Mean Number

ReleasedNumber

Recaptured N

2004-2006 1.54% 5010 77 11 2007 1.06% 1415 15 2 2008 2.30% 1612 37 2

-5.00%

-2.50%

0.00%

2.50%

5.00%

7.50%

10.00%

2003 2004 2005 2006 2007 2008 2009

Cap

ture

Effi

cien

cy P

erce

ntag

e

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

0.0%

0.5%

1.0%

1.5%

2.0%

2.5%

3.0%

0 1 2 3

Cap

ture

Effi

cien

cy P

erce

ntag

e

Day (1) or Night (2) experiment

2004

2005

2006

2007

2008

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

0.0%

0.5%

1.0%

1.5%

2.0%

2.5%

3.0%

0 50 100 150 200 250

Cap

ture

Effi

cien

cy P

erce

ntag

e

Secchi Depth (cm)

2004 to 2007 Day2004 to 2007 Night2008 Night

Figure 22. Plot of estimated capture efficiency versus secchi disk depth for 1+ coho salmon

releases, 2004 - 2008.

0.0%

0.5%

1.0%

1.5%

2.0%

2.5%

3.0%

0 500 1000 1500 2000 2500 3000

Cap

ture

Effi

cien

cy P

erce

ntag

e

Flow (cfs)

2004 to 2007 Day

2004-2007 Night

2008 Night

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).

Model Parameter

Estimated Coefficients t statistic

Signifi- cance

95% Confidence Interval for B

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).

Model Parameter

Estimated Coefficients t statistic

Signifi- cance

95% Confidence Interval for B

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

Estimated Production 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).

0

1,000

2,000

3,000

4,000

5,000

6,000

0

1,000

2,000

3,000

4,000

5,000

6,000

1/19 2/3 2/18 3/4 3/19 4/3 4/18 5/3 5/18 6/2 6/17 7/2

Estim

ated

Num

ber o

f 1+

Coh

o M

igra

nts

Mea

n Fl

ow (c

fs)

Date

Estimated Migrants Captured (n=83,608)Flow (cfs)

Figure 24. Estimated daily migration of unmarked age 1+ coho with mean daily flows, 2008.


31

0%

25%

50%

75%

100%

1/18 2/2 2/17 3/3 3/18 4/2 4/17 5/2 5/17 6/1 6/16 7/1

Perc

ent M

igra

tion

Date

May 15th

May 20th

May 25th

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.

Mark Type

Date

Number Released

Number Captured

Estimated Production for Each Release

Group

In River Mortality for Each Release Group

Total Number

Captured

Total Estimated Production Start End

CWT (Voights)*

25-Apr

29-Apr 45,300 551 34,873 23%

11,451 724,747

AD (Voights)* 25-Apr

29-Apr 708,500 9,909 627,152 11%

AD + CWT (Lake

Kapowsin) 3-Mar 3-

Mar 93,000 991 62,722 55%

AD + CWT (Voights)*

25-Apr

29-Apr 45,300

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.

20

25

30

35

40

45

50

55

60

65

6 8 10 12 14 16 18 20 22 24 26

Fork

l Len

gth

(mm

)

Statistical Week

70

75

80

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 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 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.

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

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

6.00%

2003 2004 2005 2006 2007 2008 2009

Estim

ated

Cap

ture

Effi

cien

cy

Year

Wild - Nighttime

Hatchery - Nighttime

Hatchery - Daytime

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.

-5.00%

-2.50%

2003 2004 2005 2006 2007 2008 2009

Es

Year

0.00%

2.50%

5.00%

7.50%

10.00%

12.50%tim

ated

Cap

ture

Effi

cien

cy

Hatchery

Wild

n=7

n=6 n=8 n=1

n=3

n=1

n=3

n=2n=2

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

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

6.00%

0 50 100 150 200 250

Cap

ture

Effi

cien

cy P

erce

ntag

e

Secchi Depth (cm)

Hatchery - Daytime


Wild - Nighttime

2008 Hatchery - Nighttime

2008 Wild - Nighttime

Figure 29. Plot of estimated capture efficiency versus secchi disk depth for chum releases, 2004 – 2008.

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

6.00%

0 1000 2000 3000 4000 5000

Cap

ture

Effi

cien

cy P

erce

ntag

e

Flow(cfs)

Hatchery - Daytime


Wild - Nighttime

2008 Hatchery - Nighttime

2008 Wild - Nighttime

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.


37

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%

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

0 1 2 3 4

Estim

ated

Cap

ture

Effi

cien

cy

GroupDaytime Hatchery Nighttime Hatchery Nighttime Wild

n=7n=15

n=11

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%.

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.

