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Assessment of Chinook and Coho Smolt / Fry Migration at the Puntledge Diversion Dam Eicher Fish Screens

2011

11.Pun.04

Prepared for:

Comox Valley Project Watershed Society PO Box 3007

Courtenay, BC V9N 5N3

Prepared by:

E. Guimond 1 and J.A. Taylor 2

Prepared with financial support of:

Fish and Wildlife Compensation Program on behalf of its program partners BC Hydro,

the Province of B.C. and Fisheries and Oceans Canada

June 2012

1 E. Guimond 473 Leighton Ave. Courtenay, BC V9N 2Z5 [email protected]

2 J.A. Taylor and Associates Ltd 11409 Sycamore Dr. Sidney, B.C. V8L 5J9 [email protected]

Puntledge River Eicher Screen Assessment 2011 11.PUN.04

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EXECUTIVE SUMMARY

In light of knowledge acquired over the past decade on the migration behaviour of Puntledge River summer Chinook salmon, Fisheries and Oceans Canada (DFO) have begun implementing changes to their production strategy for both wild and hatchery summer Chinook and coho salmon. Summer Chinook hatchery smolts will be imprinted and released in Comox Lake to encourage adult returns back to the lake where they will have greater survival success. Similarly, coho fry will also be released in the upper watershed which provides an abundance of high quality spawning and rearing habitat for this species. The success of this strategy is dependent on the safe passage of juveniles to the estuary during their downstream migration past the diversion dam.

The primary objectives of the 2011 Assessment of Chinook and Coho Smolt / Fry Migration at the Puntledge Diversion Dam Eicher Fish Screens were to:

i. Determine the efficiency of the Eicher screen (in Intake #4) which diverts

juvenile fish away from the turbines. ii. Estimate the differential entrainment of coho smolts between the two

intakes at the penstock (i.e. Intake #4 vs. Intake #3). iii. Determine the timing and estimate the numbers of wild Chinook and

hatchery coho and Chinook lake releases from the upper watershed (above the diversion dam).

iv. Determine diurnal migration patterns during different flows and stages of migration.

Fish sampling was conducted at the Eicher Evaluation facility from May 2 to July 29, 2011 and from October 6 to December 10, 2011. The facility allows diverted fish from one of two Eicher screens below the penstock intakes to be counted and analyzed before they are returned to the river. Batches of marked hatchery Chinook and wild coho smolts were released at two locations during the study: 1) directly into the penstock immediately upstream of Eicher Screen #2 through a new fish delivery pipe, and 2) approximately 500 m upstream of the diversion dam in the headpond.

The efficiency of the Eicher screens to divert juvenile fish from becoming entrained in the turbine was calculated at 95.6% (range 90% - 100%) for coho and 89.2% (range 86.2% – 96.6%) for Chinook smolts.

Proportional entrainment, or the percentage of juveniles entrained in each penstock intake, was determined through the use of Radio Frequency Identification (RFID) technology. Fish implanted with passive integrated transponder (PIT) tags were


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enumerated by detection arrays (antennas) that monitored the outfall from Intake #3 as well as the assessment facility (Intake #4). Under maximum generation (i.e. penstock discharge ~26 m3/s) and when river discharge ranged from 31.9 to 36.4 m3/s in Reach B, the proportion of fish that were entrained by Intake #3 was significantly higher to that by Intake #4 (57.5% versus 42.5% respectively; z = 4.25 p =


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TABLE OF CONTENTS

Executive Summary......................................................................................................... ii Table of Contents ............................................................................................................ iv List of Figures .................................................................................................................. v List of Tables .................................................................................................................... v List of Appendices............................................................................................................vi 1 INTRODUCTION .....................................................................................................1

1.1 Background..........................................................................................................2 1.2 Goals and Objectives...........................................................................................3

2 STUDY AREA ...........................................................................................................4 2.1 Eicher Fish Sceens...............................................................................................4 2.2 Evaluation Facility...............................................................................................7

3 METHODS.................................................................................................................8 3.1 Fish Catch Monitoring.........................................................................................8 3.2 Eicher Screen Efficiency Study Design ..............................................................9 3.3 Population Estimation Study Design.................................................................10

3.3.1 Calculation of mark releases ............................................................................. 10 3.3.2 Estimation method ............................................................................................ 12

3.4 Diurnal Migration..............................................................................................13 3.5 Proportional Entrainment ..................................................................................14

3.5.1 PIT Tag Application and Detection .................................................................. 15 3.5.2 Analysis............................................................................................................. 15

4 RESULTS.................................................................................................................16 4.1 Hydrologic Conditions ......................................................................................16 4.2 Eicher Screen Efficiency ...................................................................................18 4.3 Population Estimates .........................................................................................19

4.3.1 Population estimate for coded-wire tagged Chinook........................................ 22 4.3.2 Population estimate for adipose clipped coho................................................... 23 4.3.3 Biological Data ................................................................................................. 24

4.4 Bias ....................................................................................................................26 4.5 Diurnal Migration..............................................................................................33 4.6 Proportional Entrainment ..................................................................................35 4.7 Fall Juvenile Migration......................................................................................37

5 DISCUSSION...........................................................................................................40 6 RECOMMENDATIONS ........................................................................................41 7 ACKNOWLEDGEMENTS ....................................................................................42 8 REFERENCES ........................................................................................................43


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LIST OF FIGURES

Figure 1. Location map of the Puntledge River watershed and lower river features. ........5

Figure 2. Pathways for downstream migration of fry and smolts at the Puntledge diversion dam (from Bengeyfield 1995). ...........................................................................6

Figure 3. Schematic showing a top and sectional view of an Eicher screen inside a penstock..............................................................................................................................7

Figure 4. Puntledge River mean hourly discharge for the Comox dam sluice gates (CMC), penstock turbine flows (PUN G.S.) and Gauge 6 below the diversion dam (WSC Gauge No. 08HB084) for the period a) May 1 - July 31, 2011 and b) Oct. 1 – Dec. 11, 2011. Population estimate releases and diurnal migration assessment events are indicated with symbols. ....................................................................................................17

Figure 5. Daily movement of a) coho and b) Chinook juveniles through the evaluation facility. Numbers have been adjusted to account for fish that were marked and re-released upstream. ............................................................................................................20

Figure 6. Length frequency histograms for sub-samples of a) coho (1+ and 2+), b) Chinook (0+ hatchery releases and wild smolts) and c) sockeye/kokanee captured at the Eicher Assessment facility in 2011. .................................................................................25

Figure 7. Frequency distribution of population estimates for a) coho and b) Chinook, from a parametric bootstrap procedure involving 1,000 iterations. The superimposed curve illustrates departure from normality. ......................................................................27

Figure 8. Flow levels (bars) and recaptures of (a) marked coho and (b) Chinook (lines). Release dates are identified by red arrows. ......................................................................31

Figure 9. Catches of un-marked and marked coho in relation to flows............................32

Figure 10. Frequency of screen cleaning cycles for a two week period during peak smolt migration in 2010 when operating on a pressure triggered system. 1 indicates screens are in the closed “fishing” position; 0 indicates screens are in the open “cleaning” position...........................................................................................................................................38

Figure 11. Daily captures (all salmonids) at the Eicher evaluation facility from Oct-Dec 2011 with discharge. Duration of screen lock-out events are illustrated with red and green symbols at the top of the chart................................................................................39

LIST OF TABLES

Table 1. Numbers of coho and Chinook released in the Puntledge penstock during screen efficiency trials. The numbers recovered 2 hours after release and 24 hours after release, represent an absolute count (Wolf traps were fishing at 100%).......................................18


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Table 2. Marking and release timing, abundances and mark types for a) coho and b) Chinook. ...........................................................................................................................19

Table 3. Estimates of population size derived from recovery sampling by the Wolf trap a) coho, b) Chinook. Capture probabilities (trap efficiencies) are provided by release stratum. .............................................................................................................................21

Table 4. Length (mm), weight (grams) and Fulton’s condition factor (K) for sub-samples of coho and Chinook captured at the Eicher Assessment facility in 2011 and 2010. ......26

