Assessment of Chinook and Coho Smolt / Fry …a100.gov.bc.ca/appsdata/acat/documents/r41644/12.PUN.04...Assessment of Chinook and Coho Smolt / Fry Migration at the Puntledge Diversion

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

2012 - 2013

12.Pun.04

Prepared for:

Comox Valley Project Watershed Society PO Box 3007

Courtenay, BC V9N 5N3

Prepared by:

E. Guimond 1, J.A. Taylor 2, and M. Sheng 3

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

September 2013

1 E. Guimond - 473 Leighton Ave., Courtenay, BC V9N 2Z5 2 J.A. Taylor and Associates Ltd - 11409 Sycamore Dr., Sidney, B.C. V8L 5J9 3 M. Sheng - Fisheries and Oceans Canada, 3225 Stephenson Point Rd., Nanaimo, BC V9T 1K3

Puntledge River Eicher Screen Assessment 2012 12.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 2012 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) in diverting

emergent Chinook from entrainment in the turbine. ii. Estimate the proportional entrainment of coho smolts between the two

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

released coho and Chinook migrants from the upper watershed (above the diversion dam).

Fish sampling was conducted at the Eicher Evaluation facility from 1 May to 5 August 2012, and from 5 February to 2 August 2013. The facility diverts fish from one of the two operating Eicher screens below the penstock intakes into sampling chambers where each species are counted and analyzed before they are returned to the river. No fish sampling was conducted from April 3 – 18, 2013 during BC Hydro’s maintenance shutdown when the evaluation facility was not operating.

Batches of marked hatchery Chinook and chum salmon, and wild coho smolts were released at three locations during the study to conduct various experimental trials: 1) directly into the penstock immediately upstream of Eicher Screen #2 through the fish delivery pipe, 2) behind the trash rack on the diversion dam at Intake #4, and 3) approximately 500 m upstream of the diversion dam in the headpond.

The population estimate for the 2012 coho out migration was a Pooled Petersen Estimate of 41,513 (95% CI 39,272 – 43,753). The estimate for Chinook migration was derived using a Darroch Maximum Likelihood Estimator and totalled 84,263 (95% CI 63,652 – 104,874). Peak migration occurred on 22 May for coho, with a maximum daily


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count of 1,037 smolts at the Evaluation facility, and on 31 May for Chinook, with 564 individuals captured. Estimates for adipose clipped coho and coded-wire tagged Chinook populations in 2012 were 6,388 (95% CI 6,106 – 6,669) and 63,591 (95% CI 47,789 – 79,392), respectively.

Population estimates for summer Chinook migration in 2013 (brood year 2012 wild Chinook) were calculated for two time series - an early emergent spring component between February and early April 2013, and a later summer component from late April to the beginning of August 2013. The two periods were separated by a 2 week window during the maintenance shutdown when no capture data was available. The estimate of total Chinook numbers migrating during the spring and summer periods was 39,744 (95% CI 13,219 – 66,268), and 7,252 (95% CI 6,217 – 8,287) respectively. The combined estimate of 46,996 individuals for 2013 chinook fry was an underestimate, due to poor capture probabilities in the early series caused by the extremely poor screen efficiency (i.e. high mortality). This does not include an interpolated estimate of a further 17,000 fry that may have migrated during the maintenance shutdown period. Therefore, the total migration may have approached 65,000 Chinook fry if the interpolated data approximated the actual number of migrants in early to mid April.

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 enumerated by a detection array (antenna) that monitored the outfall from Intake #3 while PIT tagged fish entrained in Intake #4 were recaptured in the Wolf traps (at 100% collection capacity) and identified by a handheld portable Reader. The results from 6 trials for all turbine flows, corroborated the 2012 findings, with Intake #3 entraining a significantly greater proportion of juvenile coho recoveries than Intake #4, (56.2% vs. 43.8%). As in 2012, Intake #3 collected significantly greater than 50% of detected fish (z = 2.361 p = 0.009), again indicating that, on average, the two intakes do not collect equal proportions of migrants. Combining the results from the two years of data collection also indicates that Intake #3 entrains more fish than Intake #4.

Eicher screen efficiency was assessed on (emergent) Chinook fry before (Feb/March 2013) and after (Apr/May 2013) the screens were cleaned during BC Hydro’s maintenance shutdown of the Puntledge generating facility. The efficiency of Screen #2 to divert hatchery Chinook fry (FL = 50 mm) was <0.1% and 28.6% in the pre-maintenance test releases in the penstock and at the intake respectively. Following the maintenance period, efficiency was 85.6% and 85.7% at the two locations.


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TABLE OF CONTENTS

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

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

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

3 METHODS ................................................................................................................. 8 3.1 Juvenile Migration Monitoring ............................................................................ 8 3.2 Population Estimation Study Design ................................................................... 9

3.2.1 Calculation of mark releases .............................................................................. 10 3.2.2 2012 Population estimation method ................................................................... 11 3.2.3 2013 Population estimation method ................................................................... 12 3.2.4 Rotary screw trap assessment ............................................................................ 14

3.3 Proportional Entrainment .................................................................................. 15 3.3.1 Analysis .............................................................................................................. 15

3.4 Eicher screen efficiency on Chinook fry ........................................................... 16 4 RESULTS ................................................................................................................. 17

4.1 Hydrologic Conditions 2012-2013 .................................................................... 17 4.2 2012 Population Estimates (Brood Year 2010 Coho and 2011 Chinook) ......... 19

4.2.1 Coho (Brood Year 2010) ................................................................................... 20 4.2.2 Chinook (Brood Year 2011) .............................................................................. 23 4.2.3 Population estimate for 2012 adipose clipped CWT coho (2010 brood year) ... 24 4.2.4 Population estimate for 2012 CWT Chinook (2011 brood year) ....................... 26 4.2.5 2012 Biological Data (Brood Year 2010 coho and 2011 Chinook) ................... 28

4.3 2013 Population Estimates (Brood Year 2012 Chinook) .................................. 29 4.3.1 Emergent Chinook fry and smolts ..................................................................... 29 4.3.2 2013 Biological Data (Brood Year 2012 Chinook) ........................................... 32

4.4 Bias .................................................................................................................... 34 4.4.1 2012 coho and Chinook populations .................................................................. 34 4.4.2 2013 Chinook population ................................................................................... 40

4.5 Proportional Entrainment .................................................................................. 42 4.6 Eicher Screen Efficiency ................................................................................... 46


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5 DISCUSSION ........................................................................................................... 48 6 RECOMMENDATIONS ........................................................................................ 52 7 ACKNOWLEDGEMENTS .................................................................................... 56 8 REFERENCES ........................................................................................................ 57

LIST OF FIGURES

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

Figure 2. Schematic showing a top and sectional view of an Eicher screen inside a penstock. ............................................................................................................................. 6

Figure 3. Pathways for downstream migration of fry and smolts at the Puntledge diversion dam (from Bengeyfield 1995). ........................................................................... 7

Figure 4. Puntledge River mean hourly discharge for Reach B (Comox dam sluice gate discharge), penstock Turbine Flows and Gauge 6 below the diversion dam (WSC Gauge No. 08HB084) for the three monitoring periods a) May 1 - July 31, 2012 and b) Feb 1 – April 2, 2013 and c) April 3 – July 31, 2013. Marked fish releases for population estimate (PE) trials are indicated by symbols. .................................................................. 18

Figure 5. Daily movement of a) coho and b) Chinook juveniles through the evaluation facility in 2012 with Puntledge River discharge measured at Gauge 6 below the diversion dam. 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+) and b) Chinook (0+ hatchery releases and wild smolts) captured at the Eicher assessment facility in 2012. ................................................................................................................. 28

Figure 7. Daily catches of 0+ Chinook fry in the evaluation facility. .............................. 30

Figure 8. Length frequency histograms for sub-samples of wild summer-run Chinook captured at the Eicher assessment facility between February and July 2013. .................. 33

Figure 9. Frequency distribution of 2012 population estimates for a) total coho and b) total Chinook juveniles from a parametric bootstrap procedure involving 1,000 iterations. The superimposed curve illustrates departure from normality. ...................... 36

Figure 10. Relationship between catches of juvenile Chinook and discharge measured at the CMC sluice gate. ........................................................................................................ 39

Figure 11. Frequency distribution of 2013 population estimates for a) early and b) late Chinook juveniles from a parametric bootstrap procedure involving 1,000 iterations. The superimposed curve illustrates departure from normality. ........................................ 41

Figure 12. Flow chart of Brood Year 2012 summer Chinook migration at the Puntledge diversion dam Eicher screens, illustrating the survival and mortality rates on the timing segments of outmigration and adult returns. .................................................................... 53


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LIST OF TABLES

Table 1. Timing of activities for the 2012 evaluation of natural and hatchery summer Chinook and coho production in the Upper Puntledge watershed. .................................... 4

Table 2. Marking and release timing, abundances and mark types for 2012 a) coho and b) Chinook. ....................................................................................................................... 19

Table 3. 2012 Estimates of recapture probabilities (trap efficiencies) by release stratum for a) 2010 brood year coho, b) 2011 brood year Chinook. Capture probabilities reflect recaptures from a release stratum, specific to the initial recovery stratum. ..................... 21

Table 4. Data matrix for input into the SPASS program, showing the distribution of recaptured marked coho with catch and release totals for the respective strata. .............. 22

Table 5. Data matrix for input into the SPASS program, showing the distribution of recaptured marked Chinook with catch and release totals for the respective strata. ........ 24

Table 6. Data matrix for input into the SPASS program, showing the distribution of recaptured marked coho with catch and release totals for the respective strata, along with totals for catches of adipose clipped coho. ....................................................................... 25

Table 7. Data matrix for input into the SPASS program, showing the distribution of recaptured marked Chinook with catch and release totals for the respective strata, along with totals for catches of CWT Chinook. ......................................................................... 26

Table 8. Length (mm), weight (grams) and Fulton’s condition factor (K) for sub-samples of coho and Chinook captured at the Eicher Assessment facility from May - July 2012. .......................................................................................................................................... 29

Table 9. Estimates of recapture probabilities (trap efficiencies) by release stratum for Chinook. Capture probabilities reflect recaptures from a release stratum, specific to the initial recovery stratum. .................................................................................................... 32

Table 10. Length (mm), weight (grams) and Fulton’s condition factor (K) for sub-samples of Chinook captured at the Eicher Assessment facility from February - July 2013. ................................................................................................................................. 34

Table 11. Comparison of levels of precision for the 2012 total coho and Chinook population estimates, obtained from 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). ................................................................................................................................. 35

Table 12. Comparison of levels of precision for spring and summer Chinook population estimates, obtained from 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). .............................................. 42


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Table 13. Fate of PIT tags released above the penstock intakes in 5 trials between May 14 and June 16, 2012. Totals for Intake #4 include antenna detections plus tags that were not detected but were physically recovered from the Wolf traps. ........................... 43

Table 14. Fate of PIT tags released above the penstock intakes in 6 trials between May 3 and June 27, 2013. A seventh trial was incomplete due to an unplanned spill at the diversion dam. .................................................................................................................. 45

Table 15. Proportions of PIT tagged coho entrained by the intakes at two generating flows. ................................................................................................................................ 45

Table 16. Numbers of Chinook and chum fry released in the Puntledge penstock and at the intake during screen efficiency trials conducted before and after screen maintenance. Recoveries were over a 24 hour period and represent an absolute count (Wolf traps were fishing at 100%). .............................................................................................................. 47

Table 17. Summary of coho fry releases, captures and population estimates at the Eicher Evaluation facility from 2010 to 2012. ............................................................................. 48

Table 18. Chinook scale loss measured at the Elwha Dam Eicher Screen, 1991-92. ..... 54

LIST OF APPENDICES

APPENDIX A - Numbers of juvenile coho and Chinook captured daily in the evaluation facility in 2012. ................................................................................................................. 60

APPENDIX B - Numbers of juvenile Chinook captured daily in the evaluation facility in 2013. ................................................................................................................................. 62

APPENDIX C– Photos ..................................................................................................... 63

APPENDIX D - FWCP Financial Statement ................................................................... 66

APPENDIX E - Performance Measures ........................................................................... 67

APPENDIX F - Confirmation of FWCP Recognition ..................................................... 68


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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 Puntledge watershed production strategy is highly dependent on successful juvenile migration past the diversion dam. The primary goal of


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this study 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 estimated based on results from evaluations of the Eicher screen at Elwha Dam (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) only provided information on juvenile migration timing and patterns, population estimates and differential entrainment in the two penstock intakes, but did not measure the specific diversion efficiency of the Puntledge Eicher screens.

BC Hydro has recently implemented new more stringent Eicher screen pressure protection limits for cycling the screen into the cleaning position to protect the aging woodstave penstock. BC Hydro staff has 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


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impacted the overall performance of the Eicher screens, significantly increasing 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-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 were either pulled through the screen, became impinged on the face of the screen, or were seen sliding up the screen, often colliding with debris lodged on the screen and likely getting injured or killed (Bengeyfield 1995). The screens were originally designed to divert 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 2012/2013 encompassed 3 primary objectives:

i. Determine the efficiency of the Eicher screen (in Intake #4) in diverting emergent Chinook from entrainment in the turbine.

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

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

These objectives were assessed during three periods as outlined in Table 1.


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Table 1. Timing of activities for the 2012 evaluation of natural and hatchery summer Chinook and coho production in the Upper Puntledge watershed.

Timing of Monitoring Period Year Project

Objective Description

May 1 - July 31 2012 ii • Natural and hatchery coho smolt migration from the upper watershed (above the diversion dam)

May 1 - July 31 2012 ii • Survival of Chinook smolts from a second hatchery release in Comox Lake in May 2012 (pending approval of a separate proposal)

Feb 1 - March 31 2013 i • Eicher screen efficiency trials on emergent Chinook fry

Feb 1 - March 31 2013 ii • Assessment of natural summer Chinook production above the diversion dam for Brood Year 2012 adults (emergent fry migration)

April 1 - 30 2013 ii • Assessment of natural Chinook production during BCH shutdown – RST addendum

May 1 – July 31 2013 ii • Assessment of natural summer Chinook production above the

diversion dam for Brood Year 2012 adults (later Chinook fry migration)

May 1 - 31 2013 iii • Assessment of differential entrainment in Intakes #3 and #4

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 Screens

Twin intakes at the Puntledge 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).


