Subyearling Chinook Salmon Fate Determination ...

PNWD-4128

Subyearling Chinook Salmon Fate Determination Pilot Study in Priest Rapids Pool, 2009 FINAL REPORT

G. A. McMichael R. A. Buchanan B. J. Bellgraph K. A. Deters J. A. Carter

J. R. Skalski E. V. Arntzen J. P. Duncan A. Solcz K. D. Ham

Battelle Pacific Northwest Division Richland, Washington 99352

Prepared for Public Utility District No. 2 of Grant County Ephrata, Washington 98823 under Contract Number 430-2464

January 2010

Subyearling Chinook Salmon Fate Determination Pilot Study in Priest Rapids Pool, 2009 FINAL REPORT Prepared for Public Utility District No. 2 of Grant County P.O. Box 878 Ephrata, WA 98823

Prepared by Geoffrey A. McMichael1 Rebecca A. Buchanan2 Brian J. Bellgraph1 Katherine A. Deters1 Jessica A. Carter1 John R. Skalski2 Evan V. Arntzen1 Joanne P. Duncan1 Andrew Solcz1 Kenneth D. Ham1

1

Battelle–Pacific Northwest Division P.O. Box 999, MS K6-85 Richland, WA 99352 2

Skalski Statistical Services 11804 8th Avenue NW Seattle, WA 98177

January 2010

Executive Summary To determine whether the Juvenile Salmon Acoustic Telemetry System (JSATS) technology was suitable for conducting subyearling Chinook salmon survival studies in the Priest Rapids Project, we tagged 546 Priest Rapids Hatchery-origin subyearling fall Chinook salmon (mean fork length = 104 mm) with a newly developed delayed-start acoustic transmitter weighing 0.43 gram in air. Each transmitter had a tag life of 45 days after its 14-day ‘sleep’ phase. Tag burden (weight of tag in air/weight of fish in air) ranged from 2.0% to 5.6% and averaged 3.8%. Prior to their release, tagged fish were allowed to recover from surgery for 15 days. To assess migratory delay and survival of subyearling Chinook salmon in Priest Rapids Pool, a total of 399 acoustictagged subyearling Chinook salmon were released into the Wanapum Dam tailrace on the evening of 16 June 2009. To estimate the survival of subyearling Chinook salmon passing through Priest Rapids Dam, a total of 102 acoustic-tagged fish were released into the Priest Rapids Dam tailrace on the evening of 18 June 2009. At each release location, the total samples were divided evenly between helicopter and boat releases. A total of 41 tags were retained in the laboratory to assess tag life; more than 95% of those tags exceeded the estimated tag life of 60 days following activation. A total of 23 autonomous acoustic receivers were deployed over 80 km of the Columbia River between the Wanapum Dam tailrace (Rkm 664.8) and the old Hanford town site (Rkm 584). Most receivers were deployed in a pattern intended to allow for the assessment of the fate (alive or dead) of tagged fish that failed to emigrate from Priest Rapids Pool. The specific objectives of this pilot study were to 1) estimate the combined probability of migration and survival of acoustic-tagged subyearling Chinook salmon from Beverly to Priest Rapids Dam; 2) estimate proportions of acoustic-tagged subyearling Chinook salmon that a) migrated and survived, b) delayed migration and survived (residualized), and c) died within two reaches of Priest Rapids Pool; and 3) estimate survival of acoustic-tagged subyearling Chinook salmon through Priest Rapids Dam passage. A variation on the standard single release-recapture methods was used to estimate the probabilities of migration and survival, migratory delay (residualization), and mortality within the Priest Rapids Pool. Fish detected on the Priest Rapids Dam forebay array were used to form a virtual release that was paired with the Priest Rapids Dam tailrace release group to estimate dam passage survival through Priest Rapids Dam. The JSATS technology performed very well for the assessment of subyearling Chinook salmon migratory behavior and survival in the Priest Rapids Pool in 2009. Detection probabilities were high (89.8%–99.6%) throughout the study area. An estimated 83% migrated and survived from the Beverly array (Rkm 662.6) to the forebay at Priest Rapids Dam. Estimated survival through the upper portion of Priest Rapids Pool was very high; 98.7% of the tagged fish were estimated to have survived from Beverly to near an off-channel slough referred to as Lake Geneva (Rkm 651.8). The largest apparent loss of tagged subyearling Chinook salmon occurred between Lake Geneva and the Priest Rapids Dam forebay; an estimated 16% were lost (84% survival) in this reach. Travel time information showed that tagged fish traveled quickly through the upper portion of the Priest Rapids Pool and slowed considerably as they entered the wider portion of the reservoir near Lake Geneva. © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

iii

Estimated survival through Priest Rapids Dam was high (94%) for acoustic-tagged subyearling Chinook salmon. The Priest Rapids Dam tailrace release group had an estimated survival to Vernita Bridge (Rkm 626.7) of 100%, indicating that there was no post-release mortality (which often results in an overestimation of dam passage survival in paired-release survival estimates). Using the delayed-start tags in combination with the 15-day post-tagging recovery period provided an opportunity to select fish with no apparent deleterious effects from the tagging procedure. This post-tagging recovery improved our ability to release actively migrating fish and to meet survival model assumptions to avoid bias in results. The post-tagging recovery period used in this JSATS pilot study (15 days) was within the range of previous studies (3–30 days) to examine subyearling Chinook salmon survival through the Priest Rapids Project that used passive integrated transponder (PIT) tag technology. Priest Rapids Pool and Dam survival estimates obtained with the JSATS in this pilot study compared well and, in some cases, were higher than survival estimates based on PIT-tagging studies conducted in the Priest Rapids Project between 2001 and 2003. The 2009 Battelle JSATS pilot study provided precise survival estimates over a large number of reaches within the study area using 501 tagged fish. By comparison, more than 50,000 PIT-tagged fish on average were released annually in the previous studies of subyearling survival through the Priest Rapids Project. Detections of acoustic-tagged fish from this pilot study as they migrated through the lower Columbia River and estuary indicated fish survived well through the time they entered the Pacific Ocean. The use of the JSATS in this pilot study shows that it is an effective and efficient system for studies of migratory behavior and survival of subyearling Chinook salmon in the Columbia River system.

© 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

iv

Acknowledgments We appreciate the support we received from the staff of Public Utility District No. 2 of Grant County. Specifically, we thank Curt Dotson, Rob Weedmark, and Ed Perez. Battelle staff and research associates who worked on this project were Jenny Panther, Kasey Knox, Brett Pflugrath, John Stevenson, Katie Ovink, Jim Boyd, Daniel Deng, John Serkowski, and Christa Woodley. Peter Westhagen at the University of Washington assisted in data processing. Andrea Currie provided editorial assistance.


v

Table of Contents Executive Summary ....................................................................................................................... iii Acknowledgments........................................................................................................................... v Acknowledgments........................................................................................................................... v 1.0

Introduction ......................................................................................................................... 1

2.0

Study Area .......................................................................................................................... 3

3.0

Methods............................................................................................................................... 6

4.0

5.0

3.1

Tag-Life Assessment .............................................................................................. 6

3.2

Fish Tagging ........................................................................................................... 8

3.3

Fish Releases ......................................................................................................... 10

3.4

Acoustic Receiver Deployment and Servicing ..................................................... 12

3.5

Autonomous Acoustic Receiver Data Processing................................................. 15

3.6

Data Analyses ....................................................................................................... 15

Results ............................................................................................................................... 25 4.1

Survival Effect of Tagger and Release Type ........................................................ 25

4.2

Tag Life Adjustment ............................................................................................. 26

4.3

Arrival Distributions and Mixing of Paired Releases ........................................... 30

4.4

Survival Past Priest Rapids Dam .......................................................................... 31

4.5

Reach Survival in Priest Rapids Pool ................................................................... 32

4.6

Fate Assessment in Priest Rapids Pool ................................................................. 33

4.7

Travel Time ........................................................................................................... 34

Discussion ......................................................................................................................... 36 5.1

Travel Time ........................................................................................................... 36

5.2

Effect of Migration Delay on Survival Probabilities ............................................ 36

5.3

Tagging and Handling Effect ................................................................................ 38

5.4

Helicopter versus Boat Releases ........................................................................... 39

5.5

Conclusions ........................................................................................................... 39

6.0

Recommendations ............................................................................................................. 41

7.0

Literature Cited ................................................................................................................. 43 © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

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List of Figures 1

Columbia River between Wanapum Dam and Hanford town site, Washington ..................... 3

2

Columbia River between Wanapum Dam and Vernita Bridge, Washington. ......................... 4

3

Mean daily discharge at Priest Rapids Dam on the Columbia River between 15 June and 31 August 2009. .................................................................................... 5

4

Tag life curve for 2009 Grant County JSATS acoustic tags. .................................................. 6

5

Length frequency distribution of subyearling Chinook salmon tagged with JSATS acoustic tags on 1 June and 3 June 2009. .................................................................... 8

6

Weight frequency distribution of subyearling Chinook salmon tagged with JSATS acoustic tags on 1 June 3 June 2009. .......................................................................... 9

7

A JSATS-tagged subyearling Chinook salmon in light anesthetic undergoing acoustic tag code interrogation during release tank loading on 16 June 2009 ...................... 10

8

Release of JSATS-tagged subyearling Chinook salmon from helicopter and boat release tanks into the tailrace of Priest Rapids Dam at 2012 hours on 18 June 2009.......................................................................................................................... 12

9

The JSATS autonomous acoustic receiver mooring design used to collect behavior and survival data on subyearling Chinook salmon in the Priest Rapids Project in 2009. ..... 14