Table 5. Comparison of levels of precision for coho and Chinook population estimates, obtained form all temporal strata based on the normal approximation and bootstrapping. Bootstrap estimates were based on the hypergeometric distribution and 95% confidence intervals are provided in uncorrected and bias corrected form. Relative precision is assessed by the coefficient of variation (CV)...................................................................28

Table 6. Release and recovery of marked a) coho and b) Chinook juveniles, including capture probabilities, for concurrent flow levels. .............................................................30

Table 7. ANOVA comparing juvenile Chinook migration in 2010 and 2011 as rates of movement (number.hr-1) during 3 periods: Morning (04:00 – 10:00hrs), Daytime (10:00 – 22:00) and Nighttime (22:00 - 4:00). ............................................................................35

Table 8. Fate of PIT tags released above the penstock intakes in 5 trials. Totals for Intake #4 include antenna detections plus tags that were not detected but were physically recovered from the Wolf traps..........................................................................................36

Table 9. Total number and size range of salmonids captured at the Eicher Assessment facility, October – Dec 2011 at 69% fishing efficiency. ..................................................37

Table 10. Estimated time the Eicher fish screens were out of fishing position for regular cleaning and lock-outs, from October to December 10, 2011..........................................39

LIST OF APPENDICES

APPENDIX A - Numbers of juvenile coho and Chinook captured daily in the evaluation facility...............................................................................................................................46

APPENDIX B - FWCP Financial Statement....................................................................48

APPENDIX C - Performance Measures...........................................................................49

APPENDIX D - Confirmation of FWCP Recognition.....................................................50

APPENDIX E - Photos.....................................................................................................51

APPENDIX F - Fish delivery pipe for the Puntledge penstock. ......................................53


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1 INTRODUCTION

Access to and utilization of habitat above BC Hydro’s diversion dam is critical to the sustainability of summer Chinook and coho salmon production in the Puntledge watershed. Past studies on summer Chinook migration in the Puntledge River have indicated that summer Chinook adults that arrive in the lower Puntledge River prior to late-June have a greater success migrating to the upper river (at or above the diversion dam) compared to those that arrive later in the summer (95% versus 50% success rate). The success of early arriving fish is attributed to cooler migration temperatures in the river, low recreational use, and spring freshet spills that are more likely available to aid upstream Chinook migration into Comox Lake. In contrast, later arriving Chinook must contend with warmer river temperatures, lower flows, and a high level of disturbance from swimmers, particularly at Stotan and Nib falls, two areas that present some of the greatest challenges for migration. Studies have also shown that Chinook that are able to hold in the cooler depths of Comox Lake throughout the summer have a spawning success rate of 95% compared to ≤ 50% for fish that hold below the diversion dam (Guimond and Taylor 2009).

This clearly demonstrates that the most productive strategy for summer Chinook adults is to migrate into Comox Lake early, (i.e. before July), hold in the lake during the summer and then spawn above the diversion dam at the lake outlet (headpond) or in the two main Comox Lake tributaries (Upper Puntledge and Cruickshank rivers). Similarly for coho, Fisheries and Oceans Canada (DFO) estimates that there is an abundance of high quality spawning and rearing habitat in the upper Puntledge watershed for both coho adults and juveniles.

The Puntledge Hatchery Program has adopted these watershed species requirements into their own Production Strategy. DFO will begin to imprint and release summer Chinook hatchery smolts in Comox Lake. This will encourage the hatchery returns to migrate back to the lake where they will have the greatest chance of survival. A greater proportion of the earlier returning summer Chinook will be utilized for hatchery broodstock which is expected to re-build the earlier component of the summer Chinook returns thus improving migration success to the upper watershed. The hatchery will also avoid producing coho smolts which have to be reared during the summer under greater risk of disease outbreaks and mortality from high water temperatures, and instead, release coho fry into the upper watershed.

The success of any upper watershed production strategy is highly dependent on successful juvenile migration past the diversion dam. The primary goal of this study


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was to evaluate the current fish passage efficiency at the Eicher screens and determine whether they are operating at an acceptable level (i.e. >95%). This study also monitored coho and Chinook smolt migration timing and calculated population estimates for both juvenile coho and summer Chinook in the upper river (upstream of the diversion dam).

1.1 Background

In 1955, BC Hydro’s Puntledge River hydroelectric facility increased the diversion of streamflow to the penstock for power generation, from 8.57 m3/s to 28.34 m3/s (300 cfs to 1000 cfs). This resulted in a significant increase in the proportion of downstream migrating juveniles becoming entrained in the penstock, and a subsequent increase in juvenile mortality as they passed through the turbine at the power plant. Several years of trials using various behavioural devices to deter fish from entering the Puntledge River intakes did not result in a significant reduction in entrainment in the intakes (Bengeyfield and Smith 1989; Bengeyfield 1990). Finally in 1993, Eicher fish screens were installed at the Puntledge diversion dam after studies conducted on screens at the Elwha Dam near Port Angeles, WA indicated passage survival (diversion efficiency adjusted for 96-hr survival) was ≥ 98.7% for coho, Chinook and steelhead smolts (EPRI 1992).

Following installation of Eicher screens at the Puntledge diversion dam, a reduction in juvenile salmonid mortality from ~58% through the turbine to less than 1% by bypassing the turbine was reported (Bengeyfield 1995). Evaluations conducted at the Puntledge Eicher screens in 1993 and 1994 (Bengeyfield 1994 and 1995) determined the rates of direct and latent mortality on wild and hatchery juvenile salmonids moving past the screens but did not measure the diversion efficiency of the Eicher screens. These studies and other evaluations performed between 1996 and 2005 (Bengeyfield 1997; Addy 1999; Tryon 2008) also provided information on juvenile migration timing and patterns, population estimates and differential entrainment in the two penstock intakes.

BC Hydro has recently implemented new more stringent pressure protection limits to protect the aging woodstave penstock. BC Hydro staff have also observed increases in fouling of the screens. Proliferation of the freshwater diatom Didymosphenia geminata (Didymo) in the watershed may be a source of the problem. Both of these factors have likely impacted the overall performance of the Eicher screens, increasing significantly the frequency of cleaning cycles. If the screens do not self-clean (i.e. debris does not adequately flush off) the protection limit system locks-


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out the screens in the non-fishing (open) position until it can be manually reset by BC Hydro staff that must travel from Campbell River. BC Hydro has reported several incidences of lock-outs in recent years. During this period entrainment of juveniles through the penstock turbines is 100%. DFO is concerned that overall screen efficiency is now significantly lower and has been poorly estimated in past studies.

Of particular interest is the impact of the Eicher screens on the early migrating Chinook fry that emerge in the headpond. In 1994, Bengeyfield (1995) conducted an efficiency trial using chum fry (41-54 mm FL). Results indicated an overall mortality rate of 3.5%, though this value is likely underestimated. Observations made through the viewing ports in the penstock found that some of the fry disappeared completely through the screen, some became impinged on the face of the screen, or were seen sliding up the screen, often colliding with debris that was lodged in the screen (Bengeyfield 1995). The screens were originally designed to pass 37 mm (FL) Chinook salmon migrants, but they have never adequately been evaluated for Chinook fry at the Puntledge diversion dam due to the absence of adult Chinook spawning above the dam over the 10 year period after their installation. With the restoration of summer Chinook spawning habitat in the headpond in 2005, there has been consistent yearly use by Chinook spawners. Optimum efficiency of screen operation on small fish is now paramount.

1.2 Goals and Objectives

The assessment of Chinook and coho smolt / fry migration at the Puntledge diversion dam Eicher fish screens in 2011 encompassed 4 primary objectives:

i. Determine the efficiency of the Eicher screen (in Intake #4) which diverts juvenile fish away from the turbines.

ii. Estimate the differential entrainment of coho smolts between the two intakes at the penstock (i.e. Intake #4 vs. Intake #3).

iii. Determine the timing and estimate the numbers of wild Chinook and hatchery coho and Chinook lake releases from the upper watershed (above the diversion dam).

iv. Determine diurnal migration patterns during different flows and stages of migration.


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A secondary objective was to monitor migration from October to December. A record of fish captures versus time and discharge will provide a better understanding of migration behaviour during this period, and will help to assess the potential impacts of higher debris loads and greater cleaning frequency and possible lock-out of the screens on migrating fish at this time of year.

