THE IMPACTS OF FINE SEDIMENTS AND VARIABLE FLOW …

THE IMPACTS OF FINE SEDIMENTS ANDVARIABLE FLOW REGIMES

ON THE HABITAT AND SURVIVAL OF ATLANTIC SALMON (Salmo salar) EGGS

by

J. Jason Flanagan

Bachelor of Science (Biology), University of New Brunswick, 1996

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

Master of Science

In the Graduate Academic Unit of Biology

Supervisor:

Supervisor: Rick Cunjak, Ph.D., UNB Biology

Examining Board: Fred Whoriskey, Ph.D., Atlantic Salmon FederationKaty Haralampides, Ph.D., UNB Civil Engineering

This thesis is accepted.

_____________________________________Dean of Graduate Studies

THE UNIVERSITY OF NEW BRUNSWICK

January, 2003

© J. Jason Flanagan, 2003

ii

Dedication

To my wife Stephanie who has always been there to support me, and remind me to be

proud of my accomplishments. I am very proud indeed, but most of all for having

someone like her in my life!

iii

Abstract

This thesis evaluated a newly modified incubation basket design and applied this method

to study the impacts of two human-made disturbances on survival and habitat of

incubating Atlantic salmon (Salmo salar) eggs. In Catamaran Brook (Miramichi) the

effects of fine sediments (<2mm) from forestry activities were investigated, and in rivers

within the Tobique River Basin the effects of variable flow regimes from hydroelectric

dams were assessed.

Using baskets buried in situ, the overall mean survival to the eyed stage in Catamaran

Brook from 1994-1997 was 80% (range 65-98%) and from 1998-2000 was 95% (range

83-100%). Emergence survival was generally much more variable and ranged from 2 to

83% from 1994-1997 and 47 to 85% in 1998-2000. The percent fines measured in 1998-

99 and 1999-00 was <13%, which suggested fine sediment amounts in Catamaran Brook

were minimal compared to the literature and did not negatively affect egg survival.

In the Tobique River Basin from 1997-2000, rivers regulated by hydroelectric dams in

the headwater reaches showed lower mean survivals to the eyed and hatch stages than in

an unregulated, control river. The regulated rivers also experienced more discharge and

temperature variability during the winter, an advancement of embryo development

(degree-days), and a higher incidence of scour of the streambed, which are all believed to

have negatively affected survival.

iv

Acknowledgements

This project would not have been possible if not for the time and effort contributed by

many hard working and knowledgeable individuals. To those who helped me in the field,

as well as the members of my Supervisory and Examining Committee's, I owe a great

deal of gratitude.

I am particularly indebted to my Supervisor, Dr. Rick Cunjak, who showed me much

patience, provided a vast amount of insight into this project, and gave me a great deal of

uplifting advice when I needed it - thanks Rick! I am also especially thankful to Mr.

Peter Hardie for all of his input on the topic of Atlantic salmon, Catamaran Brook and

egg incubation baskets, among others, and to Mr. Ross Jones for his knowledge and

involvement in all aspects of the Tobique River Study.

I was also lucky enough to be surrounded by a number of good friends who helped me in

one way or another. I look forward to our continued friendship.

Lastly, financial support for this research was provided by the Department of Fisheries

and Oceans, Habitat Management Branch, Moncton and partially through research

assistantships from the University of New Brunswick.

v

Table of Contents

Dedication ........................................................................................................................... ii

Abstract .............................................................................................................................. iii

Acknowledgements............................................................................................................ iv

Table of Contents................................................................................................................ v

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

List of Figures ..................................................................................................................... x

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

General Introduction ........................................................................................................... 1

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

Atlantic salmon life cycle ........................................................................................... 3

Studies............................................................................................................................. 4

Catamaran Brook (Impacts of fine sediments on egg survival and habitat) ............... 4

Tobique River Study (Impacts of flow regulation on egg habitat and survival) ........ 6

References....................................................................................................................... 8

CHAPTER 2 ..................................................................................................................... 17

Relationship between fine sediments and the survival of incubating Atlantic salmon

(Salmo salar) eggs in Catamaran Brook........................................................................... 17

Abstract ......................................................................................................................... 18

Introduction................................................................................................................... 19

