FRY STOCKING AND ADULT TRANSLOCATION AS STRATEGIES TO ADDRESS PATCHINESS IN ATLANTIC SALMON (SALMO SALAR L.) SPAWNING DISTRIBUTIONS WITHIN CLEARWATER BROOK, NB

by

Christopher B. Connell

Bachelor of Science, University of New Brunswick, 1993

A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of

Master of Science

in the Graduate Academic Unit of Biology

Supervisor: R.A. Cunjak, Ph.D., UNB Biology Examining Board: Gerald Chaput, Dept. of Fisheries and Oceans Canada Katy Haralampides, Ph.D., UNB Engineering

This thesis is accepted by the Dean of Graduate Studies

THE UNIVERSITY OF NEW BRUNSWICK

January, 2005

© Chris B. Connell, 2004

Abstract

Passive integrated transponder (PIT) technology was used to monitor the pre-spawning

movement and spawning distribution of adult Atlantic salmon (Salmo salar L.) in

Clearwater Brook, a tributary stream basin (335 km2) of the Miramichi River catchment

in New Brunswick, Canada. Between 1999 and 2000, transponders (31.8 mm long and

3.9 mm in diameter) were surgically implanted into the musculature of 579 salmon

captured at a fish-counting fence 19 km above the confluence with the mainstem. Field

performance and efficiency of stationary and a newly designed portable detection system

were evaluated based on tagged fish movements. The individual spawning positions of

wild, hatchery-origin and adult translocated salmon were examined to elucidate the

relative effectiveness of fry-stocking and adult translocation as stock enhancement

strategies. Known tagging related mortalities were low (0.35%). Stationary readers were

> 95% efficient, had a tag detection range of 40 cm and could detect tagged salmon

moving at ground speeds as high as 4.0 m/s. A portable detection system proved

effective at locating salmon within deep water sections of the brook and was used to

locate 45% of the tagged fish in the river. Prior to spawning, a greater proportion of

early-run hatchery-origin salmon (38.8% of tagged sample) exhibited ‘roving’ behaviour

in the study area relative to their wild counterparts (8.8% of tagged sample). During the

spawning period, 25% of wild and 26.9% of hatchery-origin male grilse exhibited roving

behaviour. The translocation of 20 adult salmon resulted in a 3.1% to 5.8% gain in upper

reach egg deposition. Hatchery-origin adults increased upper reach egg deposition by

4.8%. Both enhancement strategies resulted in proportional increases in adult spawners

i

within the target reach and appear to have unique applications for supplementing areas of

low natural production or re-establishing juvenile salmon populations within a river.

ii

Table of Contents

List of Figures................................................................................................................... vi

List of Tables .................................................................................................................. viii

CHAPTER 1...................................................................................................................... 1

Introduction........................................................................................................... 2

Research Objectives.............................................................................................. 9

Thesis Overview .................................................................................................... 9

References............................................................................................................ 11

CHAPTER 2.................................................................................................................... 19

Abstract................................................................................................................ 20

Introduction......................................................................................................... 21

Introduction......................................................................................................... 21

Study Area ........................................................................................................... 22

Materials and Methods....................................................................................... 25

Atlantic salmon captures........................................................................... 25

Stationary PIT tag readers........................................................................ 28

Portable PIT tag reader............................................................................ 31

Assessing tagging related mortality.......................................................... 33

Field-testing PIT tag reader stations........................................................ 33

In-river movements of PIT tagged salmon prior to spawning .................. 36

Statistical analyses.................................................................................... 36

Results .................................................................................................................. 37

Atlantic salmon captures, 1999 and 2000................................................. 37

iii

PIT tagging ............................................................................................... 38

Tagging related mortality ......................................................................... 39

Performance of PIT tag reader stations ................................................... 40

Movement, behaviour and distribution of PIT tagged Atlantic salmon.... 44

Discussion ............................................................................................................ 47

References............................................................................................................ 58

CHAPTER 3.................................................................................................................... 77

Abstract................................................................................................................ 78

Introduction......................................................................................................... 79

Study Area ........................................................................................................... 82

Materials and Methods....................................................................................... 86

Clearwater Brook Atlantic salmon stocking program.............................. 86

Adult Atlantic salmon captures................................................................. 87

PIT tagging ............................................................................................... 88

PIT tag monitoring.................................................................................... 89

Adult salmon translocation ....................................................................... 91

Stream habitat and egg deposition rate .................................................... 92

Redd surveys ............................................................................................. 93

Statistical analyses.................................................................................... 94

Results .................................................................................................................. 95

Atlantic salmon captures and PIT tagging ............................................... 95

Adult salmon translocation ....................................................................... 98

Wild and hatchery-origin adult Atlantic salmon spawning distribution 100

iv

Discussion .......................................................................................................... 103

Wild Atlantic salmon spawning distribution........................................... 104

Stocking hatchery-reared underyearling Atlantic salmon...................... 104

Adult Atlantic salmon translocation ....................................................... 107

Cost-benefit of Atlantic salmon fry stocking and adult translocation .... 109

References.......................................................................................................... 111

CHAPTER 4.................................................................................................................. 130

General Discussion............................................................................................ 131

References.......................................................................................................... 135

Appendix I ..................................................................................................................... 136

Historic electrofishing, fry drift and fry stocking data pertinent to Atlantic

salmon research in Clearwater Brook, NB..................................................... 136

Appendix II.................................................................................................................... 146

Daily captures of Atlantic salmon at the Clearwater Brook counting fence in

1999 and 2000 .................................................................................................... 146

v

List of Figures Figure 1.1. Life cycle of the Atlantic salmon (Salmo salar) and general timing of

salmon life-stages in the Maritimes. (Graphics provided by the Atlantic Salmon Federation, St. Andrews, NB)...................................................... 16

Figure 1.2. Map showing the Clearwater Brook catchment within New Brunswick’s

Miramichi River watershed....................................................................... 17 Figure 1.3. Map of Clearwater Brook displaying the location of the fish counting

fence ( ) and the areas defined as the lower, middle and upper reach.... 18 Figure 2.1. Map displaying the position of the Clearwater Brook catchment within

New Brunswick’s Miramichi River catchment......................................... 66 Figure 2.2. Clearwater Brook and the locations of passive integrated transponder

reader stations operated in 1999 and 2000................................................ 67 Figure 2.3. Photo of the Clearwater Brook counting fence........................................ 68 Figure 2.4. Photos illustrating the PIT tagging process and orientation of tag as it is

inserted...................................................................................................... 68 Figure 2.5. Representation of a PIT tag reader station installed in Clearwater Brook

(not to scale).............................................................................................. 69 Figure 2.6. Photos illustrating the vertically oriented PIT tag detection loop antenna

and the adjacent fencing to ensure that all tagged fish pass through the RF field. .......................................................................................................... 70

Figure 2.7. Location of the fish counting fence, PIT tag reader stations (CRx), pools

surveyed with a portable PIT tag reader, and release sites (CTRx) of wild PIT-tagged adult Atlantic salmon in Clearwater Brook, NB.................... 71

Figure 2.8. Photo of the pool sweeping technique used to detect PIT tagged salmon

resting in holding areas. ............................................................................ 72 Figure 2.9. Proportion of PIT-tagged Atlantic salmon at-large detected using a

portable PIT tag reader in Fence Pool, Brook Pool and Bridge Pool – Clearwater Brook, 1999. ........................................................................... 73

Figure 2.10. Number of salmon PIT tagged per day (counting fence), number of unique

PIT detections per day (reader stations), water level at trap (___), and mean daily water temperature at trap (----) in Clearwater Brook, 1999............. 74

vi

Figure 2.11. Number of salmon PIT tagged per day (counting fence), number of unique PIT detections per day (reader stations), water level at trap (___), and mean daily water temperature at trap (----) in Clearwater Brook, 2000............. 75

Figure 2.12. Average number of days between Atlantic salmon PIT tagging and

subsequent tag detection at reader stations in Clearwater Brook, 2000. .. 76 Figure 3.1. Map displaying the position of the Clearwater Brook catchment within

New Brunswick’s Miramichi River Basin.............................................. 121 Figure 3.2. The location of the fish counting fence, PIT tag reader stations (CRx),

adult salmon translocation sites (CTRx), Avenor bridge pool, and the upper, middle, and lower reaches of Clearwater Brook, NB. ................. 122

Figure 3.3. The location of PIT tag reader stations (CRx), pools surveyed with a

portable PIT tag reader, and the sub-reaches located upstream of the fish counting fence on Clearwater Brook, NB............................................... 123

Figure 3.4. The distribution sites (CSx) of hatchery-reared Atlantic salmon fry within

Clearwater Brook, NB (1996 to 2003).................................................... 124 Figure 3.5. Percentage of translocated wild, adult Atlantic salmon that moved

downstream and were detected at a PIT tag reader station within 24-h following translocation. .......................................................................... 125

Figure 3.6. Percentage of free-swimming and translocated wild female adult Atlantic

salmon that were present and are presumed to have spawned in the upper reach of Clearwater Brook, 1999. ........................................................... 125

Figure 3.7. The percentage of wild and hatchery origin PIT tagged salmon present in

the upper study reach of Clearwater Brook in 1999 and 2000. .............. 126 Figure 3.8. Sub-reach egg deposition rate from wild Atlantic salmon plotted against

the migratory distance from the fence to the sub-reach in Clearwater Brook, 2000. R2 values shown. .............................................................. 127

Figure 3.9. Sub-reach egg deposition rate from hatchery-origin Atlantic salmon

plotted against the migratory distance from the fence to the sub-reach in Clearwater Brook, 2000. R2 values shown. ............................................ 127

Figure 3.10. Egg deposition rates of wild and hatchery origin PIT tagged Atlantic

salmon to each of the sub-reaches monitored in Clearwater Brook in 2000. (d = upstream migratory distance from the counting fence to the spawning site).......................................................................................................... 128

vii

Figure 3.11. Percentage of preferred salmon spawning habitat located in the upper reach of Clearwater Brook relative to the percentage of wild or hatchery-origin eggs carried to the upper reach during spawning in 1999 and 2000.................................................................................................................. 129

List of Tables

Table 2.1. Water chemistry in the upper, middle and lower reaches of Clearwater

Brook in August of 1998. (Analyses performed by NB Department of Environment). ........................................................................................... 62

Table 2.2. Biological characteristics (fork length and sex), PIT tag number, transfer

date, and release site of adult Atlantic salmon translocated to the upper reach of Clearwater Brook, NB. ............................................................... 63

Table 2.3. Number and percentage of adult salmon captured and implanted with

passive integrated transponder tags at the Clearwater Brook counting fence between June and October, 1999..................................................... 64

Table 2.4. Number and percentage of adult salmon captured and implanted with

passive integrated transponder tags at the Clearwater Brook counting fence between June and October, 2000..................................................... 64

Table 2.5. The percentage of wild and hatchery origin grilse and MSW salmon

captured at the Clearwater Brook counting fence prior to September, 1999 and 2000.................................................................................................... 64

Table 2.6. The number and proportion of PIT-tagged Atlantic salmon that exhibited

pre spawning roving behaviour in Clearwater Brook, 2000. .................... 65 Table 2.7. The number and proportion of PIT-tagged Atlantic salmon that exhibited

roving behaviour during spawning period in Clearwater Brook, 2000. ... 65 Table 3.1. Total wetted stream area and preferred salmon spawning area within the

middle and upper reaches and within the sub-reaches upstream of the fish counting fence on Clearwater Brook, NB............................................... 114

Table 3.2. Biological characteristics (fork length and sex), PIT tag number, transfer

date, and release site of adult Atlantic salmon translocated to the upper reach of Clearwater Brook, NB. ............................................................. 114

viii

Table 3.3. Number and percentage of adult salmon captured and implanted with passive integrated transponder tags at the Clearwater Brook counting fence between June and October, 1999. ........................................................... 115

Table 3.4. Number and percentage of adult salmon captured and implanted with

passive integrated transponder tags at the Clearwater Brook counting fence between June and October, 2000................................................... 115

Table 3.5. The percentage of wild and hatchery origin grilse and MSW salmon

captured at the Clearwater Brook counting fence prior to September of 1999 and 2000......................................................................................... 115

Table 3.6. The number of PIT tagged wild and translocated Atlantic salmon detected

at the CR2 reader station (mainstem upper reach) and the number of female salmon therein that are believed to have spawned upstream of CR2 - Clearwater Brook, 1999........................................................................ 116

Table 3.7. The number of PIT tagged wild and translocated Atlantic salmon detected

at the CR4 (Northeast Branch upper reach) reader station and the number of female salmon therein that are believed to have spawned upstream of CR4 - Clearwater Brook 1999. ............................................................... 116

Table 3.8. The number and percentage of eggs calculated to be contributed to the

upper and middle reaches of Clearwater Brook by wild, translocated and hatchery-origin PIT tagged salmon in 1999............................................ 117

Table 3.9. Estimated egg distribution and gain/loss in egg contribution as a result of

adult Atlantic salmon translocation in Clearwater Brook 1999.............. 117 Table 3.10. Egg deposition rates to the mid and upper Clearwater Brook study reaches

from PIT tagged wild and hatchery origin Atlantic salmon in 1999 and 2000......................................................................................................... 118

Table 3.11. Relative egg contributions and deposition rates from wild and hatchery

origin PIT tagged female salmon by sub-reach, Clearwater Brook - 2000.................................................................................................................. 119

Table 3.12. Results of redd surveys conducted on Clearwater Brook, 1999-2002... 120 Table 3.13. Estimated egg contributions to the middle and upper reaches of Clearwater

Brook by wild and hatchery-origin salmon in 1999 and 2000................ 120

ix

CHAPTER 1

The status of Atlantic salmon (Salmo salar L.) in Clearwater Brook: introduction and overview.

Introduction

The Atlantic salmon (Salmo salar L.) is a famed and highly sought-after sport fish that is

an important cultural, social, and economic resource. This is particularly true in the

Canadian Maritimes, where in New Brunswick alone, the recreational Atlantic salmon

fishery is estimated to contribute $28.6 million in direct expenditures to the economy

each year (MacIntosh, 2001).

Globally, a decrease in the productive range and abundance of Atlantic salmon, coupled

with the continued decline of wild Atlantic salmon stocks in the North Atlantic Ocean

(Mather et al. 1998; Parrish et al. 1998) has made the species the focus of substantial

research and management directed towards increasing and conserving remaining

populations. Unfortunately, the substantial decline in Atlantic salmon numbers observed

over the past century is largely believed to be the result of increased human pressure on

the resource (WWF, 2001).

In New Brunswick, considerable annual recreational and commercial harvests of Atlantic

salmon were common from the mid 1800’s to early 1900’s and it is speculated that a

poorly regulated fishery, coupled with augmented fishing pressure and habitat destruction

during the 20th Century were primary factors that contributed to the long-term decline of

New Brunswick’s salmon stocks (Thomas, 2001).

In Canada, the native range of Atlantic salmon includes many of the inland waters of

northern Québec, Labrador, Newfoundland, New Brunswick, Nova Scotia and Prince

2

Edward Island. In the marine environment the Atlantic salmon is found throughout most

of the North Atlantic Ocean (Scott and Crossman, 1998).

The Atlantic salmon is an anadromous fish that requires freshwater riverine habitat for

reproduction and juvenile rearing, whereas the marine environment provides abundant

food resources for the fish to maximize growth and fecundity (Mills, 1991) (Figure 1.1).

In Maritime rivers, Atlantic salmon spawning (mating) generally occurs between mid-

October and mid-November, during which time the female excavates a depression in the

gravel and deposits her eggs therein. Once fertilized by the male salmon, the eggs are

covered with gravel by the female and left to incubate over the winter months. Atlantic

salmon hatch from the egg in late April and emerge from the gravel in late May or early

June (Randall, 1982; Johnston, 1997; Flanagan, 2003). Soon after emergence these

salmon ‘fry’ begin to feed by establishing territories in the brook and grow to a sufficient

size to emigrate to the marine environment.

In most New Brunswick rivers, when salmon parr reach 11-16 cm in length and are 2.5 to

3.5 years of age, they undergo physiological changes in preparation for emigration into

the marine environment as ‘smolt’ (Hutchings and Jones, 1998). Smoltification generally

occurs between mid-April and mid-June and commences just prior to downstream

migration. After one to two years of growth at sea, sexually mature Atlantic salmon begin

returning to their native rivers as early as June. Fish returning to spawn after one year of

growth in the marine environment are termed ‘grilse’ and generally have a fork length of

< 63 cm (Chaput et al., 1999). Salmon that spend at least two years at sea before

3

spawning are referred to as ‘multi-sea winter salmon’ (MSW’s) and generally have a fork

length ≥ 63 cm. Following spawning, salmon return to the ocean and if they survive to

spawn a second or more times they are termed ‘repeat spawners’ and are also classified

as MSW salmon.

A number of variables (habitat, water quality, food availability) affect the productivity of

salmon rivers and have a significant influence on salmon spawning escapement (number

of spawning salmon) and egg deposition (number of eggs spawned per unit of available

habitat) (Symons, 1979). It is widely accepted that juvenile salmon production is

maximized when spawning escapement and egg depositions meet optimum levels for a

given river system (Elson, 1975). Accordingly, the vast majority of Atlantic salmon

management and research efforts have focused on freshwater life stages, with the hope

that an increase in juvenile salmon production will yield improved adult salmon returns

to the rivers.

Fishery managers have employed many strategies to optimize the freshwater production

of Atlantic salmon, the most common of which is the use of a fish hatchery to supplement

wild stocks through artificial reproduction and rearing. Hatchery rearing generally

involves artificially spawning eggs and milt from adult fish and rearing the fertilized ova

in a controlled environment to maximize survival. In the case of supplemental Atlantic

salmon stocking programs, progeny from hatchery rearing are generally stocked back to

their river of origin soon after hatch when they begin to feed (‘feeding fry’), or 4-6

months after they hatch (underyearlings). In some cases, enhancement strategies may

4

involve continued hatchery rearing and the stocking of parr, smolt or even mature adults

back to the river (Saegrov and Skilbrei, 1996; Youngson and Verspoor, 1998).

Hatchery-based enhancement programs have been widely challenged because stocked

fish can reduce the genetic robustness of wild fish, and are potential vectors for disease

introductions (Gross 1998). When stocked on top of natural production that is at or near

carrying capacity wild fish may suffer adversely from increased competition with

released fish (Einum and Fleming 2001). The vigour and performance of hatchery

produced fish relative to wild fish has also been questioned and a number of studies have

investigated potential differences in growth, survival and behaviour of wild and hatchery

origin salmonids (Sosiak et al., 1979; Shustov et al., 1981; Kennedy et. al. 1993;

O’Grady, 1983; Bachman, 1984; Johnsen and Ugedal, 1986; Svasand 1993). Behavioural

comparisons between stocked and wild salmon have mostly focussed on the fry to smolt

life stages, with fewer studies investigating the potential behavioural differences between

hatchery-origin and wild adult salmon prior to and during spawning (Jonsson et. al.,

1991; Fleming and Gross, 1992; Heggberget et. al., 1993). As an enhancement strategy, it

is expected that salmon stocked to a river will survive to maturity and return to spawn

naturally near the site to which they were stocked. The success of this type of strategy

depends on the performance and survival of juvenile fish, but is highly predicated on the

ability of stocked fish to imprint and subsequently ‘home’ to the stocking site as mature

adults. Several studies have investigated homing and straying behaviour in wild and sea-

farmed Atlantic salmon (Heggberget et al. 1993) whereas few published studies have

compared the homing behaviour of wild and hatchery-reared salmon in the same river. As

5

pointed out by Potter and Russell (1994), studies for Atlantic salmon have only compared

the behaviour of wild fish with hatchery fish released as smolts (Jonsson et al. 1991).

Despite the extensive use of hatcheries to compensate for shortfalls in wild salmon

production, no published studies were found that evaluated the effectiveness of targeted

Atlantic salmon fry stocking (undertaken to compensate for locally reduced wild

production), based on adult returns and egg contributions of stocked fish to the target

area.

Considering the aforementioned evidence indicating that hatchery-based stocking

programs often cause deleterious impacts to wild salmon populations, alternate stock

enhancement strategies need to be considered now, more than ever. Indeed, other

strategies to optimize the natural production of wild salmon have been investigated. For

instance, Youngson and McLaren (1998) described and evaluated the relocation of

naturally spawned salmonid ova as a technique to compensate for disproportionate egg

distributions by wild fish. Dempson et al. (1999) evaluated cage rearing of wild Atlantic

salmon smolts as a strategy to enhance salmon populations and several studies have

investigated strategies to improve the quality and productivity of salmon spawning and

rearing habitat (eg Semple, 1987; Mih, 1978). Also, while few published studies have

reviewed the strategy of adult salmonid translocation (Saunders and Smith, 1962;

Kennedy et al., 1977), this technique has been used in an attempt to achieve a local

increase in spawning density and egg depositions at or near the release site. In the case of

Atlantic salmon the technique generally involves capturing wild adult pairs within a river

just prior to spawning, and physically transporting and releasing these fish within the

6

same river in an area with diminished or no wild production. Unfortunately, the

effectiveness of this strategy in compensating for a local absence or reduction in the

number of wild salmon spawners has not been well documented and most published

studies involved translocating adult fish between rivers rather than within the same river

(Kennedy et al., 1977). No studies were found that examined the behaviour, movement

and, spawning distribution of Atlantic salmon following relocation within the same river.

In May of 1999 I began my research project in Clearwater Brook (New Brunswick,

Canada) to compare the pre-spawning behaviour and spawning distribution of: 1) wild

Atlantic salmon, 2) adult returns of Atlantic salmon that were hatchery reared and

stocked to the upper reaches as 0+ underyearlings, 3) wild origin adult salmon that were

translocated to upriver reaches just prior to spawning.

Clearwater Brook (46o42’ N, 66o48’ W) is a fifth-order tributary that flows into the main

Southwest Miramichi River 125 km above the head of tide (Figure 1.2). The brook flows

unrestricted within a forested catchment (335 km2) that is located almost wholly on

private land owned by two forestry companies (J.D. Irving, Limited and Bowater

Canadian Forest Products, Incorporated). As a result of limited public access, the annual

angling effort in Clearwater Brook is less than 200 rod-days (M. Price, Bowater, pers.

comm.), and is focused primarily in the lower eightkilometres of the river.

Since 1996, J.D. Irving Limited (JDI), the primary landowner of the upper 48 km of

Clearwater Brook, in partnership with the Atlantic Salmon Federation (ASF), has

7

conducted research with to investigate strategies to optimize salmon production in the

middle and upper reaches. Initial findings noted reduced densities of wild young-of-the-

year salmon in the upper reach relative to the middle and lower reaches (Figure 1.3,

Appendix I.1 – Appendix 1.6). This was hypothesized to be due to some of the following

factors: 1) inferior spawning or juvenile rearing habitat; 2) fewer adult salmon (per unit

of spawning habitat) migrating to and depositing eggs in the upper reach; 3) large

numbers of fry emigrating from the upper reach to the middle and lower reaches.

Preliminary investigations indicated that local reductions in upper reach juvenile salmon

densities were a function of reduced adult spawning escapement and egg deposition

(McCabe and Connell, 1997; Appendix I). As a counter-measure, between 25,000 and

64,000 Atlantic salmon underyearlings were stocked annually to the upper reach of

Clearwater Brook since 1996 (Appendix I.8). All stocked fish were progeny of

broodstock collected from Clearwater Brook the previous year and all fish were marked

with an adipose fin clip prior to stocking.