2 STUDY AREA

The Puntledge River Watershed encompasses a 600 km2 area west of the city of Courtenay (Figure 1). The lower Puntledge River flows from Comox Lake in a north-easterly direction for 14 km where it joins with the Tsolum River. From this point downstream the river is called the Courtenay River, and flows for another 2.9 km into the Strait of Georgia. BC Hydro operates an impoundment dam at the outlet of Comox Lake and a diversion dam 3.7 km downstream. A 5 km long penstock conveys water from the diversion dam to the Puntledge River Generating Station (Powerhouse) located 6.8 km upstream from the estuary.

2.1 Eicher Fish Sceens

Twin intakes at the diversion dam entrain a proportion of migrating fish from the upper river into two smaller penstocks, each equipped with an eliptical wedgewire Eicher screen oriented at 16.5 degrees to the flow in the penstock (Bengeyfield 1994). As fish approach the screen they are diverted into a bypass pipe located at the top of each penstock pipe and returned to the river downstream of the dam (Figure 2). Fish may also pass over the diversion dam during spill events, or through a small spillway adjacent the intakes (Figure 3).

The Eicher screens operate year round and can automatically rotate into a non-fishing position to remove debris on the screens. During these cleaning cycles, the screens are tilted to a horizontal position which allows the flow of water in the penstock to sweep the screens clean. During this cleaning phase, fish can be entrained into the turbines. BC Hydro can regulate the frequency of these cycles so that the screens will automatically rotate from the fishing position into the cleaning position every few hours for a duration of approximately 180 seconds per cycle. The screens can also be triggered to cycle out of the fishing position by a pressure sensing system, whereby debris build-up on the screens causes a change in pressure beyond specified limits.


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Figure 1. Location map of the Puntledge River watershed and lower river features.


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Figure 2. Pathways for downstream migration of fry and smolts at the Puntledge diversion dam (from Bengeyfield 1995).

When this threshold pressure protection limit is reached the screens move into a cleaning position. These limits are established to protect the aging woodstave penstock and prevent equipment damage from over pressurization (Tryon 2008).


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2.2 Evaluation Facility

The studies on coho and Chinook migration were conducted at the evaluation facility located at the diversion dam which was constructed in 1993 for assessing the Eicher screens after installation (Figure 3). Only one screen can be sampled by the evaluation facility at one time. Fish that reach Eicher screen # 1 (in Intake #3) are diverted into the bypass pipe and discharged directly to the river below the diversion dam. Fish in Intake #4 are conveyed from the bypass pipe into the Evaluation facility which consists of an energy dissipation chamber, wolf traps, collection tanks, evaluation tank, and a downwell and outfall pipe (Figure 3). Bypass flow enters the bottom of the dissipation chamber where velocity is reduced before spilling over an 8 ft wide stoplog weir. The elevation of the weir determines the bypass flow and therefore the sweeping velocity at the top of the Eicher screen.

TOP VIEW

SECTIONAL VIEW

Figure 3. Schematic showing a top and sectional view of an Eicher screen inside a penstock.


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Three Wolf traps constructed of aluminum and wedgewire screen were mounted along the crest of the stoplog weir to screen out fish and small debris into separate collection tanks. Each Wolf trap was 6.5 ft (2.0 m) long and 1.5 ft (0.45 m) wide and they were spaced along the weir with one at the centrepoint and the others approximately 8 in (0.2 m) from the right and left sides of the weir. Each trap could be vertically adjusted to control the delivery of water, fish and debris into the collection tanks. Water screened from the traps, and unscreened discharge flowing over the weir dropped into a downwell chamber and then flowed through a 2 ft (0.6 m) diameter pipe to the river

The collection tanks were accessed from inside a laboratory building where they could be individually drained into a rectangular evaluation tank for counting and analysis of the catch. Following biological sampling, fish could be returned directly to the river from inside the lab through a 4 in. (100 mm) diameter flex hose in the wall of the building, which conveyed fish to the downwell chamber. Refer to Bengeyfield (1995) for further details on the layout and operation of the evaluation facility.

3 METHODS 3.1 Fish Catch Monitoring

Catch monitoring was conducted daily from May 2 to July 29, 2011 and from October 6 to December 10, 2011 with a two man crew. Trap catches were inspected once per day in the morning, but up to four times per day during diurnal migration assessments. Captured fish were netted into shallow basins, identified to species, examined for marks and counted. Subsamples of the fish caught in the traps were periodically measured for length and weight. Fish were anaesthetized in small batches using Alka-Seltzer. Fork length (from tip of nose to fork in caudal fin) was measured to the nearest mm on a plastic measuring board and weight (to the nearest 0.1 gram) was measured using an Ohaus electronic balance (Scout® Pro).

In preparation for mark/recapture and efficiency trials requiring marked fish for release in the headpond or into the penstock, coho smolts that had been captured by the Wolf traps were retained in two 5 ft (1.5 m) diameter fibreglass rearing tanks located within the fenced compound at the evaluation facility. Water for the tanks was supplied from the dissipation chamber and each tank was covered with nylon shade cloth to deter predators and prevent fish from jumping out. Chinook smolts from Puntledge Hatchery


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were used for marked releases. Three to five days prior to the scheduled trial, a mark was applied to the required number of test fish in the tanks. Mutilation marks constituted the majority of marks applied: upper or lower caudal fin clip, right or left ventral fin clip. On a few occasions a Pan Jet dental inoculator (Herbinger et al. 1990) was used to apply a sub-dermal tattoo of Alcian Blue dye to the caudal fin (coho juveniles only). Extra crew were required for safety and/or procedural demands during marking and test fish releases.

3.2 Eicher Screen Efficiency Study Design

One of the key objectives of the 2011 studies was to determine the degree to which the Eicher screens successfully divert juvenile fish through the bypasses, thereby circumventing the turbines. In 2010 we were unable to obtain accurate data on the diversion efficiency due to the inability to introduce test fish directly into the penstock where they had no opportunity to swim back upstream into the forebay.

A new fish delivery system was installed on the penstock in April 2011 that could release adequate sample sizes of marked fish during the efficiency trials. Marked test fish were introduced directly into the penstock in small batches through a 3 inch (760 mm) diameter metal pipe (Appendix F). The pipe was attached to the penstock at an existing viewing port, approximately 25 m downstream of the intake opening at the forebay, and just upstream of the Eicher screen (Appendix E Photo 1). An absolute count of the recovered test fish by the Wolf traps, set at 100% trapping efficiency provided an accurate estimate of screen efficiency. This was accomplished using wooden panels that could be inserted between the Wolf traps along the weir to deflect all flow into the 3 Wolf traps, thus increasing trapping efficiency from 69% to 100%. The time required for fish to travel from the release location just upstream of the Eicher screen to the evaluation facility and into the Wolf traps was expected to be relatively short.

A minimum of 100 uniquely marked coho and 200 Chinook were used for each trial and a total of six trials were completed for each species on three different days. To ensure that efficiency tests were not compromised by a cleaning cycle, the Eicher screen was manually set to the fishing position and monitored during the trials by a BC Hydro electrician. Screens were returned to their original setting following the trials.


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3.3 Population Estimation Study Design

Estimation of the populations of juvenile coho and Chinook moving downstream past the diversion dam were made using the stratified mark/recapture design described by Carlson et al. (1998). The method requires the application of unique mark types within designated marking periods to provide an estimate of capture probability (trap efficiency) over time, so that variation in efficiency can be addressed within the assumption of reasonable consistency in strata. This approach requires temporal stratification such that each trap efficiency trial is discretely paired with one capture period.

The primary assumption of the method is that marked fish become fully integrated into the migrating population, so that consistent proportionality of marks is achieved. This was accomplished by dispersing fish across the width of the river channel from a canoe, approximately 500 m upstream of the intakes. In 2010 we tested the assumption that capture efficiency was not dependant on the release location for Chinook juveniles, by releasing individuals in mid-river and along the right and left banks and subsequently determining the proportions re-captured in the Wolf traps. There was no significant difference among release locations, so we can assume that the marked fish behave similarly to the wild migrants. Consequently, losses of fish past the capture point i.e. by spillage over the diversion dam and through the spillway opening beside the entrainment intakes, are expected to be proportional for marks and wild smolts. This, in turn, permits the deliberate alteration of trapping efficiency by the Wolf traps during Eicher screen efficiency testing, if necessary (see Sec 3.2).