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


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TOP VIEW

SECTIONAL VIEW

Figure 2. Schematic showing a top and sectional view of an Eicher screen inside a penstock.

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 difference in pressure up and downstream of the Eicher screen. When a specified threshold pressure protection limit is reached the screens drop 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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Figure 3. Pathways for downstream migration of fry and smolts at the Puntledge diversion dam (from Bengeyfield 1995).

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


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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.

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 Juvenile Migration Monitoring

Monitoring juvenile migration at the Eicher Evaluation facility was conducted during three periods: 1 May to 5 August, 2012, 5 February to 2 April, 2013, and 19 April to 2 August, 2013. Trap catches were inspected once per day in the morning, but up to three times per day during screen efficiency assessments. Captured fish were netted into shallow basins in small groups, 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 (FL), from tip of nose to fork in caudal fin, was measured to the nearest mm on a


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plastic measuring board and weight (to the nearest 0.1 gram) was measured using an Ohaus electronic balance (Scout® Pro).

Occasionally throughout the migration monitoring period coho smolts captured at the facility were retained in two 5 ft (1.5 m) diameter fibreglass rearing tanks located at the site for Population Estimate mark/recapture trials (see Section 3.2). 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, either an upper or lower caudal 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). Chinook fry and smolts from Puntledge Hatchery were used for test releases and marked with a caudal fin clip for larger fish, or a Bismarck Brown-Y immersion bath for fry (see Section 3.4).

3.2 Population Estimation Study Design

An alternative method for assessment of population size for juvenile coho and Chinook moving downstream past the assessment facility was required to deal with anomalous movement patterns of marked fish in 2012. Previously, the 2010 and 2011 estimates were generated using the stratified mark/recapture design of Carlson et al. (1998). The method requires that the application of unique mark types is conducted within designated marking periods, with subsequent recovery of marks within defined capture periods. Consequently, capture probabilities can be calculated for discrete periods during the migration, within which we can be reasonably certain that conditions did not change substantially. Decisions on the degree of temporal stratification can be made during the program, however, it is necessary to constrain the recovery of mark releases in each trap efficiency trial to a single capture period. Unfortunately, in 2012 the recovery of marks over two capture periods was encountered in both the coho and Chinook programs, violating the above premise. Consequently a maximum likelihood estimation method that could account for prolonged movement of marks through the counting facility was employed, as described below.

The 2013 Chinook data were more tractable, since none of the recaptures occurred outside the defined capture period. Consequently, the stratified population estimates previously employed in 2010 and 2011 were appropriate. These are described in the following material.

All of the other basis assumptions of the method, as reported in previous years (e.g. Guimond and Taylor 2011) were maintained in the current study. These included


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the requirement for marked fish to become fully integrated into the migrating population, so that consistent proportionality of marks is achieved.

3.2.1 Calculation of mark releases

The method used to provide prediction regarding the number of marks required for release in each time period was revisited using the probabilities of recapture determined for coho and for Chinook in the 2011 program. In the case of coho, the average capture probability was 19%, substantially larger than in 2010 (average 15.5%). However, the efficiency trials varied widely (range 4.5% to 32.9%). Consequently, we examined the effect of the average probability versus a less efficient (13%) trial. As in the previous year, we planned to utilize the Wolf traps at 100% efficiency for as much of the study as possible. This contributes to an underestimate of the overall prediction of efficiency, resulting in a conservative total for required marks, based on a total relative error ( hr ) set at ±15% for 95% precision.

a) Coho

Strata totals from the 2011 migration were used to estimate the proportion of the population encountered in each time period (φh) over a total of 5 strata. Details of the values for parameters used in the calculation are given in Guimond and Taylor (2011). 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).

Using the upper value for probability of recapture (19%) resulted in a minimum of 281 marked coho required for release in each stratum. We considered this total to


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fall below a conservative level, should conditions in 2012 prove to be less conducive to high capture rates by the Wolf traps. Using a more cautious level of 13% recapture provided a minimum of 411 releases per stratum. This was close to the predicted size of releases in the previous year: in an abundance of caution, we elevated the calculated release levels from 345 to an average of 435 in 2011. The final release total per stratum was set at 400 in the present study.

b) Chinook

The 2011 average probability of capture for Chinook was 13% with a narrower range of values than determined for coho (9.7% to 17.3%). Using this value for the 2012 program, with the parameterization for the model from 2011, set over 7 strata, provided a stratum relative error ( tr ) of 33% . The required minimum number of marks

was 306, which was adopted since it conformed exactly to the average release in 2011. This estimate was also adopted for the 2013 releases.

3.2.2 2012 Population estimation method

All population statistics from the 2012 data were generated using the statistical software package SPAS (stratified population analysis system) of Arnason et al. (1996). Estimation of population size for the coho and Chinook migrations were initially made using the pooled Petersen estimator (PPE) which, if unbiased, has greater precision than stratified estimators. However, bias can result from violations of the basic assumptions, including lack of closure of the population, resulting in a non-zero probability of recovery of marks from the capture (marking) strata in one of the final (recapture) strata. Subsequently, stratified population estimates were generated from a maximum likelihood estimator developed by Darroch (1961), and incorporating the modifications made by Plante (1990). These determine population size based on summed estimates for individual release or recovery strata. The data was subjected to pooling of strata to determine if precision and accuracy of the estimates could be improved. In conjunction with the estimates, two measures of constant capture efficiency over time and equal proportions of marked versus unmarked fish among recovery strata were performed to determine the overall validity of pooling. Examination of the appropriateness of specific pooling steps was provided by Plante’s Goodness of fit test (G square) and its equivalent chi-square form.


12

The precision of the estimate and the potential degree of bias was assessed using the parametric method described by Carlson et al. (1998), applied in a slightly different manner, depending on whether the PPE or MLE was adopted as the final population total.

In the case of the Darroch MLE, 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/()()( 2

1−−=

−∧

=

∧

∑ Bv j

B

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).

For assessment of the PPE, an overall series of 5 samples each with 1000 values of jhm were drawn based on the total marks released and the total catch over the

collapsed strata. The bootstrap mean of the pooled estimates was calculated along with appropriate confidence intervals as above.

3.2.3 2013 Population 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:


13

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 hNN1

ˆˆ (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 or 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:

)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 calculated as described above for coho, using a parametric bootstrap approach.


14

3.2.4 Rotary screw trap assessment

BC Hydro conducts maintenance of the Puntledge Generating Facility annually in April and again in September. During this 2-3 week maintenance period, the penstock is drained for inspection, and the generating facility is shutdown. Therefore most of the river flow passes over the diversion dam and we are unable to capture migrating fish at the evaluation facility.

Interpolation of Chinook fry catch data during the shutdown is one method of providing the missing information to complete an overall population estimate on natural summer Chinook production. However, the usefulness of this method may be constrained by migration timing, in the event that an obvious peak of early movement is not captured by sampling prior to April. In this case we have no ability to depict the size or timing of the peak movement. Consequently, interpolation by means such as fitting polynomials, or merely by applying smoothing techniques to provide an interpolated curve, will not be useful. The result would be to underestimate that portion of the migration not directly sampled.

In order to address the limitations in this approach, we proposed to use a Rotary Screw Trap (RST) in the river to supplement the migration data during the BCH shutdown period in order to ensure a more accurate population estimate on natural summer Chinook production. A rotary screw traps consist of a cone, supported on two pontoons, with interior baffles to trap and direct fish to a live-box (Appendix C Photo 1).

Approval for the additional project activity and funding was granted by the FWCP Coastal Board in January 2013 and installation and safety planning was completed following several discussions and input from BC Hydro and DFO. On April 4, 2013, a 6 ft diameter RST was deployed in Reach B, approximately 150 m upstream of the diversion dam (Appendix C Photo 2). The site was selected for its access, security and anchoring features and more suitable physical characteristics than other locations upstream where the river is wider and slower.

Unfortunately, due to lower than anticipated river velocities at the site for proper functioning of the trap, we could not obtain any capture data during the shutdown period. Although velocities at the site under similar flow conditions when the generating facility was operating (February) were within the range for operating the RST, we suspect that the shutdown of the generator may have altered the hydrology at the dam, thus affecting proper operation of the RST.


15

3.3 Proportional Entrainment

Past estimates of differential entrainment, or the % of juveniles entrained in each penstock intake (Bengeyfield 1997, Tryon 2008) are confounded by losses of marked fish in spills over the diversion dam and through the headpond bypass opening. In 2012, and again in 2013, 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 an antenna that monitored the outfall from Intake #3. The antenna was connected to a reader that recorded the time and unique numeric identifier of the PIT tag as it passed through the antenna array which was embedded in a fibreglass pipe that was installed on the outfall pipe in 2012 (Guimond and Taylor 2012).

Groups of coho salmon smolts captured at the evaluation facility in May and June 2013, 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 4 individual trials using approximately 100 coho smolts per trial were conducted in May and June 2013 to test entrainment at a penstock discharge of ~26 m3/s, (24 MW generation). Two trials were also completed at 11.8 m3/s (10 MW generation), but a third trial at this flow could not be completed. For all trials, 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 array. Test fish were released across the width of the headpond from a boat, at least 500 m upstream of the intakes. PIT tagged fish were detected by the antenna on the outfall pipe of Intake #3 while PIT tagged fish entrained in Intake #4 were recaptured in the Wolf traps (which were set to trap at 100% collection capacity) and identified by a handheld portable Reader (Oregon RFID, Portland, OR).

3.3.1 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 is 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


16

n is the total sample size. The 95% confidence interval for the observed proportion of entrained smolts

was determined from:

CI = ( )

nppp z

−± ∝

12/

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=( )

npp

pp00

01

1−

−

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

3.4 Eicher screen efficiency on Chinook fry

The efficiency of the Eicher screen to bypass emergent Chinook fry (average FL = 39 mm) in February/March 2013 was tested using the fish delivery system installed on the penstock in 2011. Marked test fish were introduced directly into the penstock in small batches through a 3 inch (760 mm) diameter metal pipe 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. 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 achieved 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. In addition, trials were also conducted at the intake using the system employed in our 2010 trials (Guimond and Taylor 2011).


17

Fall Chinook fry from Puntledge Hatchery (average FL = 45 mm) were used as a surrogate for summer Chinook to test screen efficiency (two trials at each release location), in addition to chum salmon (one trial at each location). For each trial, fry were marked using an immersion bath containing Bismarck Brown Y in solution (1 gram Bismarck Brown Y to 50 L water) to produce a whole body mark (Appendix C Photo 3). Fry were counted out and placed in the dye immersion bath with aeration for approximately 2.5 - 3 hours. A small number of marked fry were kept in the facility as a control to monitor mortalities associated with the marking, and dye retention. Dyed fish could be easily distinguished from unmarked fish one week after immersion in the dye. To ensure that efficiency tests were not compromised by a cleaning cycle, the Eicher screen was manually set to the fishing position and monitored by a BC Hydro electrician. Screens were returned to their original setting following the trial.

4 RESULTS 4.1 Hydrologic Conditions 2012-2013

Mean hourly discharge for the Puntledge River including BC Hydro Gauge 6 flows in Reach C (WSC Gauge No. 08HB084), Comox impoundment dam (CMC) sluice gate releases (Reach B discharge) and the Puntledge Generating Station (penstock turbine flows), was obtained from BC Hydro Power Records, and are illustrated in Figures 4a, 4b and 4c corresponding to the three monitoring periods outlined in Section 3.1.

A high snowpack level in 2011/2012 allowed the Puntledge Generating Facility to operate at maximum generation throughout most of the monitoring period in 2012, except during a few brief events in May when turbine flow was lowered to facilitate DFO personnel to safely conduct snorkel surveys in the lower river (Figure 4a). Weekly pulse flows for summer Chinook migration commenced on 4 July 2012. Peak discharge recorded at Gauge 6 was 96.7 m3/s on 27 May 2012.

From 1 February to 31 March 2013, river flows were relatively stable apart from the 48-hr winter/early spring pulse flows (Figure 4b). From mid-November until the maintenance shutdown at the beginning of April 2013, BC Hydro restricted generation to below 20 MW (maximum turbine flow = 22.5 m3/s). Attempts to increase turbine flows for greater power generation above 20 MW caused the Eicher screens to lock open due to elevated penstock pressure differentials (BC Hydro 2013 unpublished report).


18

May 1 - July 31, 2012

0

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1-M

ay

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ay

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ay

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ay

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ay

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ay

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ay

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ay

2-Ju

n

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un

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ul

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ug

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char

ge (m

3 /s)

Turbine FlowReach B Discharge Gauge #6 DischargeCoho PE TrialsChinook PE Trials

a)

February 1 - April 2, 2013

0

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eb

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eb

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eb

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ar

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Turbine FlowReach B Discharge Gauge #6 DischargeChinook PE Trials

b)

April 3 - July 31, 2013

0

20

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3-A

pr

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ay

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ay

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ay

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n

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un

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un

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l

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l

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ul

27-J

ul

1-Au

g

Dis

char

ge (m

3 /s)

Turbine FlowReach B Discharge Gauge #6 DischargeCoho PE TrialsChinook PE Trials

c)

Figure 4. Puntledge River mean hourly discharge for Reach B (Comox dam sluice gate discharge), penstock Turbine Flows and Gauge 6 below the diversion dam (WSC Gauge No. 08HB084) for the three monitoring periods a) May 1 - July 31, 2012 and b) Feb 1 – April 2, 2013 and c) April 3 – July 31, 2013. Marked fish releases for population estimate (PE) trials are indicated by symbols.


19

BC Hydro conducted a scheduled maintenance shutdown of the Puntledge Generating Station from April 3 - 18, 2013 (Figure 4c). During this period the generating station was not operating (i.e. turbine flow = 0), and flows through Reach C were increased. Following the maintenance shutdown, the generating facility operated at full capacity into early June, and turbine flow averaged 26.5 m3/s. Turbine flow varied between 7 and 27 m3/s for the remainder of the monitoring period, which included turbine flow reductions to accommodate a revised weekly summer pulse flow schedule beginning 13 June 2013. Peak discharge recorded at Gauge 6 was 118.34 m3/s on 9 June 2013.