Study Site ...................................................................................................................... 20

Methods ........................................................................................................................ 21

Results........................................................................................................................... 29

vi

Egg-to-Fry Survival in Catamaran Brook, 1994 - 1997 ........................................... 29

Eyed Survival, 1998-99 & 1999-00 .......................................................................... 30

Emergence Survival, 1998-99 & 1999-00 ................................................................ 30

Intragravel Temperatures and Degree Days ............................................................. 31

Fine Sediments.......................................................................................................... 32

Discussion..................................................................................................................... 34

Eyed Survival............................................................................................................ 34

Emergence Survival .................................................................................................. 35

Fines.......................................................................................................................... 37

Incubation Basket Method ........................................................................................ 39

References..................................................................................................................... 43

CHAPTER 3 ..................................................................................................................... 66

The effects of regulated stream flow on the survival of Atlantic salmon (Salmo salar)

eggs in the Tobique River, New Brunswick ..................................................................... 66

Abstract ......................................................................................................................... 67

Introduction................................................................................................................... 68

Study Area .................................................................................................................... 70

Methods ........................................................................................................................ 71

Results........................................................................................................................... 75

Egg survival .............................................................................................................. 75

Discharges 1998, 1999 and 2000.............................................................................. 76

Temperatures and Degree Days ................................................................................ 77

Fine Sediments.......................................................................................................... 79

vii

Discussion..................................................................................................................... 79

Unregulated (control) River...................................................................................... 80

Regulated Rivers....................................................................................................... 82

References:.................................................................................................................... 87

CHAPTER 4 ................................................................................................................... 104

General Discussion ......................................................................................................... 104

Discussion................................................................................................................... 105

Incubation Basket Method and Design ....................................................................... 105

Survival Studies .......................................................................................................... 107

References................................................................................................................... 112

APPENDIX I .................................................................................................................. 115

Calculations of Dimensions of the Incubation Baskets Used in the Current Studies ..... 115

APPENDIX II ................................................................................................................. 117

Survival and Sediment Data for Individual Baskets from Catamaran Brook Study 1994-

1997 and 1998-2000 ....................................................................................................... 117

APPENDIX III................................................................................................................ 121

Survival Estimates from Individual Incubation Baskets in the Tobique River Study 1998-

2000................................................................................................................................. 121

VITA

viii

List of Tables

Table 1-1: Approximate number of accumulated degree-days for different stages of

development in incubating Atlantic salmon embryos. All values are to

median eyed, hatch and swim-up (emergence) stages and were based on

hatchery experiments. ............................................................................... 12

Table 2-1: Atlantic salmon egg survival (%) from Catamaran Brook, New

Brunswick, 1994-1997 and 1998-2000. Data for 1994-1997 were

collected by personnel from the Department of Fisheries and Oceans and

were not hatchery corrected. Baskets in column n3 were not included in

survival estimates. In 1999-2000, four baskets (2 Middle reach and 2

Lower reach) were removed at the hatch stage (not shown). ................... 49

Table 2-2: Survival (%) of Atlantic salmon eggs to the hatch stage in the Middle

reach (site-1) and Lower reach, Catamaran Brook 1999-00..................... 50

Table 2-3: Percent fines by weight (g) from incubation baskets buried in Catamaran

Brook for the years 1998-2000. Gorge (1998-99) three baskets removed

from analysis at emergence stage due to significant change in habitat. ... 51

Table 2-4: Volume occupied by gravel/substrate in incubation baskets in 1998-99 and

1999-00. Volumes and percentages calculated based on the volume

2513cm3 of the baskets. Numbers in brackets are baskets that were not

included in calculation because of lost sediments. ................................... 52

Table 2-5: Percent volume of fines accumulated in baskets in Catamaran Brook in

1998-99 and 1999-00. Values calculated as percent volume of basket

ix

(2513.27cm3). Gorge reach (1998-99) three baskets were removed from

analysis at emergence stage due to a significant change in habitat. ......... 53

Table 3-1: Summary of site locations and changes made throughout the course of the

egg incubation studies in the Tobique River, fall (1997) – spring (2000).93

Table 3-2: Mean egg survival in incubation baskets from 1998-2000 in rivers from

the Tobique River basin, New Brunswick. ............................................... 94