The number of marks that were required to be released in order to achieve an appropriate level of accuracy for a desired degree of precision, was determined from the migration timing of coho and Chinook in the previous year of the program. The proportional rates of migration for coho and Chinook were used to generate the necessary parameters to calculate the required sample size for mark releases per stratum.

3.3.1 Calculation of mark releases

The 2010 study generated good probabilities of recapture for both coho (15.5% on average) and for Chinook (12.9% on average). Therefore we set these values as the predicted efficiency of the collection system, a combination of entrainment proportion and Wolf trap efficiency. We also planned to utilize the Wolf traps at 100% efficiency


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for as much of the study as possible, so that the overall prediction of efficiency would be an underestimate. Consequently, in order to achieve a population estimate (N) within 15% relative error with 95% confidence (α=0.05) calculation of the number of juveniles that would be required to be marked would be conservative.

As in 2010, the possibility of using captures in the Wolf traps, as well as hatchery raised juveniles suggested that juvenile numbers would not be a limiting factor in all but the initial and final strata. Therefore, the total relative error ( hr ) was set at ±15% for

95% precision.

a) Coho

Strata totals from the 2010 migration were used to estimate the proportion of the population encountered in each time period (φh): a total of 5 strata were anticipated for 2011, given a provisional migration duration of April to July. These were 6.8%, 37.7%, 34.2%, 9.3%, and 12.0%. The operating efficiency of 15.5% was assumed to be appropriate, as described above. Assuming a constant relative error (i.e.

Lrrr === ....21 ) then the expected stratum relative error ( tr ) was estimated to be 28%

from:

∑ =

=L

h h

th

rr

1

2φ (1)

and the number of marks required for release per stratum was calculated from:

)100(h

h eKM = (2)

where K is a constant described by the power function y=3E+6x-1.8893 constructed for α=0.05 from data given in Carlson et al. (1998). A minimum of 345 marked coho were then required for release in each stratum. b) Chinook

A total of 7 strata were anticipated for Chinook, comprising proportional migration levels 17.5%, 5.6%, 5.5%, 24.2%, 27.2%, 14.4% and 25.6%. The expected stratum relative error ( tr ) was estimated to be 35% in this case, and the minimum

number of marks was 260, for an overall capture efficiency of 13%.


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3.3.2 Estimation method

The common Petersen estimator for population size, incorporating the Chapman (1951) modification for small sample bias, was used to provide an estimate of the overall population, including marked smolts, from release catch and recapture data. This estimator compensates for the tendency of the simple Petersen to overestimate the true population, particularly at low sample sizes, but requires recaptures to exceed 7 in a given stratum (Robson and Regier 1964). Strata estimates are from:

1

)1)(1(ˆ+

++=

h

hhh m

MnN -1 (3)

where hN̂

= estimate of population size for stratum h hM = number of marked smolts in stratum h hn = number of smolts in the WOLF TRAP catch in stratum h hm = number of recaptured marks in stratum h Total smolt abundance is given by: ∑ ==

L

h hNN

1ˆˆ (4)

Given that predicted release of marks plus total catches in the Wolf traps was

expected to be less than the anticipated population of smolts, the result is an approximately unbiased estimate.

The tally of marked smolts from Wolf trap catches represents sampling without replacement and, hence, the distribution of hm for ranges of hM and hn , is

hypergeometric. However, for populations greater than 100, simpler distributions, such as the binomial and normal, are satisfactory approximations (Robson and Regier 1964). Given the very large smolt population size, the normal approximation to the variance for hN̂ is adequate, in the form:

v( hN̂ ) = )2()1())()(1)(1(

2 ++−−++

hh

hhhhhh

mmmnmMnM

(5)

and the overall variance is:


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)ˆ()ˆ(1∑ ==

L

h hNvNv (6)

(see Seber 1982:p60 for conditions to satisfy an approximately unbiased estimate of variance).

Approximate 95% confidence limits for N̂ are:

±1.96 )ˆ(Nv (7)

Consistency in the capture efficiency of the Wolf traps through time was examined using a χ2 contingency test.

The precision of the estimate was assessed using the parametric method described by Carlson et al. (1998). The number of recaptures in each stratum ( hm ) was treated as

hypergeometrically distributed with parameters { hN̂ , hM and hn }. One thousand random variates jhm were drawn from the hypergeometric distribution using Systat©

and used to calculate jhN̂ from equation 3. The bootstrap variance is given by:

)1/()()( 21

−−=−∧

=

∧

∑ Bv jB

jθθθ

where θ is the object of interest, here hN̂ , and −

θ is the bootstrap mean of the stratum

estimates ∧

jθ . The precision of the estimate of population size was calculated as bias-corrected

percentile confidence intervals (Efron and Tibshirani 1993), where: ( )96.12/ ±Φ= OLOWERUPPER ZP following calculation of the constant oZ (p185). 3.4 Diurnal Migration

We again used three time periods, representing Morning (04:00 – 10:00 hrs), Nighttime (22:00 – 04:00 hrs) and Daytime (10:00 - 22:00 hrs) to investigate temporal patterns of migration. Counts of juvenile coho and Chinook were made in each time


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period, over three trials on 16th-17th May, 24th-25th May, and 31st May-1st June. A fourth trial was conducted on 11th – 12th June, during a period of lower density of migration by coho. The timing of each trial corresponded to approximately equivalent flows (range 6.81 to 7.01 m3/s).

Hourly rates of movement were derived from the count data. Comparison of migration totals and rates among time periods was performed by analysis of variance (ANOVA). A second analysis was performed on the combined trials from 2010 and 2011. Assumptions of normality and equality of variances were tested using Kolmogorov-Smirnov and Levene’s tests, respectively. Individual comparisons were made using a pairwise Tukey’s Honestly-Significant-Difference test or the more conservative Games-Howell test, as appropriate: the Games-Howell test is a modified HSD test which is appropriate when the homogeneity of variances assumption is violated.

3.5 Proportional Entrainment

An assessment of differential entrainment (i.e. the % of juveniles entrained in each penstock intake) is complicated by potentially large variation over different intake flows. Data from Bengeyfield (1997) indicates that the capture rate for Intake #4 was significantly lower (19% versus 41%) under low discharges (chi square 10.50 p = 0.0012). Failure to incorporate this degree of variation into the subsequent calculation of migrant populations, e.g. by using simple proportions as in Bengeyfield (1997), results in the addition of an unknown degree of bias. A more recent estimate of entrainment over a series of trials at various discharges suggest that Intake #4 (i.e. the penstock monitored by the evaluation facility), passes on average, 25% of juvenile salmon (Tryon 2008). This was higher than the range of values measured in the 2010 study (16.3 – 20.7%), however, the latter estimate of differential entrainment was confounded by losses of marked fish in spills over the diversion dam and through the headpond bypass openings.

In the 2011 study, we circumvented these issues through the use of Radio Frequency Identification, or RFID technology. Fish implanted with passive integrated transponder (PIT) tags were enumerated by detection arrays (antennas) that monitored the outfall from Intake #3 as well as the assessment facility (Intake #4). Each antenna was connected to a reader that recorded the time and unique numeric identifier of the PIT tag as it passed through the array. The antenna installed on the “unmonitored” outfall pipe from Intake #3 was embedded in a fibreglass pipe that was custom


15

fabricated to replace a section of the existing steel outfall pipe. This replacement was necessary because steel shields the radio frequency from the detection equipment which drastically reduces antenna efficiency (Appendix E, Photo 4). Installation of the equipment could only be completed during the maintenance shutdown when the penstock was drained, thus postponing testing until 2012.