4.2 2012 Population Estimates (Brood Year 2010 Coho and 2011 Chinook)

A total of 2,369 coho smolts were released for population estimation over the 5 recapture periods of the 2012 sampling season. Upper 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. The minimum number of marks was released in all periods except late May (Table 2) when only 315 smolts were available: this was not problematic, given the very high recapture efficiencies. Chinook releases totalled 1,553 with alternating mutilation marks again employed to identify individual release strata (Table 2).

Table 2. Marking and release timing, abundances and mark types for 2012 a) coho and b) Chinook.

Marking Date Release Date Mark Type1 Number Marked Number Released

a) Coho 11-May 11-May LC 410 409 15-May 16-May UC 420 420 21-May 22-May LC 420 418 29-May 29-May UC 317 315 5 June 9-Jun LC 402 401 13-Jun 16-Jun UC 409 406

Total 2369 b) Chinook 23-May 23-May LC 324 324

9-June 9-June LC 300 299 20-June 20-June UC 300 300 4-July 4-July LC 302 302 12-July 12-July UC 328 328

Total 1553 1 UC upper caudal, LC lower caudal


20

4.2.1 Coho (Brood Year 2010)

Relative daily coho smolt migration, as depicted by the Wolf trap collections, is illustrated in Figure 5a. Since the Wolf trap efficiency was maintained at 100% throughout the program, the numbers of juveniles plotted in Figure 5a are directly comparable and illustrate catch levels over all dates.

Coho Migration May - Aug 2012

0

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ay

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ber c

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a)

Chinook Migration May - Aug 2012

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Total 0+CNGauge 6 Discharge

b)

Figure 5. Daily movement of a) coho and b) Chinook juveniles through the evaluation facility in 2012 with Puntledge River discharge measured at Gauge 6 below the diversion dam. Numbers have been adjusted to account for fish that were marked and re-released upstream.


21

Catches were adjusted to account for recoveries of juveniles that were re-released, following marking, for use in efficiency trials. A total of 13,453 coho smolts were captured during the program. Peak migration occurred on 22 May, with a count of 1,037 smolts: a second, large movement occurred on 1 June (811 smolts) but this was short lived (Figure 5a). Although the timing of migration was very similar to the previous year, it was more concentrated in 2012. In the 10 day period between May 16 and 25, 52% of the total migration from the headpond (6,964 smolts) passed through the collection facility (Appendix A).

Recapture probabilities for 1+ coho were substantially higher in comparison with those calculated in 2011. A total of 822 marks from 2,369 releases were recovered over the course of the study. Unlike the previous year, no periods had low recapture rates and the range was much narrower, from 27.9% to 45.0%, averaging 34.6 % (Table 3a). In contrast, the average recapture probability in 2011 was 19%.

Table 3. 2012 Estimates of recapture probabilities (trap efficiencies) by release stratum for a) 2010 brood year coho, b) 2011 brood year Chinook. Capture probabilities reflect recaptures from a release stratum, specific to the initial recovery stratum.

Release End Date Catch Marked Releases Recaptures Capture

a) 16-May 1,722 409 124 30.3%21-May 3,787 420 153 36.4%28-May 4,293 418 188 45.0%4-Jun 2,288 315 110 34.9%12-Jun 1,407 401 112 27.9%28-Jul 778 406 135 33.3%

Total 14,275 2,369 822 34.6%

b) 8-June 4,736 324 27 8.3%19-June 2,287 299 74 24.7%3-July 2,220 300 80 26.7%11-July 1,506 302 75 24.8%5-Aug 2,037 328 119 36.3%

Total 12,786 1,553 375 24.2%

The initial data matrix for calculation of the estimated coho migration size is provided in Table 4. The extended travel times for some fish skewed recoveries as shown in the matrix where releases in a majority of release periods persisted into the subsequent recovery periods. This did not appear to be a factor in the longer final stratum. Although only a small number of fish was involved, these contributed to bias by reducing the probability of capture in a given stratum, affecting the proportions of


22

marks sampled. The potential for further bias to have arisen from violation of the assumption that marked and unmarked fish are equally susceptible to capture, is examined in a later section.

Table 4. Data matrix for input into the SPASS program, showing the distribution of recaptured marked coho with catch and release totals for the respective strata.

Release Period

No. Released

Recapture Week 1 2 3 4 5 6

1 409 123 1 0 0 0 0 2 420 0 153 2 1 0 0 3 418 0 0 188 1 0 0 4 315 0 0 0 111 7 2 5 401 0 0 0 0 113 6 6 406 0 0 0 0 0 108

Total Catch

1429 3277 5096 1842 1331 1300

These data were first evaluated using the PPE, resulting in an estimate of 41,513 (95% CI 39,272 – 43,753). The matrix was then assessed for validity of the assumptions necessary for complete pooling: that is the summing of all temporal strata to construct the estimate. Two χ2 tests were applied to evaluate a) the consistency of proportions of marked animals across strata and b) whether complete mixing of marked and unmarked coho occurred, based on the recovery probabilities across strata. It should be noted that failure to pass either test does not invalidate legitimate pooling of the data. In fact, few biological populations conform to the conditions required by these tests so that a majority of data produce significant (p<0.05) test results (Arnason et al. 1996). The first test did not support full pooling of the data (χ2 = 42.3 p<0.001 with 5 df) contraindicating generation of an unbiased PPE. The test for equal proportions of marks produced χ2 = 130.3 p<0.001 with 6 df. This also suggests that some degree of bias in the PPE may be present.

The Darroch maximum likelihood (ML) estimator provided a population estimate from the initial data matrix of 39,404 (95% CI 37,293 – 41,515). However, Plante’s G-square and chi-square goodness of fit tests indicated a relatively poor fit to the data (both tests p<0.01). Further stratified population estimates were generated from pooling of the various release and recapture strata: this involves strata manipulation to produce the best fit to the data without excessive strata combination. Few combinations resulted in any improvement and the best fit was achieved by simply combining release strata 1 and 2 and also strata 5 and 6. The Darroch ML estimator for these data produced a population estimate of 39,389 (95% CI 37,281 – 41,478), very similar to the original


23

estimate. Both goodness of fit tests indicated improved fit to the data at p = 0.08 (chi square = 5.09). The probabilities of recapture for the combined strata were very similar to those of the original estimates in Table 3, ranging from 28.1% to 45.3%. Although both of the tests for pooling remained highly significant, the fact that the maximum likelihood estimate lies within the confidence interval for the PPE recommends the latter estimate of 41,513, which has the added benefit of a more precise confidence interval (CV 2.8%). Consequently, we have adopted the Pooled Petersen Estimate of 41, 513 (95% CI 39,272 – 43,753) as the best estimate of coho migration in 2012.

4.2.2 Chinook (Brood Year 2011)

The daily Chinook juvenile catches fluctuated considerably, with two peaks exceeding 500 fish per day and a third just over 450 (Figure 5b): the largest totalled 564 individuals on 31 May. The average daily catch over the study was 128 individuals. A total of 12,411 Chinook were captured between 1 May and 5 August, adjusted for exclusion of efficiency trial releases. There were 375 recaptures from 1,553 marks released.

With the exception of the first release period (8.3% Table 3b), capture probabilities for Chinook showed limited temporal variation (remaining range 24.7% - 36.3%). These values were more similar to those of coho, unlike the lower efficiencies recorded in 2011 which ranged from 9.0% to 18.7% and averaging 13.1% over all periods. In the present study the average capture probability was 24.2%, which was lowered by the initial estimate noted above.

As for coho, individual stratum data were combined to form an overall population estimate for the upper Puntledge system Chinook. The PPE for total Chinook numbers was 50,178 (95% CI 45,984 – 54,373). The data matrix used for this and subsequent calculations is provided in Table 4.

Recaptures of marked Chinook also occurred in periods beyond the designated recapture strata (Table 5). Overall, the percentage of Chinook that were delayed in recapture catches was substantially larger than the equivalent number of coho (6.6% Chinook versus 2.9% for coho). It was assumed that this would result in the usual lack of agreement with the hypotheses that the probability of re-sighting a marked fish is independent of its release stratum and that equal expected mark/unmarked ratios are achieved in the final strata. Consequently, the chi-square tests were not supportive of full pooling of the data i.e. generation of an unbiased PPE (complete mixing test 73.3 p<0.001 4df and equal proportions of marks 191.4 p < 0.001 4df).


24

Table 5. Data matrix for input into the SPASS program, showing the distribution of recaptured marked Chinook with catch and release totals for the respective strata.

Release Period

No. Released

Recapture Week 1 2 3 4 5

1 324 27 0 0 0 0 2 299 0 74 9 0 0 3 300 0 0 83 4 0 4 302 0 0 0 75 4 5 328 0 0 0 0 119

Total Catch

4709 2213 2128 1427 1914

The initial Darroch ML estimate was 84,186 (95% CI 63,576 – 104,796) very much higher than the PPE and far outside the confidence limits of the latter estimate. Having established significant bias in the PPE, attempts were made to improve the fit of the data. Unusually, the matrix was fairly resistant to pooling of release and recapture data, as indicated by Plante’s G-square and chi-square tests. In particular, the analysis was sensitive to combining the first and second recovery strata, in an attempt to smooth the recapture probabilities, which were very different (8.3% versus 27.8% over all recovery strata). The best fit was achieved with limited pooling, combining recapture weeks 3 and 4, although the effect on the estimate was small. The Darroch ML estimator for these data provided a population estimate of 84,263 (95% CI 63,652 – 104,874), with both goodness of fit tests indicating a good fit to the data at p = 0.95 (G square and chi square 0.76 p=0.38 1df). Both of the tests for pooling continued to provide results that were highly significant (complete mixing test 73.3 p<0.001 4 df and equal proportions of marks 187.7 p < 0.001 3df) illustrating the disparity in probability of capture over the recovery weeks mentioned previously. This identifies significant bias in the PPE. Consequently, the best estimate of the proportion of migration that occurred during the study is the Darroch Maximum Likelihood Estimate of 84,263 (95% CI 63,652 – 104,874). This estimate also lies outside the 95% confidence interval for the Pooled Petersen, further indicating that bias is unaccounted for in the latter.

4.2.3 Population estimate for 2012 adipose clipped CWT coho (2010 brood year)

Puntledge Hatchery released a total of ~1.8 million coho fry into Comox Lake in 2011. Of these, approximately 200,000 were adipose clipped and coded-wire tagged (CWT). A relatively small total of 1,374 adipose clipped 1+ age juvenile coho were


25

captured during the study, representing 9.6% of all captures. This was somewhat larger than the 2011 total of 1,291 which comprised 7.0% of catches. Based on the matrix shown in Table 6, the PPE was 6,388 (95% CI 6,106 – 6,669). This estimate has high precision (CV 2.2%) and likely has low associated bias, similar to the estimate for all juvenile coho described previously.

Table 6. Data matrix for input into the SPASS program, showing the distribution of recaptured marked coho with catch and release totals for the respective strata, along with totals for catches of adipose clipped coho.

Release Period

No. Released

Recapture Week 1 2 3 4 5 6

1 409 123 1 0 0 0 0

2 420 0 153 2 1 0 1

3 418 0 6 188 1 0 1

4 315 0 0 0 111 7 2

5 401 0 0 0 0 113 6

6 406 0 0 0 0 0 108

Total Catch

260 568 725 253 167 223

The Darroch ML estimator for the above data provided a population estimate of 6,056 (95% CI 5,787 – 6,325), although with both goodness of fit tests indicating a poor fit to the data at p < 0.01 (G square and chi square = 2.0). While both tests for pooling returned results that were highly significant (complete mixing test 42.3 p<0.001 5df and equal proportions of marks 184.3 p < 0.001 5df) the close agreement between the PPE and Darroch estimates suggests that bias is not of concern. Additional efforts to improve the fit of the data were resisted by the matrix with only limiter pooling tending towards a non-significant result in the chi-square tests. The final matrix combined recapture weeks 5 and 6, which increased the average recapture probabilities for this period and reduced the range of these values over the program (28.1% to 45.3%). The Darroch ML estimate was 6,042 (95% CI 5,776 – 6,307). Although there was little difference in the initial and final estimates, both goodness of fit tests indicated a substantially improved fit to the data at p = 0.33 (G square and chi square = 0.94 1df).

Although the Darroch estimate lies just outside the PPE 95% confidence range, the difference is so small that it is reasonable to ignore any small amount of bias in the latter. A conservative approach is to adopt the PPE as the best estimate. Therefore we recommend the Pooled Petersen Estimate of 6,388 (95% CI 6,106 – 6,669) to represent


26

the proportion of escapement that occurred during the study. This estimate has the additional benefit of highest precision (CV 2.2%).

4.2.4 Population estimate for 2012 CWT Chinook (2011 brood year)

Construction of a population estimate CWT 0 + juvenile Chinook was performed using the release and recapture data detailed in the previous section. Therefore, the matrix for analysis is similar to that used to estimate the numbers of total Chinook juveniles, following incorporation of CWT catches (Table 7). The estimated proportion of CWT Chinook in daily catches was assessed on eight occasions from May to July. However, sampling was not systematic, presenting similar problems to analysis as those encountered in the 2011 program. In 2012, at least one set of observations was generated in each recapture period. However, since the analytical method did not rely on discrete recapture periods for specific mark release strata, the approach to predicting CWT abundance was amended. Sampling for the proportion of CWT’d juveniles was initiated on 29 May and continued the next day. The first proportion was applied to catches up to and including 29 May. The subsequent estimate was applied to the period until a further sampling for CWTs was conducted, on 6 June. Each subsequent estimate was then used to calculate CWT totals for the time period ending with the next sampling date.

Table 7. Data matrix for input into the SPASS program, showing the distribution of recaptured marked Chinook with catch and release totals for the respective strata, along with totals for catches of CWT Chinook.

Release

Period

No.