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

0 50 100 150 200 250

Cap

ture

Effi

cien

cy P

erce

ntag

e

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

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

0 500 1000 1500 2000 2500

Cap

ture

Effi

cien

cy P

erce

ntag

e

Flow (cfs)

Figure 33. Plot of estimated capture efficiency of wild chum salmon versus flow for Puyallup River smolt trap data 2004-2008.

Estimated Production 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

0

15,000

30,000

45,000

60,000

75,000

90,000

0

1,250

2,500

3,750

5,000

6,250

7,500

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

Estim

ated

Num

ber o

f Chu

m M

igra

nts

Mea

n Fl

ow (c

fs)

Date

Chum Migrants (n = 593,973)

Mean Flow (cfs)

Figure 34. Daily estimated migration of chum fry with mean daily flows, 2008.

May 9th

April 29th

May 16th

0%

25%

50%

75%

100%

Perc

ent M

igra

tion

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).

24

26

28

30

4 6 8 10 12 14 16 18 20 22 24

Fo

Statistical Weeks

32

34

36

38

40

42

44

46

rk L

engt

h (m

m)

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

0.00%

0.50%

1.00%

1.50%

2.00%

2.50%

3.00%

3.50%

4.00%

2003 2004 2005 2006 2007 2008 2009

Estim

ated

Cap

ture

Effi

cien

cy

Year

Figure 37. Summary of capture efficiency estimates, by statistical week, for wild pink releases conducted in 2004, 2006 and 2008.

0.00%

0.50%

1.00%

1.50%

2.00%

2.50%

3.00%

3.50%

4.00%

2003 2004 2005 2006 2007 2008 2009

Estim

ated

Cap

ture

Effi

cien

cy

Year

n=7

n=8n=8

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

0.00%

1.00%

2.00%

3.00%

4.00%

5.00%

6.00%

7.00%

500 1,000 1,500 2,000 2,500

Estim

ated

Cap

ture

Effi

cien

cy

Flow (cfs)

2004

2006

2008

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%

Estimated Production

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).

0.00E+00

2.75E+05

5.50E+05

8.25E+05

1.10E+06

1.38E+06

1.65E+06

1.93E+06

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

1/26 2/10 2/25 3/11 3/26 4/10 4/25 5/10 5/25

Estim

ated

Num

ber o

f Pin

k

Flow

(cfs

)

Date

Pink Migrants (n = 14,936,007)

Flow (cfs)

Figure 40. Daily estimated migration of pink fry with mean daily flows, 2008.

0%

25%

50%

75%

100%

1/26 2/10 2/25 3/11 3/26 4/10 4/25 5/10 5/25

Perc

ent M

igra

tion

Date

April 11th

April 20th

April 28th

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.

539

156

250

7439

7754

25

189

0

100

200

300

400

500

600

2000 2001 2002 2003 2004 2005 2006 2007 2008

Unm

arke

d St

eelh

ead

Cap

ture

d

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

80

100

120

140

160

180

200

220

240

2 4 6 8 10 12 14 16 18 20 22 24 26

Mea

n Le

ngth

(mm

)

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

Type Attribute Count Mean Min. Max St. dev.

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.

Mark Type Date Number Released Number Captured Capture Percentage

Start EndAD (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)* (2006) 29-Apr 29-Apr 201,900 270 0.13% AD (Voights)* (2005) 1-Apr 15-Apr 207,400 470 0.23% 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

Puyallup River Juvenile Salmonid Production Assessment Project 2008 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.

0

5

10

15

0

1,000

2,000

3,000

1/18 2/2 2/17 3/3 3/18 4/2 4/17 5/2 5/17 6/1 6/16

Stee

lhea

d M

igra

n

Flow

(c

Date

20

25

30

35

4,000

5,000

6,000

7,000

ts C

aptu

red

fs)

Migrants Captured (n=187)

Flow (cfs)

Figure 44. Daily catch of steelhead migrants with mean daily flows, 2008.

Puyallup River Juvenile Salmonid Production Assessment Project 2008 47


48

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.


49

• 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.


50

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.


51

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;


52

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.

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.

R² = 0.8367

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

500,000 1,000,000 1,500,000 2,0

% In

-riv

er M

orta

lity

Total Number of Marked Chinook Released00,000

2005

2006

2008

2007

2004

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).

R² = 0.8789

0.00%

0.50%

1.00%

1.50%

2.00%

2.50%

3.00%

3.50%

4.00%

4.50%

0 1,000 2,000 3,000 4,000 5,000 6,000 7,000

Fres

hwat

er S

urvi

val E

stim

ate

Peak incubation flow (cfs) on South Prairie Creek

2008

2007

2004

2006

2005

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


55

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.


56

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=00060,00065>

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.

http://www.rmis.org/

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.

Dates Stat Week

Average Fork

Length (mm)

Max Min Standard Deviation N

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.