3.5.1 PIT Tag Application and Detection

Groups of Coho salmon smolts captured at the evaluation facility were marked with an upper or lower caudal fin clip, and PIT tagged using standard procedures and methods developed by the Pacific States Marine Fisheries Commission for tagging salmon in the Columbia River, available at the website http://php.ptagis.org/wiki/images/e/ed/MPM.pdf. A total of 5 individual trials using approximately 100 coho smolts per trial were conducted in May 2012 to test entrainment at a penstock discharge of ~26 m3/s, or full penstock load. We used 12.0 mm x 2.12 mm half duplex (HDX) tags and multiplex HDX readers (Oregon RFID, Portland, OR) to record tagged fish as they passed the antenna arrays. Test fish were released across the width of the headpond from a boat, at least 500 m upstream of the intakes. Tagged fish were enumerated by the detection arrays, but fish entrained in Intake #4 were also recaptured in the Wolf traps which were set to trap at 100% collection capacity, and counted. This allowed us to assess the true efficiency of the Wolf traps.

3.5.2 Analysis

The trials for proportion of PIT tagged fish that are entrained into the respective intakes provide us with binomially distributed data. Consequently, the reliability of the estimates for proportional entrainment are calculated as:

Standard error of the entrainment percentage = ( ) 100*/ npq

where: p is the probability of an individual being entrained in a given intake q is the probability of entrainment in the other intake, and n is the total sample size. The 95% confidence interval for the observed proportion of entrained smolts

was determined from:

CI = ( )

nppp z

−± ∝

12/


16

where p is the sample proportion, and z 2/∝ is the upper z value corresponding to half the desired alpha level.

The hypothesis that there was no difference between the observed proportions of entrained coho was tested using a z-test: the z statistic can be used because the distribution of sample proportions is approximately normal for large samples.

The z statistic is obtained from:

Z= ( )n

pppp

00

01

1−

−

where P1 is the observed proportion and P0 is the hypothesised proportion.

4 RESULTS 4.1 Hydrologic Conditions

Mean hourly discharge for the Puntledge River including BC Hydro Gauge 6 flows in Reach C (WSC Gauge No. 08HB084), Comox impoundment dam sluice gate releases (Reach B discharge) and the Puntledge Generating Station (penstock turbine flows), for the duration of each study period was obtained from BC Hydro Power Records, and is illustrated in Figure 4. BC Hydro conducted a scheduled maintenance shutdown of the Puntledge Generating Station from April 6 - 29, 2011. During this period the generating station was not operating (i.e. turbine flow = 0), and flows through Reach C were increased. Furthermore, from April 6 – 13th the penstock was drained for inspection and maintenance of the Eicher screens. Following inspection and screen cleaning, the penstock was filled and operational, but only for domestic and conservation (Puntledge Hatchery) water use.

A record snowpack during winter 2010/2011 resulted in a significant number of regulated spill events from the Comox dam in order to manage the reservoir levels. Following the maintenance shutdown, BC Hydro operated the generating station at full capacity (~26 m3/s based on BC Hydro records) throughout the summer, except during the migration pulse flows. Therefore lower penstock discharges were not available to test screen efficiency as proposed.


17

a). Puntledge River Discharge May 1 - July 31, 2011

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Figure 4. Puntledge River mean hourly discharge for the Comox dam sluice gates (CMC), penstock turbine flows (PUN G.S.) and Gauge 6 below the diversion dam (WSC Gauge No. 08HB084) for the period a) May 1 - July 31, 2011 and b) Oct. 1 – Dec. 11, 2011. Population estimate releases and diurnal migration assessment events are indicated with symbols.


18

4.2 Eicher Screen Efficiency

With the installation of the new fish delivery system in the penstock, the potential loss of marked fish in the trial was eliminated. Although passage of fish from the release location to the evaluation facility was fairly quick, a small proportion of fish from each release group were observed holding in dead zones or low turbulent pockets in the dissipation chamber for extended periods. However, all fish had passed over the weir and into the collection boxes within 24 hours after release.

Table 1 provides results from 6 trials each for coho and Chinook, on three sampling days. The average recovery rate in all coho trials was 95.6% (range 90% - 100%). The average recovery rate for Chinook for all trials was 89.2% (range 86.2% – 96.6%). The lower efficiency for Chinook may be attributable to their smaller size.

Table 1. Numbers of coho and Chinook released in the Puntledge penstock during screen efficiency trials. The numbers recovered 2 hours after release and 24 hours after release, represent an absolute count (Wolf traps were fishing at 100%). 2 hrs post release 24 hrs post release

Date of release Species

Number released # % # %

a) coho

13-May CO 100 81 81.0 90 90.0

13-May CO 95 71 74.7 91 95.8

26-May CO 100 85 85.0 98 98.0

26-May CO 100 69 69.0 91 91.0

14-Jun CO 101 86 85.1 100 99.0

14-Jun CO 100 80 80.0 100 100.0

Average 95.6

b) Chinook

13-May CN 200 173 86.5 173 86.5

13-May CN 195 163 83.6 168 86.2

26-May CN 151 125 82.8 131 86.8

26-May CN 150 123 82.0 132 88.0

14-Jun CN 151 128 84.8 138 91.4

14-Jun CN 149 114 76.5 144 96.6

Average 89.2


19

4.3 Population Estimates

A total of 2,180 coho smolts were marked for population estimation over the 5 recapture periods of the program. Upper caudal and lower caudal fin clips were used in rotation to distinguish individual trial strata: releases by mark type and period are provided in Table 2. In all marking periods, smolts were available in sufficient numbers to exceed the minimum target (345 individuals) for release: in some cases a substantially greater number were released (range 375 – 469, Table 2).

Chinook releases totalled 2,029 with alternating mutilation marks again used to identify individual release strata (Table 2).

Table 2. Marking and release timing, abundances and mark types for a) coho and b) Chinook.

Marking Date Release Date Mark Type 1 Number Marked Number Released

a) Coho

16-May 16-May LC 463 463

24-May 24-May UC 432 431

31-May 31-May LC 441 441

6&7 June 07-Jun UC 375 374

22-Jun 22-Jun LC 469 469

b) Chinook

16-May 16-May LC 302 302

24-May 24-May LC 305 302

31-May 31-May UC 307 307

07-Jun 07-Jun LC 311 311

22-Jun 22-Jun UC 301 301

24-Jun 24-Jun LC 503 503 1 UC upper caudal, LC lower caudal

a) Coho

Relative daily coho smolt migration, as depicted by the Wolf trap collections, is illustrated in Figure 5a. It should be noted that Wolf trap efficiency was adjusted between 69% and 100% to accommodate the Eicher screen efficiency tests. Therefore, the numbers of juveniles plotted in Figure 5 are not directly comparable over all dates.


20

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Figure 5. Daily movement of a) coho and b) Chinook juveniles through the evaluation facility. Numbers have been adjusted to account for fish that were marked and re-released upstream.

a).

b).


21

Additionally, catches were adjusted to account for recoveries of juveniles that were re-released, following marking, for use in efficiency trials. A total of 18,541 coho smolts were captured during the program. Peak migration occurred on 19 May, with a count of 1,297 smolts: a second, large movement occurred on 31 May (1,014 smolts) but overall migration was lower around this time. During the 10 day period between May 16 and 25, 40% of the total migration from the headpond (7,402 smolts) was recorded (Appendix A). A total of 421 marks from 2,180 releases were recaptured over the course of the study.

Capture probabilities for the Wolf traps ranged widely, from 4.5% to 32.9%, and averaged 19.0 % (Table 3a). The obvious temporal variation (Pearson chi-square, χ2 = 202.8, df = 4, p < 0.001) meant that the data could not be pooled over all periods to provide a Petersen estimate since it is probable that such an estimate would incorporate bias. Instead, the individual period estimates were summed to provide an overall population estimate for the Puntledge upper system. The potential bias resulting from heterogeneous capture efficiencies is investigated in a later section of this report.

Table 3. Estimates of population size derived from recovery sampling by the Wolf trap a) coho, b) Chinook. Capture probabilities (trap efficiencies) are provided by release stratum.