10 Release locations of fish, virtual releases of fish, and hydrophone deployments for the 2009 subyearling Chinook salmon acoustic-tag study. ........................ 17 11 Relationship between φ, ψ, and µ in a single reach and time period for a singlerelease group.......................................................................................................................... 18 12 The paired release-recapture design used to estimate dam passage survival at Priest Rapids Dam ................................................................................................................. 21 13 Observed tag failure times from the tag life study and fitted three-parameter Weibull curve ........................................................................................................................ 26 14 Three-parameter Weibull survivorship curve for tag life vs. timing of downstream detections of subyearling fall Chinook salmon smolts at Beverly, Lake Geneva, Priest Rapids BRZ, Vernita Bridge, and Hanford Town ....................................................... 27 15 Arrival distribution of Wanapum and Priest Rapids tailrace releases at Vernita Bridge ....................................................................................................................... 30 16 Arrival distribution of Wanapum and Priest Rapids tailrace releases at Hanford Town ...................................................................................................................................... 31 17 Passage index of subyearling Chinook salmon passing McNary Dam on the Columbia River, Washington/Oregon, 2009 ......................................................................... 38


vii

List of Tables 1

Tag code and lifespan for expired JSATS acoustic tags from 2009 Grant County tag life study .................................................................................................................................. 7

2

Tagging and release information subyearling Chinook salmon implanted with JSATS acoustic tags in June 2009 ........................................................................................... 9

3

Locations of acoustic receivers used to collect behavior and survival data on subyearling Chinook salmon in the Priest Rapids Project in 2009. ...................................... 13

4

Detection histories and expected probabilities of occurrences for releases V2 and R2 for the acoustic-tag study. ..................................................................................... 23

5

Number of subyearling fall Chinook salmon tagged at each release site by tagger and release type in 2009. ....................................................................................................... 25

6

Survival by tagger and release type for Wanapum and Priest Rapids tailrace releases to Vernita Bridge ..................................................................................................... 25

7

Survival by tagger for Wanapum and Priest Rapids tailrace releases to Vernita Bridge. ...................................................................................................................... 26

8

Survival by release for Wanapum and Priest Rapids tailrace releases to Vernita Bridge ....................................................................................................................... 26

9

Estimated probabilities of an JSATS acoustic tag being active when a subyearling fall Chinook salmon smolt arrived at the detection locations for releases from Wanapum and Priest Rapids tailrace, and for the virtual release in the Priest Rapids forebay....................................................................................................................... 29

10 Estimated detection probabilities at survival gates between the Wanapum tailrace and Hanford Town................................................................................................................. 31 11 Capture histories for Priest Rapids BRZ and tailrace releases of subyearling fall Chinook salmon smolts at Vernita Bridge and Hanford Town in 2009 ................................ 32 12 Estimated survival of Priest Rapids BRZ virtual release and Priest Rapids tailrace release to Vernita Bridge, and estimated survival past Priest Rapids Dam.......................................................................................................... 32 13 Estimated survival of the Wanapum tailrace release through reaches within the Priest Rapids Pool and through the Priest Rapids Project ..................................................... 33 14 Alternative scenarios used for sampling intrareach receiver detections, the number detected in the combined samples, and estimates of intrareach receiver detection probability, number of tagged fish present on 18 July 2009, joint probability of delay and survival to 18 July, and probability of mortality between Beverly and Priest Rapids BRZ before 18 July. ..................................................... 34 15 Average travel times in days through each reach for fish released in Wanapum tailrace and in Priest Rapids tailrace ..................................................................................... 35


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List of Appendices Appendix A – Water quality monitoring in fish release tanks.................................................... A-1 Appendix B – Release tank evaluation using the Sensor Fish device ........................................ B-1 Appendix C – Detection of JSATS acoustic-tagged subyearling Chinook salmon in the lower Columbia River and Pacific Ocean ................................................. C-1


ix

1.0

Introduction

Columbia River basin juvenile fall Chinook salmon Oncorhynchus tshawytscha have been documented to express at least two types of migratory life histories—a subyearling smolt that exhibits relatively directed migration seaward during the summer or fall after its emergence, or an extended rearing strategy in which the juvenile fish remains within freshwater through the first winter following emergence and then migrates seaward as a yearling smolt (also termed reservoir type; Connor et al. 2005; McMichael et al. 2008). This variability in life history trajectories presents challenges when attempting to understand the survival of juvenile fall Chinook salmon as they migrate through hydroelectric developments in the Columbia River basin. Survival models used with tagging technologies include assumptions that all tagged fish have an equal chance of being ‘recaptured.’ If tagged fish elect to extend their rearing prior to exiting a study area, they will be counted as mortalities, when in fact they may still be alive but not migrating. Thus, the term joint probability of migrating and surviving often is applied to subyearling Chinook salmon survival results (Skalski 1998; Zabel et al. 2005; McMichael et al. 2008). McMichael et al. (2008) developed an autonomous acoustic receiver deployment approach and associated statistical models to estimate the proportions of JSATS acoustic-tagged fish that failed to exit a given reach that were either alive or dead at the end of a given period (e.g., the end of the tag-life period). Application of this model in the Snake River showed that upward of 10% of the tagged subyearling fall Chinook salmon remained within Lower Monumental Reservoir for extended periods prior to emigrating during the winter or following spring (McMichael et al. 2008; Buchanan et al. 2009). In an attempt to determine whether the extended rearing phenomenon might partially explain poor survival of subyearling Chinook salmon tagged in 2008 (e.g., 51% estimated survival from Beverly to Priest Rapids Dam forebay; Sullivan et al. 2008), the Public Utility District No. 2 of Grant County contracted Battelle–Pacific Northwest Division to conduct a pilot study. The study sought to determine whether the approach Battelle researchers had developed for the application of the Juvenile Salmon Acoustic Telemetry System (JSATS) technology was suitable for conducting subyearling Chinook salmon survival studies in the Priest Rapids Project. A further goal was to collect information that would be useful in guiding future studies of subyearling Chinook salmon survival in terms of addressing assumptions relevant to statistical survival model development. The objectives of this pilot study were to 1) estimate the combined probability of migration and survival of acoustic-tagged subyearling Chinook salmon from Beverly to Priest Rapids Dam; 2) estimate proportions of acoustic-tagged subyearling Chinook salmon that a) migrated and survived, b) delayed migration and survived (residualized), and c) died within two reaches of Priest Rapids Pool; and 3) estimate survival of acoustic-tagged subyearling Chinook salmon through Priest Rapids Dam. This report documents the pilot study and its outcomes. The study site on the Columbia River is described in Section 2. Methods employed during the study, including equipment and data analysis protocols, are detailed in Section 3. Results are presented in Section 4, followed by detailed discussion of the findings in Section 5 and a presentation of recommendations in Section 6. Appendix A documents the methodology Battelle employed to monitor water quality in the fish release tanks while en route to the study site after tagging. Appendix B provides a description of how Sensor Fish devices were used to evaluate conditions in the fish release tanks prior to and during release into the river for the study. Appendix C provides details on detections © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

1

of JSATS acoustic-tagged subyearling Chinook salmon in the Lower Columbia River and the Pacific Ocean.


2

2.0

Study Area

The geographic area for this pilot study was in the Priest Rapids Project (Federal Energy Regulatory Commission License 2114) on the Columbia River in southeastern Washington. The primary focus of the study was on the lower 25 km of the reservoir upstream of Priest Rapids Dam (Priest Rapids Pool), between river kilometers (Rkm) 665 and 640. However, the study area also encompassed stretches of the river both upstream and downstream of the Priest Rapids Pool. The tagged fish were released upstream in the tailrace of Wanapum Dam, and acoustic telemetry autonomous receivers were deployed between Rkm 665 and 584 (Figures 1 and 2).

Figure 1.

Columbia River between Wanapum Dam and the old Hanford town site, Washington. Red markers indicate acoustic telemetry receiver locations. Tagged fish were released in the Wanapum and Priest Rapids dam tailraces as denoted by the green stars.

Figure 2 shows a more detailed view of Priest Rapids Pool to better illustrate the locations of autonomous receivers.


3

Figure 2.

Columbia River between Wanapum Dam and Vernita Bridge, Washington. Red markers indicate acoustic telemetry receiver locations.

Mean daily discharge through Priest Rapids Dam during the study period declined from an average of 152 thousand cubic feet per second (kcfs) during the first 2 weeks of the study (16–30 June) to an average of 81 kcfs during the last 2 weeks of the study period (17–31 August; Figure 3).


4

200 180 160

Discharge (kcfs)

140 120 100 80 60 40 20 0

Date (2009)

Figure 3.

Mean daily discharge at Priest Rapids Dam on the Columbia River between 15 June and 31 August 2009.


5

3.0

Methods 3.1

Tag-Life Assessment

JSATS acoustic transmitters used in this pilot study were a new duty cycle design built by Advanced Telemetry Systems specifically for the needs of this pilot study. These transmitters (tags) were 12 mm long, 5 mm wide, and 4 mm thick and weighed 0.43 gram in air. Residual mass in water was 0.29 gram. Transmitters were programmed to emit a coded pulse every 7 sec at a frequency of 416.7 kHz for 24 hr following activation (by acoustic signal), then ‘sleep’ for 14 days, and then resume transmitting again following the 14-day sleep period. Expected tag life from the time of activation was 60 days (45-day life after resuming transmissions). Tag life was assessed by continually monitoring 41 tags in a 2-m circular tank with flow-through ambient Columbia River water at the Pacific Northwest National Laboratory (PNNL) Aquatics Research Laboratory (ARL) in Richland, Washington, beginning 22 to 24 days after tag activation. To monitor tag life, two (90° × 180°) hydrophones were placed at 90° and 180° positions along the inner wall of the tank. The hydrophones were angled approximately 45° off the tank bottom, so the hydrophones pointed upward and toward the center effluent screen. Each activated tag was placed in a perforated opaque bag with a 5-mm glass marble for weight. The bags were attached to a foam ring that rotated around a center standpipe. The JSATS detector program recorded acoustic waveforms transmitted by the acoustic tags. These waveforms were translated into unique tag codes using the Waveform Utility Decoder programs. Once the individual tag codes were translated, a post-processing/data filtering program removed noise, accounted for multipath signals, and summarized data on an hourly basis. 110 100 90 80 70

Percent

Tags included in the tag-life assessment were activated in two lots (31 May [n = 35] and 2 June [n = 6]). Tag-life testing began on 23 June and ended on 8 September 2009, for a total study period of 77 days (beginning 22 to 24 days after activation). An equipment failure on 26 August resulted in a 39-hr period during which no data were collected. Four tags died during that time. The death date/hour of these tags was estimated as hour 20 of the outage. Of the 41 tags tested, 95.1% had tag lives longer than 76 days followed by a drastic increase in tag death rates during the 19-day period between days 76 and 95 (Figure 4, Table 1).