In 1998, when stocked fry were first observed returning to Clearwater Brook as mature

adults, the following questions were posed: 1) are these ‘hatchery-origin’ salmon homing

to the upper reach of the brook?; 2) to what extent do hatchery-origin returns contribute

to egg deposition in the upper reach? In a companion study a portion of wild adult

Atlantic salmon were collected in Clearwater Brook just prior to spawning and relocated

to the upper reach.

8

Research Objectives

The general objective of this research was to evaluate the success of juvenile stocking

and adult translocation as strategies to increase Atlantic salmon spawning escapement in

a targeted reach of Clearwater Brook. More specific objectives of the study were: 1) to

assess the feasibility of using passive integrated transponder (PIT) technology to track the

movement and spawning distribution of a large number of adult Atlantic salmon in a

remote intermediate-sized river; 2) to assess if stocked juvenile salmon exhibit reach-

specific homing behaviour when returning to the river to spawn as adults; 3) to determine

the egg contributions to the upper reach from hatchery-reared salmon relative to wild

salmon; and, 4) to examine if wild adult salmon remain in the area to which they were

relocated during the spawning period thereby increasing the potential egg deposition and

production within that river reach.

Thesis Overview

The two major components of this study are discussed in separate chapters. Chapter 2

presents the technical details and findings associated with the use of PIT tag technology

to monitor the movement and spawning locations of adult Atlantic salmon in a remote

intermediate-sized river such as Clearwater Brook. The feasibility, challenges, and

limitations of PIT technology as used in this study are reviewed and discussed.

Additionally, observations and trends in the pre-spawning movement and behaviour of

PIT tagged salmon within the middle and upper reach of Clearwater Brook are presented.

Chapter 3 focuses on the in-river distribution and relative spawning locations of hatchery-

origin, wild, and translocated adult Atlantic salmon monitored within Clearwater Brook.

This chapter evaluates the effectiveness of fry stocking and adult translocation as

9

management strategies to increase spawning escapement in a river reach where salmon

spawning was considered sub-optimal. The methods and results of these two potential

stock enhancement strategies are presented along with a discussion of the relative

advantages and limitations of each technique.

10

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England. Aquaculture and Fisheries Management 25/2: 31-44.

Randall, R.G. 1982. Emergence, population densities, and growth of salmon and trout fry

in two New Brunswick streams. Canadian Journal of Zoology 60: 2239-2244.

13

Saegrov, H. and Skilbrei, O.T. 1996. May stocking programs affect the predator stocks

and decrease the survival of the wild Atlantic salmon juveniles? International

Coucil for the Exploration of the Sea C.M. 1996/T:34.

Saunders, J.W. and Smith, M.W. 1962. Transplantation of brook trout (Salvelinus

fontinalis (Mitchell)) within a small stream system. Fisheries Research Board of

Canada. Biological Station, St. Andrews, NB. 7p.

Semple, J.R. 1987. A simple and effective method of cleaning gravel of Atlantic salmon

spawning habitat. Canadian Manuscript Report of Fisheries and Aquatic Sciences

No. 1933. 9p.

Scott, W.B. and Crossman, E.J. 1998. Freshwater Fishes of Canada. Galt House

Publications Ltd., Oakville. 966p.

Shustov, Y.A., Shchurov, I.L., and Smirnov, Y.A. 1981. Adaption times of hatchery

salmon, Salmo salar, to river conditions. J. Ichtyol. 20:156-159.

Sosiak, A.J., Randall, R.G., and MacKenzie, J.A. 1979. Feeding by hatchery-reared and

wild Atlantic salmon (Salmo salar) parr in streams. J. Fish. Res. Board Can. 36:

1408-1412.

Svasand, T. 1993. Are reared juveniles fit for release into the wild? International Coucil

for the Exploration of the Sea C.M. F:34.

Symons, P.E.K. 1979. Estimated escapement of Atlantic salmon (Salmo salar L.) for

maximum smolt production in rivers of different productivity. J. Fish. Res. Board

Can. 36: 132-140.

Thomas, P. 2001. The Lost Land of Moses: The Age of Discovery on New Brunswick's

Salmon Rivers. Goose Lane Editions, Fredericton. NB. 254p.

14

World Wildlife Fund (WWF). 2001. Henning R∅ed, editor. The status of wild Atlantic

salmon: A river by river assessment. 184p.

Youngson, A.F. and McLaren, I.S. 1998. Relocation of naturally-spawned salmonid

ova as a countermeasure to patchiness in adult distribution at spawning. Scottish

Fisheries Report 61/1998 13p.

15

Saltwater –Marine environment

Saltwater –Marine environment

Salmon feed and reach sexually maturity - 1 to 2 yrs at sea

Figure 1.1. Life cycle of the Atlantic salmon (Salmo salar) and general timing of

salmon life-stages in the Maritimes.

Adult salmon migrate to rivers (summer -fall)

Spawning occurs in late October and early November

Egg incubate over winter

Eggs hatch in May

Juvenile salmon stay in river for 2 – 3 years

Freshwater –River environment

Salmon feed and reach sexually maturity - 1 to 2 yrs at sea

“Smolt”migrate to sea - May

Adult salmon migrate to rivers (summer -fall)

Spawning occurs in late October and early November

Egg incubate over winter

Eggs hatch in May

Juvenile salmon stay in river for 2 – 3 years

Freshwater –River environment

“Smolt”migrate to sea - May

Salmon feed and reach sexually maturity - 1 to 2 yrs at sea

“Smolt”migrate to sea - May

Adult salmon migrate to rivers (summer -fall)

Spawning occurs in late October and early November

Egg incubate over winter

Eggs hatch in May

Juvenile salmon stay in river for 2 – 3 years

“Smolt”migrate to sea - May

Adult salmon migrate to rivers (summer -fall) Juvenile

salmon stay in river for 2 – 3 years

Spawning occurs in late October and early November

Salmon feed and reach sexually maturity - 1 to 2 yrs at sea

Salmon feed and generally reach sexual maturity in 1 to 2 years

Freshwater –River environment

Egg incubate over winter

Freshwater –River environment

Eggs hatch in May

16

Miramichi River Basin

Ott er Br ook

Moose Br ook

Lake Br ook

Cl earwat er

NE B r Cle a rwa ter

B r oo k

Br oo k

McCoy B rook

Turnbul l B rook

Fair ley

Brook

Redstone Brook

SW Miramichi River

0 90 180 Kilometers

N

Clearwater Brook catchment

Figure 1.2. Map showing the Clearwater Brook catchment within New

Brunswick’s Miramichi River watershed.

17

ÊÚ

$T$T

SW Miramichi River

Clearw

ater Brook

Turnbull Bk

Lake

Bk

NE B

r Clea

rwat

er

McCoy Bk

Redstone Bk

Fairl

ey B

k

Otter B

k

Moose Bk

0 10 20 Kilometers

N

ÊÚ Fish Counting Fence

Lower Reach 19km

Middle Reach 14.5 km

Upper Reach 14.5 km + Northeast Branch

Figure 1.3. Map of Clearwater Brook displaying the location of the fish counting

fence ( ) and the areas defined as the lower, middle and upper reach.

18

CHAPTER 2

Using passive integrated transponder (PIT) technology to monitor the pre-spawning movement patterns of adult Atlantic salmon within Clearwater Brook, New

Brunswick.

Abstract

This study used passive integrated transponder (PIT) technology to monitor the in-river

movements of Atlantic salmon (Salmo salar), with both stationary and portable Texas

Instruments Radio Frequency Identification systems. This study was conducted in 1999

and 2000 in Clearwater Brook, a 335 km2 sub-catchment of the Miramichi River basin in

New Brunswick. Adult salmon were easily and quickly (< 45 sec) tagged by intra-

musculature implantation of 32 mm long by 3.9 mm diameter transponders with a tagging

mortality as low as 0.35%. Stationary readers could detect tags as far as 40 cm from the

plane of the antenna and swimming fish at grounds speeds up to 4.0 m/s. Readers, as

positioned, were estimated to have tag detection efficiencies > 95% when functioning

properly. High water, power supply and data logging problems had the potential to

reduce tag detection efficiency and data accuracy. Operation of stationary readers in wide

river reaches (15-20m) was logistically more complex and generally less reliable when

compared with small (<3m width) stream installations. A portable device was designed

and proved effective for locating and identifying tagged salmon in holding pools ≤3 m

deep.

20

Introduction

Monitoring the distribution and movement of fish in natural stream environments is often

the most effective way to answer questions about fish ecology. While traditional fish

movement studies often required physically recapturing or observing fish to identify a

mark or tag, many present day studies remotely monitor tagged fish by using radio

frequency, ultrasonic (acoustic) and even satellite positioning technology. These ‘new’

technologies are limited because they require an internal power supply which reduces the

tags longevity and the minimum size and the cost of the device (Berman and Quinn,

1991). Consequently, these ‘active’ tags are only useful for short-term studies, usually <1

year, while their cost is generally prohibitive for studies which involve monitoring large

numbers of fish. Furthermore, the size of these tags usually precludes their use for

research on small-bodied fish < 12 cm (e.g., Adams et al, 1998).

Radio Frequency Identification (RFID) technology first appeared in industrial tracking

and access applications in the 1980’s and was innovatively applied as a method to

monitor and track fish in the late 1980’s and early 1990’s (see Prentice et al., 1990).

Over the past decade RFID based Passive Integrated Transponder (PIT) technology has

become an increasingly common tool for studying fish in laboratory and field settings.

Passive integrated transponders that are typically used for fisheries research are small

cylindrical tags (< 32 mm long x 3.9 mm diameter) that consist of a glass encapsulated

coil antenna and radio-frequency (RF) microchip (figure 2.4). PIT tags rely on an

external electromagnetic (EM) field to temporarily energize the RF chip and transmit a

unique RF code. Specially designed tag detection equipment is used to generate the EM

21

field and to receive and decode the RF transmission. Because PIT tags are small,

waterproof, relatively inexpensive (< $5 CAD, each), and have an indefinite lifespan they

are a potentially excellent tool for monitoring the individual movement of small-bodied

fish and/or large numbers of fish at a reasonable cost. Recent improvements in the

detection capabilities of PIT tags have increased their use and effectiveness for

conducting fish tracking and movement studies in streams (Prentice et al., 1990; Castro-

Santos et al., 1996; Armstong et al., 1996; Roussel et al., 2000; Barbin-Zydlewski et al.,

2001), however, it is still accepted that the applicability of the technology is restricted

since the tag’s primary limitation is that it must enter a localized EM field to be detected.

The present chapter describes the use of PIT technology to study the pre-spawning

movements and behaviour of several hundred adult Atlantic salmon (Salmo salar) within

an intermediate-sized river, with particular focus on the design and field performance of

the PIT tag detection systems.

Study Area

Clearwater Brook is a fifth-order tributary of the Southwest Miramichi River located in

central New Brunswick, Canada (46o42’ N, 66o48’ W) (Figure 2.1). The river flows for

60 km in a southerly direction from one spring-fed and three lake-fed headwater

tributaries (Figure 2.2). It has an average channel width of 16.5 metres and a mean slope

of 1%. In midsummer, mean daily water temperatures throughout the river rarely exceed

20oC and all other water quality parameters tested within Clearwater Brook also indicate

suitable conditions for salmonid production (Table 2.1). The Clearwater Brook

22

catchment (335 km2) is 4.3% of the Southwest Miramichi River basin and is almost

wholly situated in the gated forest management land owned by J.D. Irving, Limited and

Bowater Canadian Forest Products Incorporated. As a result of this controlled public

access, the river receives only limited recreational use, most of which is in the form of

Atlantic salmon angling from two private fishing camps located in the lower eight

kilometres of the river.

The primary anthropogenic influence to Clearwater Brook is forest harvesting. The brook

has retained much of its remote and pristine quality and shows little evidence of impacts

to aquatic habitat as a result of adjacent land disturbances. Based on photo-interpretation,

the forest cover in the Clearwater Brook catchment is 22% tolerant hardwood (sugar

maple - Acer saccharum, and yellow birch - Betula alleghaniensis), 19% softwood (red,

black and white spruce species - Picea spp., and balsam fir - Abies balsamea), 27%

softwood plantation (black and white spruce, and jack pine - Pinus banksiana), and 13%

naturally regenerating spruce and fir species. The remaining 19% of the catchment is

comprised primarily of mixed stands of tolerant and intolerant hardwood species (aspen -

Populus spp., white birch - Betula papyrifera) and a variety of softwood species (white

and red pine - Pinus spp., eastern white cedar - Thuja occidentalis, eastern hemlock -

Tsuga canadensis , fir and spruce).

Since 1996 the brook has been the site of an Atlantic salmon research and management

project (McCabe and Connell, 1997; Whoriskey, 1998). A detailed stream habitat survey

conducted in 1996 using criteria defined by the New Brunswick Department of Natural

23

Resources and Energy (Hooper and McCabe, 1998), characterized the substrate within

Clearwater Brook as predominantly rubble (33%), rock (29%), and gravel (20%) with

boulder (11%), sand (6%), and fine (1%) substrates accounting for a small proportion of

the wetted streambed. A total of 461,350 m2 of wetted stream habitat was identified in

the upper and middle reach of the brook and of this, 217,660 m2 was characterized as

preferred salmon spawning habitat (McCabe and Connell, 1997).

Atlantic salmon is the predominant fish species in Clearwater Brook; however, brook

trout (Salvelinus fontinalis), slimy sculpin (Cottus cognatus), white sucker (Catostomus

commersoni), blacknose dace (Rhinichthys atraulus), and American eel (Anguilla

rostrata) are also known to occur throughout the brook.

Since 1997, annual adult Atlantic salmon spawning returns to Clearwater Brook were

estimated to be in excess of 1000 fish. This conservative estimate is based on an annual

mean return of 810 adult salmon to a fish counting fence located 19 km upstream from

the mouth of the brook between 1997 and 2002 (Connell, 2003). The Clearwater Brook

system is an important spawning and nursery area for Atlantic salmon, as evidenced by

the presence of substantial high quality habitat, significant annual adult salmon returns,

and high juvenile densities (≥ 90 fry/100m2, ≥ 20 parr/100m2) throughout the mid and

lower reaches of the brook (Connell, 2003).

24

Materials and Methods

Atlantic salmon captures

From early July to late October a metal “A-frame” fish-counting fence similar to the

design described by Anderson and McDonald (1978) was installed in Clearwater Brook

at a location 19 kilometres upstream from the Southwest Miramichi River in 1997 to

2003 (Figure 2.2, Figure 2.3). This fence was equipped with an upstream trap and was

able to capture upstream-migrating fish > 35 cm in fork length. Rarely, exceptionally

high water events provided fish with limited opportunities to bypass the trap by finding

holes underneath the fencing or by swimming around the ends of the fence. The fish trap

was checked daily and all captured Atlantic salmon were measured for fork length (± 0.1

cm), examined for external tags or marks, and sexed based on phenotypic characteristics.

Any salmon missing most or all of its adipose fin was considered a ‘hatchery-origin’ fish

because this same mark was applied to all underyearling salmon stocked annually to the

upper reach since 1996. Following the collection of biological information salmon were

immediately released upstream of the counting fence. Atlantic salmon adults < 63 cm

fork length are referred to as grilse. Those of fork length ≥ 63 cm are referred to as multi-

se-winter salmon (MSW).

In 1999 and 2000 this facility was used to capture and collect biological information from

all upstream migrating adult salmon for the present study. No high water events were

known to have compromised the fence and allowed salmon to bypass the facility in these

years. In both years a portion of the captured salmon were implanted with passive

integrated transponder tags prior to their release upstream of the fence. In 2000, scale

25

samples were randomly collected from 126 salmon for age analysis. Age was determined

from these scales according to methods described by Power (1987) and the mean length

of Atlantic salmon, grouped by years of sea growth (sea-age), was calculated.

PIT Tagging

Based on work conducted by USGS researchers at the Conte Anadromous Fish Research

Center in Turner Falls, MA (Barbin-Zydlewski et al. 2001; Castro-Santos et al., 1996) the

TIRIS (Texas Instruments Radio Frequency Identification System) PIT equipment was

determined to be the preferred fish tagging technology for the current study. Relative to

alternate radio frequency or ultrasonic transmitter tag systems, Texas Instruments based

PIT technology offered the following advantages in monitoring adult salmon movement

and distribution in Clearwater Brook: 1) lower tag cost (~ $5), which made it

economically feasible to tag in excess of 500 Atlantic salmon; 2) smaller tag size, which

permitted a rapid and less invasive tagging procedure; 3) improved tag detection ranges

with TIRIS half-duplex tags relative to alternate PIT tag systems (e.g. Biomark’s 23 mm

tag); 4) ‘custom’ tag detection stations (RF antennas) that meet specific site installation

requirements can be constructed with the TIRIS system.

Texas Instruments 32 mm read/write glass-encapsulated passive integrated transponder

tags (RI-TRP-WR2B) were surgically implanted into adult Atlantic salmon. These tags,

weighing 0.8 grams (in air), were coded with a unique identification number and tested

prior to tagging. Due to the brief time necessary to implant a PIT tag into an adult

Atlantic salmon (~ 45 seconds), fish were not anaesthetized during the tagging procedure.

26

Rather, salmon captured at the counting fence were placed in an inverted horizontal

position in a specially designed measuring box such that the ventral surface of the fish

was exposed. The box maintained water over the fish’s gills and a wet chamois cloth was

placed over the head to help pacify salmon during the tagging procedure. Following the

removal of two to three scales anterior the tip of the right pelvic fin, a 4 mm long x 2 mm

deep incision was made in the ventral musculature using a number 11 curved scalpel. The

incision commenced approximately 30 mm anterior to the tip of the right pelvic fin and

was drawn lengthwise toward the caudal fin. A PIT tag taken from a 70% isopropyl

alcohol solution was inserted into the incision and oriented axially into the musculature

of the fish. To prevent the tag from entering the peritoneal cavity, downward force was

minimized and the tag was tilted horizontally as it was forced into the musculature

located anterior to the incision (Figure 2.4). Following tagging, the PIT identification

number was scanned and recorded with a handheld TIRIS tag reader (RI-HHU-W3AG-

00), and a topical antibiotic cream (Polymyxin B) was applied to the tagging incision.

Prior to releasing the salmon upstream of the trap, its fork length (mm) was measured and

the sex of the fish was assessed based on phenotypic characteristics.

An effort was made to PIT tag and monitor all female salmon (wild and hatchery-origin)

with the exception of the 12 wild females removed from the river in support of the

hatchery stocking program. Additionally, nearly all male hatchery-origin salmon and a

random selection of wild male salmon were PIT tagged and released upstream of the

fence so that pre-spawning movements and spawning distributions of various groups of

salmon could be compared.

27

Stationary PIT tag readers

The movement and distribution of PIT tagged Atlantic salmon were monitored in the

middle and upper reaches of the Clearwater Brook via a series of “tag reader stations”. In

1999, one reader station was established to monitor salmon movement in the main stem

of Clearwater Brook 14.8 km upstream from the counting fence (CR2). A second station

was installed within the Northeast Branch tributary 900 metres upstream from its

confluence and 13.2 kilometres upstream of the counting fence (CR4) (Figure 2.2). In

2000, two additional reader stations were installed 6.7 km (CR1) and 21.8 km (CR3)

upstream of the Clearwater Brook counting fence (Figure 2.2). Reader stations were

installed in June, prior to the capture of Atlantic salmon at the counting fence, and

removed in early November (06 to 12) in both years.

Reader station components Reader stations consisted of a wire loop RF field transmit/receive antenna regulated by a

Texas Instruments (TIRIS) Series 2000 PIT reader (Figure 2.5). This system generated a

134.2 kHz electromagnetic signal in the antenna through which adult salmon were forced

to pass when moving past the reader station. When a PIT tagged fish entered this

electromagnetic (RF) field, a capacitor within the tag was energized and the tag’s code

was transmitted to the TIRIS reader equipment. Once detected by the reader, the tag’s

signal was decoded and relayed to a Hewlett-Packard (HP) palmtop computer where a

custom software program (written in BASIC by Dr. A. Haro, USGS, Turner Falls, MA)

logged the time, date and tag identification number each time a tag was “read”. The HP

palmtop computer (1000CX or 200LX) was connected to a TIRIS Series 2000 control

28

module (RI-CTL-MB2A) via an RS232 connection. A TIRIS Series 2000 high

performance remote antenna RFM reader module (RI-RFM-008B) was connected to the

control module via a proprietary interface to form the Series 2000 “reader”. These

components, and two deep-cycle lead-acid 12-V batteries (60 A h), were housed inside a

large weatherproof plastic container situated outside of the flood zone on the stream bank

adjacent to the reader antenna. Twin-axial shielded wire was used to connect the RFM

module to a TIRIS Series 2000 antenna-tuning module (RI-ACC-008B). The antenna-

tuning module completed the connection between the “reader” on the stream bank, and

the RF wire-loop antenna in the brook. The antenna-tuning module was housed in a metal

waterproof box that was fastened above high water to a wooden frame used to support the

wire loop RF antenna (Figure 2.5). Logging data on the HP palmtop computer, as

opposed to a laptop, minimized power consumption and enabled the reader stations to

operate continuously for up to 96 hours on a set of freshly charged batteries.

The TIRIS Series 2000 tag reading equipment is half-duplex, meaning that it must rapidly

cycle between a transmit and a receive mode in order to detect and decode PIT tag

identification numbers. Essentially, the system must first transmit the RF field necessary

to energize a PIT tag, and then immediately receive the tags RF signal response. This

process limits the speed at which a tag can be consecutively ‘read’ as the transmit/receive

or “interrogation” cycle must repeat between tag detections. At peak performance, the

system was capable of interrogating tags every 100 ms.

29

Antenna design

Customized wire loop antennae were designed and tested in an effort to maximize the tag

detection capabilities of the RF field while also achieving an antenna opening large

enough to allow salmon to pass through, unobstructed. The Texas Instruments “Antenna

Design Program” (ADP) (Texas Instruments, Austin, TX) computer software was

initially used to determine the optimum inductance and power associated with various

antenna dimensions and designs. With the aid of the ADP software it was determined that

only a few antenna designs maximized the strength of the antenna’s RF field while also:

1) meeting the dimensions required for installation in Clearwater Brook; and, 2) creating

an antenna opening that provided unobstructed adult salmon passage. Dry land testing of

these various antenna options was conducted to determine the configuration that provided

optimum tag read distances without introducing “dead-spots” within the RF field. For

testing, each antenna was laid out on a flat horizontal surface in keeping with the number

of loops and dimensions calculated from the antenna design software. The TIRIS

equipment was connected to the test antenna and the antenna-tuning module was adjusted

to achieve the inductance that maximized the RF field around that antenna. This tuning

process was aided with the use of a voltmeter in contact with each conductor of the twin

axial wire at the connection from the RFM reader module; a series of jumpers and a fine-

tuning screw on the antenna-tuning module were adjusted until the voltage from the RFM

module was maximized. A 32 mm PIT tag was held perpendicular to the antenna and

moved slowly towards the RF field. This process was repeated several times and each

time the tag was introduced to a different area of the energizing field to simulate a tagged

fish passing through the antenna opening at various locations. Observations of the tag

30

read distance of each antenna tested made it possible to select the antenna design that

maximized tag detection capabilities.