Dates Stat WeekAverage

Fork Length (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.


Fork Length (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 33/17-3/23 12 38.15 42 34 1.93 263/24-3/30 13 38.88 48 33 2.20 1433/31-4/6 14 37.95 51 31 1.95 2624/7-4/13 15 38.97 48 32 2.04 328

4/14-4/20 16 39.31 55 33 2.95 5184/21-4/27 17 39.03 51 31 2.56 2464/28-4/4 18 39.42 58 30 3.00 3375/5-5/11 19 40.18 77 31 4.81 318

5/12-5/18 20 41.23 62 34 5.88 605/19-5/25 21 39.91 64 34 5.84 855/26-6/1 22 39.25 43 36 2.99 46/2-6/8 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.


Fork Length (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.

Dates Stat Week Average Fork Length (mm) Max Min Standard

Deviation N

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 34/14-4/20 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 Date Year Release

TimeDay or Night

Glacial Period*

Number Released

Number Recaptured

Capture Efficiency

Secchi Depth (cm)

Flow (cfs)

5/19/2004 2004 1500 D 1 800 5 0.00625 104 1,4805/25/2004 2004 1530 D 1 601 5 0.00832 150 1,1106/1/2004 2004 1600 D 1 628 5 0.00796 65 2,7406/4/2004 2004 1550 D 1 609 5 0.00821 82 1,9806/7/2004 2004 1615 D 1 610 5 0.00820 66 2,370

6/10/2004 2004 2015 N 1 613 2 0.00326 94 2,0506/15/2004 2004 2200 N 1 610 9 0.01475 113 1,7506/17/2004 2004 2230 N 1 595 3 0.00504 130 1,6106/22/2004 2004 1630 D 2 604 5 0.00828 34 1,6406/23/2004 2004 2200 N 2 610 20 0.03279 13 1,8807/1/2004 2004 2115 N 2 608 36 0.05921 28 1,3907/6/2004 2004 1730 D 2 602 15 0.02492 32 1,3707/7/2004 2004 2200 N 2 615 30 0.04878 30 1,310

7/12/2004 2004 1745 D 2 609 18 0.02956 30 1,0707/13/2004 2004 2145 N 2 419 23 0.05489 18 1,2705/2/2005 2005 2107 N 1 1,011 26 0.02572 139 1,7005/3/2005 2005 1115 D 1 1,017 1 0.00098 163 1,810

5/17/2005 2005 2130 N 1 855 17 0.01988 72 2,4405/18/2005 2005 1145 D 1 1,025 7 0.00683 84 2,3106/7/2005 2005 2115 N 1 806 19 0.02357 144 1,380

6/22/2005 2005 2045 N 2 804 27 0.03358 33 1,7506/23/2005 2005 1115 D 2 804 5 0.00622 29 1,7407/12/2005 2005 1145 D 2 812 27 0.03325 29 1,3407/12/2005 2005 2045 N 2 828 53 0.06401 28 1,2104/18/2006 2006 2052 N 1 512 17 0.03320 206 1,6304/28/2006 2006 1000 D 1 556 1 0.00180 175 1,5305/15/2006 2006 2145 N 1 801 16 0.01998 100 1,4765/25/2006 2006 2105 N 1 810 28 0.03457 79 1,8796/13/2006 2006 2130 N 2 591 23 0.03892 40 2,1726/14/2006 2006 945 D 2 605 12 0.01983 43 2,3333/8/2007 2007 1830 N 1 503 11 0.02187 200 2,420

4/10/2007 2007 2004 N 1 522 16 0.03065 180 1,8905/8/2007 2007 2130 N 1 510 8 0.01569 135 1,480

5/11/2007 2007 1400 D 1 507 4 0.00789 200 1,4306/6/2007 2007 1120 D 2 493 14 0.02840 34 1,8506/7/2007 2007 2130 N 1 265 2 0.00755 61 1,290

6/11/2007 2007 2145 N 1 384 4 0.01042 63 1,6102/11/2008 2008 2115 N 1 520 24 0.04615 78 2,8703/5/2008 2008 1115 D 1 500 13 0.02600 229 1,170

3/19/2008 2008 1415 D 1 509 32 0.06287 219 1,3603/21/2008 2008 2030 N 1 509 6 0.01179 220 1,2003/25/2008 2008 2230 N 1 496 27 0.05444 211 1,0905/24/2008 2008 2200 N 2 556 43 0.07734 48 2,6106/2/2008 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.