60 50 40 30 20 10 0 0

10

20

30

40

50

60

70

80

90

Days Since Activation

Figure 4.

Tag-life curve for acoustic tags assessed in Columbia River water during the fate determination study, 2009.


6

100

Table 1.

Tag code and lifespan for expired JSATS acoustic tags from 2009 tag-life assessment. Expected ping rate interval = 7 sec; expected lifespan = approximately 60 days.

Death Date Total Lifespan % Total Expected Lifespan (2009) (d) (60 d) 1 Jul 30.6 51.0 14 Jul 41.6 69.3 16 Aug 76.6 127.7 19 Aug 77.8 129.7 17 Aug 78.1 130.2 18 Aug 78.4 130.7 18 Aug 78.5 130.8 20 Aug 79.3 132.1 19 Aug 79.5 132.4 19 Aug 79.6 132.7 20 Aug 80.6 134.3 20 Aug 80.5 134.1 20 Aug 80.7 134.5 21 Aug 87.9 136.6 21 Aug 82.0 136.6 22 Aug 82.3 137.1 22 Aug 83.1 138.5 22 Aug 83.0 138.3 24 Aug 83.3 138.8 23 Aug 83.5 139.2 25 Aug 84.3 140.4 23 Aug 84.1 140.2 23 Aug 84.3 140.4 24 Aug 84.4 140.6 24 Aug 84.5 140.8 24 Aug 84.5 140.9 24 Aug 84.9 141.5 24 Aug 85.0 141.7 24 Aug 85.1 141.8 24 Aug 85.1 141.9 25 Aug 85.7 142.8 26 Aug 87.1a 145.1a 26 Aug 87.1a 145.1a a 26 Aug 87.0 145.0a a 26 Aug 85.2 142.0a 28 Aug 88.5 147.4 28 Aug 88.3 147.2 28 Aug 88.6 147.7 29 Aug 89.7 149.5 31 Aug 92.0 153.4 3 Sep 95.0 158.3 Mean 81.6 136.1 a Equipment failure resulted in a 39-hr period during which data were not collected. Death date/hour for tags that died during this time were estimated as the middle of the data gap. Unique Tag Code G722FFB2D G722F3BE7 G722E5E79 G722D6911 G722F6DE1 G722E73A7 G722E3E1C G722F4F7E G722F7363 G722F2104 G722E9D51 G722EA2AE G722E7DB8 G722E88F3 G722FB574 G722EE435 G722DAA39 G722EFAB7 G722F723D G722E9671 G722E2902 G722EF32B G722F5EBD G722CC487 G722F1826 G722F3AB9 G722F9068 G722E86EC G722F0127 G722E3B23 G722CC1B8 G722F6B3C G722F8A8B G722F9A16 G72310CEA G722D4591 G722E60D8 G722ECD8A G722F08BB G7232DCE8 G722ECA09

Activation Date (2009) 31 May 2 Jun 31 May 2 Jun 31 May 31 May 31 May 2 Jun 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 2 Jun 31 May 2 Jun 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 31 May 2 Jun 31 May 31 May 31 May 31 May 31 May 31 May


7

3.2

Fish Tagging

Fall Chinook salmon were transported as fry to the ARL in Richland, Washington, on 6 February 2009 (2008 brood year) from Priest Rapids Hatchery on the Columbia River. Prior to surgery, juveniles were held in two circular tanks with volumes of 1,882 L and 1,112 L. Acoustic transmitter implantation surgeries took place on 1 June for the Wanapum tailrace release group and on 3 June for the Priest Rapids tailrace release group. On both tagging days, the same four experienced taggers performed similar numbers of implantation surgeries. Any fish exhibiting signs of disease or injury were rejected for tagging. At the time of surgery, implanted individuals had a mean length of 104 mm (range 92–122 mm) and mean weight of 11.8 grams (range 7.7–21.1grams) for both groups combined (Figures 5 and 6). 12

10

Percentage

8

6

4

2

0 92

94

96

98

100 102 104 106 108 110 112 114 116 118 120 122 Length (mm)

Figure 5.

Length frequency distribution of subyearling Chinook salmon tagged with JSATS acoustic tags on 1 June and 3 June 2009.

Study fish were implanted using a method similar to that described by Deters et al. (2009) but with the following differences: incisions were approximately 5 mm long, fish were implanted with a JSATS acoustic transmitter only (no passive integrated transponder was implanted), and incisions were closed using two simple interrupted sutures of 5-0 absorbable monofilament (Monocryl, Ethicon Endo-Surgery, Inc., Cincinnati, Ohio). The 501 tagged fish released had a mean tag burden equal to 3.8% (range 2.0%–5.6%) of their body weight in air (Table 2). Release type (helicopter or boat) was designated following surgery; nearly even numbers of fish from each surgeon were systematically assigned to each release type (helicopter or boat).


8

25

Percentage

20

15

10

5

0 7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

Weight (g)

Figure 6.

Weight frequency distribution of subyearling Chinook salmon tagged with JSATS acoustic tags on 1 June and 3 June 2009.

Table 2.

Tagging and release information for subyearling Chinook salmon implanted with JSATS acoustic tags in June 2009. Fish size information as well as tag burden (weight of tag in air/weight of fish in air, expressed as a percentage).

Weight Range (g)

Mean Tag Burden (%)

Tag Burden Range (%)

Tagging Date

Release Date

Release Location (Rkm)

1 Jun

16 Jun

668

Helicopter

200

104

92–120

11.6

7.7–20.2

3.8

2.1–5.6

1 Jun

16 Jun

668

Boat

199

104

95–122

11.6

8.4–21.1

3.8

2.0–5.1

3 Jun

18 Jun

638

Helicopter

51

104

95–121

12.5

8.9–20.6

3.6

2.1–4.8

3 Jun

18 Jun

638

Boat

51

104

95–116

12.5

8.0–20.8

3.6

2.1–5.4

Release Type

n

Mean Length (mm)

Length Range (mm)

Mean Weight (g)

The Wanapum and Priest Rapids release groups were placed in two identical circular tanks (1,390 L) following recovery from surgery and remained there until the day of release. Fish were supplied with river water (mean 16.3°C) and experienced a natural photoperiod. Fish were fed Bio-Oregon feed (Bio-Oregon, Longview, Washington) at a rate of 1.8% body weight per day for 3 days following surgery, then switched to SilverCup medicated feed (Nelson & Sons, Inc., Murray, Utah) at the same rate, from day 4 to day 10 post-surgery during a period when five mortalities occurred in the Wanapum tailrace release group (of 437 tagged). There were no mortalities prior to release in the Priest Rapids tailrace release group (of 109 tagged). Between day 10 and 24 hr prior to release, fish were again fed the Bi-Oregon feed at a rate 1.8% body weight per day.


9

3.3

Fish Releases

Fifteen days following surgery (16 and 18 June for Wanapum and Priest Rapids release groups, respectively), fish were removed from the holding tank and lightly anesthetized with a dose of 40 mg of tricaine methanesulfonate (MS-222)/mL of water until they reached stage 3 anesthesia (as described by Summerfelt and Smith 1990). A single fish was placed inside a plastic 2-L pitcher filled with the same dose ofanesthetic. Transducers for each of two portable acoustic receivers (Model N202 acoustic nodes, Sonic Concepts, Inc., Bothell, Washington) also were placed in the pitcher (Figure 7).

Figure 7.

A JSATS-tagged subyearling Chinook salmon in light anesthetic undergoing acoustic tag code interrogation during release tank loading on 16 June 2009.

Each acoustic receiver was connected to a laptop computer via a serial cable. For each release day, the file of acoustic tag codes for the helicopter release group was loaded onto one laptop designated as helicopter while the file of codes for the boat release group was loaded onto a second laptop (boat). On each laptop, a graphical user interface developed for use with the portable receivers was used to display only the decoded messages that matched acoustic tag codes in a lookup table on that laptop. The same tag code was read (decoded) twice to verify that the decoding was accurate. After successfully decoding each tag code, the researcher watching the laptops communicated a 4-digit section of the code to another individual, who confirmed that this code was in the original tagging file. At this time, both individuals had to be in agreement on the release type (helicopter or boat). A third person was responsible for examining the incision location and overall health (based on external examination). Because 546 fish were tagged and only 500 were to be released, it was necessary to cull some fish in order to use the transmitters for the tag-life study. Reasons for rejection included excessive amounts of © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

10

fungus covering the wound, severe ulceration or redness, tearing sutures, or simply needing to supply transmitters for the tag-life study. With the release type confirmed, fish acceptable for release were placed in their respective temporary holding containers—covered 5-gal buckets filled with fresh water and designated as either helicopter or boat. When 10 fish of a single release type were collected, the fish were transferred to their respective transport vessel, one of two rectangular 950-L stainless steel tanks, which were supplied with flow-through river water. Once the last fish was placed into the transport tanks, the water was turned off, and the tank became a closed, recirculating system with oxygen supplied throughout the transport period. Transportation to Wanapum Dam took approximately 95 min, while the drive to Priest Rapids Dam lasted only 65 min. After receiving flow-through river water at Priest Rapids Dam for about 20 min, the Priest Rapids tailrace helicopter release group was then transported to Wanapum Dam (where the helicopter loading area was located). Water quality was monitored during transport and throughout the release (Appendix A). Transport tanks doubled as release tanks because they were fitted with release spouts. At Wanapum Dam, a boom truck positioned the Wanapum boat release tank on the stern of an 8-m-long boat. The Wanapum helicopter release tank was lifted into the air with a helicopter. Both tanks were driven to the release location (Rkm 668), and the fish were released to the river at 2014 hours Pacific Daylight Time (PDT) for the helicopter release group and at 2018 hours for the boat release group. The Priest Rapids tailrace releases were executed similarly; the boat release tank was loaded onto the boat with a crane at Priest Rapids Dam (approximately 1957 hours PDT). The helicopter release tank, however, was picked up by the helicopter at Wanapum Dam at 2000 hours. The boat and helicopter then traveled to the release location (Rkm 638). The fish were released to the river at 2011 hours for the Priest Rapids helicopter release group and at 2012 hours for the boat release group (Figure 8). Fish were released in the evening to reduce the probability of avian predation on recently released fish.