Released

Recapture Week

1 2 3 4 5

1 324 27 0 0 0 0

2 299 0 74 9 0 0

3 300 0 0 83 4 0

4 302 0 0 0 75 4

5 328 0 0 0 0 119

CWT Catch

3635 1852 1675 1100 1157

During the study 1,493 Chinook were checked for the presence of a CWT, resulting in an average tag incidence of 70.5% (1,053 CWT individuals). Our


27

estimation method, above, resulted in an overall total of 9,044 individuals in the sampled population which is somewhat higher than the 8,706 CWT’d fish that would be estimated using the average tag frequency. However, in the absence of random or systematic sampling, this current method is more likely to have produced totals that are representative of the overall composition of CWT Chinook catches, taking into account the substantial fluctuations in proportions of tagged fish encountered during sampling (48.8% to 85.0%).

A PPE estimate of 36,965 CWT Chinook fry (95% CI 33,893 – 40,038) results from analysis of CWT incidence in the 0+ Chinook population. The estimate was derived using the mark releases reported above for total Chinook (Section 4.2). Consequently, the capture probabilities are the same as in the previous calculation and we expected that this estimate also incorporates some degree of bias. Not surprisingly, the initial analysis resulted in the usual lack of agreement with the hypotheses that the probability of recapturing a marked fish is independent of its release stratum and that equal expected mark/unmarked ratios are achieved in the final strata. Consequently, the chi-square tests were not supportive of full pooling of the data: only the equal proportions test provides a different probability than reported in the previous section for all Chinook, due to the different catch totals for CWT fish (equal proportions of marks 258.7 p < 0.001 4df).

The initial Darroch ML estimate of 63,529 (95% CI 47,728 – 79,330) is much larger than the above total: once again, the PPE confidence interval does not include the ML estimate and appears to be substantially biased. Similar to the total Chinook matrix, pooling of strata to improve the fit of the data was problematic. A reasonable permutation resulted from combining recovery strata 2 and 3, but the best fit occurred from merging weeks 3 and 4. This produced a Darroch ML estimate of 63,591 (95% CI 47,789 – 79,392) with both the G-square and chi-square tests indicating significant agreement (0.76 p=0.38 1df). The MLE is proposed as the most accurate estimate of CWT Chinook migration over the 2012 program. However, it should be noted that this estimate does suffer from unquantified error in the assessment of CWT frequency. Due to the method of calculating CWT incidence, the estimate is potentially an overestimate of the total, but is anticipated to represent a relatively minor discrepancy. Using the average CWT frequency of 70.5% of the total Chinook outmigration gives a total of 59,405 which is only 6.6% lower than the maximum likelihood estimate. We recommend the Darroch ML Estimate of 63,591 (95% CI 47,789 – 79,392) as the best estimate of CWT chinook.


28

4.2.5 2012 Biological Data (Brood Year 2010 coho and 2011 Chinook)

Length frequency histograms for coho and Chinook smolts captured at the Eicher evaluation facility in 2012 are illustrated in Figure 6 a & b. For coho, a fork length of 130 mm was used to arbitrarily differentiate age 2+ smolts from 1+ smolts, as per Bengeyfield (1997). Table 8 summarizes statistics for length (mm), weight (grams), and Fulton’s condition factor (K) for coho and Chinook captured in 2012, where K = (W / L3 ) x 100,000.

Coho 2012

0

5

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15

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45

50

35 40 45 50 55 60 65 70 75 80 85 90 95 100

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190

Fork Length (mm)

Num

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f fis

h

MayJune

1+ 2+

a)

Chinook 2012

0

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60

70

80

35 40 45 50 55 60 65 70 75 80 85 90 95 100

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165

170

175

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190

Fork Length (mm)

Num

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f fis

h

MayJuneJuly

b)

Figure 6. Length frequency histograms for sub-samples of a) coho (1+ and 2+) and b) Chinook (0+ hatchery releases and wild smolts) captured at the Eicher assessment facility in 2012.

Average 1+ coho smolt size (fork length) ranged from 100 mm in May to 96 mm in June. The majority of 2+ coho smolts were captured in May and averaged 144 mm.


29

Statistics on adipose clipped coho smolts were not calculated discretely from non-clipped coho since Puntledge Hatchery marks only a portion of the total coho fry outplanted in the upper watershed, or 200,000 of a total of 1.8 million fry released in 2011.

Captures of coded wire tagged (CWT) Chinook in 2012 were recorded within a few days after release in Comox Lake (May 22, 2012) and observed for the duration of the monitoring period, accounting for between 49% and 85%.of the daily Chinook catch. Average juvenile Chinook size (fork length) throughout the monitoring period ranged from 53 mm in May increasing to 85 mm in July (Table 8). Captures of wild Chinook in May and early June were usually differentiated from CWT hatchery Chinook by their smaller size. Four juvenile Chinook ranging from 99 to 144 mm were captured in May and assumed to be yearling (1+) Chinook.

Table 8. Length (mm), weight (grams) and Fulton’s condition factor (K) for sub-samples of coho and Chinook captured at the Eicher Assessment facility from May - July 2012.

2012 Length (mm) Weight (g) K

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

Coho1 1+ May 175 100 11.55 77 129 10 3.7 4.1 24.2 0.97 0.09 0.72 1.34

Jun 99 96 7.84 84 120 8.5 2.12 5.0 14.5 0.94 0.06 0.78 1.14

Coho 2+ All 55 144 10.71 130 181 29 7.5 19.2 61.4 0.95 0.06 0.83 1.14

Chinook2 0+ May 170 53 8.33 36 72 1.6 0.83 0.3 3.9 1.00 0.16 0.51 1.84

Jun 210 74 6.33 56 90 4.1 1.11 1.7 7.9 1.07 0.06 0.84 1.19

Jul 169 85 6.78 61 108 6.5 1.52 2.4 12.7 1.02 0.08 0.87 1.37 1 combined unmarked (wild and hatchery) coho and adipose clipped (hatchery only) coho 2 combined unmarked (wild) and coded wire tagged (hatchery released) Chinook

4.3 2013 Population Estimates (Brood Year 2012 Chinook)

4.3.1 Emergent Chinook fry and smolts

The failure to sample the Chinook fry movement during the period of maintenance from April 3 to 18, effectively split the population estimates into two series, bracketing the period of missing data. There were no available data sufficient to accurately interpolate between these series, although a crude estimate was constructed,


30

based on the variance over catches in the month prior to closure of the assessment facility (see below).

Between 8 February and 2 April (spring period), a total of 1,339 Chinook fry were captured, excluding marked releases, with a daily maximum catch of 116 fry on 20 March. Following the closure of the evaluation facility during the maintenance period, a further 1,856 fry were collected between 19 April and 2 August, with a daily maximum of 72 individuals on 21 June (Appendix B). The pattern of daily migration is illustrated in Figure 7.

In the latter period, the numbers of Chinook fry captured were substantially lower than the equivalent in 2012, where the daily peaks in movement exceeded 450 fish on three occasions. In 2013, more than 60 fry were captured on only two occasions during the summer. The lower catches would be expected since fewer adults spawned above the diversion dam in 2012 (167 adults in 2012 versus 350 in 2011), and no coded-wire tagged Chinook were released in Comox Lake in 2013.

Chinook migration Feb - Aug 2013

0

20

40

60

80

100

120

3-Feb 23-Feb 15-Mar 4-Apr 24-Apr 14-May 3-Jun 23-Jun 13-Jul 2-Aug

Num

ber c

aptu

red

0

20

40

60

80

100

120

Dis

char

ge (m

3 /s)

TOTAL 0+ CN Reach B Discharge

Figure 7. Daily catches of 0+ Chinook fry in the evaluation facility.

Capture probabilities for the Wolf traps were extremely low during the initial collection period, ranging from 1.9% to 3.5% (Table 9). Only 19 Chinook were recovered from 650 marked releases. This likely resulted from impingement losses of marked fry during a sustained period when the Eicher screen was coated in debris.


31

Efficiency trials conducted during this period, prior to screen maintenance, were extremely low (see Section 4.6). Consequently, losses of both marked and wild Chinook fry are anticipated to be very high: we have assumed that the losses of both groups were proportional for the purposes of population estimation. Temporal changes in the capture efficiencies measured in February and March were not significant (Pearson chi-square, χ2 = 1.14, df = 2, p = 0.564) which would permit pooling of the data over the three collection periods to form the estimate. However, individual period estimates were calculated to facilitate analysis of possible sources of bias (section 4.4.2) and to enable calculation of a crude estimate of population size from interpolated data.

The estimate of total Chinook numbers migrating during the spring was 39,744 (95% CI 13,219 – 66,268). Precision was poor overall (19.7% for all data) and ranged from 30.8% to 40.0% among strata. Interpolation, based on the variance characteristics of early catches, suggested that a further 17,000 fry migrated during the shutdown for maintenance. This number is highly speculative, however, and has not been incorporated into the overall estimate.

The first release of marks in the summer period was confounded by an unplanned turbine shutdown which resulted in a very high proportion of marks not being entrained. Only 3.6% of the mark group were recovered: a total of 11 recaptures from a release of 306 marked fry. Although this proportion is similar to the spring period, in that case losses of both marked and wild Chinook extended throughout the strata, consequently, the capture probability was relatively stable. In the case of the 27 May releases, the transient nature of the event would have affected predominately the recovery of marks, with subsequent re-establishment of generating flows allowing an increased capture rate of wild fry beyond the period when marked fish were available to be recaptured. To compensate, the data from the May release were prorated for a five day period, and incorporated into the second recapture stratum, resulting in a capture efficiency of 40.2% (Table 9). This provided an estimated 2 recaptures from 61 mark releases, and adjusted the overall data for the first summer stratum to 146 recaptures from a catch of 1,247 fry (Table 9). In contrast to the spring, capture efficiencies in the summer period were very much improved and ranged from 16.6% to 41.9%, with an average of 32.0 % (Table 9). There was sufficient temporal variation (Pearson chi-square, χ2 = 98.3, df = 5, p < 0.01) so that the data could not be pooled over all periods to provide a Petersen estimate due to the potential for incorporation of bias. Consequently, the individual period estimates were summed to provide an overall population estimate. The potential bias resulting from heterogeneous capture efficiencies is investigated in section 4.4.2.


32

A total of 7,252 Chinook fry (95% CI 6,217 – 8,287) was calculated for the summer portion of the migration. The precision of the estimate was extremely good for combined data (3.7%) with the largest variance associated with the final stratum estimate (Table 9). As capture probabilities increased, the precision of strata estimates also improved, with CV < 5% in stratum 3 (Table 9).

Our final estimate of 2013 fry movement results from combining the two periods of migration (not including interpolated data) to give an underestimate for the overall migration of 46,996 individuals. The total migration may have approached 65,000 Chinook fry if the interpolated data approximated the actual number of migrants in early to mid April.

Table 9. Estimates of recapture probabilities (trap efficiencies) by release stratum for Chinook. Capture probabilities reflect recaptures from a release stratum, specific to the initial recovery stratum.

Release End Date

Catch Marked Releases

Recaptures Population Estimate

upper 95% CL

lower 95% CL

CV Capture

Probability

a)

13-Mar 515 240 8 13,817 22,146 5,488 30.8% 3.3%19-Mar 274 210 4 11,605 20,696 2,514 40.0% 1.9%02-Apr 569 200 7 14,321 23,425 5,217 32.4% 3.5%

Interpolated data1 683 17,186 28,123 6,248 32.5% 3.5%Total2 1358 650 19 39,744 66,268 13,219 19.7% 3.1%

b)

19-Jun 1,247 363 146 3,090 3,451 2,729 5.9% 40.2%27-Jun 415 300 125 994 1,104 884 5.6% 41.7%04-Jul 238 303 127 568 618 517 4.6% 41.9%16-Jul 241 303 59 1,226 1,465 987 9.9% 19.5%

02-Aug 230 350 58 1,374 1,648 1,101 10.2% 16.6%Total 2,371 1,680 515 7,252 8,287 6,217 3.7% 32.0%

1 These data reflect only an estimate of potential catches, based on the variance of earlier data. The capture probability, and hence recaptures, was assumed to have been the same as in the preceding stratum. 2 Totals do not include the estimate from interpolated data, which is included only to suggest the possible magnitude of the migration during the maintenance period.

4.3.2 2013 Biological Data (Brood Year 2012 Chinook)

Length frequency histograms for Chinook captured at the Eicher evaluation facility from February to the end of July, 2013, are illustrated in Figure 8. In 2013 coded wire tagged Chinook from Puntledge Hatchery were not released into Comox Lake due to insufficient numbers of fry available to tag. Therefore all Chinook captures


33

Figure 8. Length frequency histograms for sub-samples of wild summer-run Chinook captured at the Eicher assessment facility between February and July 2013.

February / March

0153045607590

35 40 45 50 55 60 65 70 75 80 85 90 95 100

105

110

115

120

125

130

135

140

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150

Fork Length (mm)

Num

ber o

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n = 96

April / May

05

1015202530

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1015202530

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n = 93


34

at the evaluation facility in 2013 represent natural production from brood 2012 summer Chinook that spawned above the diversion dam, with the exception of 1+ Chinook captured in April/May that were of either wild or hatchery origin.

Average juvenile Chinook size (fork length) throughout the monitoring period ranged from 39 mm in February/March, increasing to 92 mm in July (Table 10).

Table 10. Length (mm), weight (grams) and Fulton’s condition factor (K) for sub-samples of Chinook captured at the Eicher Assessment facility from February - July 2013.

2013 Chinook Length (mm) Weight (g) K

Timing n Mean SD Min Max Mean SD Min Max Mean SD Min Max

Feb/Mar 96 39 1.61 35 44 0.5 0.10 0.3 0.9 0.84 0.16 0.58 1.52

Apr/May 49 49 5.38 37 62 1.26 0.43 0.3 2.4 1.02 0.14 0.59 1.29

Jun 107 75 7.29 60 95 4.46 1.37 2.1 8.8 1.03 0.08 0.86 1.28

Jul 93 92 7.84 69 110 8.1 2.03 3.2 13.8 1.02 0.07 0.81 1.19

4.4 Bias

4.4.1 2012 coho and Chinook populations

The 2012 study results diverged substantially in the degree of precision generated by the respective data for Chinook and coho. In the case of the later, high precision was generated through the PPE for both total population size (CV = 2.8%) and for AD clipped juveniles (CV = 2.2%). In contrast, both total and CWT Chinook numbers were best estimated by a maximum likelihood method, with substantial bias evident in the PPE.