Antenna construction and installation

Rectangular wooden frames measuring 3.5 metres wide by 0.81 metres tall were

constructed from ‘2x4’ lumber. Two loops of PVC-jacketed, 12 gauge, seven-strand

copper wire were affixed to the inside of the wood frame with plastic cable ties. The

antenna was installed in a vertical orientation such that fish could swim through the

rectangular frame. The widest axis of the antenna was oriented perpendicular to the river

flow, such that the antenna spanned further across the brook than vertically in the water

column. In order to minimize any obstruction to adult salmon movement the antenna

frame was positioned in the river thalweg, where migrating salmon were most likely to be

travelling, and the lower portion of the antenna frame was partially imbedded in the

substrate of the streambed. Sections of A-frame counting fence were erected adjacent to

the reader antenna to ensure that all fish > 35 cm in length were directed into the tag

detection field as they moved past the reader station (Figure 2.6). It was assumed that the

large opening of the antenna (3.5 m x 0.8 m) oriented in the river thalweg allowed

migrating fish to pass unhindered through the reader station.

Portable PIT tag reader

The stationary PIT tag reader system is dependent on the movement of tagged fish past

the fixed RF antenna location. During low, warm water conditions, the holding (staging)

behaviour commonly exhibited by Atlantic salmon necessitated the use of an alternative

31

PIT tag reading techniques for locating tagged fish. To gain more precise information

about the holding location of PIT tagged salmon distal to fixed reader stations, a portable

tag reader system was designed and operated during early August (3,4,5) and September

(1,3,14) of 1999 in Fence Pool, Brook Pool or Bridge Pool, located 100, 4000, and 6500

metres, respectively, upstream of the Clearwater Brook counting fence (Figure 2.7).

The portability of the reader system was increased by enclosing the core components of

the reader station (control module, remote antenna reader, power supply and palmtop) in

a large plastic box that could be floated in-stream. A single loop of PVC-jacketed, 12

gauge, seven-strand copper wire was affixed between two 4-m long wooden poles with

plastic cable ties to form an RF antenna 7.3 metres wide and 66 centimetres tall. The two

extremities of the wire loop were run 2 metres up one pole and connected to the antenna

tuning module affixed to the pole. Twenty metres of twin axial wire formed the

connection between the pole mounted antenna and the reader equipment situated in the

plastic box. Two methods were used in recording PIT tags with the portable reader.

‘Pool sweeping’ involved stretching the antenna across the head of a pool and slowly

moving it downstream keeping the plane of the antenna as vertical as possible and the

lower loop of the antenna as near to the stream bottom as possible (Figure 2.8). Two

people manipulating the 4-m long wooden poles located at each end of the wire loop

antenna were required to keep the wire taught and control the movement of the antenna

as it was swept downstream. A third person was needed to monitor and move the tag

reader equipment and palmtop computer floating near the edge of the pool. Atlantic

salmon tended to congregate in the tail of the pool as the antenna was swept downstream.

Once the antenna neared the lower end of the pool, fish passed through the antenna as

32

they swam upstream towards the head of the pool. In some pools, boulders made it

difficult to ensure that the lower portion of the wire loop remained close to the stream

bottom while sweeping through the pool. In these instances, the portable reader was kept

stationary at the preferred salmon holding location and snorkelling or wading was used to

temporarily displace and drive fish through the RF antenna. In an effort to increase the

likelihood of reading all tagged fish present in a pool, multiple passes were made (15

minutes rest period between passes) until no new tags were detected.

Assessing tagging related mortality

Dead adult salmon have been recovered on the upstream side of the Clearwater Brook

counting fence on multiple occasions (< 5 per year). Because some of these fish were

highly decomposed and others appeared to have died just prior to recovery, it was

assumed that mortalities associated with complications from PIT tagging were likely to

drift downstream and be recovered against the counting fence. In-river post tagging

mortalities were monitored daily at the Clearwater Brook counting fence and to a lesser

extent at salmon holding pools upstream of the fence. All dead salmon recovered in

Clearwater Brook were thoroughly examined and scanned for the presence of a PIT tag.

Field-testing PIT tag reader stations

Reliability

The reliability of reader stations was critical to the present study because a failure of PIT

tag detection equipment or a breach in the fencing adjacent to the to RF antenna

permitted PIT tagged salmon to pass, undetected, through a reader station. While in

33

operation, each reader station was visited every two to three days in order to download

data from the palmtop computer and to supply freshly charged batteries to the system. On

these occasions, reader stations were tested to determine if they had functioned properly

since the previous visit. Testing involved passing a PIT tag through the antenna field and

ensuring that the correct tag ID number, date and time was recorded by the palmtop

computer. Additionally, the fencing adjacent to the antenna opening was visually

inspected for breaches through which adult salmon could have passed undetected.

Tag detection distance

After each reader station was installed in the brook and ‘tuned’ to maximize the power of

the antenna field, a test was performed to assess the effective tag ‘reading’ distance of the

system. One person slowly moved a PIT tag (held with its longest axis parallel to the

river flow) towards the RF field of the antenna while a second person watched the

palmtop computer and alerted the ‘tag mover’ as soon as the tag’s ID number was

recorded. This process was repeated no less than 50 times and each time the tag

approaching the antenna at different locations. The tag detection range was roughly

estimated as the mean distance from the plane of the antenna coil to the point where the

tag was first ‘read’.

Tag detection efficiency

Between October 12 and 13, 1999, 20 PIT-tagged adult salmon were translocated from

the counting fence to the upper reach of Clearwater Brook, upstream of the PIT tag reader

stations (CR2 or CR4). Salmon were measured and examined to determine their fork

34

length, sex, and origin (hatchery or wild), and a PIT tag was implanted into each salmon

selected for translocation. The 20 salmon randomly selected for the translocation study

were transported in a 900 litre insulated holding tank to one of three relocation sites as

follows: CTR1) eight Atlantic salmon (four females, four males); CTR2) eight Atlantic

salmon (four females, four males); CTR 3) four Atlantic salmon (two females, two

males) (Figure 2.7). Nine of the ten female and five of the ten male translocated salmon

exceeded 63 cm (FL) and the range of all of these fish was 60 cm to 94 cm (FL) (Table

2.2).

The presence of a known number of translocated PIT-tagged fish above each reader

station provided an opportunity to assess the tag detection efficiency as these fish moved

downstream past the reader station. It was assumed that each of the 20 tagged fish moved

downstream past the reader station prior to early November, when the stations were

removed for winter. The tag detection efficiency was calculated based on the number of

PIT tagged salmon translocated above a given reader station and the proportion

subsequently detected by that reader station. In addition to the reader efficiency

assessment provided by monitoring translocated salmon, the operation of the counting

fence and four PIT tag reader stations in 2000 provided an opportunity to identify

“missed tags”.

These gaps were instances when a tagged fish was known to have passed through a

reader station (detected downstream and subsequently upstream or vice versa) without

35

being detected. Given the layout of capture and tag detection locations, ‘missed tags’

could only be identified from data recordings at CR1 and CR2.

In-river movements of PIT tagged salmon prior to spawning

Adult salmon captures at the fish counting fence (date, sex and length) coupled with data

(location, date, timing, frequency) from detections of PIT tagged Atlantic salmon, by

stationary and portable PIT tag readers, provided an opportunity to investigate the pre-

spawning movements of adult salmon within the middle and upper reaches of Clearwater

Brook. In 1999 and 2000, adult salmon of varying length and sex were captured on

different days at the counting fence and the individual movements of 585 of these fish

were monitored relative to multiple PIT tag reader locations over as many as five months.

The date and time of counting fence captures and PIT tag detections were compiled

electronically and grouped based on a variety of adult salmon characteristics including:

sex, run-timing, fork length, salmon origin (wild vs. hatchery), and permutations thereof.

Grouped data were examined graphically to determine if similarities in pre-spawning

movements could be observed.

Statistical analyses

Z tests were performed to determine if the sex ratio of wild origin grilse or MSW salmon

varied significantly between years. The z-test procedure could not be validly applied to

assess observed difference in the sex ratio of hatchery-origin grilse and MSW salmon due

to small sample sizes. Z tests were further used to investigate differences in the

36

proportion of early-run salmon between the wild and hatchery-origin groups and between

grilse and MSW salmon within these groups. These analyses were performed using

SAS/STAT ® software (SAS Institute Inc., 1999).

The 95% confidence interval for several calculated proportions were derived without a

correction for continuity (Newcombe, 1988).

Results

Atlantic salmon captures, 1999 and 2000

In 1999, the Clearwater Brook counting fence operated from June 4 to October 21 and

captured a total of 890 Atlantic salmon (409 multi-sea-winter and 481 grilse); 33 of these

(3.7%) were identified as hatchery-origin salmon. The first salmon capture was recorded

on June 12, and 317 (24.2%) salmon arrived at the fence prior to September (‘early--run’

fish). Females accounted for 15.5% of wild grilse (n=401), 72.4% of wild, multiple sea-

winter salmon (n=456), 24.0% of hatchery-origin grilse (n=25) and 50.0% of hatchery-

origin MSW salmon (n=8).

In 2000, the fish counting fence operated from May 30 to November 3 and captured 715

Atlantic salmon (197 multi-sea winter salmon and 518 grilse), of which 33 were of

hatchery-origin. The first salmon was captured June 28, and 176 (20.4%) salmon were

early-run fish. Female salmon accounted for 5.1% of wild grilse (n=490), 72.4% of wild

MSW salmon (n=192), 7.1% of hatchery-origin grilse (n=28) and 100% of hatchery-

origin MSW salmon (n=5) captured in 2000. Sex ratios varied significantly between

37

years for wild grilse (z=0.105, P<0.001), but not for wild MSW salmon (z=0.02, P=

0.98).

Based on scale samples randomly collected from salmon captured at the fish fence in

2000, one-sea winter (1SW) salmon had a mean fork length of 57.1 ± 0.6 cm (n=60,

range = 50.0 cm to 62.5 cm), two-sea winter (2SW) salmon averaged 81.5 ± 1.5 cm

(n=58, range 72 cm to 95 cm), and three sea-winter (3SW) salmon averaged 92.7± 10.6

cm (n=8, range 76 cm to 109.5 cm).

PIT tagging

Passive integrated transponder tags were inserted into 354 (41.3%) of 857 wild salmon

and 27 (81.8%) of 33 hatchery-origin salmon captured at the Clearwater Brook counting

fence in 1999 (Table 2.3). All hatchery-origin female salmon (n=10) and 73.9% (17 of

23) of hatchery-origin male salmon received tags, whereas 88.9% (321 of 361) wild

female salmon and 6.7% (33 of 496) of wild male salmon were PIT tagged. The pressure

needed to insert a PIT tag was found to result in egg expulsion from some fish during the

peak of the spawning period. As a result, 14 wild female MSW salmon and two wild

female grilse captured after October 19 did not receive tags. Additionally, 12 wild MSW

salmon that were removed from the river for hatchery broodstock did not receive a tag.

In 2000, 165 (24.2%) of 682 wild salmon and all 33 hatchery-origin (7 female and 26

male) salmon captured at the counting fence were PIT tagged (Table 2.4) Egg expulsion

prevented two wild MSW female salmon from being tagged during late October of 2000

and 12 wild MSW females were not tagged as they were collected for hatchery

38

broodstock. A total of 147 (89.1%) of 165 wild female salmon and 18 (3.5%) of 518 wild

male salmon received a PIT tag in 2000.

Tagging related mortality

Over the two year tagging period, 2 of 579 (0.35%) PIT tagged adult salmon were

recovered dead against the Clearwater Brook counting fence. The first post-tagging

death was a 100 cm (FL) wild female salmon tagged on October 18, 1999 and recovered

on October 19, 1999. The brief time (1d) between tagging and death suggested that this

fish died as a result of the tagging procedure; haemorrhaging at the site of tag insertion

supported this suspicion. The second mortality was a 75 cm (FL) wild female salmon,

tagged on June 30, 2000 and recovered dead at the counting fence on August 4, 2000. It

unlikely that this mortality was directly related to the tagging procedure as the fish

survived for upwards of 36 days following its initial capture at the fence; a visual

inspection of the fish did not provide any clues as to the direct cause of death. Assuming

that all tag related salmon mortalities were recovered and that both of these were caused

by the tagging procedure, a mortality rate of 0.35% is attributed to PIT tagging of adult

Atlantic salmon in Clearwater Brook from 1999 to 2000. Comparatively, 0.49% (5 of

1020) of the salmon measured and released without PIT tags in 1999 and 2000 were

subsequently recovered dead against the fence. Again, this mortality rate assumes that all

salmon that died as a result of handling at the counting fence were successfully

recovered. Also, because the fence operated without incident in 1999 and 2000, it was

assumed that no salmon were successful in bypassing the facility without being counted.

It is possible that fish died upstream of the counting fence (as a result of handling or PIT

39

tagging) and were removed by predators or did not drift downstream to the fence.

Consequently, these mortality rates are conservative.

Performance of PIT tag reader stations Reader station reliability Each time a reader station was visited, a PIT tag was manually passed through the

electromagnetic field of the antenna to ensure that the station functioned properly since it

was last inspected. In over 120 visits to each reader station there were only two instances

when the tag reader equipment did not detect the test tag.

On October 21, 1999 the memory capacity of the palmtop computer at the CR2 reader

station was overloaded by near continual readings of a 75.0 cm PIT tagged female

salmon. This fish accounted for over 11,000 of the 18,660 tag readings logged in the

active data file when the maximum storage capacity of the palmtop computer was

reached. While the data recorded prior to this point were not lost, no additional tag

detection information was stored until the palmtop computer was manually reset (24-

hours later). For three days prior to this event, multiple tag recordings of the same fish

were detected on the CR2 reader equipment. The presence of a salmon redd four metres

upstream of the CR2 antenna was noted during this time and suggested that the spawning

female was resting within the antenna field as she tended the upstream redd. On multiple

occasions tagged salmon were detected within the antenna field for extended periods of

time (generally less than five minutes) or several times with a brief interval between

detections. While most common during October due to the number of fish passing

40

through reader stations, these events did not occur exclusively during the spawning

period.

In mid August of 1999, the CR2 PIT tag reader station equipment failed when the voltage

output from the external batteries dropped below the minimum requirement (+9.6 VDC)

necessary to externally power the palmtop computer. In the absence of a suitable external

power supply, the palmtop computer was able to operate for only a short period on its

onboard AA battery power source. Once this power supply failed, the palmtop computer

turned off and any tag detection information temporarily stored in the active data-logging

file was lost. It is unknown if any PIT tagged fish moved past the CR2 reader station over

a 48-hour period during this event. Fortunately, few fish were detected prior to or

following this equipment failure, suggesting that salmon were not moving during this

period.

High water, rather than equipment failure, accounted for the majority of the reliability

issues encountered with the operation of PIT tag reader stations in Clearwater Brook. On

three occasions between 1999 and 2000, river flooding caused problems with reader

station equipment. In these instances fence sections adjacent to the antenna were

breached and fish were able to pass by the station without swimming through the RF

field. High water caused a breach in the fencing at the CR2 reader in the afternoon of

October 14, 1999 and prevented repair of the station until 16h00 on October 19. It is

unknown how many PIT tagged salmon passed through the CR2 station during this 120

41

hour interval, however, substantial tag detections prior to and following this event

suggest that a number of tag detections were missed.

Similarly on July 3, 2000 the fence sections located adjacent to the antenna at reader

stations CR1 and CR2 were breached due to high water. Water levels continued to delay

the repair of the CR2 reader station until July 6, while damage to fencing material

prevented the re-installation of CR1 until July 18, 2000. The day following re-installation

(July 19) a small breach was detected at reader station CR1 and repairs were made on

July 20, 2000. It is clearly possible that PIT tagged fish were able to move past these

reader stations while the fence sections were breached. Fortunately, however, these

stations were only compromised in early July of 2000, with only three tagged fish present

in the river prior to repair of station CR2 and an additional four fish tagged at the fence

following repair of CR2 but prior to the re-installation of CR1.

PIT tag detection distance

Testing the detection capabilities of the reader antennae indicated that, with the PIT tag

oriented horizontally in the water column and parallel to the river flow, the effective read

range was 0.20 metres on each side of plane of the antenna coil. Assuming the passive

integrated transponder is similarly oriented as tagged fish pass through the antenna array

(as is likely the case), and that fish follow the shortest linear path through the antenna

field, the minimum effective length of the detection field is 0.40 metres. Based on the rate

of PIT tag recordings for salmon that passed directly through the RF antenna field,

average tag detection rates varied from 7 to 10 reads / second. Given the effective length

42

of the detection field, Clearwater Brook PIT tag detection systems were calculated to be

effective at recording fish passing through the antenna at ground speeds as high as 4.0

m/s.

PIT tag detection efficiency

Eleven of the twelve (91.7%, C.I. = 64.6% to 98.5%) tagged salmon translocated to the

upper reach in the main stem of Clearwater Brook (CTR2 and CTR3) were subsequently

recorded (pre and/or post-spawning) at the CR2 reader station, located downstream of the

relocation site. Similarly, six of the eight (75%) (C.I. = 40.9% to 92.9%) tagged salmon

translocated to the Northeast Branch of Clearwater Brook (CTR1) were later recorded

downstream at the Northeast Branch reader station (CR4). It is possible that the three

undetected fish died or remained above the reader stations and did not move downstream

prior to the removal of the PIT tag reader stations in early November.

In 2000, all of the 79 PIT tags recorded at the CR2 or CR4 reader stations were

previously detected at the CR1, indicating that the CR1 reader was 100% efficient (C.I. =

95.4% to 100%) at detecting these upstream migrating fish. Comparatively 5 of the 37

tagged salmon that migrated between the CR1 and CR3 stations were not detected at

CR2, suggesting that this station was 86.5% efficient (C.I. = 72.0% to 94.1%) at

detecting these upstream migrants. Interestingly, all of the ‘missed’ tag detections appear

to have occurred between October 18 and October 25, and during the period when the

CR2 reader was not functioning or was logging frequent tag detections due to adjacent

spawning by a tagged female.

43

Movement, behaviour and distribution of PIT tagged Atlantic salmon

Timing of adult Atlantic salmon captures In 1999, there was no significant difference in the proportions of early-run wild salmon

(25%, n= 857) and hatchery-origin salmon (23.7%, n= 33) (z= -0.164, p=0.87, Table 2.5).

A comparison of one sea-winter and multi sea-winter salmon captures found only minor

differences in the proportion early-run hatchery and wild salmon captured in 1999, none

of which were statistically significant (p>0.5). In 2000, a significant difference (z=-0.187,

P=0.015) was observed between the proportion early-run hatchery-origin (42.4%, n=33)

and wild salmon (23.8%, n=682). This difference was most pronounced for multi sea-

winter fish, with 80.0% of hatchery-origin MSW’s (n=5) and only 15.6% of wild MSW’s

(n=192) returning prior to September, however, the statistical significance of the

observed difference could not calculated (n=5).

Pre-spawning distribution and movement Individual PIT tagged salmon movement prior to spawning was diverse, however, a

number of patterns in fish migration were observed. First, many of the salmon destined

for the upper reach of Clearwater Brook held in pools located < 6.5 km upstream of the

Clearwater Brook counting fence prior to spawning with nearly 50% of the PIT tagged

salmon detected in Bridge Pool, Brook Pool or Fence Pool at the beginning of September

(Figure 2.9).

Three tagged salmon detected in Brook Pool in early September were previously detected

at CR2 (14.2 km upstream of the fence) in late June and early July, indicating that these

44

fish moved upstream a substantial distance after they were captured, but returned

downstream to a primary salmon resting pool located 4-km upstream of the fence.

Similar ‘roving’ behaviour was observed in 2000, when five male grilse (4 hatchery-

origin) and one female grilse moved upstream from below CR1 to (or beyond) CR2 in

August. All of these fish dropped downstream below the CR1 reader, with the exception

of one hatchery-origin male grilse that remained between the CR1 and CR2 reader. The

average ‘trip time’ of this roving movement was 4.5 days and was completed in as few as

two and as many as ten days. In addition to these grilse movements, two tagged female

salmon migrated upstream of the CR1 reader and subsequently dropped back downstream

within two days in August of 2000. This roving behaviour was observed in 21.7% of

grilse (n= 29) and 11.1% of the MSW salmon (n= 18) that were captured and PIT tagged

prior to September (2000) and was more common among hatchery-origin salmon (38.5%)

than wild salmon (8.8%) (Table 2.6); none of the ‘late-run’ fish exhibited this type of

movement. Despite this limited roving behaviour, it appeared that most salmon accessing

upper reaches of Clearwater Brook did so only just prior to spawning. While some

salmon began moving into the upper study reach in late-September, the majority of

upstream fish movement did not occur until mid-October when most fish were captured

at the fence (Figure 2.10). Data from 2000 provides evidence of a delayed upstream

migration of early-run salmon to the upper study reach, when only 17 (36%) of the 47

early-run tagged salmon migrated to the CR1 reader station (6.7 km upstream of the

fence) prior to September; and only six tagged salmon (12.8%) continued upstream to the

CR2 reader (14.2 km above fence). None of the salmon PIT tagged in 2000 migrated to

the CR3 (21.7 km upstream) or CR4 (NE Branch, 13.2km upstream) reader stations prior

45

to October (Figure 2.11). Similarly, in 1999, the earliest tagged salmon detections in the

Northeast Branch (CR4) occurred on September 23 and 24 from two male grilse (1 wild,

1 hatchery-origin); the remaining migrants to the Northeast Branch were not detected

until after October 9, and just prior to spawning.

Given that salmon entering the study area in autumn had less time to reach spawning

grounds it is not surprising that the average number of days between PIT tagging and tag

detections at reader stations varied between early-run and fall run salmon; clearly early-

run salmon took longer to migrate upriver than fall-run salmon (Figure 2.12).

Differences in the number of days to CR1 and CR2 between early-run hatchery-origin

and wild salmon are probably explained by the higher incidence of pre-spawning roving

behaviour by the hatchery-origin grilse.

After October 10 of 2000, and principally during the salmon spawning period, 13 PIT-

tagged salmon were observed roving between reader stations in a pattern that differed

from the ‘typical’ spawning movements of other tagged fish. Most tagged salmon moved

upstream just prior to spawning and remained in a single study reach during the spawning

period, after which they returned downstream with little delay (late October to early

November). However, seven hatchery-origin male grilse, four wild male grilse, one wild

female grilse, and one wild female MSW salmon exhibited repeated and wide ranging

movements (upwards of 15 km) among readers stations during mid to late October. This

pattern was observed in just over 26.2% (C.I.=15.3% to 41.1%) of male grilse and only

46

4.0% (C.I.=0.07% to 19.5%) of female grilse and 0.8% (C.I.=0.14% to 4.3%) of female

salmon (Table 2.7).

Discussion

The objectives of the present chapter were to assess the feasibility, performance and

challenges of monitoring PIT tagged adult Atlantic salmon in Clearwater Brook and to

document patterns in the pre-spawning movements of tagged salmon within in the brook.

The innovative use of passive integrated transponder tags made it feasible to monitor 579

adult Atlantic salmon within Clearwater Brook during the summer and autumn of 1999

and 2000 and provided some new information about the pre-spawning movement patterns

and distributions of these fish.