Table 3-3: Mean volume of fine sediments measured from different sites in the

Tobique River basin, 1998-2000. Percent fines calculated based on the

volume occupied within the basket = 2984.51cm3. .................................. 95

x

List of Figures

Figure 1-1: Life cycle of Atlantic salmon (Salmo salar). Pictures courtesy of

Mactaquac Fish Culture Station (Department of Fisheries and Oceans) and

Peter Hardie (DFO, Moncton). ................................................................. 13

Figure 1-2: Characteristics of salmonid redds, showing how river water flows through

the redd. Adapted from Peterson (1978).................................................. 14

Figure 1-3: The Miramichi River Basin (shaded area) within the Province of New

Brunswick. Location of the Catamaran Brook study area is also shown. 15

Figure 1-4: The Tobique River Basin (shaded area) within the Province of New

Brunswick, showing different hydroelectric facilities (i.e., dams). .......... 16

Figure 2-1: Map of Catamaran Brook, including sites used in 1998-99 and 1999-2000.

................................................................................................................... 54

Figure 2-2: Detailed description of incubation baskets used in 1998-99 and 1999-00 at

Catamaran Brook. ..................................................................................... 55

Figure 2-3: Conceptual illustration of the arrangement of incubation baskets in the

streambed at different reaches in Catamaran Brook, as they pertain to

different forestry impacts (e.g. timber harvest block)............................... 56

Figure 2-4: Diagram of an incubation basket buried in the streambed substrate. ....... 57

Figure 2-5: Emergence basket in situ (A) schematic, (B) actual picture looking

through water. ........................................................................................... 58

Figure 2-6: Annual survival of Atlantic salmon eggs to the eyed stage, by study reach

in Catamaran Brook. ................................................................................. 59

xi

Figure 2-7: Annual emergence survival of Atlantic salmon eggs, by reach in

Catamaran Brook. Graph shows interaction effect of year and reach on

egg survival to emergence. ....................................................................... 60

Figure 2-8: Daily emergence of Atlantic salmon alevins from all incubation baskets

combined by reach in Catamaran Brook in 1998-99 (A) and 1999-00 (B).

................................................................................................................... 61

Figure 2-9: Mean survival including standard error bars at eyed, hatch and emergence

stages in 1999-00. Survival between stages in the Middle reach (site-1)

and Lower reach were not statistically different (p=0.17 (Middle) and

p=0.27 (Lower)). Mean percent volume of fines at each stage also shown.

................................................................................................................... 62

Figure 2-10: Average daily intragravel temperatures by reach for 1998-99 (A) and

1999-00 (B)............................................................................................... 63

Figure 2-11: Accumulated degree-days by reach for Atlantic salmon eggs in Catamaran

Brook in 1998-99 (A) and 1999-00 (B). “Eyed” refers to the day on which

incubation baskets were removed from the streambed. ............................ 64

Figure 2-12: Regression of percent survival vs. percent volume of fines at the eyed and

emergence stages in Catamaran Brook for 1998-99 and 1999-00. R2

values shown............................................................................................. 65

Figure 3-1: Map of St. John River in New Brunswick, Canada, showing the major

dam obstructions on the mainstem of the river and the three dams of

interest in this study. ................................................................................. 96

xii

Figure 3-2: Tobique River basin showing tributaries and sites used in each year of this

study.......................................................................................................... 97

Figure 3-3: Incubation basket (s) used to study egg survival of Atlantic salmon eggs in

the Tobique River Basin. .......................................................................... 98

Figure 3-4: Mean survival (with standard error bars) of Atlantic salmon eggs to the

eyed stage for the years 1999 and 2000. Graph shows effects of year and

site on egg survival. .................................................................................. 99

Figure 3-5: Mean survival (with standard error bars) to the hatch stage of Atlantic

salmon eggs incubated in egg baskets in 4 rivers tributary to the Tobique

River, 1999-2000. n is the number of baskets used to determine the mean

survival.................................................................................................... 100

Figure 3-6: Mean daily discharges for regulated and unregulated rivers in 1998, 1999

and 2000. Gulquac River discharges represented by discharges measured

in the 'unregulated' Grande Rivière. All discharges adjusted for the same

drainage area of 193km2. ........................................................................ 101