Unfortunately, the analytical package provided by Arnason et al. (1996) does not include formal tests for bias incorporated by the various estimators. Generally, the PPE is the more precise estimator, but can incorporate substantial bias if there are differences in capture rates over time, particularly if this occurs between marked and unmarked fish. Examination of the potential degree of bias was, therefore, performed by bootstrapping.


35

Bootstrapping indicated that, for coho, recovery of marks in pooled strata agreed strongly with the underlying hypergeometric distribution and that precision was increased over that available from the normal approximation. The confidence intervals indicate that bias in the estimate was very low: the bias corrected 95% CI was extremely small (1.1%) as were the uncorrected bounds. Figure 9a illustrates the frequency distribution of bootstrap values, which, although close to the normal distribution, showed some loss of symmetry at medium values (Anderson-Darling statistic 1.026 p=0.01).

The ratio of skewness 0.11 to its standard error 0.077 was 1.4, indicating that the asymmetric tails shown in Figure 9 are not sufficient to bias the estimate of population size. Similarly, the degree of kurtosis (-0.25) does not suggest a significantly peaked distribution (kurtosis/se ratio 1.6) where central values are over represented (Figure 9). Consequently departure from normality is moderate and we do not expect that the degree of error incorporated into the bootstrap estimate would be large.

The results for Chinook were similar, although precision was lower for both the Darroch ML and bootstrap estimates (Table 11). Bootstrapping again provided tighter confidence intervals (bias corrected 8.9%), although the two estimates were essentially equal. In this case, the frequency distribution (Figure 9b) did not depart from normalcy (Anderson-Darling statistic 0.52 p=0.15): the slight degree of kurtosis indicated by the peak in middle level replicates was not significant. However, this raises the question of how significant bias was incorporated into the PPE, which accounted for only 59% of the MLE (50,178).

Table 11. Comparison of levels of precision for the 2012 total coho and Chinook population estimates, obtained from 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 Estimator Estimate Variance 95% C I CV

a) coho

Normal approximation PPE 41,513 1.31E+06 39,272 – 43,753 2.8

Bootstrap (uncorrected) 41,568 8.95E+07 40,662 – 42,505 1.1

Bootstrap (bias corrected) 40,624 – 42,464 1.1

b) Chinook

Normal approximation MLE 84,263 1.11E+08 63,652-104,874 12.5




36

b

a

Figure 9. Frequency distribution of 2012 population estimates for a) total coho and b) total Chinook juveniles from a parametric bootstrap procedure involving 1,000 iterations. The superimposed curve illustrates departure from normality.


37

The assumptions that are required to be fulfilled for the unbiased estimation of population size using a Petersen estimator have been dealt with in detail by a number of authors e.g. Seber (1982), Arnason et al. (1996). They are examined here briefly, in conjunction with assessment of compliance in the present study.

a) No mark loss – the primary issue here is short term mortality effects i.e. between release and recapture, although reporting of marks can influence the estimate, particularly if marks are indistinct or susceptible to removal. Marking mortality was assessed during the program, and was found to be inconsequential. Only 1 incidence of mortality was recorded on one occasion, 9 June, from a total of 300 marked Chinook.

b) Population closure – closure has different implications for stratified versus non-stratified designs. For this project, it requires that all of the population is encompassed within the sampling period. At the conclusion of the project only a small number of Chinook were still being caught in the Wolf traps (63 in the final 5 days; Appendix A), and there was sufficient time following the final release of marked Chinook on 12 July to be certain that no further recoveries would be made: sampling concluded on 5 August. While the effect on the estimate would be small, we acknowledge that sampling was concluded prior to cessation of migration, and, consequently, this would have contributed to a slight underestimate of population size.

c) All fish share the same probability of capture, or, an equal probability of being examined for marks. Since the Wolf traps were set to 100% efficiency for all entrained fish, this avoids the potential for size selectivity to influence catchability, which is a feature of most capture gear (Ricker 1975). In any event, increased catchability of a segment of the migration does not necessarily produce bias in the stratum estimates. Since the marked releases constitute a random sample, the recovery sample can be selective as long as this is independent of mark status (Seber 1982). It was assumed that the release sites were sufficiently far from the capture sites that random mixing of marks with the unmarked population would occur. This was assessed in the 2010 study and no difference in the recovery of marked fish was noted among three release locations (Guimond and Taylor 2011). Additional discussion appropriate to this assumption is provided below.

d) Constant probability of capture – ideally, catchability should remain stable throughout the study. A particularly important source of uncertainty is the variation in capture probability over time, which can be exacerbated by the


38

potential for smolts to move in schools, as opposed to moving independently. This may result in greater than expected variation in capture probabilities (overdispersion) and increased bias. Temporal stratification, as employed in the present study, can minimize bias by compensating for events, such as fluctuations in discharge. Throughout the study probability of capture was high and had low associated variability for coho (mean 34.6% SD 0.059). For Chinook, capture probability was depressed in the early stage of the outmigration (8.3%) and showed greater variability (SD 0.10 range 8.3 – 36.3 Table 3). This may have reduced the overall precision of the estimate, but the effect was small, as indicated in Table 11.

e) All marks are recovered or move past the recapture site – this generally addresses the potential for marks from a release stratum to occur in more than one recovery period and was accommodated in this study by the use of maximum likelihood analysis. As mentioned above, the possibility that some portion of the final mark releases may not have had the opportunity of being sampled in Wolf trap catches was negated by the length of time that sampling continued after the final mark release (24 days versus the average capture period of 12.6 days).

f) Finally, minimum sample size is of concern, but is generally dealt with through calculation of appropriate levels of marks to be released into the population, as in each year of the current studies. The 2012 coho and Chinook data fully comply with the requirements for mark releases and subsequent level of sampling of the migration. Under unusual circumstances, however, appropriate sampling may fall below the conventional levels required to ensure that substantial bias is not incorporated into the estimates. This is relevant for the 2013 emergent Chinook program and is explored more fully in the following section.

The use of temporal stratification in assessing population size provides for some degree of control over variation in capture probabilities caused by factors such as water temperature and hydrological events that influence migration parameters. Since both marked and unmarked fish were expected to be equally affected, variation was expected to be low, however, patterns of movement of juveniles may have resulted in discrepancies in how well mark releases represent overall movement of wild fish within a stratum. In 2011, BC Hydro instigated an unusually high frequency of water releases, designed to proactively control flood events generated by the high snowpack.


39

Consequently, recovery of marked fish took place over widely differing river stages and mark releases were performed on two occasions in June, at higher than normal flow levels. The marks that were released during higher flows experienced lower recapture probabilities, particularly in the case of coho, although for both species 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=<0.001). In 2012, there was less variation in the flow regime, with only one substantially higher flow during a release of marked coho juveniles (77.95 m3/s versus the mean for all releases of 42.11 m3/s SD 17.8 measured at the CMC sluice gate). Even so, recovery of marks was moderately negatively correlated with discharge (Pearson correlation coefficient -0.62 p=0.184). For Chinook, there was lower variability in discharge (mean = 33.08 m3/s SD = 3.46) and a slight positive correlation was found with mark recoveries (Pearson correlation coefficient 0.20 p=0.74). It appears that in 2012, there was no significant degree of bias that resulted from discharge levels during marked Chinook releases. Similarly, during the period 9 May to 3 June only a weak linear relationship was evident between total catches in the Wolf traps and discharge (Figure 10; r2 = 0.10 p = 0.11). This suggests that the overall pattern of movement of Chinook was not strongly influenced by discharge; therefore, we do not anticipate that the integration of marked fish into the population would be affected by the flows encountered on the release date.

Figure 10. Relationship between catches of juvenile Chinook and discharge measured at the CMC sluice gate.


40

4.4.2 2013 Chinook population

In contrast to the 2012 population estimates, a number of factors contributed to significant bias in the early Chinook estimate of migration. The most prominent was the loss of capture efficiency by the evaluation facility, most probably caused by impingement of fry on the Eicher screen (see section 4.6). This resulted in substantial bias in the stratum estimate, by reducing the total number of recaptures below 7 individuals, the level at which Robson and Regier (1964) calculated that we can be 95% certain that bias associated with the estimate is negligible. Validity in a Petersen estimate necessitates that the product of the number of marks ( hM ) and the catch size

( hn ) is at least 4 times the population size ( hN̂ ). The small catch size in stratum 2 (274

individuals Table 9) resulted in the product just exceeding this level, at 4.96 times the stratum estimate of 11,605 fry. This, in itself is not a significant source of bias: Robson and Regier (1964) calculate that a product of 3 hN̂ will generate an underestimate of 5%,

while 4 hN̂ will result in ~2%. However, in combination with the failure to recapture 7

marks, the likelihood of significant bias in the estimate is high. Strata 1 and 3 had larger catches (Table 9) and, therefore, a more substantial multiple of population size than stratum 2. It should be noted, however, that the calculated products of 9 and 8, respectively, for these strata are in stark contrast to those in the early summer periods, which ranged from 125 to 146, providing a much greater degree of protection against bias in the population estimate.

This is evident from the bootstrap data which provide an estimate of 48,049 fry (95% bias adjusted CI 32,527 – 105,481), in the spring migration, considerably higher than the Petersen estimate of 39,744 (Table 12a). The former also indicates a significant departure from normality (Andersen Darling statistic 36.5 p <0.01) due to a number of bootstrap replicates in excess of 100,000 fry (Figure 11a). Consequently, there is a shift in the confidence bounds due to the asymmetry in the distribution. This was significant and relatively severe (the ratio of skewness 1.74 to its standard error 0.077 was 22.6). The degree of kurtosis (4.06) indicates a significantly peaked distribution (kurtosis/se ratio 26.2) where central values are over represented (Fig 11a). However, the left, or negative skewness, does not counteract the right tail of the distribution, consequently the bootstrap data provide a larger overall estimate of the population, driven by the extremely low capture probability in stratum 2, with very low mark recoveries. This is the primary source of underestimation of the spring migration, although the numbers of recaptures in the other two strata were only slightly better (Table 9).


41

Figure 11. Frequency distribution of 2013 population estimates for a) early and b) late Chinook juveniles from a parametric bootstrap procedure involving 1,000 iterations. The superimposed curve illustrates departure from normality.


42

The summer estimate provided by bootstrapping was much closer to the stratum estimates at 7,182 (95% bias adjusted CI 6,587 – 7,531). Similarly, the bootstrap CV as substantially closer to that of the stratum estimates (Table 12b).

The shape of the bootstrap distribution (Figure 11b) was normal (Andersen Darling statistic 0.56 p = 0.15), with only slightly elongated right tails: skewness (0.241) was just significant (skewness/se ratio 3.1). Kurtosis showed no significant departure from normality (0.253, kurtosis/se ratio 1.63). The similarity between the Petersen estimate and the bootstrap estimate indicates that bias in the estimate was very low: similarly the bias corrected 95% CI was very small (6.6%) as were the uncorrected bounds. Although, as described above, the first, combined, recapture stratum was very large, this did not contribute to appreciable bias in the estimate.

Table 12. Comparison of levels of precision for spring and summer Chinook population estimates, obtained from 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) spring

Normal approximation 39,744 6.11E+07 13,219 – 66,268 19.7



b) summer

Normal approximation 7,252 6.83+04 6,217 – 8,287 3.7


Bootstrap (bias corrected) 6,587 – 7,531 3.4 4.5 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


43

range 9.6% to 37.0%, Chinook range 8.8% to 22.1%). However, this is not a true reflection of the fraction of migrants entrained by the intake contributing to the assessment facility.

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. Over five trials conducted in 2012, the mean number of fish entrained by intake #3 was 57.5% (95% CI 52.7 – 62.3%) of all tags detected (Table 13), while intake #4 captured 42.5% (95% CI 37.6-47.3%). These proportions are reduced when the total number of tags released is employed in the calculation, including those that were not located by either of the antennas. Accordingly, intake #3 collected 43.9% and intake #4 captured 32.4%. The latter calculation is in better agreement with the proportions found before the use of PIT tags, however, the estimate is larger than the means of the estimates described above, 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. A substantial proportion of tags were never located (23.8%), presumably having bypassed the intakes and migrated over the diversion dam spill.

Table 13. Fate of PIT tags released above the penstock intakes in 5 trials between May 14 and June 16, 2012. 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 found1

1 106 55 40 11

2 105 29 48 28

3 106 46 31 29

4 103 55 24 24

5 102 44 26 32

Totals 522 229 169 124 1some tags were not detected nor recovered by trap collection and presumably bypassed both intakes and migrated over the diversion dam spill


44

While the results of the five tests were somewhat variable, only one test indicated that intake #4 entrained more fish (trial 2, 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 overall (z = 4.25 p = <0.001). However, we also wanted to be certain that the degree of precision in the estimates is great enough to also reject the null hypothesis of equal proportions of entrainment. Testing the entrainments against 50% in each case indicated a significant difference. That by intake #3 was significantly higher (z = 2.79 p=0.003), while 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 repeated the experiment in 2013, again using PIT tags, in a series of 7 trials between May 3 and June 27, 2013. The results from 6 trials are reported in Table 14: the 7th trial on May 26 was considered to be incomplete due to an unplanned spill at the diversion dam. These results corroborated the 2012 findings, with extremely similar proportions of tags collected by the two intakes. Intake #3 again entrained a greater proportion of coho (56.2% of all recoveries 95% CI 52.7 – 62.3%) in comparison with intake #4 (43.8% 95% CI 38.7 – 48.9%). The proportions were significantly different (z = 3.34 p = 0.001). As in 2012, the former was also significantly greater than 50% of tags collected (z = 2.361 p = 0.009), while the latter was significantly less than 50% (z = -2.355 p = 0.009).

As for the 2012 data, both proportions were reduced by incorporating all PIT tag releases into the calculation. The mean percentage of all releases entrained by intake #3 over the 6 trials was 33.8% (95% CI 30.0 – 37.6%), while intake #4 captured 26.4% (95% CI 22.9-29.9%). While these percentages are lower than those calculated for 2012, they are comparable in term of the relative capture efficiency of the two intakes: the ratio of entrainment in 2012 was 1.35:1 and 1.28:1 in 2013. Intake #3 again captured significantly more juvenile coho than intake #4 (z = 2.818 p = 0.005).