Pre-spawning movement patterns of adult Atlantic salmon

An examination of the capture dates and pre-spawning movements of wild and hatchery-

origin adult salmon identified some patterns and differences in behaviour. Anecdotal

information that most salmon do not migrate to the middle and upper reaches of

Clearwater Brook until just prior to spawning were supported by the finding that less than

25% of wild adult Atlantic salmon were captured at the Clearwater Brook counting fence

prior to September in 1999 and 2000. Hatchery-origin fish were also predominantly

(75%) ‘late-run’ in 1999. However, in 2000 a significantly higher proportion of hatchery-

origin adult salmon were captured at the fish trap prior to September (42.4%) when

compared to early-run returns of wild salmon (23.8%). This observation is important

since Laughton and Smith (1992) found that early-run grilse and two-sea winter Atlantic

47

salmon were likely to originate from headwater reaches, whereas Smith et al. (1998)

noted that late-run fish tended to spawn in lower river reaches. Accordingly, the higher

proportion of early-run hatchery-origin salmon returns could support this finding since

most hatchery-raised fish were stocked to the headwaters of Clearwater Brook.

Of further interest was the observation that many of the salmon captured and tagged at

the fish trap prior to September exhibited ‘roving’ or exploratory movement patterns.

This behaviour was observed in 21.7% of early-run grilse, 11.1% of early-run MSW

salmon and none of the late-running (September / October) salmon captured in 2000. I

speculate that this roving behaviour was associated with fish searching for suitable pools

in upriver reaches. As documented in 1999 and 2000, roving fish moved upstream, by as

much as 20 kilometres, only to return back downstream to holding areas located within 6

km of the counting fence. The fact that most salmon returned back downstream where

they remained in holding pools until spawning time is not surprising since a detailed

habitat analysis of Clearwater brook found no exceptional holding pools further than 10

km upstream of the fish fence (McCabe and Connell, 1997). Roving salmon completed

this exploratory movement in as few as two days and as many as 10 days with an average

trip time of 4.5 days; 38.5% of early-run hatchery-origin salmon (n=13) and only 8.8% of

early-run wild salmon (n=34) exhibited roving behaviour. The reason for this discrepancy

is unknown but may be related to imprinting and homing behaviour. This is supported by

the observation that fish which exhibited pre-spawning roving behaviour had higher

upstream spawning positions (mean = 15.9 km upstream of fence) relative to early-run

salmon that did not ‘rove’ (mean = 10.0 km upstream of fence).

48

It was evident in both 1999 and 2000 that most salmon, and particularly female salmon,

used an “11th hour” strategy, either waiting downstream of the fence or within pools just

upstream of the fence until just before spawning time. Most salmon located upstream of

the fence did not move into the upper reach until the second week in October. When

these fish did move upstream, the movements appeared deliberate with fish moving

quickly to a sub-reach, remaining within that reach during the spawning period, and then

returning back downstream. Wide scale movements of male grilse were noted. From

October 10th until early November of 2000, 26.9% of tagged hatchery male grilse (n=26)

and 25% of tagged wild male grilse (n=16) moved upwards of 15 km between reader

stations in patterns that differed from most other fish during the spawning period. While

no male MSW salmon were interpreted to have exhibited this same behaviour it is

important to note that only data from 2000 provided sufficient resolution (four reader

stations) to elucidate this behaviour and unfortunately only two male MSW salmon

carried PIT tags in 2000. It was presumed that the exploratory movement exhibited by

male salmon during spawning was associated with mate seeking and it is not surprising

that some males would ‘cover more ground’ as a strategy to find a receptive female to

mate with. Competition among male salmonids for access to spawning females has been

well documented (Keenlyside and Dupuis, 1998; Evans, 1994) and because large size

provides a competitive advantage for access to spawning females (Fleming et al., 1996,

1997) it is possible that roving behaviour is a strategy by which small males avoid

competition with large males in favour of seeking an untended female. Accordingly it

would be expected that roving males would be smaller than males that did not rove.

49

There was no significant difference (p>0.05) in the fork length of male grilse that roved

(mean FL= 57.6 cm) during spawning compared with the fork length of non-roving males

(mean FL= 56.8 cm).

Fleming and Gross (1992) found that hatchery-origin male coho salmon (Onchorhychus

kisutch) were less active, less aggressive and exhibited less spawning behaviour than wild

males, whereas Jonsson et al. (1990, 1991) found that during spawning hatchery-reared

Atlantic salmon tended to rove more within the river than did wild salmon. Assuming

that similar behaviour in hatchery-origin Atlantic salmon would be reflected in mate-

seeking behaviour, it is possible that hatchery-origin salmon would be less aggressive

than wild males and would consequently spend more time randomly searching for a mate

rather than choosing to compete. Alternately, reduced spawning activity could translate to

fewer hatchery-origin males seeking out prospective mates and thus the proportion of

hatchery fish exhibiting mate seeking would be less than that of wild fish. Either way, the

proportion of hatchery-origin and wild male grilse that exhibited this behaviour was

comparable in the present study. It must be noted that the distance (5+ km) between PIT

tag reader stations was too large to detect localized movements (±1km) of salmon. Since

the present study could not detect movement patterns of salmon over small spatial scales

it is probable that roving behaviour in spawning males was far more extensive than

reported.

50

Using PIT tags to monitor adult Atlantic salmon

The ability to individually identify and monitor several hundred adult salmon in this

study required two things: 1) the use of a uniquely identifiable tag with a tagging

technique that resulted in low post-tagging mortality rates and excellent tag retention

rates; and 2) the ability to efficiently detect individual tagged fish as they moved within

the Clearwater Brook study area. The brief tagging time and small incision required to

implant a 32 mm long PIT tag in large-bodied fish (>35 cm) appears to have caused

minimal stress and resulted in low mortality rates. Known tagging related mortalities

were low (0.35%) and comparable with mortalities observed in untagged salmon

(0.49%). While no published studies were found that specifically examined mortality

rates associated with intra-musculature PIT tagging of Atlantic salmon, Barbin-

Zydlewski et al. (2001) reported survivals in excess of 99% for hatchery and stream-

reared parr that were internally tagged with 23 mm passive integrated transponders. The

retention rate of PIT tags could not be quantified in the present study, however, several

studies have shown that PIT tags are superior to external tags for long-term studies. For

example, Baxter et al. (2001) found that double tagged bull trout (Salvelinus confluentus)

had an average PIT tag retention rate of 86.3% and an average Floy tag retention rate of

64.3% after two years. While there is no published information on the retention rate of

PIT tags implanted into the musculature of adult Atlantic salmon, Clugston (1996) noted

that intra-muscular injection PIT tagging in Gulf sturgeons (Acipenser oxyrinchus

desotoi) resulted in long-term tag retention rates near 90%. Roussel et al. (2000) reported

tag retention rates of 85% to 100% for PIT tags implanted into the peritoneal cavity of

juvenile Atlantic salmon. Since it is possible for PIT tags implanted into the peritoneal

51

cavity to be expelled through the vent, especially during spawning, it is likely that intra-

musculature PIT tagging results in better long-term tag retention rates. Furthermore,

intra-muscular tagging techniques are less invasive and have reduced risk of causing

infection or damage to internal organs when compared with methods used to implant a

tag in the peritoneal cavity.

Because the performance of this specific reader station configuration had not been tested

in a similar remote intermediate sized river it was essential that the system be field tested

over the duration of this study. Stationary readers were effective at recording PIT tagged

adult salmon moving through the antenna at ground speeds as high as 4.0 m/s and were

comparable with result published by Castro-Santos et al. (1996) who used a similar PIT

tag detection system and noted that tags externally affixed to adult American shad (Alosa

sapidissima), blueback herring (Alosa aestivalis), and gizzard shad (Dorosoma

capadianum) were detected at grounds speeds of up to 3.5 m/s. In 1999, reader stations

were estimated to be 91.7% and 75% efficient at detecting PIT tagged salmon. These

estimates are presented as conservative values since they are based on the probable

downstream movement of a known number of PIT tagged fish released upstream of each

reader station. It is possible that undetected fish died or remained above the reader

stations and were therefore erroneously assumed to have passed through reader stations

undetected. Additionally, since downstream moving fish may have higher ground speeds

and are less likely to be oriented parallel to river currents (Downing et al., 2001) it is

possible that tag reader stations were less efficient at detecting downstream movements

of tagged fish. This supposition is supported by observations that PIT tagged shad (Alosa

52

spp.) were less frequently detected when moving downstream and more frequently

detected when moving upstream through a fishway (A. Haro, pers. comm., 2000). In

2000, tag reading efficiencies of upstream swimming salmon were estimated at 86.5% to

100%. Preliminary problems with the data-logging equipment were overcome but likely

resulted in missed tag detections. When functioning properly, tag detection efficiencies of

stationary readers employed in the present study were estimated to be > 95%.

The construction and use of a portable system to detect quiescent PIT tagged salmon

located in pools within Clearwater Brook proved effective for detecting tagged salmon at-

large within Clearwater Brook during early September, when few fish were actively

moving throughout the brook. A maximum effective antenna width of 7.3 metres was

achieved using a vertically oriented a single wire loop that was 66 cm in height. While

the antenna was not tall enough to cover the upper portion of the water column within

most pools, it was effective in detecting tagged salmon since most fish remained on the

stream bottom when the device was used. Although using the ‘sweeping’ or ‘driving’

technique to cause salmon to pass through the antenna field did cause substantial fish

movement within a pool, it did not appear to cause fish to displace from the pool. It was

felt that sequential tag detection attempts could be conducted to ensure that all tagged fish

were ‘read’ provided that: 1) no more than three attempts were conducted in a single pool

in one day; 2) fish were permitted to ‘settle back’ into normal holding positions within

the pool following each tag reading event (minimum 15 minutes); 3) an effort was made

to minimize stress on fish by sweeping the antenna very slowly and staying out of the

deep portion of the pool or, 4) when driving fish, by avoiding antagonistic movements

53

that caused erratic fish responses. The present study was the first to design and use a

portable PIT tag detection system with a river-wide antenna to detect PIT tagged adult

fish in deep water, however, recent studies have described the use of portable antenna

‘wands’ to detect and record the positions of PIT tagged juvenile salmon in shallow river

segments (Roussel et al., 2000; Barbin-Zydlewski et al., 2001). The development of

portable PIT tag detection systems has greatly improved the applicability of passive radio

frequency identification technology to conduct fish movement studies of small-bodied

fishes in shallow rivers and to actively search for larger tagged fish in pool habitats in

rivers of moderate size.

PIT tag monitoring: problems and solutions Despite the multiple advantages of passive radio frequency identification systems to

conduct fish monitoring studies several limitations of this equipment were identified

based on its application in the present study. Using passive integrated transponder tags to

monitor the movement of several adult Atlantic salmon in Clearwater Brook presented a

number of challenges. The greatest of these was associated with the lack of a continuous

power supply for operation of the stationary tag reading systems. Lead-acid 12-volt

batteries were an effective way to power tag reading equipment. However it was essential

that charged batteries be maintained at each reader station to avoid data loss. To ensure

adequate power was always supplied to the equipment, two to three batteries were

connected in parallel and were changed with freshly charged batteries every three to four

days. Likewise, active data logging files were saved and transferred to a laptop computer

at similar intervals. During the cooler temperatures of late fall, reader stations were

checked, data were stored and batteries were changed every two to three days.

54

A second major challenge encountered in the present study involved properly interpreting

the distribution of tagged salmon based on PIT tag detections at reader stations. In most

cases the movement of a tagged salmon through a reader station was easily identified as a

single tag reading event with a rapid series of detections of only one tag number over a

brief period of time (<20sec.) In some cases, intermittent recordings of a single PIT tag

number occurred over several minutes or hours. In these instances it was impossible to

know if fish were passing through the RF field or were merely approaching the antenna

without passing through it. Resolving the true position of these fish required subsequent

tag detections at an upstream or downstream location. In rare instances, multiple fish in

the antenna field or unusual tag orientations may have reduced tag detection efficiency or

prevented the equipment from registering a tag passage. Doubling the number of PIT tag

reader stations to four in 2000 made it much easier to document the position of individual

tagged fish prior to and during spawning.

A problem with ‘squatters’ or tagged fish that remained in the antenna field for extended

periods of time was encountered in this study. On these infrequent occasions, thousands

of tag readings had to be sorted, and it was discovered that too many (~18,500 +) tags

detections resulted in an overload of the temporary storage capacity of the palmtop

computer. When this happened no data were lost, however, no further tag detections were

stored until the active data file was transferred from the palmtop and reset. A second

problem with the continuous logging of a fish resting in the RF field is the possibility that

a second tagged fish passing through the antenna may not be detected because the RFID

55

equipment will only read the strongest RF tag signal in the antenna field. To address the

problem of continuous tag recordings, a timeout feature was added to the data-logging

program (A. Haro, USGS, Turner Falls, MA) which forced the palmtop to stop recording

a repeated tag number after a specified amount of time. For instance, if the data-logging

file was initialized with a three-minute timeout specified by the user, a tagged fish in the

RF field would be recorded for three minutes and then be ignored by the logging software

until a new tag was detected. While the timeout feature of the data logging software is

effective at reducing the number of tag recordings from a fish resting in the detection

field, this does not address the problem of missed tag recordings of fish that pass through

the field while a squatter fish is transmitting a stronger RF signal. Presumably this would

be rare, as the squatter would need to hold in the strongest part of the field while another

tagged fish passed through the antenna.

The need to construct and maintain sections of A-frame fencing adjacent to PIT tag

detection stations presented the greatest problems during this study. This fencing was

necessary to ensure that tagged fish moved through the reader antenna when passing by a

reader station. Maintaining several sections of fence during high water events proved

onerous; on two occasions fence sections at Clearwater Brook reader stations were

breached due to high water. One of these events, which occurred just prior to the

spawning period, most certainly resulted in missed tag detections. Single antenna PIT tag

detection systems installed in stream segments wider than three to four metres have a

higher risk of failure, particularly when installed in high gradient stream sections that

have periodic high river discharges. Fortunately, small river installations (< 4 meters

56

width) are better able to withstand high discharge conditions since a single antenna can

be installed across the entire channel without the need for fencing. In larger rivers it may

be preferable to use multiple readers and antennae oriented side by side to cover the

entire river width. This would avoid the need for fencing but would incur the additional

expense of multiple readers and would still be somewhat vulnerable to high water since

the antennae would require mid-river supports.

The following additional points are provided to other researchers considering the use of

PIT technology to conduct movement studies on fish in natural river environments:

• PIT tag monitoring provides a means of discerning the movement, migration timing,

survival, and distribution of fish. The fact that this information was collected without

physically recapturing the tagged animal precluded the collection of post-tagging

biological information. When such information is required, capture techniques such

as electrofishing and traps must be used in conjunction with PIT tagging.

• Twin antenna arrays which would require a tagged fish to pass through two

independent readers at a single location could be used to increase tag detection

efficiencies and to help discern if a PIT tag moved upstream or downstream through a

tag reading station.

• A data logging program with a timeout feature should be used if there is a likelihood

that tagged fish will reside within the antenna array for extended periods of time. To

avoid problems with simultaneous tag detections antennas should be installed in a fast

flowing area and substrate that fish could use as cover should be removed from the

vicinity of the tag detection field.

57

References

Adams, N.S., Rondorf, D.W., Evans, S.D., Kelly, J.E., and Perry, R.W. 1998. Effects of

surgically and gastrically implanted radio transmitters on swimming performance

and predator avoidance of juvenile Chinook salmon (Oncorhynchus tshawytscha).

Can. J. Fish. Aquat. Sci. 55: 781-787.

Anderson, T.C. and McDonald, B.P. 1978. A portable weir for counting migrating fishes

in rivers. DFO Fisheries and Marine Service Technical Report 733, St. John’s,

NFLD. 13 p.

Armstrong, J.D., Braithwaite, V.A., and Rycroft, P. 1996. A flat-bed passive integrated

transponder array for monitoring behaviour of Atlantic salmon parr and other fish.

J. Fish Biol. 48: 539–541.

Barbin-Zydlewski G., Haro A., Whalen K.G., and McCormick, S.D. 2001. Performance

of stationary and portable passive transponder detection systems for monitoring of

fish movements. J. Fish Biol. 58: 1471-1475.

Baxter, J.S., Westover, B., Down, T., and Snelson, S. 2001. Retention of Floy tags and

passive integrated transponder tags in a wild bull trout (Salvelinus confluentus)

population one and two years after tagging. Bull Trout II Conference Proceedings,

pp. 177-180.

Berman, C.H. and Quinn, T.P. 1991. Behavioural thermoregulation and homing by spring

Chinook salmon Oncorhynchus tshawytscha (Waldbaum), in the Yakima River. J.

Fish. Biol. 39: 301-312.

Castro-Santos T., Haro A., and Walk, S. 1996. A passive integrated transponder (PIT) tag

system for monitoring fishways. Fisheries Research. 28:253-261.

58

Connell, C.B. 2003. J.D. Irving, Limited fisheries program report for 2002. J.D. Irving,

Limited Woodlands Division. Saint John, New Brunswick 67 p.

Clugston, J.P. 1996. Retention of T-bar anchor tags and passive integrated transponder

tags by Gulf sturgeons. N. Am. J. Fish.. Manag. 16: 682-685.

Downing, S. L., Prentice, E.F., Peterson, B.W., Nunnallee, E.P., and Jonasson, B.F. 2001.

Development and evaluation of passive integrated transponder tag technology:

annual report, 1999 to 2000. Report to the U.S. Department of Energy, Bonneville

Power Administration, Division of Fish and Wildlife, Project 83-319, Contract

307-00001, 31 p.

Evans, D.M. 1994. Observations on the spawning behaviour of male and female adult sea

trout, Salmo trutta L., using radio-telemetry. Fish Manag. Ecol. 1: 91-105.

Fleming, I.A. and Gross, M.R. 1992. Reproductive behaviour of hatchery and wild coho

salmon (Oncorhynchus kisutch): does it differ? Aquaculture.103: 101-121.

Fleming, I.A., Jonsson, B., Gross, M.R., and Lamberg, A. 1996. An experimental study

of the reproductive behaviour and success of farmed and wild Atlantic salmon

(Salmo salar). J. Appl. Ecol. 33: 893-905.

Fleming, I.A., Lamberg, A., and Jonsson, B. 1997. Effects of early life experience on the

reproductive performance of Atlantic salmon. Behav. Ecol. 8: 470-480.

Hooper, W.C. and McCabe, L. 1998. Procedure Manual for Aquatic Habitat Inventories

in New Brunswick Streams. New Brunswick Department of Natural Resources

and Energy. (draft working document).

59

Jonsson B., Jonsson N., and Hansen, L.P. 1990. Does juvenile experience affect

migration and spawning of adult Atlantic salmon? Behav. Ecol. Scoiobiol. 26:

255-230.

Jonsson B., Jonsson N., and Hansen, L.P. 1991. Differences in the life history and

migratory behaviour between wild and hatchery-reared Atlantic salmon in nature.

Aquaculture 98: 69-78.

Keenlyside, M.H.A. and Dupuis, H.M.C. 1998. Courtship and spawning competition in

pink salmon (Oncorhynchus gorbusha). Can. J. Zool. 66: 262-265.

Laughton, R. and Smith, G.W. 1992. The relationship between date of river entry and the

estimated spawning positions of Atlantic salmon (Salmo salar L.) in two major

Scottish east coast rivers. P. 423-433. In: Priede, I.G. and Swift, S.M. [eds.].

Wildlife telemetry: remote monitoring and tracking of animals. Chichester, Ellis

Horwood.

McCabe, L., and Connell, C.B. 1997. Clearwater Brook / Little Main Restigouche

Fisheries Assessment Project, 1996. New Brunswick Department of Natural

Resources and Energy. Internal Report.

Newcombe, R. G. 1998. Two-sided confidence intervals for the single proportion:

comparison of seven methods. Statistics in Medicine. 17: 857-872.

Power, G. 1987. Scales in the Balance. Atlantic Salmon Journal 37(4): 14-17.

Prentice, E.F., Flagg, T.A., and McCutcheon, S. 1990. Feasibility of using implantable

passive integrated transponder (PIT) tags in salmonids. American Fisheries

Society Symposium. 7: 317-322.

60

Roussel, J.-M., Haro. A., and Cunjak, R.A. 2000. Field test of a new method for tracking

small fishes in shallow rivers using passive integrated transponder (PIT)

technology. Can. J. Fish. Aquat. Sci. 57:1326-1329.

Smith, G.W., Nelson, K., Youngson, A.F., and Carss, D. 1998. The movements and

estimated spawning positions of late-running adult Atlantic salmon (Salmon salar

L.) returning to the Aberdeenshire Dee. Fisheries Research Services Report.

Aberdeen, Fisheries Research Services 3/98, 19 p.

Whoriskey, F.W., Connell, C.B., and Perley, L. 1998. Little Main Restigouche River and

Clearwater Brook: report on 1998 field work. Atlantic Salmon Federation

collaborative research program report. 49 p.

61

Table 2.1. Water chemistry in the upper, middle and lower reaches of Clearwater Brook in August of 1998. (Analyses performed by NB Department of Environment).

Analysis

Units

Upper Reach

Middle Reach

Lower Reach

Alkalinity - Grans (CaCO3) mg/l 10.9 11.4 10.5 Alkalinity – Phenol mg/l 0 0 0 Aluminum ug/l 120 102 99.4 Ammonia – Total mg/l L0.010 L0.010 L0.010 Antimony ug/l L1.0 L1.0 L1.0 Arsenic ug/l L1.0 L1.0 L1.0 Cadmium ug/l L0.1 L0.1 L0.1 Calcium – Dissolved mg/l 3.5 3.8 3.8 Chlorine mg/l 0.717 0.863 0.82 Chromium ug/l 0.6 0.6 0.7 Color 40 40 40 Conductivity μS/cm 33.3 34.9 32.8 Copper ug/l L0.5 L0.5 2.1 Dissolved Nitrite mg/l L0.05 L0.05 L0.05 Fluoride mg/l L0.100 L0.100 L0.100 Hardness mg/l 12.4 13.2 12.8 Iron mg/l 0.112 0.096 0.096 Lead ug/l L1.0 L1.0 L1.0 Magnesium mg/l 0.9 0.9 0.8 Manganese mg/l L0.010 L0.010 L0.010 Nickel mg/l L0.010 L0.010 L0.010 Nitrate mg/l 0.15 0.13 0.09 Nitrous mg/l 0.2 0.18 0.14 pH 7.21 7.33 7.32 Potassium mg/l 0.206 0.229 0.273 Sodium mg/l 1.6 1.5 1.6 Sulfate mg/l 2.44 2.51 2.53 Suspended Solids mg/l T 0 T 0 T 1 Tot Kjeldahl Nitrogen mg/l 0.22 0.21 0.22 Total Organic Carbon mg/l 8.4 7.3 6.7 Total Phosphorus mg/l 0.006 L0.005 L0.005 Turbidity NTU 0.3 0.1 0 Zinc mg/l L0.010 L0.010 0.075

L – indicates value less than minimum detectable limit (shown after L)

62

Table 2.2. Biological characteristics (fork length and sex), PIT tag number, transfer date, and release site of adult Atlantic salmon translocated to the upper reach of Clearwater Brook, NB.