Figure 3-7: Mean daily intragravel temperatures measured during incubation in the

regulated Dee, Don and Serpentine (1999) rivers and the unregulated

Gulquac River in 1998, 1999 and 2000. ................................................. 102

Figure 3-8: The average accumulated degree-days for each river (all sites combined)

during incubation in 1998, 1999 and 2000. ............................................ 103

1

CHAPTER 1

General Introduction

2

Introduction

Atlantic salmon (Salmo salar) have been living in, and returning to, many of Canada’s

Maritime streams for millenia and some of the world’s most famous salmon rivers are

found in the Maritimes. Today however, the number of Atlantic salmon in these streams

is discouraging and population numbers often do not meet suggested conservation limits

(Chaput, 1998).

Many factors have been blamed for the declining numbers of salmon, and most are

associated with the effects from human activities in and around river systems (WWF,

2001). In New Brunswick rivers such as the Miramichi and St. John, forestry activities

and the construction of dams for hydroelectric power generation, respectively, are

thought to contribute to the declines of Atlantic salmon. The present research study was

initiated to address the potential impacts of these two activities on the early life stage

survival of Atlantic salmon in tributaries within the St. John and Miramichi River basins.

The studies were carried out over two years in Catamaran Brook (Miramichi River basin)

and in the Upper St. John River area (Tobique River basin). In this chapter, the Atlantic

salmon life cycle and the goals of the research are outlined; chapters 2 and 3 examine the

studies in Catamaran Brook and in the Tobique River basin, respectively; whereas

chapter 4 summarizes the conclusions from each of the two preceding chapters and

outlines what I believe are the significant findings of this research.

3

Atlantic salmon life cycle

In autumn, Atlantic salmon spawn in the gravel bottom of freshwater streams, typically at

the tails of pools, near the head of riffles (Gibson, 1993; Fleming, 1996). The female

deposits her eggs in a "redd" often buried 20 - 30cm deep in the gravel. The depth at

which female salmonids bury their eggs depends on the size of the spawning female

according to Crisp and Carling (1989). Once the eggs have been buried, they are left in

the gravel during the winter months where they incubate until the following spring (Scott

and Crossman, 1998). By March, Atlantic salmon in the Maritimes have usually reached

the eyed stage. In April the fish hatch and remain in the gravel living solely off their yolk

sac. Within four to six weeks of hatching and when their yolk sac is almost completely

absorbed, the fish emerge from the gravel into the stream (Figure 1-1). Emergence for

Atlantic salmon is often nocturnal (Bardonnet et al., 1993) and in Maritime streams

usually occurs during June. Randall (1982) and Johnston (1997) reported peak

emergence near mid-June for Atlantic salmon in Catamaran Brook. Similarly, Cunjak et

al. (2002) found peak emergence occurring from 09 June to 14 June in the Morell River,

P.E.I. Once the fish have emerged they establish a territory and begin feeding, and in

some cases the salmon may drift variable distances downstream (Johnston, 1997).

Success during the incubation period (i.e. in the redd) is primarily dependant on

intragravel flow (Chapman, 1988). As Peterson (1978) showed, the formation of the redd

creates an environment that typically provides sufficient intragravel flow to allow

delivery of oxygen and the removal of wastes that is necessary for salmon eggs to

4

successfully incubate over winter (Figure 1-2). However, human activities like forestry

and hydropower generation may disturb the stream environment such that characteristics

of the redd (e.g. intragravel flow) are affected and survival during the incubation period

may be reduced (Snucins et al., 1992). In other words, salmon eggs are entirely

dependent on the conditions of the environment that surrounds them. In addition,

disturbances to the stream environment can have even greater consequences for egg

survival because salmon are immobile during this time (Kocik and Taylor, 1987).

There is little doubt then, that the intragravel period is a critical time for all salmonids

(MacKenzie and Moring, 1988; Pauwels and Haines, 1994) and, that the loss of

freshwater habitat is a major contributor to the declining numbers of Atlantic salmon

stocks worldwide (Gibson, 1993). It is also why survival during the early life stages of

the Atlantic salmon life cycle needs to be fully understood in order to help conserve the

species.