45

Table 14. Fate of PIT tags released above the penstock intakes in 6 trials between May 3 and June 27, 2013. A seventh trial was incomplete due to an unplanned spill at the diversion dam.

Trial Tags

released Intake # 3 Intake # 4

Generating

flow

1 100 39 22 24MW

2 99 33 41 24MW

3 102 37 36 24MW

4 104 48 27 10MW

5 100 22 22 10MW

6 101 26 12 24MW

Totals 606 205 160

Because there were substantially lower generating flows during two of the trials (Table 14) we also compared the mean entrainment rates at 24MW versus 10MW. Although intake #3 appeared to capture a larger percentage of tags at both flow rates (Table 15), the difference was significant only for the 10MW generating flow (z = 2.295 p = 0.022), in contrast to the overall results. There was no significant difference in the percentages of recaptures between the flow levels at either intake #3 (z = -0.180 p = 0.857) or #4 (z = 0.955 p = 0.339).

Table 15. Proportions of PIT tagged coho entrained by the intakes at two generating flows.

Generating

flow Intake # 3 95% CI Intake # 4 95% CI

24MW 33.6% 29.9 - 38.2 27.6% 23.2 - 32.0

10MW 34.3% 27.8 - 40.8 24.0% 18.2 - 29.9

Combining both years of data indicates that intake #3, on average, entrains 56.9% of coho that were recaptured (95%CI = 53.4 – 60.4). Intake #4 was responsible for collecting the remaining 43.1% (95%CI = 39.6 – 46.7%). These data are highly significantly different from each other (z = 5.323 p = <0.001) and from a null hypothesis of equal probability of captures (z = 3.813 p = <0.001).


46

4.6 Eicher Screen Efficiency

Results from several experimental trials to assess the efficiency of the Eicher screen to divert (emergent) Chinook fry are presented in Table 16. The trials involved both Chinook and chum fry (from Puntledge Hatchery) released directly into the penstock through the 3 inch delivery pipe, and, additionally, from the dam at the intake (trash rack), over two sampling periods: Feb-March, prior to the maintenance (i.e. pressure washing and inspection) of the Eicher screens, and April-May following the maintenance period. The lower than expected results obtained during the first 2 assessments of screen efficiency in February in the penstock (i.e. only 1 fish was recovered from >240 fish released), prompted further investigations at the intake trash rack using the delivery system employed in 2010 (Guimond and Taylor 2011). Chum salmon fry were also used as test fish due to their closer similarity in size (fork length) to wild Chinook compared to hatchery Chinook (mean FL = 40 mm for wild summer Chinook, 42 mm for hatchery chum, and ~50 mm for hatchery fall Chinook). Screen efficiency results for both chum and Chinook before screen maintenance were similar and were combined for an overall mean screen efficiency of <0.1% from the penstock releases, and 28.6% from the intake releases (Table 16). Our previous concerns that test fish released at the intake could swim upstream into the forebay were somewhat mitigated by the high turbine flows and smaller size of fish used compared to the trials using larger coho and Chinook smolts in 2010 (Guimond and Taylor 2011; see Section 5).

Screen efficiency (i.e. percent recovery of test fish) significantly improved following the April maintenance period for both Chinook and chum fry at each release location, (penstock and intake). Overall, the Chinook releases after maintenance, and at maximum generation (i.e. turbine flows ~26.8 m3/s) were not significantly different between the penstock and intake recoveries (z = 0.042 p = 0.966). Totals of 597 and 489 releases, respectively, had associated recoveries of 511 and 419 individuals and had near identical efficiencies of 85.6% and 85.7% (Table 16). Results from tests using chum fry were more variable at each location, and percent recovery was lower on average than Chinook. These fish demonstrated significantly higher recoveries when released at the intake compared to releases directly into the penstock (z=4.99 p= <0.01). This may be due to the fact that marked fry released behind the trashrack at the intake get distributed into the upper half of the penstock and therefore only encounter the upper half of the Eicher screen and are therefore less likely to be impinged. Fish introduced into the penstock at the base of the Eicher screen, encounter almost the entire face of the screen before entering the by-pass pipe. This likely causes a higher degree of impingement on the screens. Overall, the results from the tests at the two


47

locations, for both species, confirm that the Eicher screens are unable to meet design specifications of >95% diversion for smaller juvenile salmonids. Even after cleaning, screen efficiency was generally lower (i.e. Chum 33.7% to 70.3% and Chinook 77.2% to 91.5%) than the > 95% efficiencies calculated for coho, Chinook and steelhead fry at Elwha dam (EPRI 1992). When operating under a high debris load (before cleaning), efficiencies only reached a mean level of 28.6% (Table 16).

Table 16. Numbers of Chinook and chum fry released in the Puntledge penstock and at the intake during screen efficiency trials conducted before and after screen maintenance. Recoveries were over a 24 hour period and represent an absolute count (Wolf traps were fishing at 100%).

Penstock Intake

Date of release

Species Turbine

Flow (m3/s) Number Released

Number Recovered

% Number Released

Number Recovered

%

A. Before Maintenance

21/Feb/13 Chinook 11.4 240 1 0.4 -

28/Feb/13 Chinook 21.5 204 0 0.0 -

7/Mar/13 Chinook 22.0 - 100 25 25

13/Mar/13 Chinook 22.4 - 100 34 34

20/Mar/13 Chinook 22.4 - 33 9 27.3

20/Mar/13 Chum 22.4 - 82 22 26.8

30/Mar/13 Chum 21.7 201 0 0.0 -

Overall % Recovery <0.1 28.6

Standard Dev - 3.9

B. After Maintenance

24/Apr/13 Chinook 26.8 198 160 80.8 101 78 77.2

2/May/13 Chinook 26.9 199 184 92.5 188 172 91.5

9/May/13 Chinook 26.7 200 167 83.5 200 169 84.5

Overall % Recovery 85.6 85.7

Standard Dev 6.1 7.1

24/Apr/13 Chum 26.8 208 40 19.2 101 34 33.7

2/May/13 Chum 26.9 264 202 76.5 215 146 67.9

9/May/13 Chum 26.7 239 99 41.4 209 147 70.3

Overall % Recovery 48.0 62.3

Standard Dev 28.9 20.5

16/May/13 Chinook 11.8 200 167 83.5 199 190 95.5

16/May/13 Chum 11.8 200 173 86.5 220 145 65.9


48

An additional single release of test fish (both Chinook and chum) was conducted at each location on May 16 at a lower generation (10 MW), or a turbine flow of 11.8 m3/s. Since we were only able to complete one trial at this lower flow, the results provide little insight into any influence of reduced turbine flow on fish passage at the screens. Releases at the intake at much lower penstock discharges may increase the ability for test fish to avoid penstock entrainment during the trial. Video monitoring at the intake during a release of chum on May 16 seemed to confirm that some fish were able to swim upstream upon release at the intake. Unfortunately, we do not have a comparable observation during a release at high discharges. Chum fry during this last trial on May 16 were much larger (65-70 mm) than test fish (both Chinook and chum) released in the early trials in Feb/March (45-55 mm FL). Studies on chum fry swimming ability have shown that burst swimming speed increases with fry length, suggesting a rapid improvement of swimming ability during the fry stage (Ohkuma et al. 1998). Therefore smaller fish in earlier releases under higher discharges would have likely had less ability to avoid entrainment.

5 DISCUSSION

Contribution/survival of coho smolts from fry outplants in the Comox Lake watershed over the past 3 years of assessments at the Puntledge diversion dam Eicher screens were much lower in 2012 than previous years (Table 17). Although the population estimate is an underestimate, since we know that coho migrate all year long, a comparison over the 3 years seems to indicate that larger fry releases may not necessarily result in greater contributions/survival.

Table 17. Summary of coho fry releases, captures and population estimates at the Eicher Evaluation facility from 2010 to 2012.

Sampling

Year

Total CO fry

releases yr

prior1

May-July

CO Smolt

captures

at EEF

CO

Pop'n

Est 2 95% CI

%

Survival

Ad Clip

CWT CO

releases yr

prior

Ad clip

CO

Pop'n

Est 95% CI

%

Survival

Adults above dam3

Brood

Year #

2010 417,000 15,511 84,513 75,731 - 93,296 20.3 - - - - 2008 571

2011 1,800,000 18,541 98,295 81,408 - 115,182 5.5 200,000 7,789

7,032 – 8,545 3.9 2009 2,635

2012 1,800,000 13,453 41,513 39,272 -43,753 2.3 200,000 6,388

6,106 – 6,669 3.2 2010 n/a

2013 800,000 Not yet calculated 200,000 Not yet calculated 2011 333

EEF - Eicher Evaluation Facility; 1 Numbers are approximate; 2 Includes hatchery and wild coho recruitment; 3 Numbers are from transports to Comox Dam and video counts above the Diversion Dam


49

The coho smolt enumeration counts could not differentiate between wild smolts and unmarked hatchery smolts that originated from fry outplants. Population estimates in this report include a combined contribution. For the two fry release years (2011 and 2012) when fry releases were both ~1.8 million, the percent contribution from the hatchery (represented as the adipose clipped component) were quite similar, in contrast to the overall or total survival (5.5% in 2011 versus 2.3% in 2012). Based on the numbers of coho adults that accessed habitat in the upper watershed, either from direct trap and truck adult transports or from observed migration counted by an underwater camera at the diversion dam fishway, this wild component potentially varies yearly, with the greatest potential wild contribution occurring in 2011 (BY 2008), which may account for the larger combined contribution.

Interestingly, the highest survival (20.3%) was in 2010 when hatchery fry releases were lowest. The differences in survival versus hatchery fry loading densities may be linked to the carrying capacity of Comox Lake. This is the focus of a collaborative study with federal, provincial and community partners, and FWCP funding, to examine coho smolt production versus fry loading densities in the upper watershed, mean smolt size, and summer phytoplankton and zooplankton densities. The overall goal of this study is to provide agency direction for optimizing fish management strategies in the upper watershed, to benefit both resident and anadromous stocks. As DFO begins to implement their long term strategy of increasing coho utilization in the upper watershed, it is paramount that these factors are adequately assessed to ensure that the coho fry outplants are appropriate and that the risks to native species are minimized.

The objective of the screen efficiency assessment in February/March was to determine how well the Eicher screens divert emergent Chinook (mean FL = 39 mm) from entrainment in the turbines. Based on the results from tests conducted prior to and following the maintenance shutdown, the Eicher screens performed inadequately when they were in poor condition, (i.e. fouled with debris). Only 1 fish was recovered from 3 releases made directly into the penstock immediately upstream of the Eicher screen.

Two factors are germane to the very low recovery in the early 2013 trials (efficiency of <0.1%). The first is the location of the delivery pipe which is in close proximity to the screen. As we noted and observed from previous trials on coho and Chinook smolts, fish released at this site have no time to re-orient themselves in a “head upstream/tail downstream” position prior to passage over the screen (Guimond and Taylor 2012). This has been confirmed by visual observations in 2013. During the maintenance shutdown, BC Hydro installed a viewing stack on one of the existing skylights of the penstock situated over Eicher screen #2, in order to conduct underwater


50

video monitoring of fish releases at the screen while the generating facility was back online (Appendix C Photo 6). When screen efficiency was re-assessed following the maintenance period, we were also able to directly observe fish behaviour during passage at the screens through the viewing ports which had been partially cleaned. Similar to Bengeyfield’s observations in 1994 (Bengeyfield 1995) we observed chum, and to a lesser degree, Chinook fry, becoming impinged on the Eicher screen, or contacting and sliding up the surface of the screen temporarily (Appendix C Photo 7). This was more evident from releases directly into the penstock compared to those at the intake, and more frequent during higher turbine flows.

The second factor is the very high level of debris on the screens during the spring efficiency trials. When the penstock was drained for inspection/maintenance in April 2013, the screens were found to be almost completely covered by a thick mat of aquatic grass and other vegetation (Appendix C Photo 4). There was also an area along the length of Screen #2 where a piece of gasket was missing, thus exposing a wider gap in the screen through which small fish could potentially be entrained. This gap was approximately 7 mm wide, compared to the Eicher screen wedgewire bar spacing of 2.5 mm. Several dead chum and Chinook fry from test releases that had become impinged on the screen were also recovered (Appendix C Photo 5). This is likely the predominant factor in the low recoveries, since even the additional releases behind the trash rack intake at the dam, ~20 m upstream of the screen (average recovery 28.6 %), suggest that smaller fish are more likely to become impinged on the screen, despite being oriented in a more natural upstream position. Previously, releases at this location at the dam were thought to incorporate uncertainty regarding test fish swimming into the forebay and not becoming entrained in the penstock. Coho and Chinook smolts released in 2010 at an average discharge of 26.6 m3/s produced diversion efficiencies, over a 24 hour recapture period, of 91% and 72% respectively (Guimond and Taylor 2011). However, at the turbine discharges tested before (avg = 22.3 m3/s) and after (avg = 26.8 m3/s) maintenance in 2013, (Table 16), this is unlikely to contribute significantly to the losses of fry since emergent sized fry are clearly less able to swim upstream, compared to the much larger coho and Chinook smolts tested in 2010.

Results from screen efficiency trials conducted on Chinook (mean FL= 70 mm) and coho (mean FL= 95 mm) juveniles in May/June 2011 suggested that smaller fish may have a lower diversion efficiency (89.2% versus 95.6% efficiency respectively; Guimond and Taylor 2012). Our results from the April/May 2013 trials seem to agree with these findings, with an overall mean diversion efficiency for smaller sized (hatchery) Chinook (mean FL = 66 mm) of 85.6 %. Considering that test fish used in 2013 were much larger (i.e. both in length and weight) than wild emergent summer


51

Chinook during the evaluation period (mean FL = 40 mm), an even lower diversion efficiency might be expected for these fish, even after the screens are cleaned.

The early spring Chinook migration period (i.e. between Feb and April) which covered the first 54 days of monitoring at the evaluation facility before the maintenance shutdown, accounted for 84.6% of the total Chinook population estimate over the whole sampling period (i.e. February to August). In other words, the early spring component of the population is much larger than the later summer component which encompassed 106 days of monitoring but only 15.4% of the migrating population. Factoring in the population estimate interpolated for the period during the maintenance shutdown (i.e. 17,000 fry) reduces the proportion of fry in each period. However, the early spring mortalities due to poor screen efficiencies prior to screen maintenance in April still have a significant impact on the overall juvenile Chinook population.