11

Figure 8.

3.4

Release of JSATS-tagged subyearling Chinook salmon from helicopter and boat release tanks into the tailrace of Priest Rapids Dam on 18 June 2009. Acoustic Receiver Deployment and Servicing

Acoustic receivers (Model N201, Sonic Concepts, Inc., Bothell, Washington) were placed at 23 locations in the Columbia River between Wanapum Dam and the Hanford town site (Figure 1, Table 3). Ten of these locations were part of survival gates (multiple receivers arranged in a transect perpendicular to the river shore). Each gate had two to three acoustic receivers spaced equidistant on cross-sectional lines with spatial redundancy to maximize detection probabilities. There were three survival gates within Priest Rapids Pool and one downstream of Priest Rapids Dam, near the Vernita Bridge. One receiver was placed at Wanapum tailrace to act as an entrance receiver, and one receiver was placed at the Hanford town site to enable determination of detection probability of the Vernita Bridge array. The remaining 11 acoustic receivers were placed at approximately 2-km intervals, centered in the middle of the river beginning 2.1 km downstream of the array at Beverly and ending 1.3 km upstream of the boat restricted zone (BRZ) in the Priest Rapids forebay. The last two intrareach locations each had two receivers, dividing the river into thirds, to account for the greater width of the river near Priest Rapids Dam (Table 3).


12

Table 3.

Locations of acoustic receivers used to collect behavioral and survival data on subyearling Chinook salmon in the Priest Rapids Project in 2009. Array Code

Rkm

Number of Receivers

CR664.8

664.8

1

CR662.6

662.6

3 (survival gate)

CR660.4

660.4

1

Intrareach receiver

CR658.3

658.3

1

Intrareach receiver

CR656.2

656.2

1

Intrareach receiver

CR654.0

654.0

1

Intrareach receiver

CR651.8

651.8

CR649.6

649.6

1

Intrareach receiver

CR647.5

647.5

1

Intrareach receiver

CR645.3

645.3

1

Intrareach receiver

CR643.1

643.1

2

Intrareach receivers

CR640.9

640.9

2

Intrareach receivers

CR639.6

639.6

3 (survival gate)

Priest Rapids forebay

CR626.7

626.7

2 (survival gate)

Vernita Bridge

CR584.0

584.0

1

2

(survival gate)

Description Wanapum tailrace Beverly

Lake Geneva

Hanford town site

Each autonomous receiver consisted of a hydrophone, battery compartment, 15-sec beacon, buoy line, acoustic release (Model 111, InterOcean Systems, Inc., San Diego, California), anchor line, and anchor (Figure 9). The beacons emitted a signal every 15 sec, which was used as a confirmation that the hydrophone was working properly. Prior to deployment, each acoustic receiver was attached to an acoustic release by a 0.9-m-long bridle made of 12.7-mm-diameter braided nylon rope. Each bridle end was terminated by a braided splice around a professionally braided 9.5-mm SeaDog nylon thimble. Three yellow buoys (Model BL-6, 16.5–12.4 cm, 1.45kg buoyancy each; Bao Long Industrial Co., Ltd., Taiwan, Republic of China) were threaded on the bridle between the acoustic receiver and release (Figure 9). Depending on the water depth, each acoustic release was shackled to a 23-kg anchor with either a 1.5- or 3.6-m-long shockcorded mooring made from 12.7-mm braided nylon rope terminated by a 10-cm galvanized steel ring held by the acoustic release mechanism. The configuration of the various components of the autonomous receiver system as it was deployed in the water column is represented in Figure 9.


13

Figure 9.

The JSATS autonomous acoustic receiver mooring design used to collect behavioral and survival data on subyearling Chinook salmon in the Priest Rapids Project in 2009.

The acoustic receivers were deployed 11–12 June 2009 and maintained through 18 August 2009. The receivers were recovered and serviced once during the study period, approximately 28 days after the initial deployment. To recover each receiver, the boat was navigated close to the waypoint of the deployed receiver using a Global Positioning System (GPS) receiver and the navigation software Fugawi Marine ENC (Northport Systems Inc., Toronto, Ontario) to display the position of the boat on a laptop computer. A command unit and transducer (Model 1100E, InterOcean Systems, Inc. San Diego, California) was used to activate the acoustic release. Upon © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

14

receiving the signal from the command unit, the acoustic release opened and released the ring on the anchor line, which allowed the receiver and release to float to the surface. During servicing, the receiver batteries and the Compact Flash cards (Extreme III 1.0-GB, SanDisk Corporation) containing the data were replaced. Prior to redeployment, receiver function was tested by confirming the ability of the receiver to receive and decode beacon transmissions. The acoustic release was re-armed using hand-held magnets to activate the motor to close the link to a new anchor line attached to a new anchor. Once the boat was in position, the equipment was fed over the side as the anchor was lowered to the bottom on a slip line. When the anchor reached bottom, the actual GPS point was recorded. 3.5

Autonomous Acoustic Receiver Data Processing

Data collected by the autonomous receivers were recorded as a single text file on Compact Flash cards. Physical data (date, time, pressure, water temperature, tilt, and battery voltage) were written to file every 15 sec. Detections of transmitters were recorded in real time as they were received. Detections written to media included the individual transmitter code (TagID), time stamp, receive signal strength indicator, and a calculated measure of background noise. Each data file was transferred to a laptop computer following servicing or retrieval events. Data files from all receivers were coded with the receiver location and stored in a database developed specifically for storing and processing acoustic telemetry data. To filter out false detections (detections of TagIDs that did not meet criteria to be considered a valid detection), a post-processing program was implemented. This program required a minimum of four detections within 13 expected transmissions. The timing of expected transmissions was calculated based on the nominal ping rate interval (PRI) of the tag, which in this case was 6 sec. Because the actual PRI often differed from the nominal PRI, a multiplication factor of 1.3 was used, making the interval approximately 94 sec. Additionally, the time spacing between these detections was required to maintain a consistent pattern to be kept in the valid detection file. From the valid detection file, a detection history was created for each fish. Detection histories were analyzed to estimate survival (see Section 3.6.2). 3.6

Data Analyses 3.6.1

Tag Release-Recapture Design

A single paired release of subyearling Chinook salmon smolts was performed at Wanapum and Priest Rapids tailraces. A total of 399 acoustic-tagged subyearlings were released from the Wanapum tailrace and another 102 released from the Priest Rapids tailrace (Figure 10). The Wanapum tailrace release supplied fish to form a virtual release group at the Beverly hydrophone array. This array demarcated the upstream edge of the study area. Between Beverly and the Priest Rapids BRZ, a variation on the standard single release-recapture methods was used to estimate the probabilities of migration and survival, migratory delay (residualization), and mortality in the Priest Rapids Pool (Buchanan et al. 2009). Identification of delay would be evidence that survival is higher in the Priest Rapids Pool than estimated by standard tagging methods. © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

15

Fish that arrived at the Priest Rapids BRZ formed another virtual release that was paired with the Priest Rapids tailrace release group to estimate dam passage survival. The downstream detection arrays for this paired release-recapture design were at Vernita Bridge and the Hanford town site (Figure 10). Because the design paired already released fish with newly released fish downstream, any post-release handling mortality among the downstream group might have potentially biased estimates of dam passage survival in a positive direction. 3.6.2

Statistical Analysis

Separate data analyses were performed to investigate survival in the Priest Rapids Pool and dam passage survival through Priest Rapids Dam. 3.6.2.1 Using Single-Release Model to Estimate Migration Parameters For a single-release group (V1), three parameters were estimated in the reach between Beverly and the Priest Rapids BRZ: 1. φ , the joint probability of migrating and surviving through the reach within the study period 2. ψ , the probability of holding up (delaying) and surviving in the reach to the end of the study period; the delay parameter 3. µ , the probability of dying in the reach within the study period ( µ =1 − φ −ψ ) .


16

Wanapum Dam 399

R1

• V • • • • • •• • ••• • • • • •V • •

Beverly

1

Lake Geneva

BRZ

2

Priest Rapids Dam

R2

102

S1

S2

p1

•

•

λ1

Vernita Bridge

λ2

• Figure 10.

p2

Hanford Town

Release locations (R) of fish, virtual releases of fish (V), and hydrophone deployments (●) for the 2009 subyearling Chinook salmon acoustic-tag study.


17

The relationship between these three parameters is shown in Figure 11. Together, φ (migrate and survive), ψ (delay and survive), and µ represent all possible outcomes for a fish that entered the reach (Buchanan et al. 2009). These three parameters were estimated from the onset of the tagged fish entering the reach until the end of the study period (based on tag-life data and detections on Priest Rapids tailrace receivers).

µ

= Pr [ Death in reach and time period ] =1 − φ −ψ

φ = Pr [ Migrate and survive ] Line Detections

Intrareach Receivers ( N )

ψ = Pr [ Delay and survive ] Figure 11.

Relationship between φ (joint probability of migrating and surviving), ψ (joint probability of delaying and surviving), and µ (probability of death) in a single reach and time period for a single-release group.