Release End Date

Catch Marked Releases

Recaptures Population Estimate

upper 95% CL

lower 95% CL

CV Capture Probability

a)

23-May 8,356 463 140 27,501 31,243 23,759 6.90% 30.20%

30-May 3,088 431 95 13,933 16,340 11,525 8.80% 22.00%

06-Jun 4,749 441 145 14,380 16,253 12,507 6.60% 32.90%

21-Jun 2,232 374 20 39,981 56,139 23,824 20.60% 5.30%

29-Jul 116 469 21 2,500 3,398 1,601 18.30% 4.50%

Total 18,541 2,180 421 98,295 115,182 81,408 8.80% 19.00%

b)

23-May 159 302 41 1,154 1,429 879 12.20% 13.60%

30-May 696 302 57 3,677 4,486 2,868 11.20% 18.70%

06-Jun 1,748 307 42 12,528 15,919 9,137 13.80% 13.70%

21-Jun 3,667 311 28 39,463 52,859 26,067 17.30% 9.00%

29-Jul 1,993 804 85 18,665 22,291 15,039 9.90% 10.60%

Total 8263 2,029 253 75,487 89,798 61,175 9.67% 13.10%


22

The estimate of total coho smolt numbers was 98,295 (95% CI 81,408 – 115,182), with excellent precision (CV 8.8 %) at only 1/2 of the design target. This was biased upward by the lower recapture probabilities in the final two periods (20.6% and 18.3% CV), which resulted from the greatly reduced capture probabilities (Table 3). The flow regime during the study, designed to spill water to avoid extreme discharge through snowpack contribution, is likely to have affected recapture rates, but may not have had an overriding effect on the overall population estimate. This is discussed in detail in the following section.

b) Chinook The daily Chinook juvenile catches were much less numerous than that of coho

(Figure 5b). After applying efficiency calculations for each sampling period a total of 8,263 individuals were estimated in the captures between 2 May and 29 July. The total included 253 recaptures from 2,029 marks released. Peak movement occurred on 20 June, with 424 individuals captured.

Capture probabilities for the Wolf traps again demonstrated significant temporal variation (Pearson chi-square, χ2 = 17.6, df = 4, p < 0.01). However, values were more similar than for coho, ranging from 9.0% to 18.7% and averaging 13.1% over all periods (Table 3b). Distinctly marked releases on 22nd and 24th June were combined into a single release period, since catches could not be allocated to a specific mark after the second release. Consequently, the 9% probability of capture for the period represents an average.

Individual stratum estimates were calculated and combined to form an overall population estimate for the Upper Puntledge River Chinook. The estimate of total Chinook numbers was 75,487 (95% CI 61,175 – 89,798). Precision was again excellent for the estimate (CV 9.7%) and ranged between 9.9% and 17.3% for individual strata (Table 3b).

4.3.1 Population estimate for coded-wire tagged Chinook

On May 24, 2011, 90,000 coded-wire tagged (CWT) and unmarked (non-adipose clipped) Chinook juveniles from Puntledge Hatchery were released into Comox Lake as part of a summer Chinook imprinting/homing behaviour study. Daily catches were checked for the presence of CWT 0 + Chinook on several dates in June and July using a portable V-detector (Northwest Marine Technology Inc., WA). However, since the proportions of CWT fish were variable over the data series and the data were not collected systematically, the construction of a population estimate for these fish was not


23

straightforward. Two sets of observations were available from strata 3 and 4 of the Chinook sampling program (Table 3). Between 1st and 5th June (stratum 3) 6 counts of the proportion of CWT fish were recorded. Between 22nd June and 11th July (stratum 4), a further 4 counts were made. Rather than simply using an overall average for CWT incidence in the population to predict abundance, we wanted to maximize the information from sampling and apply the two estimates to different segments of the migration. A basic assumption of the estimation method is that temporal stratification can minimize bias from variability in capture probabilities, by compensating for events such as fluctuations in discharge. Therefore, the capture probabilities give us some indication of how similar periods of migration were, although they do not address the composition of the captures, which are normally directly assessed by counting. In order to assign the proportion of CWT encounters we examined the capture probabilities from the overall Chinook estimate. These are shown in Table 3 and were higher in the first 3 strata (range 13.6% to 18.7%) than in the final 2 periods (9.0% and 10.6%). Consequently, the estimates of proportions of CWT Chinook from stratum 3 were applied to the initial 3 strata and the data from stratum 4 was used to construct capture totals for the final 2 strata. The proportions observed on specific dates were deconstructed and an average rate of encounter for CWT fish was derived. For stratum 3 this was 59.9% and for stratum 4 it was 55.5%. These figures were used to estimate the total number of CWT Chinook that would have been encountered in each stratum catch (excluding marked releases). Over all strata the total was 4,562. Stratum catches, in conjunction with the release and recapture of marked Chinook for the periods shown in Table 3, were then used to construct the population estimate.

A total estimate of 44,669 CWT Chinook fry (95% CI 36,560 – 52,778) results from individual stratum totals, based on the two determinations of CWT incidence in the 0+ Chinook population. It should be noted that this is a relatively crude approximation and the confidence intervals assume absence of error in assessing the catch rate for tagged fish. This assumption, while untrue, cannot be quantified due to the sparseness of the actual data. However, the estimate represents 59.2% of the total Chinook outmigration over the study and is in good agreement with the overall percentage of CWT fry that were sampled in Wolf trap collections (58.9%).

4.3.2 Population estimate for adipose clipped coho

Puntledge Hatchery released a total of 1.8 million coho fry into Comox Lake in 2010. Of these, approximately 200,000 were adipose clipped. During the study we captured 1,291 adipose clipped 1+ age juveniles. Based on the release of 2,180 marked


24

coho and 421 recaptures, the estimated population size for clipped fish was 7,789 (95% CI 7,032 – 8,545) or 3.9% fry-to-smolt survival. This estimate has high precision (CV 5.0%) and likely has low associated bias, similar to the estimate for all juvenile coho, above.

4.3.3 Biological Data Length frequency histograms for the 3 most abundant salmonids captured at the

Eicher evaluation facility in 2011 are illustrated in Figure 6. For coho, a fork length of 130 mm was used to arbitrarily differentiate age 2+ smolts from 1+ smolts, as per Bengeyfield (1997), while a sub-sample of coho in 2010 were aged by scales. Captures of CWT Chinook were recorded within a few days after release and observed for the duration of the monitoring period, accounting for between 40% and 80% of the daily Chinook catch. These fish averaged 4 grams at release and were slightly larger than wild Chinook overall (Figure 6b). Table 4 summarizes statistics for length, weight, and Fulton’s condition factor (K) for coho and Chinook captured in 2011 and 2010.


25

Figure 6. Length frequency histograms for sub-samples of a) coho (1+ and 2+), b) Chinook (0+ hatchery releases and wild smolts) and c) sockeye/kokanee captured at the Eicher Assessment facility in 2011.

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26

Table 4. Length (mm), weight (grams) and Fulton’s condition factor (K) for sub-samples of coho and Chinook captured at the Eicher Assessment facility in 2011 and 2010.

Length (mm) Weight (g) K

Species Age n Mean SD Min Max Mean SD Min Max Mean SD Min Max

2011

Coho 1+ 242 95 11.7 62 129 8.4 3.4 3.1 21 0.95 0.09 0.76 1.30

2+ 18 140 10.7 130 178 26.1 6.3 20.4 47.2 0.95 0.09 0.84 1.24

Chinook1 0+ 211 70 13.6 44 97 3.8 1.8 0.7 8.5 1.01 0.11 0.77 1.44

2010

Coho2 1+ 349 100 11.6 74 139 9.9 3.7 4.3 25.8 0.97 0.08 0.62 1.49

2+ 25 162 17.0 132 187 40.5 12.5 18.5 59.9 0.93 0.13 0.54 1.32

Chinook 0+ 192 74 12.5 47 105 4.6 2.0 1 13.1 1.04 0.09 0.78 1.44

1 Includes wild production and hatchery (CWT) releases. 2 A sub-sample of coho smolts in 2010 were aged by scales.

4.4 Bias

The approach taken to estimating population size in coho and Chinook juveniles through temporal stratification addresses variation in capture probability resulting from migration timing. This includes variation caused by factors such as water temperature and hydrological events, since both marked and unmarked fish are expected to be equally affected. However, particularly in the case of coho, the wide range in capture probabilities suggests that some degree of bias is likely to have been introduced through loss of stratum consistency in periods 4 and 5. The former is the more likely to have contributed measurable error, since ~ 41% of overall migration occurred in this period, while only a small portion of the migration occurred in stratum 5 (2.5%). The degree to which the low capture probability in period 5 contributed to loss of overall precision was examined using a parametric bootstrap technique (Carlson et al. 1998), based on the hypergeometric distribution.