Contact with the Eicher screen as a result of higher debris accumulation, higher turbine flows or due to their smaller size can cause injury to fish during passage. During past years of monitoring at the evaluation facility, we observed that many smolts had sustained significant scale loss and/or injury, however we did not quantify the prevalence or magnitude of the scale loss. Bengeyfield (1994) conducted scale loss analyses on captures (coho, Chinook, sockeye and steelhead) in previous studies at Puntledge. He determined that passage through the system increased the incidence of scale loss, but did not assess injuries from screen passage versus the evaluation facility. The proportion of descaled fish - a fish which exhibits >16% combined scale on either side, based on criteria developed by the National Marine Fisheries Service (NMFS) - was greatest for sockeye smolts (20%), while 5.7% of chinook and 3.8% of coho smolts were categorized as descaled (Bengeyfield 1994). Similarly, researchers at Elwha Dam reported greater amounts of scale loss, and a greater proportion of fish categorized as “descaled” with increasing velocity at the screen (EPRI 1991). During our assessments at the evaluation facility in 2013, scale loss appeared to be more prevalent on coho smolts, prompting further testing in June (E. Guimond unpublished data). However we also observed scale loss on some chinook and chum fry used in the post maintenance efficiency trials, possibly a result of contact with the Eicher screen during passage (Appendix C Photo 8).

Coho smolts with as little as 10 % scale loss can suffer a 50 % mortality rate after 10 days in seawater (Bouck and Smith 1979). Although salinity tolerance may be restored over a five day recovery period in freshwater, during this time there is an increased susceptibility to fungal, parasitic and bacterial infections (ex. Saprolegnia, Ichthyophthirius and Furunculosis), as well as stress on organs caused by imbalances in


52

blood electrolytes, all of which can severely impact the ability of a fish to survive and smolt and escape from predators. Out-migrating smolts from the upper Puntledge River could likely reach the estuary in less than a day and could therefore experience difficulty in osmoregulation and a greater risk of mortality.

6 RECOMMENDATIONS

Over the summer of 2012, the Upper Puntledge Hatchery, located adjacent the diversion dam, was decommissioned as per an agreement reached between DFO and BC Hydro. DFO is now conducting all salmon enhancement activities at the lower hatchery, including the collection of summer Chinook broodstock and rearing of summer Chinook juveniles. They are also releasing all coho fry into Comox Lake. These initiatives are part of a new strategy that will ultimately rebuild sustainable populations of summer Chinook and coho in the upper Puntledge River watershed, DFO’s support for the closure of the upper facility and implementation of these initiatives was contingent on BC Hydro funding two critical multi-year assessments:

• the evaluation of Chinook and coho smolt migration and survival past the diversion dam, and

• the homing of adult hatchery returns into Comox Lake.

In 2011 a homing behaviour study of Puntledge summer Chinook was initiated with support from FWCP. Assessment of retuning adults over the next 2-3 years will determine whether lake releases of hatchery Chinook smolts results in more adults migrating to Comox Lake compared to standard hatchery river releases. More importantly, the success of any wild (natural) and upper watershed hatchery production strategies will hinge on the ability of juveniles to safely migrate downstream past the diversion dam and to the estuary. It is paramount that the Eicher screen infrastructure and/or operational modifications are tested and assessed to ensure that recovery of a self-sustaining population of summer Chinook in the Puntledge River is achieved.

Based on the results from studies at the Eicher Evaluation facility in 2012 and 2013, it appears that the performance of the Eicher screens can have an adverse effect on migrating juveniles during specific times of the year, and/or under certain screen and penstock flow conditions. If the ~70% Eicher screen mortality in 2013 on the early migrating summer Chinook fry continues at this high rate, the rebuilding of a self-sustainable population of summer Chinook is not likely to be achieved. Figure 12 illustrates the consequence of poor screen efficiency during the early migration period


53

Population Estimate Early emergent

migrant component

39,744 62.1%

Population Estimate Late migrant component

7,252 11.3%

Eicher screen

(diversion) efficiency

84.4%

Eicher screen

(diversion) efficiency

28.3%

Number of fry successfully

diverted 11,247 17.5%

Number of fry Lost 28,497 44.5%

Number of fry successfully

diverted 6,121 9.6%

Number of fry Lost 1,131 1.8%

Summer Chinook Adults

Recruited 60

56.1%

Lost Adult production1

43 40.2%

Lost Adult production1

4 3.7%

Interpolated Population Estimate

during shutdown 17,000 26.6%

Assume all successfully pass over

diversion dam100%

1 Used release to adult survival rates of 0.3% for smolts (late migrant component) and 0.15% for fry (spring migrants).

17,000 26.6%

Figure 12. Flow chart of Brood Year 2012 summer Chinook migration at the Puntledge diversion dam Eicher screens, illustrating the survival and mortality rates on the timing segments of outmigration and adult returns.


54

(i.e. Feb - March) on adult summer Chinook production. Due to the high uncertainty associated with the interpolated population estimate during the 2 week shutdown, the >40% loss of natural summer Chinook fry from the overall contribution is likely even greater.

One option to reduce these losses, as well as the potential losses and/or injury to all migrating fish at the penstock Eicher screens is through the use of strobe lights to deter fish from entrainment at the penstock intake. Our previous studies on temporal patterns of juvenile coho and Chinook migration at the Puntledge diversion dam during three periods (Nighttime between 22:00 – 04:00 hrs; Morning between 04:00 – 10:00 hrs; and Daytime between 10:00 - 22:00 hrs) found that smolts moved in significantly higher numbers at Nighttime (63.9 individuals.hr-1), compared to Morning (7.0 individuals.hr-1) and Daytime (23.2 individuals.hr-1; Guimond and Taylor 2012). The operation of underwater strobe lights at night has been shown to elicit an avoidance response in fish, and can be highly effective in deterring fish from entrainment at intakes (McLean 2008; Johnson et al. 2005). Thus the use of strobe lights during at night could provide a cost effective solution of reducing entrainment and potential risks associated with passage at the Eicher screens during the peak out-migration period.

Our observations on scale loss during the 2013 sampling year seem to be consistent with past studies at other facilities that indicate greater amounts of scale loss, and a greater proportion of fish categorized as “descaled” (>16% scale loss on one side) with increasing approach velocity at the screen. At Elwha Dam (EPRI 1991) the proportion of fish with >16% scale loss increased with increasing velocities. Descaling was most common on Chinook smolts, averaging 0.4% descaled at the lowest velocity tested, and increasing to 12.6% at a velocity of 2.38 m/s (Table 18). Scale loss (>16%) and other injuries also increased substantially from 8% to 40% when the screen was clogged with introduced debris that caused the head loss up and downstream of the screen to increase from 0 to 0.25 ft. Debris accumulation appears to have the most significant impact on injuries and diversion efficiency at Elwha Dam (EPRI 1991).

Table 18. Chinook scale loss measured at the Elwha Dam Eicher screen, 1991-1992.

Velocity Feet per second

Velocity Meters per second

% Chinook fry scale loss

4 1.22 0.46 1.83 2.8

7 2.13 6.7

7.8 2.38 12.6


55

The Puntledge Eicher screens were designed for a minimum fish size of 37 mm fork length, with a 58% porosity wedgewire screen (2.5 mm bar spacing), and an approach velocity of 1.83 m/s, (or 14 m3/s). The design velocity in the bypass pipe was 2.44 m/s. During the study period in 2013, maximum approach velocities were estimated at 1.77 m/sec but the by-pass pipe velocity was between 2.0 and 2.44 m/s during 80% of the study period. The consequences of deviating from these design criteria have not been closely assessed at the Puntledge Eicher screens, however it should warrant further investigation in light of the fact that increases in scale loss in Chinook fry were associated with increasing penstock velocities at the Elwha Dam Eicher screens (Table 18).

The following recommendations have been developed to support future assessment programs at the Puntledge diversion dam Eicher screens:

1. It is strongly recommended that the Eicher screens are cleaned in early February in advance of the early migration period of summer Chinook. These small fry are more susceptible than coho smolts to impingement at the screens which is exacerbated by debris build-up. A reduction in generation during this time of year may also improve passage at the screen.

2. Accumulation of debris on the screens appears to have the greatest impact on screening efficiency. Cycling the screens into the cleaning position regularly (every day during late morning when fish migration is lowest) may ensure the screens stay cleaner. Head loss or the pressure differential up and downstream of the screen should be recorded and monitored to determine if more cleaning cycles or a maintenance shutdown to pressure wash the screens is required.

3. Screen efficiency trials should be conducted in 2014 to reassess passage of emergent Chinook fry (35 - 40 mm fork length) at the screens in February and March. For these tests, selecting fall Chinook fry from Puntledge Hatchery that are as close in size as the natural summer-run Chinook population from the upper watershed would provide a more accurate assessment of efficiency during this period.

4. In addition to the four penstock plexiglass viewing ports on the side of each Eicher screen, a larger plexiglass skylight is also located on top of the penstock directly above the top end of each screen. These skylights allowed observations and video filming of fish passage during the 1994 studies (Bengeyfield 1995), and were used during trials and observations in 2013. However, even with the use of a high candle power worklight, they do not pass much light due to a thick film of algal growth on the inside of the skylights. A thorough cleaning of the


56

viewing ports and skylights on Eicher Screen #2 (Intake #4) during the maintenance shutdown in April will allow direct observations of fish behaviour as they approach and travel over the screens during efficiency trials, and enhance our knowledge on fish passage at the screens.

5. Until the issues with poor screen efficiency during the early (emergent) Chinook migration period is resolved, further releases of coded-wire tagged Chinook into Comox Lake to elicit adult homing back to the lake may need to be postponed. Failing to resolve the high mortality on early migrants starting in February greatly hinders the rebuilding efforts and severely impacts DFO’s summer Chinook recovery strategy.

6. Implement a study on the effectiveness of underwater strobe lights at the diversion dam to reduce entrainment of migrating juveniles (coho and Chinook). The effectiveness of the strobe lights can easily be assessed by monitoring and comparing the capture rate at the evaluation facility between periods when the lights are turned on and off.

7. Investigate the relationship between penstock and by-pass pipe velocity and discharge, and scale loss on Chinook and coho under different screen conditions (levels of fouling and debris accumulation).

7 ACKNOWLEDGEMENTS

We are grateful for the financial support for this study from the BC Hydro Fish and Wildlife Compensation Program (FWCP), on behalf of its program partners BC Hydro, the Province of B.C. and Fisheries and Oceans Canada. We wish to acknowledge the various staff at BC Hydro Vancouver Island Generation (VIG) for their commitment and cooperation throughout the monitoring period, in particular, Eva Wichmann, Rob Gill and the various BC Hydro staff that assisted with the assessment trials. We are also grateful to the entire staff at Puntledge Hatchery, Eamon Miyagi (DFO StAD), and Doug Poole (DFO RRD) for assistance with all activities associated with the installation and operation of the rotary screw trap, and for their support in various capacities throughout the project. Finally, we wish to extend our appreciation to Kevin Pellett (BC Conservation Foundation) for his assistance with setting up the RFID equipment, technicians D. Chamberlain, C. Frank, M. White and J. Ellefson for data collection and field testing during the study, as well as to Project Watershed Society,


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Puntledge River Restoration Committee, Ministry of Forests, Lands & Natural Resource Operations, and the K’ómoks First Nation for their continued support on the project.

8 REFERENCES

Addy, B. 1999. Eicher screen assessment - 1998. BC Hydro Bridge River Coastal Generation Power Facilities. 16 p.

Arnason, A.N., C.W. Kirby, C.J. Schwartz and J.R. Irvine. 1996. Computer analysis of data from stratified mark-recovery experiments for estimation of salmon escapements and other populations. Can Tech. Rep. Fish. Aquat. Sci. 2106 : 37p.

Beers, C. 2011. Puntledge Fish Screen Operations Summary April 2010 – March 2011. Unpubl. Rpt., BC Hydro, Vancouver Island Generation, Campbell River, B.C.

Bengeyfield, W and H. A. Smith. 1989. Evaluation of behavioural devices to divert coho salmon smolts from the penstock intake at Puntledge Generating Station. Prepared for: BC Hydro Environmental Resources, Vancouver, BC. Prepared by: Global Fisheries Consultants Ltd., White Rock, BC

Bengeyfield, W. 1990. Evaluation of an electrical field to divert coho salmon smolts from the penstock intake at Puntledge Generating Station. Unpubl. Report to B.C. Hydro Prepared by: Global Fisheries Consultants Ltd,, White Rock, BC

Bengeyfield, W. 1994. Evaluation of the Eicher fish screen at Puntledge diversion dam in 1993. Global Fisheries Consultants Ltd. White Rock, B.C. for BC Hydro, Burnaby, BC. 36 p. + app

Bengeyfield, W. 1995. Evaluation of the Eicher fish screen at Puntledge diversion dam: Year 2 (1994). Global Fisheries Consultants Ltd. White Rock, B.C. for BC Hydro, Burnaby, BC. 39 p. + app

Bengeyfield, W. 1997. Enumeration of downstream migrants at Puntledge Diversion Dam: 1996. Unpubl. Rpt. For BC Hydro, Bridge River Coastal Generation Power Facilities. 25 pp.

Bouck, G. and S.D. Smith. 1979. Mortality of experimentally descaled smolts of coho salmon (Oncorhynchus kisutch) in fresh and salt water. Transactions of the American Fisheries Society 108:67-69.

Carlson, S.R., L.G. Coggins Jr. and C.O. Swanton. 1998. A simple stratified design for mark-recapture estimation of salmon smolt abundance. Alaska Fish. Res. Bull. 5(2):88-102.

Darroch, J.N. 1961. The two-sample capture-recapture censuses when tagging and sampling are stratified. Biometrika 48: 241-260.


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Efron, B. and R.J. Tibshirani. 1993. An introduction to the bootstrap. Chapman & Hall/CRC 436p.

EPRI (Electrical Power Research Institute). 1992. Evaluation of the Eicher Screen at Elwha Dam: 1990 and 1991 Test Results. Report for EPRI by Stone and Webster Engineering Corp., Boston, and Hosey andAssociates Engineering Co., Bellevue, WA., 111 p. + app.