Capture / Translocation

Date Sex

Fork Length

(cm) Pit-tag applied

Translocation site

10/12/1999 F 90 140 CTR3 10/12/1999 F 76 134 CTR3 10/12/1999 M 60 139 CTR3 10/12/1999 M 63 142 CTR3 10/12/1999 F 82 132 CTR2 10/12/1999 F 82 141 CTR2 10/13/1999 F 77 150 CTR2 10/13/1999 F 90 149 CTR2 10/12/1999 M 61 131 CTR2 10/12/1999 M 67 137 CTR2 10/13/1999 M 72 151 CTR2 10/13/1999 M 61 153 CTR2 10/13/1999 F 79 152 CTR1 10/12/1999 F 94 130 CTR1 10/12/1999 F 83 138 CTR1 10/12/1999 F 61 143 CTR1 10/12/1999 M 92 133 CTR1 10/12/1999 M 60 136 CTR1 10/12/1999 M 92 135 CTR1 10/13/1999 M 86 148 CTR1

63

Table 2.3. Number and percentage of adult salmon captured and implanted with passive integrated transponder tags at the Clearwater Brook counting fence between June and October, 1999.

MSW salmon – multi-sea winter salmon, ≥ 63 cm fork length Grilse – one sea winter salmon, < 63 cm fork length Table 2.4. Number and percentage of adult salmon captured and implanted with passive

integrated transponder tags at the Clearwater Brook counting fence between June and October, 2000.

MSW salmon – multi-sea winter salmon, ≥ 63 cm fork length Grilse – one sea winter salmon, < 63 cm fork length

Table 2.5. The percentage of wild and hatchery origin grilse and MSW salmon captured

at the Clearwater Brook counting fence prior to September, 1999 and 2000. 1999 2000

Grilse MSW All Grilse MSW All

Wild 34.8% 10.3% 23.7% 26.9% 15.6% 23.8% Hatchery-origin 29.2% 12.5% 25.0% 35.7% 80.0% 42.4%

Probability of observed difference (two-tailed) 0.57 n/a 0.87 0.31 n/a 0.02

CapturedPIT

tagged % tagged CapturedPIT

tagged % taggedFemale MSW salmon 139 124 89.2% 5 5 100.0%

Female grilse 25 23 92.0% 2 2 100.0%Male MSW salmon 53 2 3.8% 0 0

Male grilse 465 16 3.4% 26 26 100.0%Total 682 165 33 33

Hatchery OriginW ild2000

CapturedPIT

tagged % tagged CapturedPIT

tagged % taggedemale MSW salmon 290 259 89.3% 4 4 100.0%emale grilse 71 62 87.3% 6 6 100.0%ale MSW salmon 111 14 12.6% 4 3 75.0%ale grilse 385 19 4.9% 19 14 73.7%tal 857 354 41.3% 33 27 81.8%

Hatchery orig

FFMMTo

inW ild1999

64

Table 2.6. The number and proportion of PIT-tagged Atlantic salmon that exhibited pre spawning roving behaviour in Clearwater Brook, 2000.

Hatchery-origin Wild early-run fall-run early-run fall-run

Grilse 4 0 2 0 Roving salmon (tagged) MSW 1 0 1 0

Grilse 10 18 19 20 Total (tagged) MSW 3 2 15 110

Total roving 5 0 3 0 Total tagged 13 20 34 130 Proportion roving 38.5% 0.0% 8.8% 0.0%

Table 2.7. The number and proportion of PIT-tagged Atlantic salmon that exhibited

roving behaviour during spawning period in Clearwater Brook, 2000.

Hatchery-origin Wild Female Male Female Male

Grilse MSW

salmon Grilse MSW salmon Grilse MSW

salmon Grilse MSW salmon

Number roving during spawning period

0 0 7 0 1 1 4 0

Total number tagged 2 5 26 0 23 124 16 2

% roving during spawning period

0.0% 0.0% 26.9% 4.3% 0.8% 25.0% 0.0%

65

Miramichi River Basin

Ott er Br ook

Moose Br ook

Lake Br ook

Cl earwat er

NE B r Cle a rwa ter

B r oo k

Br oo k

McCoy B rook

Turnbul l B rook

Fair ley

Brook

Redstone Brook

SW Miramichi River

0 90 180 Kilometers

N

Clearwater Brook catchment

Miramichi River basin

Figure 2.1. Map displaying the position of the Clearwater Brook catchment

within New Brunswick’s Miramichi River catchment.

66

'W

'W

'WÊÚ

$T$T

SW Miramichi River

Clearw

ater BrookCR4

CR2

CR1

CR3

Turnbull Bk

Lake

Bk

NE Br

Clea

rwat

er

McCoy Bk

Redstone Bk

Fairl

ey B

k

Otter B

k

Moose Bk

0 5 10 15 20 KilometersN

N

'W PIT Tag Reader Stations (2000 only)ÊÚ Fish Counting Fence

$T PIT tag reader stations (1999-2000)

Middle Reach14.5 km

Upper Reach 14.5km + Northeast Branch

Lower Reach 19 km

Figure 2.2. Clearwater Brook and the locations of passive integrated transponder

reader stations operated in 1999 and 2000.

67

Figure 2.3. Photo of the Clearwater Brook counting fence.

1 2

3 4

1 2

3 4

1 2

3 4

Figure 2.4. Photos illustrating the location of the incision and the technique used

to insert a PIT tag into an adult Atlantic salmon.

68

A-Frame Fencing

Wooden frame

supporting wire-loop antenna

Tuning module RI-ACC-008B

Stream bank

Stream bankWater level

Weatherproof box housing batteries, TIRIS reader and palmtop computer

Control module

Reader module Palmtop

computer / data logger

RS232 cable

Twin axial wire

12v batteries connected in parallel

Figure 2.5. Representation of a PIT tag reader station installed in Clearwater Brook (not to scale).

69

Figure 2.6. Photos illustrating the vertically oriented PIT tag detection loop antenna and the adjacent fencing to ensure that all

tagged fish pass through the RF field.

70

$Z

$Z

$ZÊÚ

$T$T

##

#

#³

#³

#³

Brook Pool

CR1

CR3

Turnbull Bk Lake

Bk

NE B

r Clea

rwat

er

McCoy Bk

Redstone Bk

Fairl

ey B

k

Moose Bk

CR2CR4

CTR1

CTR2

CTR3

Bridge Pool

Fence Pool

Clearwater Bk

0 6 12 KilometersNÊÚ Fish Counting Fence

$T PIT tag reader stations (1999-2000)

# Atlantic salmon translocation site

#³ Portable PIT tag reader sites

$Z PIT Tag Reader Stations (2000 only)

Figure 2.7. Location of the fish counting fence, PIT tag reader stations (CRx),

pools surveyed with a portable PIT tag reader, and release sites (CTRx) of wild PIT-tagged adult Atlantic salmon in Clearwater Brook, NB.

71

Figure 2.8 Photo of the pool sweeping technique used to detect PIT tagged salmon resting in holding areas.

72

0%

5%

10%

15%

20%

25%

30%

35%

Aug. 3 Aug. 4 Aug. 5 Sept. 1 Sept. 3 Sept. 14

Prop

ortio

n of

tagg

ed fi

sh a

t lar

ge

Fence PoolBrook PoolBridge Pool

Figure 2.9. Proportion of PIT-tagged Atlantic salmon at-large detected using a portable PIT tag reader in Fence Pool, Brook Pool and Bridge Pool – Clearwater Brook, 1999.

73

0

5

10

15

20

25

30

35

40

45

12-J

un

19-J

un

26-J

un

3-Ju

l

10-J

ul

17-J

ul

24-J

ul

31-J

ul

7-A

ug

14-A

ug

21-A

ug

28-A

ug

4-S

ep

11-S

ep

18-S

ep

25-S

ep

2-O

ct

9-O

ct

16-O

ct

23-O

ct

30-O

ct

0

10

20

30

40

50

60

70Fence captures

Water Depth (cm)

Daily mean watertemperature (oC)

0

5

10

15

20

0

5

10

15

20N

o. o

f sal

mon

PIT

tagg

ed /

day

No.

ofun

ique

tags

dete

cted

/day

Water Level / tem

perature

CR4 NE Branch (13.2 km upstream of fence)

CR2 (14.8 km upstream of fence)

n/a

Figure 2.10. Number of salmon PIT tagged per day (counting fence), number of unique PIT detections per day (reader stations), water level at trap (___), and mean daily water temperature at trap (----) in Clearwater Brook, 1999.

74

0

5

10

15

20

28-J

un

5-Ju

l

12-J

ul

19-J

ul

26-J

ul

2-Au

g

9-Au

g

16-A

ug

23-A

ug

30-A

ug

6-Se

p

13-S

ep

20-S

ep

27-S

ep

4-O

ct

11-O

ct

18-O

ct

25-O

ct

1-No

v

8-No

v

0

10

20

30

40

50

60Fence captures

Water level (cm)

mean daily watertemperature (oC)

0

5

10

15

20

25

0

5

10

0

5

10

0

5

10

#of s

alm

on P

IT ta

gged

/ da

y

CR2 (14.8 km upstream of fence)

CR1 (6.7 km upstream of fence)

CR3 (21.7 km upstream of fence)

CR4 NE Branch (13.2 km upstream of fence)

#of u

niqu

e PI

T ta

g de

tect

ions

/ da

y

Water Level / Tem

perature

n/a

n/a

Figure 2.11. Number of salmon PIT tagged per day (counting fence), number of unique PIT detections per day (reader stations), water level at trap (___), and mean daily water temperature at trap (----) in Clearwater Brook, 2000.

75

Figure 2.12. Average number of days between Atlantic salmon PIT tagging and

subsequent tag detection at reader stations in Clearwater Brook, 2000.

0

10

20

30

40

50

60

70

80

90

Early-runhatchery-origin

salmon

Early-run wildsalmon

Fall-run hatchery-origin salmon

Fall-run wildsalmon

Ave

rage

num

ber o

f day

s be

twee

nP

IT ta

ggin

g an

d de

tect

ion

CR1 (6.7km)

CR2 (14.8km)

CR3 (21.7km)

CR4 (NE-13.2km)

76

CHAPTER 3

Can fry stocking or adult translocation increase Atlantic salmon (Salmo salar) spawning escapement and egg depositions in a targeted river reach?

Abstract

An application of passive integrated transponder (PIT) technology was used to evaluate

the effectiveness of fry stocking versus adult translocation to address patchiness in adult

Atlantic salmon (Salmo salar) spawning distributions within the Clearwater Brook sub-

basin of the Miramichi River, New Brunswick.

Stocked underyearling salmon imprinted to the target (upper) reach, with more than 75%

of hatchery-origin present in the upper reach during spawning; however, adult return

rates of stocked fry were low (0.11%). Over the two years of this study (1999-2000)

hatchery returns contributed 50300 eggs to the upper reach and accounted for a 4.8% gain

in overall potential production in this reach. The estimated cost / benefit to upper reach

production from stocking was $520 (CAD) / 1000 eggs.

Translocating adult salmon to the upper reach just prior to spawning was equally

effective; 65% of these fish remained in the target reach during spawning. This technique

was conducted in 1999 only and resulted in an increase of 25,300 to 47,300 eggs (3.1% to

5.8%) to the upper reach. The estimated cost/benefit to upper reach production from

stocking was <$40 (CAD) / 1000 eggs.

Both strategies provided only a marginal gain to wild production in the target reach;

however translocation was only carried out at a small scale. It is suggested that adult

translocation is the preferred enhancement technique as it is less costly and less likely to

have deleterious genetic impacts on the wild salmon populations.

78

Introduction

The return of mature Atlantic salmon (Salmo salar) to their natal rivers is well

documented (Stabell, 1984; Ritter, 1989). This ‘homing’ behaviour is relatively precise

and allows salmon to return to spawn in river locations they inhabited during their

juvenile life-stages (Youngson et al. 1994; Dittman and Quinn 1994; Stewart et al. 2002).

This adult salmon homing behaviour, coupled with the fact that fry exhibit limited

dispersal from their site of emergence (Gustafson-Greenwood and Moring 1990; Crisp

1995; Raddum and Fjellheim, 1995) is suggested to restrict rates of genetic exchange

among locations and can result in genetic population structuring of Atlantic salmon at a

subcatchment scale (Garant et al. 2000; Stewart et al. 2002). Youngson and McLaren

(1998) noted that the recruitment of adult Atlantic salmon to spawning populations was

driven by homing fish and depended largely on the return of smolts that had left the same

10 km segment of river in previous years. Accordingly, a localized reduction in

spawning populations can result in low juvenile densities and sub-optimal smolt

production from discrete river segments and thereby reduce subsequent adult returns to

the river. Furthermore, Laughton and Smith (1992) found that early-run grilse and two-

sea winter Atlantic salmon were likely to originate from headwater reaches, whereas

Smith et al. (1998) noted that late-run fish tended to spawn in lower river reaches.

Assuming this correlation between run-timing and spawning reach selection is broadly

applicable, it is possible that a local decrease in smolt production from headwater habitats

could result in subsequent shortfalls in early-run spawning populations, and vice-versa.

Interestingly, work conducted since 1996 in the Clearwater Brook tributary of the

Miramichi River (NB) found that less than 25% of the wild adult spawners captured at a

79

fish counting fence (19 km up Clearwater Brook.) arrived prior to September during the

“early-run” period. Furthermore, low juvenile salmon abundance in the upper 20

kilometres of the river, relative to the lower and middle reaches, was hypothesized to be

the result of locally reduced spawning populations within the upper reach of the brook

(C. Connell, J.D.Irving Limited, unpubl.; Whoriskey et al., 1998).

Strategies to promote spawning in the upper reach of Clearwater Brook has become a

management priority. Fisheries managers began annually stocking between 25,000 to

64,000 six-month-old, hatchery-reared Atlantic salmon to these under-used habitats in the

autumn of 1996. As an enhancement strategy, it was expected that salmon stocked to the

river would survive to maturity and return to spawn naturally near the site to which they

were stocked. Thus the success of the stocking program relied on the ability of stocked

fish to imprint, survive, and subsequently “home” to the stocking site as mature adults.

An alternate technique, which involved relocating wild adult salmon to the upper reach

just prior to spawning, was also evaluated as a strategy to increase the number of

spawners and number of eggs deposited in the target reach. The latter enhancement

technique assumed that ‘translocated’ wild adult salmon would remain close to the

release site during spawning and thereby contribute to wild salmon production in that

area.

The specific objectives of the study were: 1) to assess if stocked salmon exhibited reach-

specific homing behaviour when they returned to the river as adults and thereby increased

80

egg deposition to the river segment to which they were stocked; 2) to examine if wild

adult salmon that were translocated to specific river segment remained there during

spawning and thereby increased egg deposition to that river segment; and 3) to assess the

cost-benefit and effectiveness of fry stocking and adult translocation as techniques to

increase Atlantic salmon spawning populations and egg deposition in the upper reach of

Clearwater Brook.

The following predictions were tested in examining the effectiveness of fry stocking and

adult translocations in Clearwater Brook:

1. For wild Atlantic salmon, egg deposition is inversely related to migratory distance;

that is, as the distance to access spawning habitat increases, egg deposition will

decrease.

2. For hatchery-origin Atlantic salmon egg deposition is directly related to upstream

migratory distance; that is, as the distance to spawning habitat increases, egg

deposition from hatchery-origin salmon will increase.

3. Reach-specific egg deposition can be increased through the translocation of mature

adult Atlantic salmon; that is, translocated wild female salmon will stay and spawn in

the study reach to which they have been moved.

81

Study Area

Clearwater Brook is a fifth-order tributary of the Southwest Miramichi River in central

New Brunswick (46o42’ N, 66o48’ W) (Figure 3.1) and has been the site of an Atlantic

salmon research and management project since 1996 (McCabe and Connell, 1997;

Whoriskey et al., 1998). In midsummer the brook has an average channel width of 16.5

metres and mean daily water temperatures are generally less than 20oC. Clearwater Brook

has a mean slope of 0.67%, and is just over 60 km in length. The brook flows unrestricted

in a southerly direction from one spring-fed and three lake-fed headwater tributaries

(Figure 3.2). The Clearwater Brook catchment has an area of 335 km2 which is 4.3 % of

the Southwest Miramichi River basin, and is almost wholly situated in the gated forest

management land owned by J.D. Irving, Limited and Bowater Canadian Forest Products

Incorporated. As a result of this controlled public access, the brook receives only limited

recreational use, most of which is in the form of recreational Atlantic salmon angling

from two private fishing camps located in the lower eight kilometres of the river. While

the primary anthropogenic influence to Clearwater Brook is forest harvesting, the brook

has retained much of its remote and pristine qualities and shows little evidence of impacts

to aquatic habitat as a result of adjacent land disturbances.

Based on photo-interpretation, the forest cover in the Clearwater Brook catchment is 22%

tolerant hardwood stands (sugar maple, Acer saccharum, and yellow birch, Betula

alleghaniensis), 19% softwood stands (red, black and white spruce species, Picea spp.,

and balsam fir, Abies balsamea), 27% softwood plantations (black and white spruce, and

jack pine), and 13% naturally regenerating spruce and fir species. The remaining 20% of

82

the catchment is comprised primarily of mixed stands of tolerant and intolerant hardwood

species (aspen, white birch) and a variety of softwood species (spruce, fir, white and red

pine, eastern white cedar, and eastern hemlock).

A detailed stream habitat survey conducted in 1996 characterized substrate within

Clearwater Brook as predominantly rubble (33%), rock (28.5%), and gravel (20.3%),

while boulder (11.5%), sand (5.5%) and fines (1.3%) accounted for a small proportion of

the wetted streambed. Atlantic salmon is the predominant fish species in the lower 35-40

km of Clearwater Brook and while present in the upper 20 km of the brook, beaver dams

sporadically limit adult salmon distribution and access to these upper reach habitats.

Other species of fish known to occur in Clearwater Brook include brook trout (Salvelinus

fontinalis), slimy sculpin (Cottus cognatus), white sucker (Catostomus commersoni),

blacknose dace (Rhinichthys atraulus), and American eel (Anguilla rostrata).

Since 1997, Clearwater Brook is estimated to have received annual Atlantic salmon

spawning runs in excess of 1000 fish, a conservative figure that is based on an annual

mean return (1997-2002) of 810 adult salmon to a fish counting fence located 19 km

upstream from the mouth of the brook (Connell, 2003). The Clearwater Brook system is

an important spawning and nursery area for Atlantic salmon, as evidenced by the

presence of substantial high quality habitat, significant annual adult salmon returns, and

high juvenile densities (≥ 90 fry / 100m2, ≥ 20 parr / 100m2) throughout the middle and

lower reaches of the brook (Appendix I).

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For the purposes of this research, Clearwater Brook was divided into study reaches based

on the location at which salmon were first captured as they ascended the brook and the

upstream locations at which fish with PIT tags were monitored by fixed tag reading

stations. A fish counting fence, located 19 kilometres upstream from the brook’s

confluence with the SW Miramichi River, provided the first opportunity to capture,

enumerate, and tag adult salmon migrating upstream. This counting fence location

defined the lower boundary of the middle reach. In 1999, two stationary PIT tag readers

were installed upstream of the counting fence, one of these stations (CR2) was situated in

the main stem of Clearwater Brook at a location 14.5 km upstream of the counting fence,

while the second station (CR4) was installed in the Northeast Branch of Clearwater at a

location 13.2 km upstream of the (Figure 3.2). These sites were chosen in part because

they were easily accessible but primarily because upstream of these locations, in the

“upper reach”, low juvenile abundance and reduced wild spawning were known to occur.

In 2000, two additional tag reading stations, CR1 and CR2, were installed 6.7-km and

21.8-km, respectively, upstream of the of Clearwater Brook counting fence to increase

the resolution of PIT tagged salmon detections within the study area.

In comparing results from 1999 and 2000, fish were analysed based on their distribution

in either the middle or the upper study reaches of Clearwater Brook. Fish occupying a

position upstream of reader stations CR2 or CR4 during the spawning period were

considered to have spawned in the upper reach; similarly fish positioned downstream of

these reader stations but upstream of the counting fence during the spawning period are

considered to have spawned in the middle study reach (Figure 3.2).

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The additional reader stations operated in 2000 (Figure 3.2) enabled more detailed

movement and spawning distribution analysis. In view of this, some single year analysis

of the positions of tagged salmon relative to five sub-reaches is discussed. Sub-reach “M-

1” included the 6.7 km of river between the counting fence and reader station CR1; sub-

reach “M-2” comprised 8.1 km of river upstream of CR1 to the reader stations CR2 and

CR4 (NE Clearwater Branch); sub-reach “U-1” encompassed the 7.0 km of river

upstream of CR2 to the headwaters reader station CR3; the uppermost section of

Clearwater Brook was sub-reach “U-2” and included the 8.8 km of habitat accessible to

adult salmon upstream of the CR3 reader station. Finally, sub-reach “U-3” was located

upstream of the CR4 reader station and included 10.2 km of stream habitat accessible to

adult salmon within the Northeast Branch of Clearwater Brook (Figure 3.3). Clearwater

Brook contains a minimum of 460,000 m2 of wetted habitat within the middle and upper

reaches (McCabe and Connell, 1997). This wetted stream area is nearly evenly

distributed, with the middle reach accounting for 55.8%, and the upper reach accounting

for 44.2%, of the total habitat potentially accessible to adult Atlantic salmon spawning

upstream of the counting fence (Table 3.1). Preferred spawning habitat, or the stream

areas with substrate and flow characteristics most suitable for Atlantic salmon spawning,

are less evenly distributed between reaches, with the middle reach accounting for nearly

65% (140,682 m2) of the 217,658 m2 of the total preferred spawning habitat located

upstream of the counting fence (Table 3.1).

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Materials and Methods

Clearwater Brook Atlantic salmon stocking program

Annually from 1995 to 1997, 12 male and 12 female adult Atlantic salmon broodstock

were seined in September from the Avenor Bridge Pool (Figure 3.2), located 10 km

upstream of the Clearwater Brook confluence. In 1998, broodstock collection methods

were modified to enhance the “early-run” component of adult salmon returns to

Clearwater Brook. Consequently, early-run salmon were seined from Bridge Pool (Figure

3.3) in August of 1998 and were collected from the Clearwater Brook counting fence

from June through August thereafter. Fifteen pair of broodstock were collected annually

since 1999 in an effort to increase the genetic diversity of the salmon produced for the

Clearwater Brook stocking program.

Once captured, broodstock were transported to the Miramichi Salmon Conservation

Centre (MSCC) in South Esk, New Brunswick. Between mid-October to early-November

eggs were stripped from the female fish and fertilized with milt from the males; eggs

from each female were divided into two even lots and each lot was fertilized with sperm

from a different male. Fertilized eggs were cultured until they hatched and the emergent

fry were further reared to the feeding fry stage at the MSCC hatchery. In June these fry

were transported to a satellite rearing facility located in Juniper, NB where they were

reared in dark green ten-foot diameter fibreglass tanks in water supplied from the North

Branch of the SW Miramichi River. In September, the adipose fin of each fish was

removed and in early-October these ‘adipose clipped’ salmon were distributed to several

locations throughout Clearwater Brook (Figure 3.4). At the time of stocking the mean

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fork length of these underyearling salmon varied, by year, from 8.9 cm to 10.2 cm. Since

nearly all juvenile salmon in Clearwater Brook are age 2 or 3 when they smoltify (M.

Mathews, University of New Brunswick, unpubl.), it was assumed that any adipose fin

clipped adult salmon captured during the present study (in 1999 or 2000) were stocked to

the brook as underyearlings between 1996 and 1998. In 1996 nearly 25,000 hatchery-

reared salmon were stocked and approximately 35,000 hatchery salmon were distributed

in 1997 and again in 1998 (Appendix I.8).