The virtual release of fish known to have arrived at Beverly (i.e., V1) was entered into a single release-recapture model to estimate the migration parameter φ based on the detections at the BRZ, Vernita Bridge, and Hanford Town. Detection histories from the intrareach receiver detections (see Section 3.6.2.2, Estimating Delay Numbers) were used with a multinomial markrecapture, closed-population model to estimate N1, the abundance of live tagged smolts in the reach. The probability of delaying in the reach and surviving to the end of the study, ψ1, was estimated as

ψˆ1 =

Nˆ 1 V1 ,

(1)

with variance estimate

( )

 (ψˆ ) = 1 Var  Nˆ Var 1 1 V12 .

(2)


18

The probability of death within the reach was estimated as

µˆ =1 − φˆ −ψˆ .

(3)

It was not possible to determine whether dead smolts were actively migrating or not. The ˆ variance of µ1 was estimated by

( )

( )

  φˆ + 1 Var  Nˆ = Var ( µˆ1 ) Var 1 V12 .

3.6.2.2 Estimating Delay Numbers

(4)

( Nˆ ) 1

Using the detection data from the intrareach receivers between Beverly and the Priest Rapids BRZ, we estimated the abundance of live tagged fish within the reach using a closed-population, mark-recapture model. For example, using detection data from just the last 2 days of the study, the abundance of live tagged fish in the reach was estimated using the Lincoln/Petersen model in which = Nˆ 1

( n1 + 1)( n2 + 1) − 1 ( m + 1)

(5)

and where n1 = number of live tagged fish detected on day 1 n2 = number of live tagged fish detected on day 2 m = number of tagged fish detected on days 1 and 2. The variance of Nˆ 1 was estimated by (Seber 1982, p. 60)

 Nˆ = ( n1 + 1)( n2 + 1)( n1 − m )( n2 − m ) Var 1 2 ( m + 1) ( m + 2 )

( )

(6)

The Lincoln/Petersen model assumes the population of tagged fish within the reach is closed to recruitment, death, immigration, and emigration. Recruitment and immigration are unlikely at the end of the study. Most fish entering the reach will have done so well before the end of the study. Mortality and emigration are possible within a period of a day. If they occurred, then Nˆ 1 estimates abundance on the second-to-the-last day of the study and has little or no impact on study results. Alternative sampling scenarios were used to confirm results from sampling on the last 2 days of the period. © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

19

Although data from only the last few days were analyzed to estimate migratory delay, the detections at the intrareach receivers over the course of the study were used for several purposes. Most important, the detection records at the intrareach receivers were used to develop an algorithm to identify live tagged fish and distinguish them from dead tagged fish. This algorithm was then used to determine which detections to use in the capture-recapture analysis to estimate residualization abundance. The receiver upstream of the Beverly array was used to determine whether fish migrated upriver and remained so after first entering the study area. 3.6.2.3 Estimating Dam Passage Survival Using a virtual release composed of tagged fish known to have arrived at the Priest Rapids BRZ (i.e., V2) and the tailrace release below Priest Rapids Dam (i.e., R2), we estimated passage survival through the dam with a paired release-recapture model (Figure 12). The model employed the paired release-recapture methods of Burnham et al. (1987), as described below. Survival estimates were estimated from capture histories representing detections at Vernita Bridge and Hanford Town and adjusted for the estimated acoustic tag life, as described in Townsend et al. (2006).


20

V2

BRZ

Priest Rapids Dam

R2

S1

S2

p2

p1

λ1

Vernita Bridge

λ2 Hanford Town

Sˆ SˆDam = 1 Sˆ2 Dam Passage Survival Figure 12.

The paired release-recapture design used to estimate dam passage survival at Priest Rapids Dam.

In estimating Priest Rapids Dam passage survival, the fully parameterized release-recapture model can be written as follows: n01 n10 V  n L  2  ( S1 p1λ1 ) 01 ( S1 (1 − p1 ) λ1 ) ( S1 p1 (1 − λ1 ) ) = n  n00 ⋅ ( (1 − S1 ) + S1 (1 − p1 )(1 − λ1 ) ) m01 m10 R  m ⋅  2  ( S 2 p2 λ2 ) 11 ( S 2 (1 − p2 ) λ2 ) ( S 2 p2 (1 − λ2 ) ) m  m00 ⋅ ( (1 − S 2 ) + S 2 (1 − p2 )(1 − λ2 ) ) ,


21

(7)

where n and m are the vectors of counts associated with the downstream capture histories of   releases V1 and R2, respectively (Figure 12). To account for acoustic tag failure, additional parameters were added to the above model (7) based on methods of Townsend et al. (2006). Table 4 presents the expected probabilities of occurrence for each of the possible capture histories under tag failure where L11 = probability a tag from release V2 survives the first reach P ( L12 | L11 ) = conditional probability a tag from release V2 survives the second reach given its survival to the first reach L12 = probability a tag from release V2 survives both reaches 1 and 2 L21 = probability a tag from release R2 survives the first reach

P ( L22 | L21 ) = conditional probability a tag from release R2 survives the second reach conditional on its surviving the first reach L22 = probability a tag from release R2 survives both reaches 1 and 2. The joint likelihood can be expressed as = L L ( S1 , p1 , λ1 V1 , n, L1 ) ⋅ L ( S 2 , p2 , λ2 R2 , m, L2 )     .

(8)

The estimates of survival from likelihood model (8) should be more reliable because it takes into account possible tag failure and tag-life probabilities of less than one.


22

Table 4.

Detection histories and expected probabilities of occurrences for releases V2 and R2 for the acoustic-tag study.

Release

V2

R2

Detection History

Expected Probabilities

11

S1 L11 p1 P ( L12 L11 ) λ1 = S1 p1 L12 λ1

01

S1 L11 (1 − p1 ) P ( L12 L11 ) λ1 = S1 (1 − p1 ) L12 λ1

10

S1 L11 p1 1 − P ( L12 L11 ) λ1  = S1 p1 ( L11 − L12 λ1 )

00

(1 − S1 ) + S1 (1 − L11 ) + L11 (1 − p1 ) − L12 (1 − p1 ) λ1 

11

S 2 p2 P ( L22 L21 ) λ2 = S 2 p2 L22 λ2

01

S 2 L21 (1 − p2 ) P2 ( L22 L21 ) λ2 = S 2 (1 − p2 ) L22 λ2

10

S 2 p2 1 − P L 22 L21 λ2  = S 2 p2 ( L21 − L22 λ 2 )  

00

(1 − S2 ) + S2 (1 − L21 ) + L21 (1 − p2 ) − L22 (1 − p2 ) λ2 

(

)

The estimates of the survival and capture parameters in likelihood model (8) were calculated using the estimates of tag-life probabilities (i.e., Lˆ11 , Lˆ12 , Lˆ21 , and Lˆ22 ) treated as known constants. The error in the estimation of the tag-life probabilities was then incorporated into the variance estimator for the survival parameters. The variance of the survival estimates was calculated using the expression Var ( SˆPR ) = sS2ˆ

PR

Lˆ 

(

)

+Var SˆPR Lˆ  .

(9)

The second term in Equation (9) was derived from the maximum likelihood model (8) conditioning on the tag-life probabilities (i.e., Lˆ ). The first variance component in Equation (9)  was calculated using bootstrap resampling techniques (Efron and Tibshirani 1993). Alternative estimates of Lˆ were computed by bootstrapping both the observed tag-life data and travel-time  data. For each estimated vector of tag-life parameters, survival was estimated using likelihood


23

model (8). One thousand bootstrap estimates of the tag-life parameters were calculated along with the corresponding conditional maximum likelihood estimates of survival. The first variance component in Equation (9) was then estimated by the quantity

∑ ( Sˆ

1000

sS2ˆ

PR

Lˆ 

=

b =1

ˆ b −S

)

2

(1000 − 1)

where Sˆb = the bth bootstrap estimate of survival ( b = 1, ,1000 ) , 1000

Sˆ =

∑ Sˆ b =1

b

1000 .

Tag Life. In 2009, 41 delayed-start JSATS tags were used to characterize tag life from systematically sampling tags used in the subyearling Chinook salmon study. The tags were initiated and continually monitored in ambient river water until they failed (Section 3.1). The failure time (tag life) was recorded for each of the 41 tags. The failure-time data were fit to a Weibull distribution of the form

f ( x) e =

 x −γ  −   η 

β

β −1  β  η β ( x − γ )   .

(10)

The statistical tag-life data were truncated after day 85. Tests Within a Release. The detection design for 2009 (Figure 12) did not permit calculation of Burnham et al. (1987) Tests 2 and 3. Because smolts were not physically handled during detection, there was no reason to believe upstream detection had an effect on downstream survival and detection processes. Tests of Mixing. For the estimates of project survival to be valid, the detection data need to conform to the assumptions of statistical model (8). One assumption was the downstream mixing of release groups. Chi-square R × C contingency tables were used to test the assumption of homogeneous arrival distributions for the various paired-releases. The chi-square contingency table tests of homogeneity were of the form Release V2 Arrival Date

R2

1 2

 D


24

4.0

Results 4.1

Survival Effect of Tagger and Release Type

Fish in the release groups were evenly distributed across both tagger and release type (boat versus helicopter), with the exception of tagger 5 (Table 5). Tagger 5 was omitted from the analysis assessing tagger effects. Without tagger 5, chi-square tests found good mixing among tagger and release type for both the Wanapum release (P = 0.7974) and the Priest Rapids release (P = 0.9005). Table 5.

Tagger 1 2 3 4 5 Total Tags

Number of subyearling fall Chinook salmon tagged at each release site by tagger and release type in 2009. Wanapum Tailrace Boat Helicopter 43 48 55 50 48 54 52 48 1 0 199 200

Priest Rapids Tailrace Boat Helicopter 13 14 12 14 13 10 13 13 0 0 51 51

Total Tags 118 131 125 126 1 501

Survival to Vernita Bridge below the Priest Rapids Dam was estimated for both release groups by tagger and release type both jointly (Table 6) and individually (Tables 7 and 8). No consistent evidence of a tagger or release type effect was found, so data were pooled across tagger and release type within each release group. Table 6.