Guimond, E. and J.A. Taylor. 2009. Puntledge River Radio Telemetry Study on Summer Chinook Migration in the Upper Watershed 2008. Project #08.Pun.04. Prepared for Comox Valley Project Watershed Society and BC Hydro BCRP.

Guimond, E. and J.A. Taylor. 2011. Assessment of Chinook and Coho smolt / fry migration at the Puntledge diversion dam Eicher fish screens 2010. Project #10.Pun.02. Prepared for Comox Valley Project Watershed Society and BC Hydro FWCP

Guimond, E. and J.A. Taylor. 2012. Assessment of Chinook and Coho smolt / fry migration at the Puntledge diversion dam Eicher fish screens 2011. Project #11.Pun.04. Prepared for Comox Valley Project Watershed Society and BC Hydro FWCP

Herbinger, C.M., G.F. Newkirk and S.T. Lanes. 1990. Individual marking of Atlantic salmon: evaluation of cold branding and jet injection of Alcian Blue in several fin locations. J. Fish. Biol. 36: 99-101.

Johnson, R., M. Simmons, C. McKinstry, C. Simmons, C. Cook, R. Brown, D. Tano, S. Thorsten, D. Faber, R. LeClaire, & S. Francis. 2005. Strobe light deterrent efficacy test and fish behaviour determination at Grand Coulee Dam, third powerplant forebay. Richland, WA: Pacific Northwest National Laboratory.

McLean, A.R. 2008. Strobe Lights as a Fish Deterrent. Unpublished master’s thesis. Royal Roads University.

Ohkuma, K., S. Sasaki, A. Wada, and T. Tojima. 1998. Burst swimming speed of chum salmon fry measured with a simple water tunnel apparatus. Bulletin of the National Salmon Resources Center No.1: 45-48.

Pacific States Marine Fisheries Commission. 1999. PIT Tag Marking Procedures Manual. Prepared by: Columbia Basin Fish and Wildlife Authority PIT Tag Steering Committee. http://php.ptagis.org/wiki/images/e/ed/MPM.pdf

Robson, D.S. and H.A. Regier. 1964. Sample size in Petersen mark-recapture experiments. Trans. Amer. Fish. Soc. 93 (3):215 – 226.

Seber, G.A.F. 1982. The estimation of animal abundance. 2nd ed. Griffin, London.

Tryon, L. 2008. Assessment of downstream fish migration at the Puntledge River Eicher Screen: July 2005. Lake Trail Environmental Consulting, Courtenay, B.C. for BC Hydro, Campbell River, BC. 18 p.


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APPENDICES


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APPENDIX A - Numbers of juvenile coho and Chinook captured daily in the evaluation facility in 2012.

Date 1+ COHO

(unmarked) 1+ COHO

(adipose Clip) Total 1+ COHO

2+ COHO (>130 mm)

Total 0+ CHINOOK

1-May 2 1 3 32-May 4 0 4 4 3-May 5 2 7 11 4-May 6 1 7 6 5-May 5 0 5 16 6-May 3 0 3 7 7-May 26 5 31 1 3 8-May 56 8 64 17 9-May 120 16 136 4 32

10-May 151 17 168 5 59 11-May 156 18 174 8 40 12-May 212 23 235 5 30 13-May 167 16 183 5 12 14-May 256 29 285 4 22 15-May 263 30 293 1 44 16-May 392 67 459 3 58 17-May 449 82 531 2 79 18-May 378 55 433 5 45 19-May 616 72 688 5 23 20-May 611 109 720 2 13 21-May 681 122 803 4 59 22-May 926 111 1037 1 30 23-May 842 129 971 4 94 24-May 476 67 543 3 123 25-May 707 72 779 5 423 26-May 434 18 452 3 456 27-May 175 18 193 121 28-May 130 130 63 29-May 166 166 326 30-May 180 13 193 2 252 31-May 335 25 360 2 564 1-Jun 723 88 811 304 2-Jun 93 11 104 40 3-Jun 65 2 67 40 4-Jun 27 4 31 57 5-Jun 55 1 56 87 6-Jun 99 1 100 363 7-Jun 133 133 2 503 8-Jun 153 4 157 280 9-Jun 145 20 165 209

10-Jun 269 8 277 153 11-Jun 133 13 146 147 12-Jun 177 8 185 135 13-Jun 121 10 131 287 14-Jun 205 15 220 207 15-Jun 149 22 171 270 16-Jun 113 6 119 165 17-Jun 75 7 82 280 18-Jun 51 3 54 207 19-Jun 65 7 72 153 20-Jun 45 3 48 78 21-Jun 56 1 57 159 22-Jun 43 3 46 177


61

APPENDIX A cont’d

Date 1+ COHO

(unmarked) 1+ COHO

(adipose Clip) Total 1+ COHO

2+ COHO (>130 mm)

Total 0+ CHINOOK

23-Jun 46 0 46 321 24-Jun 21 2 23 113 25-Jun 6 0 6 40 26-Jun 12 0 12 96 27-Jun 7 1 8 223 28-Jun 8 0 8 152 29-Jun 6 0 6 214 30-Jun 5 0 5 2 184 1-Jul 8 1 9 167 2-Jul 2 0 2 141 3-Jul 4 1 5 75 4-Jul 5 0 5 51 5-Jul 3 0 3 188 6-Jul 9 1 10 277 7-Jul 2 0 2 169 8-Jul 2 0 2 248 9-Jul 0 0 0 204

10-Jul 0 0 0 198 11-Jul 0 0 0 96 12-Jul 3 0 3 186 13-Jul 0 0 0 217 14-Jul 0 0 0 186 15-Jul 0 0 0 191 16-Jul 0 0 0 143 17-Jul 0 0 0 205 18-Jul 1 0 1 114 19-Jul 1 2 3 81 20-Jul 1 0 1 82 21-Jul 0 0 0 106 22-Jul 0 1 1 12 23-Jul 0 0 0 5 24-Jul 0 0 0 2 25-Jul 0 0 0 37 26-Jul 1 0 1 45 27-Jul 0 2 2 61 28-Jul 0 0 0 71 29-Jul 0 0 0 49 30-Jul 0 0 0 2 36 31-Jul 0 0 0 26 1-Aug 1 0 1 20 2-Aug 0 0 0 5 3-Aug 0 0 0 11 4-Aug 0 0 0 2 5-Aug 0 0 0 25


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APPENDIX B - Numbers of juvenile Chinook captured daily in the evaluation facility in 2013.

Date Total 0+

CHINOOK Date Total 0+



CHINOOK

4-Feb 0 17-Mar 68 13-May 1 23-Jun 39 5-Feb 0 18-Mar 73 14-May 10 24-Jun 24 6-Feb 0 19-Mar 55 15-May 6 25-Jun 13 7-Feb 0 20-Mar 116 16-May 5 26-Jun 29 8-Feb 1 21-Mar 98 17-May 5 27-Jun 27 9-Feb 3 22-Mar 50 18-May 10 28-Jun 32 10-Feb 2 23-Mar 14 19-May 14 29-Jun 20 11-Feb 2 24-Mar 12 20-May 33 30-Jun 4 12-Feb 2 25-Mar 1 21-May 41 1-Jul 1 13-Feb 2 26-Mar 3 22-May 26 2-Jul 9 14-Feb 0 27-Mar 4 23-May 41 3-Jul 26 15-Feb 1 28-Mar 7 24-May 10 4-Jul 19 16-Feb 2 29-Mar 33 25-May 10 5-Jul 23 17-Feb 8 30-Mar 47 26-May 6 6-Jul 21 18-Feb 1 31-Mar 58 27-May 12 7-Jul 25 19-Feb 2 1-Apr 67 28-May 1 8-Jul 16

20-Feb 2 2-Apr * 52 29-May 48 9-Jul 10

21-Feb 0 19-Apr 11 30-May 23 10-Jul 22 22-Feb 2 20-Apr 69 31-May 21 11-Jul 8 23-Feb 2 21-Apr 50 1-Jun 8 12-Jul 27 24-Feb 0 22-Apr 18 2-Jun 7 13-Jul 14 25-Feb 17 23-Apr 15 3-Jun 20 14-Jul 16 26-Feb 5 24-Apr 19 4-Jun 34 15-Jul 19 27-Feb 13 25-Apr 5 5-Jun 20 16-Jul 26 28-Feb 10 26-Apr 9 6-Jun 19 17-Jul 14 1-Mar 16 27-Apr 11 7-Jun 11 18-Jul 17 2-Mar 4 28-Apr 19 8-Jun 5 19-Jul 6 3-Mar 8 29-Apr 13 9-Jun 22 20-Jul 7 4-Mar 72 30-Apr 10 10-Jun 16 21-Jul 11 5-Mar 34 1-May 24 11-Jun 16 22-Jul 3 6-Mar 37 2-May 4 12-Jun 15 23-Jul 2 7-Mar 22 3-May 10 13-Jun 12 24-Jul 5 8-Mar 27 4-May 7 14-Jun 28 25-Jul 6 9-Mar 69 5-May 8 15-Jun 23 26-Jul 14 10-Mar 13 6-May 14 16-Jun 16 27-Jul 5 11-Mar 27 7-May 8 17-Jun 45 28-Jul 13 12-Mar 47 8-May 29 18-Jun 24 29-Jul 4 13-Mar 54 9-May 35 19-Jun 20 30-Jul 9 14-Mar 34 10-May 12 20-Jun 54 31-Jul 4 15-Mar 21 11-May 9 21-Jun 72 1-Aug 2 16-Mar 19 12-May 6 22-Jun 32 2-Aug 5

* BC Hydro Maintenance Shutdown


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APPENDIX C– Photos

Photo 1. A 6 ft. diameter rotary screw trap (RST) being manoeuvred into place for assessment during the BC Hydro maintenance shutdown period in April 2013.

Photo 2. Location of the RST on river right, upstream of the diversion dam adjacent BC Hydro’s river gauging shed.

Photo 3. Chinook fry marked with an immersion bath using Bismarck Brown-Y dye prior to release in the penstock in early March 2013.


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Photo 4. Debris mat (algae and aquatic grass) coating the entire surface area of the Eicher screens, observed during the April 2013 maintenance shutdown.

Photo 5. Chinook fry mortalities removed from Eicher screen #2 during inspection in April 2013. Note the gap along the length of the screen from the missing gasket seal.

Photo 6. Viewing stack over Eicher screen #2 to allow underwater video monitoring of fish releases at the screen while generating.


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Photo 7. Impinged chum fry remaining on the Eicher screen after a test release in the penstock on April 24, 2013.

Photo 8. Evidence of scale loss on a Bismarck Brown dyed Chinook fry from impingement or contact with the screen after release at the intake on April 24, 2013.


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APPENDIX D - FWCP Financial Statement Project # 12.PUN.04 BUDGET ACTUAL

INCOME FWCP Other (Cash)

Other (in-kind) FWCP

Other (cash)

Other (in-kind)

Total by Source $96,626.20 $0.00 $16,005.00 $96,619.20 $0.00 $16,896.00

Grand Total Income (FWCP + Other) $112,631.20 $113,515.20

EXPENSES

Project Personnel

Biologist - Project coordination & management $19,375.00 $28,630.70

Technicians $51,100.00 $35,613.83

Statistician $7,952.00 $10,724.03

DFO Technicians $8,400.00 $8,400.00

DFO Biologist $3,350.00 $5,360.00

Communications $900.00 $336.84

Material and Equipment

Materials and supplies (facility maintenance, RST, RFID, safety, field sampling, misc.) $2,750.00 $5,089.47

RFID Equipment $1,750.00 $1,200.00 $1,198.84

Rotary screw trap rental & delivery $1,600.00 $1,600.00

Mileage $4,015.00 $4,125.80

Administration

Admin Fees (10%) $8,784.20 $1,455.00 $8,571.95 $1,536.00

Total Expenses $96,626.20 $0.00 $16,005.00 $94,291.46 $0.00 $16,896.00

Grand Total Expenses (FWCP + others) $112,631.20 $111,187.46

Balance (Grand Total Income - Grand Total Expenses (inclusive of GST/HST obligations) $0.00 $2,327.74


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APPENDIX E - Performance Measures Project # 12.Pun.04

Performance Measures – Target Outcomes

Project Type Primary Habitat Benefit Targeted of Project (m2)

Primary Target Species

Habitat (m2)

Est

uarin

e

In-S

tream

Hab

itat –

Mai

nstre

am

In-s

tream

Hab

itat –

Trib

utar

y

Rip

aria

n

Res

ervo

ir Sh

orel

ine

Com

plex

es

Riv

erin

e

Low

land

Dec

iduo

us

Low

land

Con

ifero

us

Upl

and

Wet

land

Impact Mitigation

Fish passage technologies

Area of habitat made available to target species

Summer Chinook and coho

3.7

km

32 k

m

>500

ha

Drawdown zone revegetation/stabilization

Area turned into productive habitat

Wildlife migration improvement

Area of habitat made available to target species

Prevention of drowning of nests, nestlings

Area of wetland habitat created outside expected flood level (1:10 year)

Habitat Conservation Habitat conserved – general

Functional habitat conserved/replaced through acquisition and mgmt

Functional habitat conserved by other measures (e.g. riprapping)

Designated rare/special habitat

Rare/special habitat protected Maintain or Restore Habitat forming process Artificial gravel recruitment

Area of stream habitat improved by gravel plmt.

Artificial wood debris recruitment

Area of stream habitat improved by LWD plcmt

Small-scale complexing in existing habitats

Area increase in functional habitat through complexing

Prescribed burns or other upland habitat enhancement for wildlife

Functional area of habitat improved

Habitat Development New Habitat created Functional area created


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APPENDIX F - Confirmation of FWCP Recognition Project Watershed booth at the Puntledge Hatchery Open House, October 2012, providing information on the assessment of Chinook and coho smolt / fry migration at the Puntledge diversion dam Eicher fish screens, and other FWCP projects, past and present.

Assessment of Chinook and Coho Smolt / Fry …a100.gov.bc.ca/appsdata/acat/documents/r41644/12.PUN.04...Assessment of Chinook and Coho Smolt / Fry Migration at the Puntledge Diversion

Documents