Adult Atlantic salmon captures

A fish counting fence, located 19 kilometres upstream from the confluence of Clearwater

Brook and the Southwest Miramichi River (Figure 3.2), provided a means of capturing

and enumerating all wild and hatchery-origin upstream migrating adult Atlantic salmon.

The metal “A-frame” fence was constructed from 3”x 3” angle iron suspended

horizontally between vertical tripods spaced 3 metres apart; one inch holes drilled

vertically at 1.5” centres enabled 7/8” galvanized pipe to be passed through the angle iron

across the width of the fence (Anderson and McDonald, 1978). The fence was installed in

an upstream pointing “V” formation at a location where the river width was

approximately 30 metres. A single two metre wide by 2.5 metre long “upstream” trap was

installed at the point of the V to capture only upstream migrating fish. This fence was

effective at catching salmonids > 35 cm in length (Connell, 1998).

Each Atlantic salmon captured in the counting fence trap was measured for fork length (±

0.5 cm) and examined to determine its sex (based on phenotypic characteristics). Fish

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were further inspected for external tags and fin clips; salmon that did not have an adipose

fin were identified as a hatchery-origin adult return. All of this information was recorded

in addition to the date and time of capture. In 2000, scale samples were randomly

collected from 126 adult salmon captured at the fish trap so that the mean fork length at

sea age could be calculated. Fish age was determined from scales according to methods

described by Power (1987).

The number of eggs carried by each female salmon (fecundity) was estimated based on

Randall’s (1985) length-fecundity relationships for one-sea winter (1SW) and multi-sea

winter (MSW) Atlantic salmon:

Grilse fecundity = e[3.1718 x ln (FL) -4.5636]

MSW salmon fecundity = e[1.4132 x ln (FL) + 2.7560]

ln(FL) = the natural logarithm of the fork length of a grilse or MSW salmon in cm; e = the base of the natural logarithm (2.718).

Fecundity estimates were calculated for comparisons of maximum potential egg

depositions by study reach and it was assumed that egg retention was negligible, thus no

corrections for potential egg loss were applied.

PIT tagging

Texas Instruments PIT tags (RI-TRP-WR2B) were used to assess the spawning

distribution of grilse and multi sea-winter salmon in Clearwater Brook in 1999 and 2000.

These cylindrical glass encapsulated tags, measuring 31.8 mm in length by 3.85 mm in

diameter and weighing 0.8g, in air, were implanted into the ventral musculature of adult

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salmon according to methods described in Chapter 2. Passive integrated transponders

were selected because they were the least expensive and invasive way to monitor the

distribution of a large number of adult salmon for the present study. Due to the relatively

low cost of PIT tags (< $5 CAD), 579 salmon captured at the Clearwater Brook counting

fence were tagged between 1999 and 2000. Since it was not possible to tag all captured

salmon, a decision was made to tag all female and hatchery-origin adult salmon and a

random sample of wild male salmon. This was done in an effort to assess egg depositions

within each study reach and in order to maximize the sample size of tagged hatchery

origin salmon. When tagged, biological data were collected and recorded as was each

salmon’s unique PIT tag number. Given the high retention rate and indefinite lifespan of

PIT tags they were an excellent choice for Atlantic salmon monitoring in this study.

However, since these tags do not have an internal power supply they can only be detected

and “read” when passed through a specially designed electromagnetic field that

temporarily powers the tag (Chapter 2, this study).

PIT tag monitoring

Once released upstream of the Clearwater Brook counting fence, the movement and

position of each PIT tagged salmon was monitored with a series of ‘reader stations’

(Figure 3.3). Two reader stations were installed in 1999. In 2000, two additional stations

were installed to provide increased tag detecting capabilities throughout Clearwater

Brook (Figure 3.3) and making it possible to examine hatchery and wild salmon

movements at a finer scale.

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Reader stations consisted of a wire loop radio frequency (RF) field trasmit/receive

antenna regulated by a Texas Instruments (TIRIS) Series 2000 antenna-tuning module

(RI-ACC-008B) and connected to a TIRIS 2000 control module (RI-CTL-MB2A),

reader module (RI-RFM-008B) and a Hewlett Packard palmtop computer (1000CX or

200LX). Two 12-volt lead-acid batteries (60 A h), connected in parallel, were used to

power the system and generate a 134.2 kHz electromagnetic signal through which adult

salmon were forced to pass when swimming by the reader station. When a PIT tagged

fish entered this electromagnetic (RF) field, a capacitor within the tag was energized and

the tag’s code was transmitted to the TIRIS reader equipment. Once detected by the

reader, the tag’s signal was decoded and relayed to the palmtop computer where a custom

software program (written in BASIC by Dr. A. Haro, USGS, Turner Falls, MA) logged

the time, date and tag identification number. Further details of the equipment, setup and

technical aspects of PIT tag reader stations are provided in Chapter 2 (this study).

PIT tag detections from each reader station were compiled so that the individual

movements of tagged salmon could be analyzed. This process made it possible to discern

where each fish was located, relative to reader stations, during the spawning period (mid

October to early November). Since the size, sex and origin (hatchery or wild) of each

uniquely tagged salmon was known, it was possible to examine and compare the

spawning distribution of these fish by sex, origin and relative size. Additionally, since the

fecundity of each tagged female salmon was estimated, the position of tagged females

during spawning enabled the calculation of the number of eggs potentially deposited

within each study reach.

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Determining the sub-reach in which each fish was located when it spawned was

challenging. Variation in the spawning date for individual fish, coupled with occasional

difficulties in resolving a fish’s position (upstream or downstream) relative to a reader

station likely introduced some error. In an effort to reduce this interpretation error, an

analysis of the 2000 data was performed based solely on the how far upstream of the

counting fence a tagged fish was known to have travelled. This “minimum” migratory

distance was assigned to each fish based on the distance from the fence to the furthest

upstream reader station at which the fish was detected.

Adult salmon translocation

To evaluate the viability of adult Atlantic salmon translocation as a means to increase egg

deposition rates in under utilized stream sections, PIT tagged salmon were transported

from the Clearwater Brook counting fence to the upper study reach of the brook. Between

11h30 and 13h30 on October 12th and 13th, 1999, 20 Atlantic salmon were distributed in

male/female pairs using a 900 litre insulated holding tank to one of three relocation sites.

The tagged salmon were translocated to three sites as follows: CTR1 (Northeast Branch

tributary), eight Atlantic salmon (four females, four males); CTR2, eight Atlantic salmon

(four females, four males); CTR3, four Atlantic salmon (two females, two males) (Figure

3.2).

Nine of the ten female and six of the ten male salmon translocated from the fence had

fork lengths equal to or exceeding 63 cm and were classified as multi sea-winter (MSW)

salmon whereas salmon with fork lengths less than 63 cm were classified as grilse.

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Translocated salmon ranged in length from 60 cm to 94 cm (FL) (Table 3.2). In order to

monitor the movement and distribution of these salmon following the relocation process,

all fish were fitted with a passive integrated transponder at the counting fence prior to

transportation to the upper reach.

Stream habitat and egg deposition rate

A detailed stream habitat assessment was conducted in 1996 to evaluate, quantify, and

spatially reference the habitat available to salmonids in Clearwater Brook (McCabe and

Connell, 1997). This survey was completed according to the standardized methods

established by the New Brunswick Department of Natural Resources and Energy and the

Gulf Region of the Department of Fisheries and Oceans (Hooper and McCabe, 1998).

The survey was conducted over the entire length of Clearwater Brook. Detailed

observations and measurements of aquatic habitat were recorded from the uppermost

point suitable for salmon production to the brook’s confluence with the Southwest

Miramichi River. The habitat parameters investigated included substrate, stream type,

wetted and bank channel widths, depth, temperatures, vegetation, in-stream cover, cold-

water inputs and habitat quality variables such as the degree of substrate embeddedness

and siltation. All observations were collected and spatially linked based on the distance

from survey start points. These data were then incorporated into a geographic information

system (GIS) database to facilitate spatial analyses of the information.

For the purposes of this study, it was necessary to examine the availability of stream

habitat relative to the number and distribution of eggs spawned by female salmon. This

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comparison enabled the calculation of the potential egg deposition rate (number of egg

deposited per square meter of habitat) within each study reach. Minimum potential

deposition rates were based on the total number of eggs spawned (within a study reach)

relative to all accessible wetted habitat located within that study reach. Since Atlantic

salmon spawning generally occurs in gravel and rubble substrates and in areas with

hydraulic conditions promoting intragravel flow (Gibson, 1993), I also calculated egg

deposition rates based on the amount of “preferred” spawning habitat within study

reaches. Preferred habitat area was computed from stream survey data as the area (m2) of

suitable sized substrate (2.6 mm – 179 mm diameter) located in areas typically used by

spawning salmon (runs, riffles).

Redd surveys

Post-spawning salmon redd surveys were conducted in the upper and middle reaches of

Clearwater Brook in late October or early November of 1998 through 2001. These

surveys were conducted to identify where and how intensively salmon spawning occurred

within the surveyed portion of the river. Salmon redds were identified from a canoe by

looking for the wide depression (60+ cm diameter) of clean gravel that is typically

formed when a female salmon buries eggs during spawning. Survey information from

1999 and 2000 was used to verify that salmon were actually spawning and distributing

eggs in study sites as indicated from their distributions shown from the PIT tag

monitoring work. In 1999 the survey included the 12.2 km of river from a point 3.4 km

upstream of CR2 to Bridge Pool (6 km upstream of the fence). In 2000 higher water

levels made it possible to conduct the survey via canoe over 24 km of the brook, from a

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point 4.8 km upstream of reader station CR3 to Brook Pool (2.5 km upstream of the

fence).

Statistical analyses

Chi-square contingency table analyses were performed using SAS/STAT ® software (SAS

Institute Inc., 1999) to test if adult salmon spawning distribution was independent of

origin (hatchery vs. wild vs. translocated). A contingency table test for heterogeneity

confirmed that the spawning distribution data for wild and hatchery-origin salmon were

homogeneous (0.25>P>0.10) between years; consequently the 1999 and 2000 data were

pooled for additional analyses. To test the significance of observed differences in the

spawning distribution of wild versus translocated female salmon it was necessary to

apply Yates’s correction to account for the small sample size (n=9) of female salmon

translocated to the upper reach.

Linear regression analyses (α=0.05) were performed to test for a correlation between

upstream migratory distance and spawning contributions (egg deposition rates) for

hatchery-origin and wild adult salmon in 2000. A similar analysis of 1999 data could not

be performed due to the reduced resolution of spawning distributions from the operation

of only two reader stations that year.

Z tests were performed to determine if: 1) the sex ratio of wild origin grilse or MSW

salmon varied significantly between years; 2) the proportion of early-run salmon within

the wild and hatchery-origin samples were significantly different; 3) the proportion of

upper reach spawners within the translocated group and the free-swimming group

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differed significantly. The z-test procedure could not be validly applied to assess

observed difference in the sex ratio of hatchery-origin grilse and MSW salmon due to

small sample sizes.

The 95% confidence intervals associated with many of the proportional data presented

herein were calculated without a correction for continuity (Newcombe, 1998).

Results

Atlantic salmon captures and PIT tagging

In 1999, the Clearwater Brook counting fence was installed on June 4th and operated until

October 21st. A total of 896 Atlantic salmon (410 multi sea-winter and 486 grilse) were

enumerated during this period, with the first of these salmon arriving at the fence on June

12th. A total of 317 (24.2%) salmon were captured at the fence prior to September and

well before the peak migration typically observed at the Clearwater Brook fence in early

to mid October (“fall-run”). Thirty-three (3.7%) of the adult salmon captured at the

counting fence were hatchery-origin fish. Females accounted for 15.5% of wild grilse

(n=401), 72.4% of wild multi sea-winter salmon (n=456), 24% of hatchery-origin grilse

(n=25) and 50% of hatchery-origin MSW salmon respectively (n=8). Passive integrated

transponder tags were applied to 321 (88.9%) of 361 wild female adult Atlantic salmon

and 33 (6.7%) of 496 wild male adult salmon captured at the Clearwater Brook counting

fence in 1999. All 10 (100%) female hatchery-origin adult salmon and 17 (68.0%) of the

25 male hatchery-origin adult salmon received a PIT tag prior to being released upstream

of the fence in 1999 (Table 3.3). An effort was made to tag all adipose-clipped and wild

female salmon. However, during the peak of the spawning period there were instances

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when the force needed to insert a PIT tag resulted in egg expulsion. Consequently, 14

female MSW salmon and two female grilse captured at the Clearwater Brook counting

fence after October 19 were not PIT tagged. Additionally, 12 wild MSW salmon were

removed from the river for hatchery broodstock and did not receive a tag. On October

19, 1999 one wild female MSW salmon was recovered dead at the counting fence one

day after it was tagged and was not included in the analysis of the pre-spawning

movements and spawning distributions.

In 2000, the Clearwater Brook counting fence operated from May 30 to November 3, and

a total of 715 Atlantic salmon (197 multi-sea winter salmon and 518 grilse) were

captured during this period (Table 3.4). The first salmon was captured at the facility on

June 28, and 176 (20.4%) salmon arrived at the fence prior to September. Thirty-three

(4.6%) of the salmon captured in 2000 were marked with a clipped adipose fin and were

assumed to be of hatchery-origin. Female salmon accounted for 5.1% of wild grilse

(n=490), 72.4% of wild MSW salmon (n=192), 7.1% of hatchery-origin grilse (n=28) and

100% of hatchery-origin MSW salmon (n=5) captured in 2000. Sex ratios varied

significantly between years for wild grilse (z=0.105, P<0.001), but not for wild MSW

salmon (z=0.02, P= 0.98). Passive integrated transponder tags were applied to 147 (90%)

of the 164 wild female adult salmon and 18 (3.4%) of the 518 wild male adult salmon

captured in 2000.

All seven hatchery-origin female and 26 hatchery-origin male adult salmon captured at

the fence in 2000 received a PIT tag. Egg expulsion prevented PIT tags from being

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inserted into two wild female salmon during late October of 2000. Also, 12 wild MSW

females were not tagged as they were collected for hatchery broodstock. One wild female

MSW salmon PIT tagged on June 30, 2000 was recovered dead at the counting fence on

August 4, 2000. This fish was not included in the analysis of salmon movements and

spawning distribution since it was unclear exactly when the fish died. Furthermore the

fish was not detected at any reader stations prior to being recovered.

Based on scale samples randomly collected from salmon captured at the fish fence in

2000, one-sea winter (1SW) salmon had a mean fork length of 57.1 ± 0.6 cm (n=60,

range = 50.0 cm to 62.5 cm), whereas two-sea winter (2SW) salmon averaged 81.5 ± 1.5

cm (n=58, range 72 cm to 95 cm), and three sea-winter (3SW) salmon averaged 92.7±

10.6 cm (n=8, range 76 cm to 109.5 cm). Spawning marks, indicative of a fish that has

previously spawned (i.e. repeat spawner), were noted on 6.9% (4 of 58) of the scales

sampled from 2SW salmon and on 62.5% (5 of 8) of the 3SW salmon scales.

In 1999, the proportion of “early-run” wild and hatchery-origin salmon did not differ

significantly (z= -0.164, p=0.87); 25.0% of fry-stocked adult returns and 23.7% of wild

fish were captured at the fence prior to September (Table 3.5). A further examination of

one sea-winter and multi sea-winter salmon captures found only minor differences in the

proportion early-run hatchery and wild salmon captured in 1999, none of which were

statistically significant (p>0.5). In 2000, however, a significant difference (z=-0.187,

p=0.015) was observed between the proportion of early-run hatchery-origin (42.4%) and

wild salmon (23.8%). This difference was most pronounced for multi-sea winter fish,

with 80.0% of hatchery-origin MSW’s and only 15.6% of wild MSW’s returning ‘early’

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Due to the small number (n=5) of hatchery-origin MSW captures, the statistical

significance of the observed difference could not calculated .

Clearly the majority of salmon entered the middle and upper study reach just prior to the

spawning period. Timing of adult Atlantic salmon captures at the counting fence were

similar in 1999 and 2000; in both years peak adult salmon captures occurred near October

15th (Appendix II).

Adult salmon translocation

The movement of translocated salmon varied among individuals but a general pattern of

downstream movement immediately following relocation was observed. Seven of the 12

salmon relocated to the upper Clearwater Brook study reach (CTR2 and CTR3) moved

downstream within a 24-hour period following translocation. Three of the four salmon

(75%) distributed at CTR2 and four of the eight salmon (50%) distributed to CTR3

moved downstream by at least 1.05 km and 2.45 km, respectively, in this 24-hour period.

Interestingly, only one of the 8 salmon (13%) distributed to the Northeast Branch of

Clearwater Brook at site CTR1 was subsequently detected when it travelled at least 2.95

km downstream to the reader station CR4 within 24 hours of relocation (Figure 3.5). One

female grilse and one female MSW salmon translocated to CTR1 (Northeast Branch) and

one female MSW salmon translocated to CTR3 were never detected following

translocation. It is possible that these fish either dropped below the reader station

undetected, remained upstream during the spawning period and did not descend until

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after the readers were removed, or died in the study reach following translocation. None

of these three undetected fish were assumed to have spawned in the upper study reach.

A higher proportion of translocated female salmon are believed to have spawned in the

upper reach when compared to the proportion of wild females that migrated from the

fence to spawn in this reach. In total, 106 of the 301 (35.2% C.I. = 30.0% to 40.8%) wild

free-swimming PIT tagged female salmon were present in the upper study reach during

spawning, while 6 of the 10 (60% C.I. = 31.3% to 83.2%) female MSW salmon tagged

and translocated to the upper study reach remained there during the spawning period.

Based on the spawning location of these fish as resolved by tag reader stations, 77 of the

301 (25.6%, C.I. = 21.0% to 30.8%) wild free-swimming tagged salmon spawned in the

mainstem portion of the upper reach, whereas 4 of the 6 (66.7%, C.I. = 30% to 90.3%)

female salmon translocated to the upper reach above CR2 remained in this study reach

during spawning (Figure 3.6, Table 3.6). Similarly, only 29 of the 311 (9.6%, C.I.= 6.8%

to 13.5%) wild free-swimming females spawned in the Northeast Branch tributary

(upstream of CR4), whereas 2 of the 4 (50.0%, C.I. = 15% to 85%) tagged female salmon

translocated to this area remained and are presumed to have spawned (Figure 3.6, Table

3.7).

The spawning distributions of free-swimming and translocated PIT tagged salmon (male

and female) differed significantly (Z= -2.108, p=0.035) based on the proportion of each

group which were upper reach spawners. In 1999, 137 of the 334 (41.0%, C.I. 35.9% to

46.4%) wild free swimming PIT tagged salmon were present in the upper study reach

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during the spawning period, while 13 of the 20 (65%, C.I. = 43.3% to 81.9%) tagged

salmon translocated to the upper study reach remained in this reach during the spawning

period. Interestingly, I calculated that 44.7% (40,063 of 89,563) of the eggs carried by

translocated females were deposited in the upper study reach during spawning in 1999.

Comparatively, 33.4% of the eggs carried by naturally migrating wild salmon were

estimated to have been deposited in the upper reach (Table 3.8). Wild and translocated

salmon contributed an estimated total of 845,167 eggs to the upper reach in 1999, 4.7%

of which were spawned by translocated females.

Given that 16.5% of the wild salmon PIT tagged at the counting fence after October 1st,

1999 were present in the upper reach during spawning, it was assumed that this same

proportion of translocated salmon would have been upper reach spawners even if they

had not been translocated. After correcting the egg contributions accordingly, it was

estimated that translocated salmon provided a net gain of 25,285 eggs to the upper study

reach and accounted for a 3.1% gain in egg contributions to the target reach (Table 3.9).

Wild and hatchery-origin adult Atlantic salmon spawning distribution

Similarities in the proportion of wild and hatchery-origin grilse and multi-sea winter

(MSW) salmon that spawned in the upper reach in 1999 and 2000 made it statistically

acceptable to pool these data for analysis (chi-square heterogeneity test: 0.10>p>0.05).

Relative to their wild (free-swimming) counterparts, hatchery-origin salmon exhibited an

increased propensity to spawn in the upper reach of Clearwater Brook. Pooled data

indicate that 75% (n=48) of hatchery-origin grilse and 72.7% (n=11) of hatchery-origin

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MSW salmon were present in the upper reach of Clearwater Brook during spawning.

Comparatively, only 46.0% (n=100) of wild grilse and 29.3% (n=375) of wild MSW

salmon traveled to the upper reach to spawn (Figure 3.7).

Chi-square analyses (corrected for continuity) of these findings confirmed a significant

difference in spawning distributions between: 1) wild and hatchery-origin grilse (x2=9.9,

df=1, p<0.002); 2) wild and hatchery-origin MSW salmon (x2=9.5, df=1, p<0.0025); and

3) wild grilse and wild MSW salmon (x2=9.2, df=1, p<0.0025). Interestingly, while the

upper reach spawning distribution of wild grilse (46.0%-upper) and wild MSW salmon

(29.3%-upper) differed, no statistically significant difference was detected between the

proportion of hatchery-origin grilse (75%-upper) and hatchery-origin MSW salmon

(72.7%-upper) that spawned in the upper reach.

The average minimum upstream migratory distance of PIT-tagged, hatchery-origin

salmon (n=32) was 15.1 km and only 8.3 km for PIT-tagged wild salmon (n=164) in

2000. The minimum upstream migratory distances of hatchery-origin fish were found to

be significantly (P<0.0001) greater than those observed for wild fish and a t-test indicated

a 97% probability that hatchery-origin adult salmon travelled at least 3-km further

upstream than did wild adult salmon in 2000.

Wild and hatchery-origin adult Atlantic salmon egg deposition

Egg deposition rates from hatchery-origin salmon were positively correlated with the

minimum distance to sub-reaches (r=0.82, r2=0.67) (Figure 3.8, 3.10, Table 3.11) and a

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one-tailed t-test confirmed the prediction that hatchery-origin salmon egg deposition rates

increased with increasing distance (p=0.045). Conversely, wild salmon egg deposition

rates were inversely correlated with distance (r= -0.875, r2=0.77) (Figure 3.9, 3.10, Table

3.11) and the prediction that wild egg deposition rates decreased with increasing distance

was confirmed (one-tailed t-test: p=0.026). When the Northeast Branch (sub-reach U-3)

was excluded from these regressions an even stronger correlation between egg deposition

rates and distance to spawning sites existed for hatchery salmon (r=0.97, r2=0.94); 94%

of the variability in mainstem egg deposition rates from hatchery-origin salmon was

explained by upstream distance (one-tailed t-test: p=0.014). When the Northeast Branch

data were excluded from the analysis of wild salmon egg deposition rates a stronger

inverse correlation was observed (r=-0.98, r2=0.96, p=0.01), and 96% of the variability in

mainstem egg deposition from wild salmon was explained by the distance to spawning

habitat.