The bootstrap data show a significant departure from normality (Anderson-Darling statistic coho 11.69 p


27

Figure 7. Frequency distribution of population estimates for a) coho and b) Chinook, from a parametric bootstrap procedure involving 1,000 iterations. The superimposed curve illustrates departure from normality.

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few extreme values: the highest value (145,842) derives from an iteration in stratum 4 that was 2.3 times the average value. The degree of kurtosis (1.65) indicates a significantly peaked distribution (kurtosis/se ratio 10.6) where central values are over represented (Figure 7a). The left, or negative, skewness counteracts the right tail of the distribution, tending towards a smaller overall estimate of the population. However, here again, departure from normality is moderate. Consequently we do not expect that the degree of error incorporated into the bootstrap estimate would be large.

Table 5 presents the 95% confidence interval calculated from the normal approximation, as in section 4.3, in comparison with the bias-corrected percentile confidence intervals (Efron and Tibshirani 1993) and associated CV. The bootstrap estimate was smaller than the pooled Petersen estimate and had wider confidence intervals.

Table 5. Comparison of levels of precision for coho and Chinook population estimates, obtained form all temporal strata based on the normal approximation and bootstrapping. Bootstrap estimates were based on the hypergeometric distribution and 95% confidence intervals are provided in uncorrected and bias corrected form. Relative precision is assessed by the coefficient of variation (CV). Technique Estimate Variance 95% C I CV

a) coho

Normal approximation 98,295 7.42E+07 81,408 – 115,182 8.8

Bootstrap (uncorrected) 94,103 8.95E+07 78,395 – 116,253 10.8

Bootstrap (bias corrected) 79,073 – 118,186 10.5

b) Chinook

Normal approximation 75,487 7.42E+07 61,175 – 89,798 9.3

Bootstrap (uncorrected) 76,675 5.95E+09 63,392 – 95,846 10.8

Bootstrap (bias corrected) 64,629 – 91,357 8.9

This loss in precision resulted from the degree of variability in the 4th stratum (22.9 CV versus 20.6 CV for the Petersen). Consequently the bootstrap estimate displayed a higher overall CV. However, the degree of bias is very small, with only a 4.3% difference in the two estimates.

The bootstrap distribution for Chinook was similarly non-normal (Anderson-Darling statistic coho 9.55 p


29

(17.3 CV; Table 3b). The population estimates for Chinook were very similar (75,487 versus 76,675 Table 5) with only a small increase shown by the bootstrapping. The 95% confidence intervals were also very similar and the degree of precision in all estimates was in good agreement, with a small reduction in the bias adjusted value (CV 8.9). There is no suggestion from these data that the Petersen estimate incorporates any significant degree of error.

The lack of significant bias in the estimates of population size indicates that there was a high degree of compliance with the assumptions of the methodology (see Seber (1982) and Arnason et al. (1996) for summaries and discussion of these). However, exogenous factors may have compromised the accuracy of segments of the population calculations.

Factors such as mark loss, primarily derived from short term mortality effects i.e. between release and recapture, were not problematic, although reporting of marks can influence the estimate, particularly if marks are indistinct or susceptible to removal. Similarly, population closure, the requirement that all of the population is encompassed within the sampling period, was not an issue. At the conclusion of the project only a small number of individuals, mostly Chinook fry were still being caught daily (~10 per day in the final week of the study). While the effect on the estimate would be small, we acknowledge that the estimates are representative of the sampling period only.

Finally, the requirement for all marks to be recovered or to move past the recapture site generally addresses the potential for marks from a release stratum to occur in more than one recovery period and was not an issue in this study since the time of travel of fish from the various release sites to the recapture site was consistently less than the stratum duration, and all captures were completed within the bounds of each stratum. More problematic may be the possibility that alternative migration routes could circumvent the sampling intake. Complete integration of marks into the population should result in consistent mark/unmarked ratios and is necessary to ensure that all smolts share the same probability of capture, or an equal probability of being examined for marks. Consequently, the release sites should be sufficiently far from the capture sites so that complete mixing would occur. The degree of mixing was tested in the previous year (Guimond and Taylor 2011) by releasing juvenile Chinook at three locations across the headpond. Respective recoveries from these locations were 20.7% mid-river, 19.5% right bank and 16.3% left bank. These proportions were not significantly different (individual comparisons Z=0.356 p = 0.723; Z=1.01 p=0.314, Z=1.506 p=0.132). This means that the degree of mixing of marked fish was likely to have been high in that year. In 2011, BC Hydro instigated an unusually high frequency


30

of water releases, designed to proactively control flood events generated by the high snowpack. Consequently, recovery of marked fish took place over widely differing river stages and mark releases were performed on 2 occasions in June, at higher than normal flow levels (Table 6).

The marks that were released during higher flows experienced lower recapture probabilities, particularly in the case of coho. However, in both cases recaptures were highly negatively correlated with flow level (coho Pearson correlation coefficient -0.92; Chinook Pearson correlation coefficient -0.88). These values suggest that, respectively, 85% and 77% of variance in recovery rates is explained by discharge levels; in both species the correlations were highly significant (n=8 p=


31

avoid recapture, possibly by being swept over the diversion dam, through the spillway or through greater entrainment by Intake #3. However, in order for this to have an effect on the population estimates, there would have had to have been no equivalent effect on the wild, non-marked, fish. Unfortunately, there is no way to determine the abundance of wild fish other than through the daily catch data which provides a relative, or indexed, picture of migration. Unlike the known numbers of marks that can be compared to recaptures, unmarked catches cannot be compared to the migration densities from which they originated.

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140

# co

ho s

mol

ts

Chinook releases

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16-M

ay-11

21-M

ay-11

26-M

ay-11

31-M

ay-11

05-Ju

n-11

10-Ju

n-11

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n-11

20-Ju

n-11

25-Ju

n-11

Date

Gau

ge 6

(cm

s)

0

10

20

30

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# ch

inoo

k sm

olts

Figure 8. Flow levels (bars) and recaptures of (a) marked coho and (b) Chinook (lines). Release dates are identified by red arrows.

a).

b).


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The relationship between catches of coho and flow is illustrated in Figure 9. Catches declined over the course of the study and were weakly negatively related to discharge (Pearson correlation coefficient -0.28). This indicates lack of predictive ability for the data (r2 = 0.04) although the relationship between juvenile catches and flows is significant (n= 114 p=


33

based on the proportions of catches in the original periods. The result was a substantial increase in population size to 139,024 coho. While this seems large, it is undoubtedly an overestimate, and is meant only to explore the potential increase that might result from bias due to high flow periods. However, it is an order of magnitude lower than the expectation for the migration from a release of 1.8 million coho fry into the upper watershed in 2010. For comparison, the estimated coho smolt migration in 2010 was 84,513 (95% CI 75,731 – 93,296; Guimond and Taylor 2011) from a hatchery release of 417,000 fry in 2009. Any potential bias due to our methodology cannot have underestimated the migration of most of these fish.

Chinook were weakly positively correlated with flows (Pearson correlation coefficient 0.34), but again this relationship has little predictive capacity (r2 = 0.12) although it is significant (n=114 p=


34

that many more Chinook fry moved during the Nighttime period than either in the morning or daytime.

An initial ANOVA of the number of coho counted by time period indicated that there were significant differences in the sample means, and therefore, migration is affected by time period. The highest number of individuals was recorded in the Nighttime period (384 juveniles compared with 284 during Daytime and 42 in Morning). However, Nighttime and Daytime totals were not significantly different (Levene’s test p


35

Table 7. ANOVA comparing juvenile Chinook migration in 2010 and 2011 as rates of movement (number.hr-1) during 3 periods: Morning (04:00 – 10:00hrs), Daytime (10:00 – 22:00) and Nighttime (22:00 - 4:00).

ANOVA

Source SS df MS F p

Regression 4529.1 2 2264.6 10.8 0.001

Residual 3770.9 18 209.5

Smolts moved in significantly higher numbers in the Nighttime (22:00 – 04:00hrs), than at the other two times: Nighttime versus Morning p=0.001, Nighttime versus Daytime p=0.009. Movement rates were equivalent in the Daytime and Morning (p=0.274). The temporal grouping explained 55% of the variation in migration rates, lower than in the previous analysis for three periods in 2011 (r2 = 0.898). The difference can be ascribed to the differences in means for Daytime and Nightime counts between years: Daytime 17.9 versus 27.6 individuals.hr-1 and Nighttime 29.7 versus 63.9 individuals.hr-1 in 2010 and 2011 respectively.