Survival by tagger and release type for Wanapum and Priest Rapids tailrace releases to Vernita Bridge. Standard errors in parentheses. Values of 1.0000 are unadjusted for tag failure. Release Type Boat

Helicopter

Tagger 1 2 3 4 1 2 3 4

Wanapum Tailrace 0.6940 (0.0741) 0.8297 (0.0573) 0.8164 (0.0615) 0.7692 (0.0584) 0.7961 (0.0637) 0.8252 (0.0594) 0.7252 (0.0648) 0.7327 (0.0688)

Priest Rapids Tailrace 1.0000 (0.0124) 1.0000 (0.0129) 1.0000 (0.0124) 1.0000 (0.0124) 1.0000 (0.0119) 1.0000 (0.0119) 1.0000 (0.0141) 0.9447 (0.0763)


25

Table 7.

Survival by tagger for Wanapum and Priest Rapids tailrace releases to Vernita Bridge. Standard errors in parentheses. Values of 1.0000 are unadjusted for tag failure. Tagger 1 2 3 4

Table 8.

Priest Rapids Tailrace 1.0000 (0.0086) 1.0000 (0.0088) 1.0000 (0.0093) 0.9841 (0.0399)

Survival by release for Wanapum and Priest Rapids tailrace releases to Vernita Bridge. Standard errors in parentheses. Release Type

4.2

Wanapum Tailrace 0.7478 (0.0493) 0.8278 (0.0421) 0.7681 (0.0457) 0.7639 (0.0466)

Wanapum Tailrace

Priest Rapids Tailrace

Boat

0.7874 (0.0331)

1.0000 (0.0063)

Helicopter

0.7690 (0.0337)

1.0000 (0.0158)

Tag Life Adjustment

Two tags in the tag-life study failed before day 70, and tag-life data were truncated after day 85 (Figure 13). Inspection of the tag-failure data found that the three-parameter Weibull distribution fit the curve well. The Weibull distribution was used for tag-life adjustments to survival estimates.

Figure 13.

Observed tag failure times from the tag-life study and fitted three-parameter Weibull curve. © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

26

Comparison of arrival timing of the release groups to the fitted tag survivorship curve shows that some tag failure had occurred by the time of smolt arrival at the downstream reaches (Figure 14). Thus, survival estimates were adjusted for tag failure. However, the estimated probability of having an active acoustic tag upon arrival at the different detection sites was consistently high,  = 0.0138) at the last receiver at Hanford Town for fish from the ranging from 0.9690 ( SE Wanapum release to 0.9772 (0.0102) at Beverly for fish from the Wanapum release (Table 9). Thus, the adjustments to the survival estimates were generally small.

(a) Arrival distribution at Beverly

(b) Arrival distribution at Lake Geneva

Figure 14.

Three-parameter Weibull survivorship curve for tag life versus timing of downstream detections of subyearling fall Chinook salmon smolts at (a) Beverly, (b) Lake Geneva, (c) Priest Rapids BRZ, (d) Vernita Bridge, and (e) Hanford Town. © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

27

(c) Arrival distribution at Priest Rapids BRZ

(d) Arrival distribution at Vernita Bridge

Figure 14 (cont).

Three-parameter Weibull survivorship curve for tag life versus timing of downstream detections of subyearling fall Chinook salmon smolts at (a) Beverly, (b) Lake Geneva, (c) Priest Rapids BRZ, (d) Vernita Bridge, and (e) Hanford Town.


28

(e) Arrival distribution at Hanford Town

Figure 14 (cont). Three-parameter Weibull survivorship curve for tag life versus timing of downstream detections of subyearling fall Chinook salmon smolts at (a) Beverly, (b) Lake Geneva, (c) Priest Rapids BRZ, (d) Vernita Bridge, and (e) Hanford Town. Table 9.

Estimated probabilities of an acoustic tag being active when a subyearling fall Chinook salmon smolt arrived at the detection locations for releases from Wanapum and Priest Rapids tailrace, and for the virtual release in the Priest Rapids forebay (BRZ). Standard errors in parentheses. Release Location

Detection Location

Wanapum Tailrace

Priest Rapids BRZ (virtual release)


Beverly

0.9772 (0.0102)

Lake Geneva

0.9769 (0.0103)

Priest Rapids forebay

0.9714 (0.0127)

Vernita Bridge

0.9696 (0.0135)

0.9699 (0.0133)

0.9771 (0.0106)

Hanford Town

0.9690 (0.0138)

0.9691 (0.0136)

0.9766 (0.0108)


29

4.3

Arrival Distributions and Mixing of Paired Releases

Inspection of the arrival distributions indicates that Wanapum and Priest Rapids tailrace releases arrived at Vernita Bridge at approximately the same time (Figure 15), although the Wanapum arrival distribution has a longer tail. The Wanapum tailrace release arrived at Hanford Town about 1.5 d after arrival of the Priest Rapids tailrace release (Figure 16).

Figure 15.

Arrival distribution of Wanapum and Priest Rapids tailrace releases at Vernita Bridge. Day 0 = day of release.


30

Figure 16.

4.4

Arrival distribution of Wanapum and Priest Rapids tailrace releases at Hanford Town. Day 0 = day of release. Survival Past Priest Rapids Dam

Detection probabilities were high with the autonomous acoustic receivers deployed as arrays. Detection probabilities were very high (over 99%) on the Beverly and Vernita arrays and slightly lower (about 90%) in areas where the reservoir was relatively wide near Lake Geneva and in the Priest Rapids Dam forebay (Table 10). Table 10.

Estimated detection probabilities at survival gates between the Wanapum tailrace and Hanford Town. Estimates were adjusted for tag failure. Detection Site Beverly Lake Geneva Priest Rapids BRZ Vernita Bridge

Detection Probability Estimate 0.9950 0.8980 0.9157 0.9955

Standard Error 0.0035 0.0173 0.0158 0.0044

A virtual release (N = 300) of Wanapum tailrace fish was identified by detection on the acoustic receiver line PRP3 located at the BRZ in the Priest Rapids forebay. This release was paired with the release (N = 102) made in the Priest Rapids tailrace. Capture histories at Vernita Bridge and Hanford Town (Table 11) were used to estimate dam passage survival at Priest Rapids using the paired release-recapture model. Estimates were adjusted for tag failure. Survival of the Priest  = 0.0211), and survival of the Rapids forebay release group to Vernita Bridge was 0.9428 ( SE Priest Rapids tailrace release group to Vernita Bridge was 1.0000 (0.0064) (Table 12). With 100% survival of the Priest Rapids tailrace release group to Vernita Bridge, there is no indication © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

31

that the downstream release group experienced post-release handling mortality. The estimate of survival from the Priest Rapids BRZ to the Priest Rapids tailrace was 0.9428 (0.0219). Table 11.

Capture histories for Priest Rapids BRZ and tailrace releases of subyearling fall Chinook salmon smolts at Vernita Bridge and Hanford Town in 2009. The 1 denotes detection; 0 denotes not detected. Detection History Release

11

01

10

00

Total

Priest Rapids BRZ

205

1

68

26

300

Priest Rapids tailrace

77

0

24

1

102

Table 12.

Estimated survival of Priest Rapids BRZ virtual release and Priest Rapids tailrace release to Vernita Bridge, and estimated survival past Priest Rapids Dam (forebay to tailrace). Estimates were adjusted for tag failure. Survival Release

Standard error

To Vernita Bridge

Priest Rapids BRZ (virtual)

0.9428

0.0211

Priest Rapids tailrace

1.0000

0.0064

Past Priest Rapids Dam 0.9428

4.5

0.0219

Reach Survival in Priest Rapids Pool

Capture histories from the Wanapum tailrace release group (N = 399) were used to estimate reach survival in Priest Rapids Pool (Beverly to Priest Rapids BRZ). Survival was estimated for the reaches from Beverly to Lake Geneva, and from Lake Geneva to the Priest Rapids BRZ (Table 13). In addition, the overall survival from Beverly to the Priest Rapids BRZ was estimated. Because fish arrived at the detection sites after the onset of tag failure (Figure 14), estimates of survival were adjusted for tag failure. Estimated survival from Beverly to Priest  = 0.0198), and estimated survival from Beverly to Vernita Bridge Rapids BRZ was 0.8319 ( SE was 0.7623 (0.0220) (Table 13). Survival from Wanapum tailrace to Beverly was estimated to be 1.0000 (0.0012), giving no indication of post-release handling mortality.


32

Table 13.

Estimated survival of the Wanapum tailrace release through reaches within the Priest Rapids Pool and through the Priest Rapids Project. PR BRZ = Priest Rapids forebay boat restriction zone. PR tailrace = Priest Rapids tailrace (Vernita Bridge). Estimates were adjusted for tag failure. Reach

4.6

Survival Estimate

Standard Error

Beverly to Lake Geneva

0.9871

0.0109

Lake Geneva to PR BRZ

0.8424

0.0206

Beverly to PR BRZ

0.8319

0.0198

PR BRZ to PR tailrace

0.9186

0.0160

Beverly to PR tailrace

0.7623

0.0220

Wanapum tailrace to Beverly

1.0000

0.0012

Wanapum tailrace to PR BRZ

0.8475

0.0231

Wanapum tailrace to PR tailrace

0.7764

0.0247

Fate Assessment in Priest Rapids Pool

The unadjusted estimate of mortality of subyearling fall Chinook salmon smolts in Priest Rapids  = 0.0198), equivalent to Pool between Beverly and Priest Rapids forebay (BRZ) was 0.1681 ( SE the complement of the estimated survival from Beverly to Priest Rapids forebay. In the presence of migratory delay in the pool throughout the detection period, this mortality estimate will be positively biased and include the probability of migratory delay. The last acoustic detection on the hydrophones at the survival gates used to estimate survival occurred on 18 July 2009, which was day 48 after tag activation and day 34 after release. Any fish that delayed within the pool and survived through this 34-day detection period will mistakenly contribute to the preliminary mortality estimate. Detections from the intrareach receivers were used to estimate the abundance of live tagged smolts present in the Priest Rapids Pool at the end of the detection period. Two temporal samples of intrareach receivers were taken at the end of the detection period. Three sampling scenarios were considered, using 6-hr and 24-hr sampling periods on 17 July and 18 July 2009, the final day of the detection period (Scenarios 1–3, Table 14). For each scenario, only a single fish was detected in either sample (Table 14). This fish was determined to be alive based on the movement patterns. With only one fish detected, we were unable to estimate abundance of live fish from the intrareach receiver samples taken at the end of the detection period. To estimate the detection probability of the intrareach receivers, additional temporal samples were taken at earlier times during the detection period, when fish were known to be present in the pool. The sampling scenarios varied in the length of each temporal sample (2 hr versus 6 hr) and in the length of the gap between the samples (2–18 hr) (Scenarios 4–8, Table 14). For each of these early sampling scenarios, the intrareach receiver detection probability was estimated ( Pˆ ) and used to estimate the abundance of delaying fish ( Nˆ ) present in the pool on © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