To compare 1999 and 2000 egg deposition rates from wild and hatchery-origin salmon,

data were reviewed at the broader “study reach” scale. Wild salmon egg deposition rates

in the upper reach were 8.4% (1999) and 52.4% (2000) less than middle reach values,

whereas hatchery-origin egg depositions values were 47.6% (1999) and 157% (2000)

higher than middle reach values (Table 3.10). Redd surveys found that spawning was

most extensive in the middle reach and support findings from PIT tag monitoring that

indicated an inverse correlation between upstream distance and spawning distributions

among wild salmon (Table 3.12)

102

Of the 217,658 square meters of preferred salmon spawning habitat located upstream of

the Clearwater Brook counting fence, 35.4% (76,976 m2) is distributed in the upper study

reach, while 64.6% (140,682 m2) is found in the middle reach. Assuming that salmon

spawning occurred based solely on habitat distribution, one would expect the proportion

of eggs deposited to each study reach to mirror the proportion of spawning habitat within

that reach. In fact, wild salmon deposited 33.4% of their eggs in the upper reach in 1999,

whereas in 2000 only 20.7% of wild salmon eggs were carried to the upper reach.

Comparatively, 44.3% (1999) and 58.4% (2000) of the eggs from hatchery-origin salmon

were deposited in the upper reach in these same years (Figure 3.11).

Based on the spawning distribution of hatchery-origin and wild female salmon in 1999

and 2000, hatchery-origin salmon were estimated to have resulted in a 4.8% increase in

egg deposition (net gain of 50,308 eggs) to the upper reach (Table 3.13). It should be

noted that the potential loss in wild adult salmon production as a result of broodstock

collection for the stocking program was not accounted for.

Discussion

Declines in adult Atlantic salmon abundance and spawning returns have prompted

fisheries managers to investigate and implement a variety of techniques aimed at

optimizing smolt production from freshwater habitats. The present study examined two

such techniques by investigating Atlantic salmon fry stocking and adult translocation as

strategies to increase egg deposition within the upper reach of Clearwater Brook in 1999

and 2000.

103

Wild Atlantic salmon spawning distribution

The disproportionate production of Atlantic salmon juveniles noted between the upper

and middle study reach was confirmed on the basis of egg deposition rates. In fact, for

wild salmon, as the distance to upstream spawning habitat increased the number of eggs

deposited per square metre of habitat was found to decrease. This middle reach spawning

‘preference’ observed in wild salmon was suspected to be a consequence of fewer wild

juveniles being produced in (and imprinting to) the upper reach. Based on the 1996 to

1998 mean wild parr densities for the upper and middle reaches, and the availability of

parr rearing habitat in those same reaches, an estimated 30% of the wild parr produced

upstream of the counting fence came from upper reach habitat. Correspondingly, 30.2%

of the wild MSW salmon captured and tagged at the Clearwater Brook counting fence in

1999 and 2000 returned to spawn in upper reach habitat whereas a higher proportion of

wild grilse (56.8%) appear to have spawned in the upper reach. The reason for the

increase proportion of upper reach spawning grilse is unknown.

Stocking hatchery-reared underyearling Atlantic salmon The ability of hatchery-raised salmon to imprint to the site at which they were released

(stocked) was a significant premise of stocking efforts within Clearwater Brook.

Monitoring the spawning distribution of adult salmon confirmed a high degree of reach-

specific homing among salmon that were previously stocked as underyearlings into the

upper reach of the brook. In fact, 73.4% of the hatchery-raised fry stocked into the

Clearwater Brook study area from 1995 to 1997 were distributed within the upper reach

(appendix I-8). Comparatively, 75% of hatchery-origin grilse (n=48) and 72.7% of

104

hatchery-origin MSW salmon (n=11) that returned to the Clearwater Brook fence in 1999

and 2000 were present in the upper reach during spawning. It is important to note that

this apparently precise imprinting is likely to have occurred because stocked salmon were

released to their ‘natal’ river at a young age. As suggested by Fleming and Petersson

(2001), releasing hatchery reared salmon to home-rivers as juveniles generally results in

increased homing precision of returning adults. Unfortunately, despite the homing

behaviour observed in adult returns of salmon stocked to Clearwater Brook, the overall

return rate was low (0.11%) with stocked salmon accounting for only 33 adult returns to

the study area each in both 1999 and 2000. Total returns of female hatchery-origin

salmon were low (n=17) and accounted for only 2.2% (78,829 of 3,612,746) of the total

estimated egg deposition within the middle and upper study reach of Clearwater Brook.

An examination of how these eggs were apportioned relative to the availability of high

quality salmon spawning habitat confirmed two predictions of this study: 1) estimated

egg deposition by wild salmon decreased with increasing upstream distance, particularly

when only mainstem spawning distributions were considered; and 2) estimated egg

deposition by hatchery-origin salmon increased as the distance to spawning grounds

increased, and again this was particularly true when only mainstem spawning

distributions were considered. The first of these findings supports the hypothesis that

reduced juvenile salmon abundances in the upper reach of Clearwater Brook are a

function of decreased spawning and egg density within this same reach. The second

finding indicates that targeted salmon stocking could potentially be used to establish self-

sustaining production in the stocked areas. Of particular interest here, was the finding that

105

egg deposition rates in the Northeast Branch of Clearwater Brook (sub-reach U-3) were

highest for hatchery-origin salmon and lowest for wild salmon, despite the fact that the

distance to U-3 was less than that to U-2 and marginally less than the distance to U-1.

The fact that these results did not correspond well with the previously stated relationships

between egg deposition rates and distance was potentially because the Northeast Branch

represents less than 4% of the preferred spawning habitat within the sub-reaches. Thus,

small variations in the number and size of female salmon (eggs) to the Northeast Branch

result in larger variation in egg deposition rates relative to other sub-reaches.

The gain in upper reach egg deposition from hatchery-origin adult returns was nominal

relative to upper reach egg contributions by wild salmon. Over the two years of this

study, hatchery salmon potentially increased total egg deposition in the upper reach by

4.8% (~50,000 eggs). The variation in this value between 1999 (2.9%) and 2000 (11.6%)

was largely a function of reduced upper reach egg deposition from wild salmon in 2000

(231827) relative to 1999 (805476) since the total number of eggs deposited to the upper

reach by hatchery fish was only slightly higher in 2000 (26818) relative to 1999 (23490).

While stocking appears to have been an effective means to increase egg depositions and,

presumably, juvenile abundance in the upper reach of Clearwater Brook, the use of this

technique has the potential to result in negative genetic impacts to wild salmon

populations within the brook. The effects of stock movement, non-random sampling of

broodfish, and forced matings that occur from hatchery rearing programs were identified

by Youngson and Verspoor (1998) as potential factors that could distort the natural

population structure of salmon within a river, even for same river stocking of first

generation hatchery progeny. Furthermore, the gain in egg to juvenile survival that results

106

from hatchery rearing results in an over-representation of parent fish genotypes at a local

scale (Ryman, 1991); this may be particularly true if hatchery fish are released in large

numbers at few locations within a river.

Adult Atlantic salmon translocation

The present study also examined the effectiveness of adult salmon translocation as a

counter-measure to uneven wild spawning distributions and reduced egg deposition in the

upper reach of Clearwater Brook. The following predictions were tested: 1) a higher

proportion of translocated salmon will spawn in the upper reach relative to free-

swimming (non-translocated) salmon; 2) proportionally, translocated salmon will

contribute more eggs to the upper reach than free-swimming wild salmon; and 3)

translocation will result in an increase in the total number of eggs deposited to the upper

reach.

Based on PIT tag monitoring data, a significantly higher proportion (x2 = 3.52, df =1,

P=0.06) of salmon translocated to the upper reach remained there during the spawning

period (65%, n=20) relative to the proportion of wild, free-swimming salmon that

travelled to the upper reach to spawn (41.0% n=334). Similarly, translocated salmon were

found to contribute proportionally more eggs (44.7%) to the upper reach than did wild

salmon (33.4%). Moreover, translocation of just 10 male-female pairs of wild adult

salmon to the upper reach resulted, at minimum, in a net gain of 25,285 eggs and a 3.1%

increase in egg deposition to the upper reach. It should be noted that three PIT tagged

female salmon (1 grilse, 2 MSW salmon) were never detected at downstream reader

107

stations following translocation. It was assumed that these fish passed through the

downstream reader station without detection prior to spawning and that they did not

contribute to upper reach production. However, it is also possible that these fish passed

downstream without detection after the spawning period or that they dropped down after

the reader stations were removed. If these fish had, in fact, spawned in the upper reach,

translocated salmon would have contributed 69% of their eggs to this reach and

accounted for a 5.8% gain (47,280 eggs) in upper reach egg deposition.

Based on the single year adult Atlantic salmon were translocated and monitored in

Clearwater Brook, it appears that this technique is a potentially effective way to

counteract patchiness or uneven distribution in adult salmon during spawning.

Translocations of a greater number of fish would likely have yielded higher egg

contributions to the enhancement reach or site. Furthermore, it is speculated that more

substantial increases in egg deposition would be achieved from the translocation of

salmon to river segments that have extremely low natural spawning escapement. Moving

sexually mature adult salmon is one of the least interventionist forms of enhancement and

genetic interactions from this technique are least likely to be problematic (Youngson and

Verspoor, 1998). Despite this, when used as a technique to re-colonize river segments

that were once isolated from wild salmon spawning (driving dams, beaver dams, natural

in-stream blockages) genotypic diversity in the resultant local population should be

maintained. Accordingly, sufficient numbers of wild fish should be translocated in order

to maximize genetic diversity in the re-established local population.

108

Cost-benefit of Atlantic salmon fry stocking and adult translocation The costs incurred from adult broodstock collection, and the hatchery rearing, marking

(fin-clipping), and distribution of juvenile Atlantic salmon to Clearwater Brook equated

to 40 cents per fry (M. Hambrook, Miramichi Salmon Conservation Centre, pers comm.).

Since only 0.11% of stocked salmon were found to return to the middle and upper

reaches of Clearwater Brook as mature adult fish (1 adult per 900 stocked juveniles;

Connell, 2003), the average cost to produce an adult salmon return via fry stocking was

approximately $400 (CAD). Thus, the 17 female and 49 male hatchery-origin adult

salmon captured at the Clearwater Brook fish fence over 1999 to 2000 were produced at a

cost of just over $26,000 (CAD) and the potential immediate gain to upper reach juvenile

salmon production from hatchery returns was estimated to be between 2.9% (1999) and

11.6% (2000) over the two years of this study. The combined two-year gain in upper

reach egg deposition from hatchery-origin adult salmon returns was assessed to be

approximately 50,000 eggs or 4.8% ($520 CAD / 1000 eggs gained in the upper reach). It

should be noted that these estimates did not account for potential loss in wild production

from the annual removal of 12 MSW female salmon to support the hatchery-rearing

program; nor were the potential future contributions from repeat spawning hatchery-

origin adults considered within the scope of this study.

Comparatively, the translocation of 20 wild adult salmon from the counting fence to the

upper reach of Clearwater Brook was conducted at less than $1000 (CAD) and this

technique was found to have potentially increased upper reach egg depositions between

109

3.1% and 5.8% (25285 to 47280 eggs) (<$40 CAD / 1000 eggs gained in the upper

reach).

Based on findings from this study, ‘home-river’ stocking of hatchery-reared

underyearling Atlantic salmon and the translocation of wild adult Atlantic salmon are

both a potentially effective technique to increase or establish salmon production in target

stream reaches. Both techniques appear to have resulted in a small contribution of eggs to

the target (enhancement) reach relative to egg depositions from wild free-swimming

salmon. However, in the case of adult translocation, this egg contribution and potential

gain in production was achieved by moving only 10 pair of salmon at a minimal cost and

effort. Further, given the potential genetic implications to wild salmon populations from

each technique it is suggested that adult translocation would provide the greatest benefit

and minimize potential deleterious genetic impacts to wild fish when used to establish (or

re-establish) juvenile salmon populations in previously vacant habitat. Clearly adult

salmon translocation is a far less costly enhancement solution to address uneven adult

salmon distribution and low egg depositions within discrete river reaches.

110

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(Salmo salar L.) in a regulated Norwegian river: hatching, dispersal and growth of

fry. Regulated Rivers: Research and Management 10: 169-180.

Randall, R.G. 1985. Spawning potential and spawning requirements of Atlantic salmon in

the Miramichi River, New Brunswick. Canadian Atlantic Fisheries Scientific

Advisory Committee Res. Doc. 85/68. 19p.

Ritter, J. A. 1989. Marine migration and natural mortality of North American Atlantic

salmon (Salmo salar L.). Can. MS. Rep. Fish. Aquat. Sci. No. 2041. 136 p.

112

Ryman, N. 1991. Conservation genetics considerations in fishery management. J. Fish.

Biol. 39 (Suppl. A): 211-224.

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estimated spawning positions of late-running adult Atlantic salmon (Salmo salar

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Aberdeen, Fisheries Research Services 3/98, 19pp.

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reference to the Atlantic salmon. Biol. Rev. 59: 333–388.

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collaborative research program report. 49 p.

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113

Table 3.1. Total wetted stream area and preferred salmon spawning area within the middle and upper reaches and within the sub-reaches upstream of the fish counting fence on Clearwater Brook, NB.

Wetted habitat Preferred spawning

habitat Reach Sub-

reach

Area (m2) % of total

area Area (m2) % of total area

M-1 126645 27.45% 63636 29.24% M-2 130871 28.37% 77046 35.40%

Middle 257516 55.82% 140682 64.63% U-1 85591 18.55% 38232 17.57% U-2 95742 20.75% 30943 14.22% U-3 22497 4.88% 7801 3.58%

Upper 203830 44.18% 76976 35.37%

Total 461346 100.00% 217658 100.00% Table 3.2. Biological characteristics (fork length and sex), PIT tag number, transfer date,

and release site of adult Atlantic salmon translocated to the upper reach of Clearwater Brook, NB.

Capture / Translocation

Date Sex

Fork Length

(cm) Pit-tag applied

Translocation site

10/12/1999 F 90 140 CTR3 10/12/1999 F 76 134 CTR3 10/12/1999 M 60 139 CTR3 10/12/1999 M 63 142 CTR3 10/12/1999 F 82 132 CTR2 10/12/1999 F 82 141 CTR2 10/13/1999 F 77 150 CTR2 10/13/1999 F 90 149 CTR2 10/12/1999 M 61 131 CTR2 10/12/1999 M 67 137 CTR2 10/13/1999 M 72 151 CTR2 10/13/1999 M 61 153 CTR2 10/13/1999 F 79 152 CTR1 10/12/1999 F 94 130 CTR1 10/12/1999 F 83 138 CTR1 10/12/1999 F 61 143 CTR1 10/12/1999 M 92 133 CTR1 10/12/1999 M 60 136 CTR1 10/12/1999 M 92 135 CTR1 10/13/1999 M 86 148 CTR1

114

Table 3.3. Number and percentage of adult salmon captured and implanted with passive

integrated transponder tags at the Clearwater Brook counting fence between June and October, 1999.

CapturedPIT

tagged % tagged CapturedPIT

tagged % taggedFemale MSW salmon 290 259 89.3% 4 4 100.0%Female grilse 71 62 87.3% 6 6 100.0%Male MSW salmon 111 14 12.6% 4 3 75.0%Male grilse 385 19 4.9% 19 14 73.7%Total 857 354 41.3% 33 27 81.8%

Hatchery originWild1999

MSW salmon – multi-sea winter salmon, ≥ 63 cm fork length Grilse – one sea winter salmon, < 63 cm fork length Table 3.4. Number and percentage of adult salmon captured and implanted with passive

integrated transponder tags at the Clearwater Brook counting fence between June and October, 2000.

CapturedPIT

tagged % tagged CapturedPIT

tagged % taggedFemale MSW salmon 139 124 89.2% 5 5 100.0%

Female grilse 25 23 92.0% 2 2 100.0%Male MSW salmon 53 2 3.8% 0 0

Male grilse 465 16 3.4% 26 26 100.0%Total 682 165 33 33

Hatchery OriginWild2000

MSW salmon – multi-sea winter salmon, ≥ 63 cm fork length Grilse – one sea winter salmon, < 63 cm fork length

Table 3.5. The percentage of wild and hatchery origin grilse and MSW salmon captured at the Clearwater Brook counting fence prior to September of 1999 and 2000.

1999 2000

Grilse MSW All Grilse MSW All

Wild 34.8% 10.3% 23.7% 26.9% 15.6% 23.8% Hatchery-origin 29.2% 12.5% 25.0% 35.7% 80.0% 42.4%

Probability of observed difference (two-tailed) 0.57 n/a 0.87 0.31 n/a 0.015

115

Table 3.6. The number of PIT tagged wild and translocated Atlantic salmon detected at the CR2 reader station (mainstem upper reach) and the number of female salmon therein that are believed to have spawned upstream of CR2 - Clearwater Brook, 1999.

Origin Sex Total Tagged

Total detectedat CR2

Females spawning

above CR2

% detected

% Spawn

Females 250 73 65 29.2 26.0 Males 9 2 22.2

Wild MSW Salmon – free-swimming Total 259 75 30.0

Females 61 22 12 36.1 19.7 Males 14 7 50.0

Wild Grilse – free-swimming Total 75 29 36.7

Females 6 5 4 83.3 66.7 Males 3 5 166.7

Wild MSW Salmon - Translocated Total 9 10 111.1

Females 0 0 0 0.00 0.00 Males 3 3 100.0

Wild Grilse - Translocated

Total 3 3 100.0

Table 3.7. The number of PIT tagged wild and translocated Atlantic salmon detected at

the CR4 (Northeast Branch upper reach) reader station and the number of female salmon therein that are believed to have spawned upstream of CR4 - Clearwater Brook 1999.

Origin Sex Total Tagged

Total detectedat CR4

Females spawning

above CR4

% detected

% Spawn

Females 250 17 17 6.8 6.8 Males 9 0 0.0

Wild MSW Salmon

Total 259 17 6.6 Females 61 14 12 23.0 19.7 Males 14 2 14.3

Wild Grilse

Total 75 16 21.3 Females 3 2 2 66.7 66.7 Males 3 3 100.0

Wild MSW Salmon - Translocated Total 6 5 83.3

Females 1 0 0 0.00 0.0 Males 1 1 100.0

Wild Grilse – Translocated

Total 2 1 50.0

116

Table 3.8. The number and percentage of eggs calculated to be contributed to the upper and middle reaches of Clearwater Brook by wild, translocated and hatchery-origin PIT tagged salmon in 1999.

Eggs by study reach

Proportion of eggs % of total egg deposition Salmon 'origin' Total

eggs Unknown Upper Reach

Middle Reach

Upper Reach

Middle Reach

Upper Reach

Middle Reach

Translocated 89563 21995 40063 27505 59.3% 40.7% 4.7% 1.7% Wild migrants 2411606 805104 1606502 33.4% 66.6% 95.3% 98.3% Total 2501169 21995 845167 1634007 33.8% 66.2% 100.0% 100.0%

Table 3.9. Estimated egg distribution and gain/loss in egg contribution as a result of adult Atlantic salmon translocation in Clearwater

Brook 1999.

Study Reach

Observed egg distribution of translocated

salmon (A)

Observed egg distribution of wild

salmon (free-swimming)

(B)

Observed egg distribution of

translocated and wild salmon (A+B)

(C)

Expected egg distribution

(assuming no translocation)

(D)

% gain / loss in egg distribution from

translocation

[(C/D) x 100] -100

Middle 27505 1606130 (83.5%)

1633635 1680915 (83.5% of C total)

-2.8%

Upper 40063 805476 (16.5%)

845539 820254 (16.5% of C total)

3.1%

Unknown 21995 21995 Total 89563 2411606 2501169 2501169 0.0%

117

Table 3.10. Egg deposition rates to the mid and upper Clearwater Brook study reaches from PIT tagged wild and hatchery origin Atlantic salmon in 1999 and 2000.

1999 2000

Wild salmon

Hatchery-origin salmon Wild

salmon Hatchery-

origin salmon

Middle reach egg deposition rate 10.28 0.21 6.33 0.08

Upper reach egg deposition rate 9.42 0.31 3.01 0.20

% difference in upper reach value -8.4% +47.6% -52.4% +157.0%

118

Table 3.11. Relative egg contributions and deposition rates from wild and hatchery origin PIT tagged female salmon by sub-reach, Clearwater Brook - 2000.

Sub-reach Total preferred spawning area

(m2)

Eggs from tagged

hatchery-origin salmon (n=6)

Hatchery-origin salmon egg

deposition rate (n=6)

Eggs from tagged wild

salmon (n=147)

Wild salmon egg deposition

rate (n=147)

% of subreach egg

contribution (hatchery-origin

salmon)

% of subreach egg

contribution (wild salmon)

M-1 63636 3553 0.056 421080 6.617 0.8% 99.2% M-2 77046 7159 0.093 469404 6.093 1.5% 98.5% U-1 38232 11411 0.298 146545 3.833 7.2% 92.8% U-2 30943 11751 0.380 70118 2.266 14.4% 85.6% U-3 7801 3656 0.469 15164 1.944 19.4% 80.6%

Total 217658 37530 0.172 1122311 5.156 3.2% 96.8%

119

Table 3.12. Results of redd surveys conducted on Clearwater Brook, 1999-2002.

Year Redd survey stretch Study reach

No. of redds

Distance (km)

Preferred spawning

habitat (m2)

redds/ spawning

habitat (#/100m2)

3.2 km above CR2 to the NE Branch upper & middle 70 6.0 25539 0.274

1999 NE Branch to Bridge Pool middle 122 6.3 70711 0.173

4.8km upstream of CR3 to CR3 (U-2) upper 7 4.8 18409 0.038

CR3 to CR2 (U-1) upper 34 7.0 38232 0.089 CR2 to CR1 (M-2) middle 111 8.5 77046 0.144

2000

CR1 to Brook Pool (M-1) middle 42 4.1 27055 0.155 Table 3.13. Estimated egg contributions to the middle and upper reaches of Clearwater

Brook by wild and hatchery-origin salmon in 1999 and 2000.

Year Study Reach

Total egg contribution from hatchery-origin

salmon

(A)

Total egg contribution from

wild salmon

(B)

% gain from hatchery-origin

salmon

(A/B) x 100 Middle 29559 1606130 1.8% 1999 Upper 23490 805476 2.9%

Middle 10713 890484 1.2% 2000 Upper 26818 231827 11.6%

Middle 40272 2496614 1.6% 1999 + 2000 Upper 50308 1037303 4.8%

120

Miramichi River Basin

Ott er Br ook

Moose Br ook

Lake Br ook

Cl earwat er

NE B r Cle a rwa ter

B r oo k

Br oo k

McCoy B rook

Turnbul l B rook

Fair ley

Brook

Redstone Brook

SW Miramichi River

0 90 180 Kilometers

N

Clearwater Brook catchment

Miramichi River basin

Figure 3.1. Map displaying the position of the Clearwater Brook catchment

within New Brunswick’s Miramichi River Basin.

121

Figure 3.2. The location of the fish counting fence, PIT tag reader stations (CRx), adult salmon translocation sites (CTRx), Avenor bridge pool, and the upper, middle, and lower reaches of Clearwater Brook, NB.

'W

'W

ÊÚ

$T$T

ââ

#Y#Y

#Y

SW Miramichi River

Clearwater

CR4

CR2

CR1

CR3

Turnbull Bk

Lake

Bk

NE Br

Clea

rwate

r

McCoy Bk

Redstone Bk

Fairl

ey B

k

Otter B

k

Moose Bk

BrookCTR3

CTR1CTR2

0 6 12 18 24 KilometersN

N

'W PIT tag reader stations (2000 only)ÊÚ Fish Counting Fence$T PIT tag reader stations (1999 & 2000)â Avernor Bridge Pool#Y Adult salmon translocation sites

Upper reach

Middle reach

Lower reach

122

$Z

$Z

$ZÊÚ

$T$T

#³

#³

#³

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CR3

Turnbull Bk Lake

Bk

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r Clea

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McCoy Bk

Redstone Bk

Fairl

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k

Moose Bk

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Bridge Pool

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water Bk

Clear

M-1M-2U-1U-2U-3

0 5 10 Kilometers

N

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$T PIT tag reader stations (1999-2000)

#³ Portable PIT tag reader sites

$Z PIT Tag Reader Stations (2000 only)

Sub-reaches M-1

M-2

U-1

U-2

U-3

Figure 3.3. The location of PIT tag reader stations (CRx), pools surveyed with a portable PIT tag reader, and the sub-reaches located upstream of the fish counting fence on Clearwater Brook, NB.