Date YearTime of Release

Number Released

Number Recaptured

Secchi Depth (cm)

Flow (cfs)

Capture Efficiency

4/14/2004 2004 1930 208 3 150 1,010 0.014405/3/2004 2004 2030 211 4 92 1,230 0.01900

3/21/2005 2005 1715 502 4 138 759 0.008003/23/2005 2005 1145 513 6 138 704 0.011703/29/2005 2005 1330 516 10 79 2,470 0.019403/31/2005 2005 1711 513 11 155 1,590 0.021404/13/2005 2005 1915 511 9 162 1,240 0.017604/14/2005 2005 1215 516 10 195 1,260 0.019404/17/2006 2006 1700 506 7 206 1,790 0.013804/27/2006 2006 2045 520 7 188 1,400 0.013505/15/2006 2006 2145 494 6 100 1,476 0.012103/21/2007 2007 1945 804 9 133 2,730 0.01119

4/12/07 2007 2030 611 6 203 1,480 0.009824/9/2008 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.

Date Year Time of Release

Day or Night

Hatchery or Wild

Number Released

Number Recaptured

Secchi Depth (cm)

Flow (cfs)

Capture 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 0.000002/25/2008 2008 1845 N H 516 7 220 1150 0.013573/25/2008 2008 2215 N H 525 11 211 1090 0.020954/16/2008 2008 2115 N W 379 6 219 1330 0.015834/24/2008 2008 2200 N W 630 12 203 908 0.019055/6/2008 2008 2225 N W 662 19 148 1700 0.02870


C3

Table C4. Capture efficiency results for wild pink, 2004, 2006 and 2008.


Date Year Time of release

Number Released

Number Recaptured

Flow (cfs)

Capture Efficiency

3/4/2004 2004 1800 19 0 1409 0.000003/5/2004 2004 1745 47 1 1310 0.021283/6/2004 2004 2000 41 1 1260 0.024393/7/2004 2004 1815 58 1 1250 0.017243/8/2004 2004 1830 96 0 1400 0.000003/9/2004 2004 1815 99 3 1700 0.03030

3/10/2004 2004 1800 92 1 1670 0.010873/11/2004 2004 1800 69 2 1450 0.028993/12/2004 2004 1830 80 3 1360 0.037503/13/2004 2004 1745 104 4 1250 0.038463/14/2004 2004 1800 72 3 1150 0.041673/15/2004 2004 1815 172 7 1110 0.040703/16/2004 2004 1815 155 4 1060 0.025813/17/2004 2004 1800 105 1 1010 0.009523/18/204 2004 1830 100 2 1100 0.02000

3/19/2004 2004 1800 110 2 1090 0.018183/20/2004 2004 1800 143 4 1030 0.027973/21/2004 2004 1830 99 2 1010 0.020203/22/2004 2004 1830 106 7 1130 0.066043/23/2004 2004 1845 105 2 1270 0.019053/25/2004 2004 800 200 6 1370 0.030003/25/2004 2004 1900 200 4 1260 0.020003/28/2004 2004 1900 506 18 1270 0.035573/31/2004 2004 800 510 21 1340 0.041184/1/2004 2004 1900 522 14 1230 0.026824/3/2004 2004 1830 514 7 885 0.013624/5/2004 2004 1945 612 13 870 0.021244/6/2004 2004 2015 510 8 825 0.015694/7/2004 2004 900 425 23 832 0.054124/9/2004 2004 1900 530 5 817 0.00943

4/12/2004 2004 1900 517 19 1120 0.036753/3/2006 2006 1645 178 2 1620 0.011243/8/2006 2006 1800 123 0 1410 0.00000

3/12/2006 2006 1900 180 4 1270 0.022223/15/2006 2006 1900 237 3 1220 0.012663/18/2006 2006 1915 251 2 1310 0.007973/21/2006 2006 1900 198 1 1200 0.005053/23/2006 2006 1900 299 0 1190 0.000003/27/2006 2006 2000 294 4 1180 0.013613/31/2006 2006 1915 211 0 1209 0.000004/3/2006 2006 2100 307 2 1350 0.006514/7/2006 2006 2030 522 4 1270 0.00766

4/11/2006 2006 2100 226 0 1339 0.000004/16/2006 2006 2115 261 6 2124 0.022994/26/2006 2006 1830 201 3 1445 0.014933/4/2008 2008 1345 290 10 1310 0.034483/8/2008 2008 1915 161 1 1030 0.00621

3/13/2008 2008 2200 493 6 1750 0.012173/15/2008 2008 2030 741 1 1640 0.001353/17/2008 2008 2100 257 5 1500 0.019463/18/2008 2008 2030 625 17 1480 0.027203/25/2008 2008 2300 751 18 1090 0.023973/30/2008 2008 1730 531 16 1050 0.030133/31/2008 2008 2045 729 7 996 0.009604/7/2008 2008 2130 509 12 1190 0.02358

4/20/2008 2008 1930 682 8 1020 0.011734/24/2008 2008 2200 732 6 908 0.00820

C4

puyallup tribe of indians smolt trap report 2008

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