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18 July 2009, the joint probability of delay and survival in the pool throughout the detection period (ψˆ ), and the probability of mortality in the pool during the detection period ( µˆ ). For the five early intrareach receiver sampling scenarios, the probability of detection ranged from Pˆ = 0.3900 to 0.9478, resulting in estimates of abundance of live delaying fish on 18 July 2009 ranging from Nˆ = 1.0551 to 2.5641 (Table 14). These abundance estimates resulted in estimates of the joint probability of delay and survival ranging from ψˆ = 0.0027 to 0.0065 and estimates of mortality ranging from µˆ = 0.1616 to 0.1654 (Table 14). The overall probability of migrating successfully out of the study area or remaining alive in the reach was then calculated  = 0.0109). to be at least 0.9898 and, at most 0.9936 ( SE Table 14.

Alternative scenarios (day, hours) used for sampling intrareach receiver detections, the number detected in the combined samples, and estimates of intrareach receiver detection probability ( Pˆ ), number of tagged fish present on 18 July 2009 ( Nˆ ), joint probability of delay and survival to 18 July (ψˆ ), and probability of mortality ( µˆ ) between Beverly and Priest Rapids BRZ before 18 July. Number Detected

Pˆ

Nˆ

ψˆ

µˆ

1

NA

NA

NA

NA

18 July, 1800–2400

1

NA

NA

NA

NA

18 July, 0000–2400

1

NA

NA

NA

NA

Scenario

Sample 1

Sample 2

1

17 July, 0600–1200

18 July, 0600–1200

2

18 July, 0600–1200

3

17 July, 0000–2400

4

23 June, 0600–1200

24 June, 0600–1200

38

0.7308

1.3684

0.0035

0.1646

5

24 June, 0600–1200

24 June, 1800–2400

45

0.7500

1.3333

0.0034

0.1647

6

17 June, 0600–1200

18 June, 0600–1200

139

0.3900

2.5641

0.0065

0.1616

7

18 June, 0600–1200

18 June, 1800–2400

156

0.7933

1.2606

0.0032

0.1649

8

16 June, 2000–2200

17 June, 0000–0200

384

0.9478

1.0551

0.0027

0.1654

4.7

Travel Time

For the Wanapum tailrace release group, average travel time through the reaches ranged from  = 0.0013), or approximately 1.8 hr, from the Wanapum tailrace release site to the 0.0760 day ( SE survival gate at Beverly, to 1.8470 day (0.0640) from the Lake Genera survival gate to the Priest Rapids forebay (BRZ) (Table 15). Average travel time from the Priest Rapids BRZ to Vernita Bridge in the Priest Rapids tailrace was 0.1768 day (0.0065), or approximately 4.2 hr. For the Priest Rapids tailrace release group, average travel time was 0.0665 day (0.0013) (1.6 hr) to Vernita Bridge and 0.2781 day (0.0046) (6.67 hr) from Vernita Bridge to Hanford Town (Table 15).


34

Table 15.

Average travel times in days (harmonic mean) through each reach for fish released in Wanapum tailrace and in Priest Rapids tailrace. Standard error and number of observations in parentheses. Release Location Reach

Wanapum Tailrace


Wanapum tailrace to Beverly

0.0760 (0.0013; n = 394)

––

Beverly to Lake Geneva

0.1571 (0.0018; n = 354)

––

Lake Geneva to Priest Rapids forebay

1.8470 (0.0640; n = 270)

––

PR forebay to Vernita Bridge

0.1768 (0.0065; n = 273)

––

PR tailrace to Vernita Bridge Vernita Bridge to Hanford Town

0.0665 (0.0013; n = 101) 0.4752 (0.0012; n = 222)

0.2781 (0.0046; n = 77)


35

5.0

Discussion 5.1

Travel Time

Travel rates (i.e., speed) of emigrating subyearling Chinook salmon in this study slowed between the release in the Wanapum Dam tailrace to Priest Rapids Dam forebay. This pattern of decreased travel rates of subyearling Chinook salmon as they move from a free-flowing environment into impounded water also occurs for juvenile salmon in other reservoirs (Venditti et al. 2000; Tiffan et al. 2009a, 2009b). Mean travel rates of subyearling Chinook salmon in this study, calculated from travel time data presented in the results, decreased from 71.1 km/day immediately after release in the Wanapum Dam tailrace to 6.6 km/day in the Priest Rapids Dam forebay. Similarly, median travel rates (calculated from travel times) of subyearling Chinook salmon tagged for a different study in 2008 through Priest Rapids Pool decreased from 80.6 km/day immediately after release in the Wanapum tailrace to 3.8 km/day in the Priest Rapids Dam forebay (Sullivan et al. 2008). Other studies also have observed this relationship between subyearling Chinook salmon travel rate and river and reservoir sections. In Little Goose Reservoir on the Snake River, median travel rates of subyearling Chinook salmon declined from 26.0 km/day in the Lower Granite Dam tailrace to 0.8 km/day in the Little Goose Dam forebay (Venditti et al. 2000). Further, subyearling Chinook salmon travel rates varied from 64.8 to 127.7 km/day upstream of Lower Granite Reservoir in the free-flowing Hells Canyon reach of the Snake River to a slower 8.7 to 27.5 km/day in the downstream half of Lower Granite Reservoir (Tiffan et al. 2009b). The decrease in travel rates as fish approach a dam may be deleterious if fish cannot pass the dam; however, subyearlings in Priest Rapids Pool showed little evidence of significant delay in the forebay and had relatively high probabilities of migrating and surviving through Priest Rapids Dam. 5.2

Effect of Migration Delay on Survival Probabilities

This study marked the second implementation of the modified single-release recapture methodology to adjust mortality estimates for migratory delay (Buchanan et al. 2009). In this instance, the estimate of the probability of delay through the end of the 34-day detection period was less than 0.01. This is considerably less than the probability of delay (0.106 through 8 weeks) estimated for subyearling fall Chinook salmon in Lower Monumental Reservoir in 2007 (McMichael et al. 2008). The low estimated delay probability in Priest Rapids Pool is based on the lack of detections on the intrareach receivers at the end of the detection period. Only a single fish was detected in the study area at the end of the detection period, and it was subsequently detected downstream. Thus, it appears that essentially no subyearling fall Chinook salmon delayed in the study area throughout the entire 34-day detection period. The low delay probability is supported by the short travel times and high estimate of the probability of migration and survival to Priest Rapids forebay (0.8320). This pattern was very different from the 2007 migration pattern of subyearling fall Chinook in Lower Monumental Reservoir on the Snake River, in which migratory delay and mortality together accounted for nearly 64% of the fish entering the reservoir (McMichael et al. 2008; Buchanan et al. 2009). Fate assessment in the study area depends in part on the decision rule used to distinguish between live and dead fish among the intrareach receiver detections. This decision rule identifies live fish based on the maximum temporal “gap” between detection events and the © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

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maximum “duration” of detection events for live fish. The maximum gap and duration values found for live fish were considerably higher in this study than in the Lower Monumental study (e.g., maximum gap = 21.4 hr versus 6.4 hr). It is possible that in the Priest Rapids study, signals from drifting tags from dead fish were classified as coming from live fish, resulting in skewed gap and duration distributions for supposed live fish. However, for this study there was no impact of the decision rule because only a single fish was detected on the intrareach receivers at the end of the detection period, and this fish was subsequently detected downstream of the study area. Therefore, using a different decision rule would not have changed the study results. Nevertheless, it may be worthwhile to reconsider the decision rule for future studies. Tagged subyearling Chinook salmon released for the current study travelled quickly, had relatively high probabilities of migrating and surviving, and had a low probability of migration delay in Priest Rapids Pool, indicating that fish did not exhibit the reservoir-type life history. However, these fish were released relatively early in the emigration period as compared to the timing of subyearling passage at McNary Dam (Figure 17; FPC 2009). Subyearlings in the current study passed Priest Rapids Dam from mid-June to early July which coincided with the early part of the subyearling Chinook salmon emigration past McNary Dam from early June to late July (FPC 2009). Early- and mid-season juvenile fall Chinook salmon migrants are generally considered to emigrate faster than late-season emigrants and are less likely to delay their migration within reservoirs than late-season emigrants in the mid-Columbia River (Tiffan et al. 2000; McComas et al. 2007, 2008) and Snake River (Connor et al. 2002, 2005; McMichael et al. 2008; Tiffan et al. 2009a). The relatively high probability of subyearling Chinook salmon delaying in the Lower Monumental Reservoir study (0.106) versus the current study (0.01) may be due to the relatively late release (i.e., August–October) of subyearlings in that study, whereas fish were released for the current study almost two months earlier. Consequently, it is possible that later-migrating fish through Priest Rapids Pool may have a higher probability of migration delay, which would affect the probabilities of migrating and surviving by overestimating the proportion of fish that are considered mortalities (Buchanan et al. 2009). Releasing study fish throughout the entire migration period in Priest Rapids Pool would allow for calculation of migration delay throughout the entire migration season. The use of hatchery fish also potentially biases migration delay probabilities in this study because hatchery fish behavior may not be representative of run-of-river and/or wild fish. Performing this study with in-river fish would allow more applicability of the results to run-of-river and wild individuals. However, natural fall Chinook salmon production upstream of the Priest Rapids Project is limited (McMichael et al. 2004a).