123

ÊÚ

&\&\&\

&\

&\

&\&\&\

&\

&\

&\&\

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&\

&\

&\

&\

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&\

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CS20CS21

CS14CS23

CS1CS19

CS2 CS17

CS3CS4

CS18

CS13 CS22

CS6

CS5

CS16

CS9

CS8

CS11

CS7CS24

CS12

CS10

0 6 12 KilometersNÊÚ Fish Counting Fence

&\ Atlantic salmon fry stocking sites (CSx)

Figure 3.4. The distribution sites (CSx) of hatchery-reared Atlantic salmon fry

within Clearwater Brook, NB (1996 to 2003).

124

0%

10%

20%

30%

40%

50%

60%

70%

80%

1.05 (C R 2) 2.45 (C R 2) 2.95 (C R 4)

D istance (km ) from tranlocation s ite to downstream reader (C R x)

Prop

ortio

n of

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up d

etec

ted

at

dow

nstre

am

read

er w

ithin

24

hrs

of tr

ansl

ocat

ion

C T R 2C T R 3C T R 1

Figure 3.5. Percentage of translocated wild, adult Atlantic salmon that moved

downstream and were detected at a PIT tag reader station within 24-h following translocation.

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Mainstem aboveCR2

Northeast aboveCR4

Mainstem aboveCR2

Northeast aboveCR4

Prop

ortio

n of

gro

up sp

awni

ng in

up

per

reac

h of

Cle

arw

ater

Bro

ok

Wild, free-swimming femalesalmon

Wild, translocated femalesalmon

Figure 3.6. Percentage of free-swimming and translocated wild female adult Atlantic salmon that were present and are presumed to have spawned in the upper reach of Clearwater Brook, 1999.

125

0%10%20%30%40%50%60%70%80%90%

100%

Wild grilse Hatchery-origingrilse

Wild MSWsalmon

Hatchery-originMSW salmon

Perc

ent o

f gro

up a

cces

sing

up

per r

each

1999 2000 Pooled data (1999 & 2000)

Figure 3.7. The percentage of wild and hatchery origin PIT tagged salmon

present in the upper study reach of Clearwater Brook in 1999 and 2000.

126

U-3U-2

U-1

M-2M-1

R2 = 0.77

R2 = 0.96

0

1

2

3

4

5

6

7

0 5 10 15 20 25

Minimum distance to sub-reach (km)

Egg

dep

ositi

on ra

tio w

ithin

sub

-rea

ch

(egg

s / m

2 of

pre

ferr

ed s

paw

ning

hab

itat)

8

Wild salmon

Linear regression line (includes Northeast Branch)

Linear regression (within mainstem only)

Figure 3.8. Sub-reach egg deposition rate from wild Atlantic salmon plotted against the migratory distance from the fence to the sub-reach in Clearwater Brook, 2000. R2 values shown.

U-3

U-2

U-1

M-2

M-1

R2 = 0.94

R2 = 0.67

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

0.50

0 5 10 15 20 25

Minimum distance to sub-reach (km)

Egg

dep

ositi

on ra

tio w

ithin

sub

-rea

ch

(egg

s / m

2 of

pre

ferr

ed s

paw

ning

hab

itat)

Hatchery-origin salmon

Linear regression line (within mainstem only)

Linear regression line (includes Northeast Branch)

Figure 3.9. Sub-reach egg deposition rate from hatchery-origin Atlantic salmon plotted against the migratory distance from the fence to the sub-reach in Clearwater Brook, 2000. R2 values shown.

127

0

1

2

3

4

5

6

7

8

Subreach M-1(d<6.7km)

Subreach M-2(6.7km<d<14.2km)

Subreach U-1(14.2km<d<21.7km)

Subreach U-2(d>21.7km)

Subreach U-3(Northeast Br.

d>13.2km)

Egg

dep

ositi

on (w

ild s

alm

on a

nd to

tal)

(Egg

s / m

2 of p

refe

rred

habi

tat)

0

0.1

0.2

0.3

0.4

0.5

0.6

Egg

dep

ositi

on (h

atch

ery-

orig

in s

alm

on)

(Egg

s / m

2 of p

refe

rred

habi

tat)

Total egg deposition

Egg deposition from wild salmon

Egg deposition from hatchery-originsalmon

Northeast Branch

TributaryUpstream Direction (mainstem)------------------------------>

Figure 3.10. Egg deposition rates of wild and hatchery origin PIT tagged Atlantic salmon to each of the sub-reaches monitored in Clearwater Brook in 2000. (d = upstream migratory distance from the counting fence to the spawning site).

128

0%

10%

20%

30%

40%

50%

60%

70%

1999 2000

% of eggs from wild salmon potentially deposited to the upper reach

% of eggs from hatchery-origin salmon potentiallydeposited to the upper reach

% of preferred spawning habitat in upper reach

Figure 3.11. Percentage of preferred salmon spawning habitat located in the upper reach of Clearwater Brook relative to the percentage of wild or hatchery-origin eggs carried to the upper reach during spawning in 1999 and 2000.

129

CHAPTER 4

General Discussion

General Discussion

A local decline in spawning populations can result in reduced juvenile densities and sub-

optimal smolt production from discrete river segments (Youngson and McLaren, 1998)

which in turn can lead to reductions in adult returns to the river. Since juvenile salmon

are subjected to density-dependent mortalities (Cunjak and Therrien, 1998) and the

highest fry mortalities occur during dispersal following emergence (Egglishaw and

Shackley, 1977), it follows that juvenile salmon survival and smolt production should

benefit from near even densities across all suitable habitat (Youngson and McLaren,

1998).

While partially affected by spatial arrangement of substrates, the natural distribution of

salmonid juveniles is highly dependent on spawning site selection by parent fish. For

instance, suitable spawning habitat generally exists in upper-river reaches but access to

these areas is more frequently restricted due to water levels or natural in-stream

blockages. These access issues can restrict spawning site selection by adult salmon and

lead to patchy juvenile densities across potential rearing habitats. It is assumed that

hatchery-reared fry stocked to areas of low natural juvenile abundance will strengthen

subsequent spawning in these areas through adult returns of stocked fish. Alternately, the

technique of relocating adult fish to under used habitats is also suggested to be a viable

method to achieve more even spawning distributions and/or increase the deposition of

eggs to river segments with low natural spawning use (Kennedy et al., 1977).

131

The present study tested the effectiveness of both of these techniques by: 1) monitoring

the number, spawning distributions and egg contributions of returning adults from the

initial years of the stocking trials; 2) monitoring the spawning distribution and egg

contributions from adult salmon that were translocated to the upper reach just prior to

spawning.

This study also aimed to confirm or disprove the prediction that wild adult egg

depositions decreased with upstream migratory distance in Clearwater Brook. This

prediction was based on observed low juvenile salmon densities, few spawning redds,

and limited fry drift from the upper reach. Finally, the feasibility of conducting fish

movement studies in a remote and relatively large river using the novel approach of PIT

tag technology was tested.

In chapter two, the performance, problems and solutions associated with PIT tag

monitoring used in the present study were discussed. Passive integrated transponders

offered an innovative, inexpensive and rapid technique for tagging several hundred

Atlantic salmon and examining individual fish movements relative to established tag

detection stations. This technology was a generally effective method to examine

spawning distributions of tagged fish throughout Clearwater Brook. However, difficulty

in resolving the direction of fish travel through individual stations sometimes provided

ambiguous data. Furthermore, since the maximum effective width of stationary antennae

designed for the present study was 3.5 metres and since river widths at reader stations

were up to 15 metres wide, fencing was necessary to ensure that all migrating tagged fish

132

passed through the antenna field. The maintenance of this fencing was problematic under

high water conditions and in two instances fish were able to bypass the tag detections

antennas due to river flooding. Other ‘learning curve’ problems, such as power supply

and data-logging difficulties, were less labour intensive to resolve and were not viewed as

an insoluble limitation. Based on this study, it is suggested that twin antenna arrays be

installed at stationary reader sites, particularly when it is important to know if a fish is

located upstream or downstream of the site. The suggested modification would require

the installation of one antenna two to three metres upstream of another antenna such that

tagged fish are sequentially detected as they pass through the site.

The novel design of a portable application of PIT technology to detect tagged fish in

holding pools was successful. This system was shown to be effective in detecting salmon

in pools up to three metres deep and 7.3 metres wide and has added another facet to use

of this technology for conducting fish tracking studies.

Chapter three presented salmon monitoring data with a particular focus on the spawning

distributions and egg contributions from wild, hatchery-origin and adult translocated

salmon. Monitoring data confirmed that wild salmon were primarily late-run fish and that

egg deposition rates by wild salmon were inversely correlated with increasing distance

upstream of the counting fence (R2=0.77 to 0.96). This observation supports findings

from Smith et al (1998) which suggest that late entering fish spawn in lower river

reaches. These data may also support a hypothesis from Youngson and Verspoor. (1998)

that reproductive isolation from spatial and temporal influences is sufficient to maintain

133

heterogeneity of allozymes at a sub-catchment scale. In other words late entering fish

may spawn later and further down the brook than early entering fish, and as a result

genetic adaptations occur that maintain this reproductive isolation. In 2000, hatchery-

origin salmon entered significantly earlier than wild salmon (p=0.015) and hatchery

salmon were found to spawn further upstream than wild salmon.

The strategies of salmon stocking and adult translocation were both marginally (3% to

6%) effective at increasing the number of eggs deposited to the upper reach of Clearwater

Brook. Egg deposition rates from hatchery origin adult salmon returns were found to be

positively correlated with upstream distance (R2=0.67 to 0.94). This study found that

both methods resulted in more even distributions of adult salmon during spawning and

can be used to increase egg depositions and potential production in areas that are

naturally ‘under-seeded’. However, since hatchery rearing programs could distort the

natural population structure of salmon within a river (Youngson and Verspoor, 1998) and

since underyearling salmon stocking is more costly than adult translocation, the latter is

suggested as a better approach to address disproportionate adult spawning distributions

and patchiness in juvenile salmon production.

134

References

Cunjak, R.A. and Therrien, J. 1998. Inter-stage survival of wild juvenile Atlantic salmon,

Salmo salar L. Fish. Manag. Ecol. 5: 209-223.

Egglishaw, H.J. and Shackley, P.E. 1980. Survival and growth of salmon, Salmo salar

L., planted in a Scottish stream. J. Fish. Biol. 16: 565-584.

Kennedy, G.J.A., Hadoke, G.D.F., and Sheldrake, D.R. 1977. Transplanting of adult

Atlantic salmon (Salmo salar L.) in the River Foyle as a viable method of

supplementing the spawning stock. Fish. Mgmt. 8/4: 120-127.

Smith, G.W., Nelson, K., Youngson, A.F., and Carss, D. 1998. The movements and

estimated spawning positions of late-running adult Atlantic salmon (Salmo salar

L.) returning to the Aberdeenshire Dee. Fisheries Research Services Report.

Aberdeen, Fisheries Research Services 3/98, 19pp.

Youngson, A.F., Jordan, W.C., and Hay, D.W. 1994. Homing of adult Atlantic salmon

(Salmo salar L.) to a tributary stream in a major river catchment. Aquaculture

121: 259–26.

Youngson, A.F. and McLaren, I.S. 1998. Relocation of naturally-spawned salmonid ova

as a countermeasure to patchiness in adult distribution at spawning. Scottish

Fisheries Report 61/1998. 13p.

Youngson, A.F. and Verspoor, E. 1998. Interactions between wild and introduced

Atlantic salmon (Salmo salar). Can. J. Fish. Aquat. Sci. 55(Suppl. 1): 153-160.

135

Appendix I

Historic electrofishing, fry drift and fry stocking data pertinent to Atlantic salmon research in Clearwater Brook, NB

136

Electrofishing Surveys Patchiness and reduced densities of juvenile salmon in the upper reach of Clearwater

Brook were the basis of this study. The density and distribution of juvenile salmon in

Clearwater Brook were determined through annual sampling initiated in 1996. Using a

Smith-Root model 12-A electrofisher, juvenile densities were calculated from removal

sampling (Zippin, 1956) conducted at as many as 14 locations throughout the mid and

upper study reaches of Clearwater Brook. All sampling was conducted in “open” sites

with wetted areas ranging between 300 and 600 square meters. Regression analyses of the

1996 to 2002 electrofishing data were performed to investigate changes in juvenile

densities that may have resulted from fry stocking and potential increased egg depositions

rates from adult hatchery returns to the upper study reach. These analyses tested for

significant positive or negative trends in fry and parr densities over this six-year period

and in all cases no significant increase or decrease in juvenile densities was noted

(p>0.15). Due to the inherent annual fluctuation in juvenile densities, small increases or

decreases in fry or parr numbers over time would be statistically difficult to detect.

Annual fluctuations in juvenile Atlantic salmon abundance are common due to yearly

variation in egg deposition levels (recruitment) and environmental influences on egg, fry

and parr survival. While these fluctuations are inherent, trends in juvenile densities can

provide a good understanding of fry and parr distributions and abundance throughout a

river system. Electrofishing conducted in Clearwater Brook from 1996 to 2002 indicates

that fry densities are lower within the upper reach relative to the middle reach (Appendix

I.1, I.3, and I.4). A similar trend in parr abundance upstream of the Clearwater Brook

counting fence (Appendix I.2, I.5, and I.6) was noted.

137

Appendix I-1: Mean Atlantic salmon fry densities (fish/100 m2) as determined by electrofishing in Clearwater Brook, 1996 to 2002.

138

Appendix I-2: Mean Atlantic salmon parr densities (fish/100 m2) as determined by electrofishing in Clearwater Brook, 1996 to 2002.

139

Appendix I.3. Density of age 0+ Atlantic salmon (fry/100m2) detected in the upper reach of Clearwater Brook, 1996 to 2002. UPPER REACH

Clearwater Average

Density 1996 1997 1998 1999 2000 2001 2002

C 20 0.50 -- -- -- -- Trace Trace -- C 24 4.49 -- -- -- Trace Trace 4.68 12.29 C 29 43.00 -- -- -- -- 57.47 39.93 31.61 C 25 1.47 Trace -- -- Trace 4.39 Trace Trace C 9 27.37 5.40 6.70 Trace 48.50 40.07 26.35 64.08 C 26 41.46 -- -- -- 48.70 63.10 16.08 37.95

Mainstem

C 2 108.09 36.40 130.10 75.20 346.60 67.36 30.90 70.10 C 11 15.74 -- Trace Trace -- 76.69 Trace Trace C 10 1.24 -- -- -- Trace -- 2.73 Trace NE Branch C 27 43.42 -- -- -- 38.60 72.01 23.21 39.86

Trace: insufficient number of salmon captured to calculate an estimate.

Appendix I.4. Density of age 0+ Atlantic salmon densities (fry/100m2) detected in the middle reach of Clearwater Brook, 1996 to 2002.

MIDDLE REACH

Clearwater Average Density 1996 1997 1998 1999 2000 2001 2002

C 3 109.16 149.90 252.40 Trace 102.90 41.16 94.08 123.20 C 6 112.11 133.10 35.60 160.10 98.80 81.92 114.98 160.25 Mainstem C 5 116.60 12.60 14.50 -- 212.90 182.97 210.24 66.38

NE Branch C 12 16.64 Trace Trace Trace 45.90 -- 19.65 -- Trace: insufficient number of salmon captured to calculate an estimate.

140

Appendix I.5. Density of wild Atlantic salmon parr (all ages) detected in the upper reach of Clearwater Brook, 1996 to 2002. UPPER REACH

Clearwater Average Density

(parr/100m2) 1996 1997 1998 1999 2000 2001 2002 C 20 0.50 -- -- -- -- Trace Trace -- C 24 10.56 -- -- -- Trace Trace 20.45 20.77 C 29 8.46 -- -- -- -- 10.14 3.91 11.34

Mainstem C 25 9.72 32.60 -- -- Trace 14.49 Trace Trace C 9 10.52 4.80 25.50 11.40 8.40 7.01 3.96 12.58 C 26 24.87 -- -- -- 20.90 22.78 32.29 23.52 C 2 11.40 7.50 16.30 16.00 16.50 7.32 9.88 6.32 C 11 4.83 -- Trace Trace -- 10.53 12.13 Trace

NE Branch C 10 6.04 -- -- -- Trace -- 17.12 Trace C 27 29.02 -- -- -- 41.30 21.34 23.88 29.56

Trace: insufficient number of salmon captured to calculate an estimate.

Appendix I.6. Density of wild Atlantic salmon parr (all ages) detected in the middle reach of Clearwater Brook, 1996 to 2002. MIDDLE REACH

Clearwater Average Density

(parr/100m2) 1996 1997 1998 1999 2000 2001 2002 C 3 27.70 22.50 42.40 Trace 42.80 32.09 24.88 28.71

Mainstem C 6 22.37 25.70 38.80 29.90 17.00 15.11 19.80 10.26 C 5 14.12 Trace 18.80 -- 21.10 7.40 14.97 8.33

NE Branch C 12 29.71 20.10 25.48 41.70 28.20 -- 33.07 --

Trace: insufficient number of salmon captured to calculate an estimate.

141

Fry Drift Monitoring

Fry drift nets were installed and monitored in 1998, 1999 and 2000 to confirm that the

disproportionate juvenile densities, noted from electrofishing, between the upper and

middle reach of Clearwater Brook were not a function of excessive fry drift from upper

reach habitats. The ability to monitor the extent and locations of drifting wild fry post-

emergence is useful in determining salmon survival during early life stages. Locations

found to have very high fry drift could indicate high spawning success and survival and,

conversely, areas with low drift could be associated with low winter egg survival or areas

with low egg deposition (few adult females reaching the area). Drift sampling equipment

and methodologies were similar to those described by Johnston (1997) and Bujold (2003)

provided an effective technique for sampling drifting aquatic organisms within the

sampled portion of the water column. In 1998, eight fry drift nets were installed and

monitored from early June to mid July at three locations; 1) 100 metres upstream of the

counting fence (3 nets); 2) in the mainstem of Clearwater Brook immediately upstream of

the confluence of the Northeast Branch tributary (3 nets); 3) five metres downstream of

the CR4 reader station on the northeast Branch tributary (2 nets). In addition to these

sites, three drift nets were monitored at the most downstream point of the upper study

reach, 75-m upstream of reader station CR2, from late May until mid July of 1999 and

2000.

As confirmed from fry drift net captures, a substantial downstream movement of fry

occurred in Clearwater Brook during the spring of 1998 through 2000. Drifting fry were

captured at all drift net sites in each of the three monitoring years. The magnitude of this

142

fry movement was highly variable between sites and years (Appendix I.7). The highest

levels of fry drift occurred in 1999, coincident with peak fry densities observed in six

years of electrofishing.

Drift sampling information suggests that the disproportionate fry abundance noted

between the upper and middle study reaches is not the result of an exodus of fry from the

headwaters to mid reach habitats of Clearwater Brook. In fact, it appears that fry drift is

less predominant in the upper reach. Overall mean fry drift values (average of the total

fry per trap per day) were highest from the middle study reach (fence location), and

nearly a third less from the upper reach (CR2). The amplified fry drift in the mid reach is

likely related to an increased abundance of newly emerged fry as a result of the higher

spawning densities in this reach.

References:

Bujold, V. 2003. Egg-to-fry survival models and drifting fry biology of wild Atlantic

salmon (Salmo salar L.). M.Sc. Thesis. Department of Biology, University of

New Brunswick, Fredericton, NB. 136p.

Johnston, T.A. 1997. Downstream movements of young-of-the-year fishes in Catamaran

Brook and the Little Southwest Miramichi River, New Brunswick. Journal of Fish

Biology 51: 1047-1062

Zippin, C. 1956. An evaluation of the removal method of estimating animal populations.

Biometrics, 12, 163-189.

143

0

50

100

150

200

250

300

350

400

450

Counting Fence Confluence of NEBranch

CR4 CR2

Tota

l fry

cap

ture

d / t

rap

1998 1999 2000

Appendix I.7. Total number of drifting salmon fry captured per trap over the same sampling periods at fry drift sampling sites in Clearwater Brook, 1998-2000.

144

Appendix I.8. Total numbers of Clearwater Brook origin underyearling salmon stocked to Clearwater Brook and its tributaries (1995 to 1998). Sites are shown in Figure 3.4.

Site No. Reach 1995 1996 1997 1998

CS18 Upper 2584 0 0 0 CS4 Upper 0 0 2000 500 CS3 Upper 0 5900 2000 0

CS17 Upper 0 0 0 0 CS2 Upper 2584 1300 2000 2500

CS19 Upper 0 0 0 0 CS1 Upper 2584 500 2000 2500

CS20 Upper 0 0 0 0 CS21 Upper 0 0 0 0 CS14 Upper 0 5900 4000 0 CS5 Upper 3876 1650 2000 2500 CS6 Upper 1938 1650 2000 2500

CS13 Upper / Middle 0 5900 2500 5500

CS7 Middle 0 0 2000 0 CS22 Middle 0 0 0 0 CS16 Middle 0 0 0 2500 CS12 Middle 0 0 2000 7500 CS8 Middle 0 0 2000 500

CS11 Middle 1970 0 4000 7500 CS9 Middle 0 400 1800 3500

CS10 Lower 0 0 4000 0 CS15 Lower 4644 1650 0 0

Upper reach 13566 19850 17250 13250 Middle reach 1970 3350 13050 24250 Lower reach 4644 1650 4000 0 15536 23200 30300 37500

Total 20180 24850 34300 37500

145

Appendix II

Daily captures of Atlantic salmon at the Clearwater Brook counting fence in 1999 and 2000

146

Appendix II.1. Daily capture and cumulative proportion of grilse (<63 cm FL) and MSW (>/= 63 cm FL) Atlantic salmon at the fish counting fence operated from 04/06/99 to 21/10/99 in Clearwater Brook, NB.

Appendix II.2. Daily capture and cumulative proportion of grilse (<63 cm FL) and MSW (>/= 63 cm FL) Atlantic salmon at the fish counting fence operated from 30/05/00 to 03/11/00 in Clearwater Brook, NB.

0

5

10

15

20

25

30

35

25-J

un

1-Ju

l

7-Ju

l

13-J

ul

19-J

ul

25-J

ul

31-J

ul

6-A

ug

12-A

ug

18-A

ug

24-A

ug

30-A

ug

5-Se

p

11-S

ep

17-S

ep

23-S

ep

29-S

ep

5-O

ct

11-O

ct

17-O

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23-O

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29-O

ct

Dai

ly c

atch

(m

sw s

alm

on o

r gril

se)

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Cum

ulat

ive

prop

ortio

n of

sa

lmon

cap

ture

d

Grilse (<63 cm FL) / day

MSW salmon (>/= 63 cm FL) / day

Cumulative % of MSW salmon

Cumulative % of Grilse

147