4.6 Proportional Entrainment

Previous estimates of the proportion of juvenile salmonids that entered Intake #3 were confounded by the diversion dam overspill and the spillway in proximity to Intake #4, both of which allowed for fish to circumvent the intakes (Guimond and Taylor 2011). The proportion of marked coho and Chinook collected by the Wolf traps at a fishing level corrected to 100% efficiency was 21.6% and 15.6%, respectively (coho range 9.6% to 37.0%, Chinook range 8.8% to 22.1%).

The use of PIT tags in 2012 enabled estimation of the proportions entrained by the respective intakes, as well as providing insight into the magnitude of losses through the alternate routes mentioned above. Of the total number of tags detected by the receivers in the five trials (Table 8), the proportion of fish entrained by Intake #3 was 57.5% (95% CI 52.7 – 62.3%) while Intake #4 captured 42.5% (95% CI 37.6-47.3%). Of the total number of tags released, Intake #3 collected 43.9%, Intake #4 captured 32.4% and 23.7% were not located by either of the antennas (i.e. likely swam over the diversion dam or through the spillway). The latter calculation is in better agreement with the proportions estimated originally in 2011, before the use of PIT tags. However, the


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estimate is larger than the means of the estimates described above (i.e. 21.6% and 15.6%), and only lies within the range measured for coho. The much larger proportion (68%) determined by Bengeyfield (1997) lies outside the confidence interval for our highest estimate. Since the initial estimates, based on the totals for all located tags, are so similar, a suitable null hypothesis for statistical testing is that there is no difference in the numbers of fish entrained by the two intakes i.e. each collects 50% of the outmigration. Table 8. Fate of PIT tags released above the penstock intakes in 5 trials. Totals for Intake #4 include antenna detections plus tags that were not detected but were physically recovered from the Wolf traps.

Trial Tags released Intake # 3 Intake # 4 Not detected1 Not found2

1 106 55 40 11 11

2 105 29 48 8 28

3 106 46 31 28 29

4 103 55 24 16 24

5 102 44 26 24 32

Totals 522 229 169 60 124 1 some tags were not detected, primarily by antenna #2 potentially due to placement in the Wolf traps 2 some tags may have bypassed both intakes and were not detected nor recovered by trap collection

A substantial proportion of tags were never located (23.8%), presumably having

bypassed the intakes, although there is potentially some detection error that may be associated with antenna #1 on the outlet from intake #3 (Eicher Screen #1). Other tags were physically recovered from Wolf trap collections, but not recorded by array #2 possibly due to the physical configuration of the collection system (see later).

While the results of the five tests were somewhat variable, only one test indicated that Intake #4 entrained more fish (62.3%). Since we consider the distribution to be binomial, however, we can estimate the reliability of a single determination: the sum of the trials rather than the mean of the series. Overall, the variation in proportion (standard error of the percent entrained by an intake) of detected fish was 2.2% representing excellent precision. Comparing the proportion of fish that were entrained by Intake #3 to that by Intake #4, the former is significantly higher (z = 4.25 p =


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entrainment by Intake #4 was significantly lower (z = -3.01 p=0,003). We reject the null and confirm that, on average, the two intakes do not collect equal proportions of migrants.

We examined the relationship between proportional entrainment and hydrologic stage, using linear regression. The proportion of tagged fish entrained by intake #3 was regressed on the average daily Comox Lake sluice gate release for the individual trial dates. The average hourly flow rates were relatively similar (range 31.9 to 36.4 m3/s) and accounted for less than 2% of variation in entrainment rates (r2 = 0.011 p = 0.69). Consequently, the differences in entrainment proportions noted above appear to be more related to individual movement patterns rather than dictated by current.

4.7 Fall Juvenile Migration

Monitoring was conducted during the fall to provide a better understanding of migration behaviour during this period, and assess the potential impacts of higher debris loads, greater cleaning frequency and possible lock-out of the screens on migrating fish at this time of year. Trap catches were inspected daily from October 6 to December 10, 2011. A total of 1643 salmonids were captured during the monitoring period with the Wolf traps fishing at 69%, including several large and sexually mature Dolly Varden and Sockeye/Kokanee (Table 9).

Table 9. Total number and size range of salmonids captured at the Eicher Assessment facility, October – Dec 2011 at 69% fishing efficiency.

Species Total Catch @ Eicher Screen #2 Fork Length Range (mm)

Coho 1,602 71 - 119

Chinook 12 110 - 171

Sockeye 14 56 - 210

Steelhead 2 91 - 325

Cutthroat 5 40 - 184

Dolly Varden 7 109 - 400

Total 1,642

Following the maintenance shutdown of the Puntledge Generating Station in

April, the Eicher screens are typically set to operate on the pressure triggered system. The frequency of screen cleanings during the peak migration period (late spring – early


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summer) may range from 4 times per day to once every four days, (Figure 10). In other words, the screens may be in an open position for ~1% to less than 0.1% of the time.

Cleaning Frequency May 16-28, 2010

0

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ay

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ay

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ay

25-M

ay

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ay

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ay

28-M

ay

Scre

en p

ositi

on

Eicher Screen #2Eicher Screen #1

Figure 10. Frequency of screen cleaning cycles for a two week period during peak smolt migration in 2010 when operating on a pressure triggered system. 1 indicates screens are in the closed “fishing” position; 0 indicates screens are in the open “cleaning” position.

By late summer or early fall, the Eicher screen cleaning operation is changed from a pressure triggered system to a programmed mode due to the accumulation of debris, leaf litter and increased flows. However, despite regular hourly cleaning cycles, screen lock-out events are common, particularly between October and December. Under an hourly programmed cleaning mode, screens would be in the open position (i.e. not fishing) for approximately 84 minutes per day, or 6% of the time. In October and November 2010, screens were locked out for an additional 5204 and 1095 minutes, respectively, over and above their regular (hourly) cleaning operation (C. Beers, unpublished data, 2011).

This increased the total estimated time out of fishing position to 16.7% and 8.3% respectively. In 2011, high flows and increased debris loads caused similar issues with screen lock-outs in October and November. However, the total estimated time the screens (either one screen or both) were out of the fishing position was significantly higher (Table 10).


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Table 10. Estimated time the Eicher fish screens were out of fishing position for regular cleaning and lock-outs, from October to December 10, 2011.

Month Screen #

Estimated time (minutes) Screens open for regular cleaning and lock-outs

Percentage of time Screens open during

month (%)

1 18852 43.6 Oct 2 11871 27.5

1 11954 27.7 Nov 2 2922 6.7

1 53 0.4 Dec (first 10 days only)

2 60 0.4

Although migration during the fall period is significantly lower than

spring/summer, these migrants have a much higher risk of mortality from screen operations/lock-outs. Figure 11 illustrates the potential impact of extended screen lock-out periods on migrating fish. This underscores the need to address screen lock-out events during non-peak periods in a timely manner to reduce the risk of injury/mortality on migrating fish.

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ct19

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ec

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res

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daily captures Net Flow at Gauge #6 Screen 2 Open Screen 1 Open

Figure 11. Daily captures (all salmonids) at the Eicher evaluation facility from Oct-Dec 2011 with discharge measured at Gauge 6. Duration of screen lock-out events are illustrated with red and green symbols at the top of the chart.


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5 DISCUSSION

With the addition of a new fish delivery system on the penstock, we were able to acquire more accurate data on screen (diversion) efficiency in 2011. The location of the delivery system, approximately 25 m downstream of the penstock intake opening, addressed the concern of test fish escaping upstream into the forebay. The proximity of the delivery pipe to the leading (upstream) edge of the Eicher screen ensured the marked releases of fish were exposed to the full length of the screen as they travelled to the by-pass. However, it did not provide the released fish sufficient time to orient themselves in a normal position (head upstream, parallel to flow) before encountering the screen. Observations made through viewing ports downstream of the release pipe during an efficiency trial at full penstock

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