37

Smolt Index

350000 300000 250000 200000 150000 100000 50000 0

Date (2009)

Figure 17.

5.3

Passage index of subyearling Chinook salmon passing McNary Dam on the Columbia River, Washington–Oregon, 2009. The shaded area indicates the mean estimated dates of passage of fish released for the current study. Tagging and Handling Effect

One of the assumptions necessary in estimating the joint probability of migration and survival using acoustic transmitters is that the surgical procedure and implanted tag do not affect the survival or behavior of the study fish. Research on the effects of surgical procedures and implanted transmitters on subyearling Chinook salmon has shown that JSATS transmitters can be implanted in subyearlings as small as 95 mm fork length and with a tag burden up to 6.7% without effects on survival (Brown et al. in press). Ongoing research at Battelle for the U.S. Army Corps of Engineers is intended to improve the methods used in JSATS transmitter implantation and to produce a standardized implantation protocol to minimize the effects of surgery on study fish. This research directly influenced the surgical methods that were used in the current study. High survival of fish during the 15-day recovery period before release and relatively high survival probabilities after release in the Wanapum and Priest Rapids tailraces verify that there was little effect of the transmitter on fish survival. In paired release dam passage survival studies in which tagging or handling effects are associated with release downstream of a dam, the direction of the bias will be positive in the survival estimate, often resulting in survival estimates exceeding100%. In the current 2009 JSATS pilot study, the fish released in the Priest Rapids Dam tailrace had an estimated survival of 100% to the Vernita Bridge array, indicating no tagging or handling effects and an unbiased estimate of survival for fish passing Priest Rapids Dam. Current research aims to improve our surgery protocols by understanding the mechanisms of wound healing to minimize tissue irritation (e.g., by choosing the best suture material, incision location, and suturing techniques; Deters et al. in press) and to determine optimal procedures for storing and using anesthesia (PNNL unpublished data). Fourteen days following surgery, monofilament suture material (Monocryl manufactured by Ethicon) had high suture and tag retention, and incisions were more healed than 7 days following surgery (Deters et al. in press). © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

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Other data also indicate that incisions of juvenile Chinook salmon held at 20°C are partially healed 14 days following surgery and are completely healed 28 days following surgery (PNNL unpublished data). Holding study fish until advanced healing occurs would be ideal in minimizing the chance of tag loss. However, 28 days of holding also would allow significant growth and a resulting size range that would be skewed toward larger individuals compared to the run at large. This would reduce the applicability of results to run-of-river fish and would add an assumption that may not be reasonably justified. Thus, we believe that the 15-day holding period of study fish following surgery was sufficient to ensure that transmitters remained in study fish during their emigration and also that size of study fish was more representative of the run-at-large at the time of release. The post-tagging recovery period in this study (15 days) was within the range used in previous PIT-tag survival studies of subyearling Chinook salmon in the Priest Rapids Project (3 to 30 days; McMichael et al. 2004b). To minimize effects of handling on fish when they were transferred into transport/release tanks, fish were not measured and weighed. Therefore, the only size data we collected on these fish were collected at the time of tagging. It is likely that fish grew in the 15 days between tagging and release. Based on previous data (McMichael et al. 2004b), we suspect that the fish were an average of approximately 10 mm longer at the time of their release than they were at the time of tagging. Detections of acoustic-tagged subyearling Chinook salmon released for the current study in the Wanapum and Priest Rapids dam tailraces as they migrated through the lower Columbia River, estuary and out into the plume indicated there was no evidence of delayed tag/tagging effects (Appendix C). 5.4

Helicopter versus Boat Releases

Experiments to determine the comparability of helicopter- and boat-released fish generally indicate that physical conditions during release were similar for helicopter and boat releases. Dissolved oxygen and temperature were usually similar between helicopter and boat release tanks. Total dissolved gas within helicopter release tanks before and during helicopter transport was either slightly higher or lower than boat release tanks. However, the boat release tank for the Priest Rapids tailrace release contained total dissolved gas levels that exceeded 120%, which may have been harmful to fish because compensation depths were not available in the release tanks. However, post-release survival of this group was 100% to Vernita Bridge. Although the exact cause of the high TDG values was not determined, it is likely that water input to the release tank during flow-through exchange at Priest Rapids Dam to reduce tank temperature may have caused the TDG increase. Examination of this water source to determine if it caused high TDG within the release tank is recommended before further use. Further, although the probabilities of migration and survival did not differ between helicopter and boat releases, the mean survival rate was lower for helicopter releases than for boat releases. Sample sizes may not have been sufficient (i.e., with high statistical power) to detect differences between the helicopter and boat releases, and thus a difference in survival rates may have been found if larger sample sizes were used. Thus, until more definitive data are available, we caution the use of helicopter releases and recommend that fish be released by boat. 5.5

Conclusions

Battelle’s application of the JSATS technology worked very well in this pilot study of juvenile fall Chinook salmon behavior and survival in Priest Rapids Pool. The delayed-start transmitters developed for this project, combined with the 15-day post-tagging recovery period, appeared to © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

39

work very well to produce actively migrating subyearling Chinook salmon. Autonomous acoustic receiver arrays were efficiently deployed and serviced, produced very high detection probabilities, and proved to be extremely reliable (i.e., no data gaps). Previous PIT-tagging survival studies have also used similar fish source and tagging, recovery, release approaches with good success. In comparison to previous studies of subyearling Chinook salmon survival using PIT tags (McMichael et al. 2004b), the JSATS acoustic-tagged fish performed as well or better. The mean 2001–2003 Priest Rapids Pool survival estimates based on PIT tags ranged from 0.77 to 0.89 and averaged 0.82 in comparison to the JSATS-derived pool survival estimate of 0.83 in 2009. In addition, the estimated mean survival through Priest Rapids Dam based on PIT-tag studies between 2001 and 2003 ranged from 0.80 to 0.94 and averaged 0.89, while the JSATS Priest Rapids Dam survival estimate from the 2009 study was 0.94. The standard error estimates of these survival estimates were comparable even though much smaller numbers of tagged fish were released in the 2009 JSATS pilot study (total N = 501) than in the previous PIT tag survival studies (total N range 29,400–79,905). Previous PITtag survival studies released an average of more than 100 times as many fish as the JSATS study in 2009. The high detection probabilities, lower sample size requirements, ability to easily deploy and maintain reliable autonomous receiver arrays in any location of interest, and the rapid turnaround time on data analyses and reporting are advantages of the JSATS over PIT-tag or other active telemetry systems.


40

6.0

Recommendations

The following list of recommendations is intended to improve the study design if future efforts are planned to address the fate determination of subyearling Chinook salmon migrating through the Priest Rapids Project. • Continue to implant only a JSATS transmitter, rather than a PIT tag and transmitter, to minimize the potential for tag burden effects on fish behavior. • Evaluate predation potential on subyearlings in the stretch from Lake Geneva to Priest Rapids Dam forebay. The Lake Geneva area is hypothesized to contain a large predator population and may significantly decrease survival rates of subyearlings passing through this reach. Predator diets (e.g., of smallmouth bass Micropterus dolomieu, northern pikeminnow Ptychocheilus oregonensis, or walleye Sander vitreus) could be specifically evaluated by removal of gut contents by gastric lavage or using a stable isotope analysis. Gastric lavage is useful in determining what a predator consumed within the last few hours; however, a more comprehensive view of diet in the short- to mid-term range (i.e., days to weeks) could be determined by analyzing stable isotope ratios of predators and prey. The extent of predation on subyearlings in the Lake Geneva area could then be compared to other reaches within Priest Rapids Pool to estimate the proportion of mortality that occurs from fish predation and if management actions to control predation are necessary. • Tag predator fish in the Priest Rapids Pool, particularly in the lower half of the reservoir, with JSATS transmitters to elucidate spatial and temporal relationships with emigrating subyearling fall Chinook salmon. This combination of the stable isotope and/or gut contents analyses would increase understanding of the fate of fish that fail to survive to the Priest Rapids Dam forebay (17% in this study) and potentially help to identify management actions to reduce losses in this area. • Evaluate avian predation using radio telemetry technology. Juvenile fall Chinook salmon implanted with radio transmitters that are removed from the water could be detected by fixed radio telemetry stations, indicating that an avian predator (e.g., Caspian tern Sterna caspia) had removed a tagged fish from the water. An estimate of the effect of avian predation could then be used to further differentiate mortality sources and explore management options. • Evaluate whether migration delay is occurring in later-migrating fish. Release subyearlings implanted with JSATS transmitters throughout the emigration period, with JSATS receiver deployment similar to 2009. Although fish did not exhibit migration delay during this study, it is possible that later-emigrating fish may be more likely to delay and, consequently, contribute to an overestimate of mortality. The information gathered would be used to account for the effect of delay on survival estimates. • Evaluate hatchery-wild differences. The use of hatchery fish for the pilot study in 2009 presents a potential bias because hatchery fish may not behave similarly to wild fish or run-of-river fish (i.e., fish already acclimated to river environment). Use of wild or runof-river fish in future efforts would improve the applicability of results to naturally produced fall Chinook salmon produced within or upstream of the Priest Rapids Project. © 2010, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS.

41

A comparative study of movement and survival of hatchery-origin versus natural-origin subyearling fall Chinook salmon would be useful in determining whether hatchery fish are suitable surrogates for wild fish in this area. However, we understand that there are logistical, sample size, and fish health constraints related to the collection of naturally produced fall Chinook salmon within the study area. • Evaluate pre-release holding times. Fish moved very quickly through the first reach after release, whether they were released in the Wanapum tailrace or the Priest Rapids tailrace. It is possible that subyearlings traveled faster downstream than they would have if they had not been held for 2 weeks before release. Thus, applicability of the delay probability (