Studies

Catamaran Brook (Impacts of fine sediments on egg survival and habitat)

The Miramichi River basin is located in the central portion of the province of New

Brunswick (Figure 1-3). Within its roughly 14 000km2 catchment, there is substantial

forestry activity which has the potential to affect the aquatic biota. For this reason, in

1990, the Department of Fisheries and Oceans (DFO) began a long-term (15 year)

5

research project to evaluate the impacts of forestry activities on aquatic biota within

Catamaran Brook, a 3rd order tributary of the Little Southwest Miramichi River (Cunjak

et al., 1990). One of the main objectives of the project was to determine the influence of

fine sediment deposition from nearby forestry activities on Atlantic salmon eggs during

incubation. It has been shown in many western streams that fines may accumulate in

sufficient quantities to alter intragravel flow thereby reducing available oxygen to eggs

and removal of wastes (Chapman, 1988; Rubin, 1995), as well as preventing emergence

of fry (Phillips and Koski, 1969).

In order to evaluate the impacts of fines on eggs in Catamaran Brook, incubation baskets

(see Appendix I) were seeded with known quantities of eggs and gravel, buried in the

stream bottom and monitored from late-October to end-June in 1998-1999 and 1999-

2000. Survival was assessed from fertilization to the eyed and emergence stages in the

first year and from fertilization to the eyed, hatch/alevin and emergence stages in the

second year. Each of these stages was easily identified at their respective time of year

and the developmental rate of the eggs was recorded as accumulated degree-days (Kane,

1988). Table 1-1 provides a list of accumulated degree-days determined in other studies

of Atlantic salmon for each stage of their life cycle.

The three main objectives of the Catamaran Brook portion of the study were to:

1. Determine if the amount of accumulated fine sediments (<2mm in diameter)

was sufficient to cause a decrease in survival of incubating eggs;

6

2. Determine if there were differences in egg survival between different reaches

within Catamaran Brook, due to varying degrees of potential impact by

forestry activities; and

3. Further evaluate the use of incubation baskets as a tool to assess egg-to-fry

survival of Atlantic salmon.

The general hypothesis for the Catamaran Brook study was that fine sediment

accumulation during incubation would negatively affect egg survival.

Tobique River Study (Impacts of flow regulation on egg habitat and survival)

The St. John River is largely influenced by hydroelectric activities, with three major

dams on the mainstem river and numerous dams on many of its tributaries (Figure 1-4).

Some of the best available spawning habitat in the St. John River is within the Tobique

River basin (DFO, 1998). Storage dams in headwater streams can threaten early life

stage survival of salmonids due to water level fluctuation (Cushman, 1985). Utilizing the

same techniques as those outlined for the Catamaran Brook incubation study, egg-to-fry

survival of Atlantic salmon was evaluated in four streams (three with dams, one control

(no dam)) within the Tobique River basin from 1998-2000. The focus of this study was

to determione whether variable flow regimes from the dams had an impact on survival of

salmon eggs during incubation. Survival to the eyed stage and hatch was determined but

survival to emergence could not be evaluated for logistical reasons. Overall, the

hypothesis was that variable flow regimes negatively affected the survival of incubating

salmon eggs.

7

It was hoped that the evaluation of the intragravel survival of salmonids with respect to

the different environmental and/or human impacts in both studies would provide further

insight into the incubation survival of salmonids. The studies may also be useful in

evaluating stream quality and habitat for these fishes and may ultimately lead to a better

understanding of how to improve these areas to aid depleted Atlantic salmon stocks

locally and worldwide.

8

References

Bardonnet, A. and P. Gaudin. 1990. Diel pattern of emergence in grayling (Thymallus

thymallus Linnaeus, 1759). Canadian Journal of Zoology 68: 465-469.

Bardonnet, A., P. Gaudin, and E. Thorpe. 1993. Diel rhythm of emergence and of first

displacement downstream in trout (Salmo trutta), Atlantic salmon (S. salar) and

grayling (Thymallus thymallus). Journal of Fish Biology 43: 755-762.

Chapman, D.W. 1988. Critical review of variables used to define effects of fines in redds

of large salmonids. Transactions of the American Fisheries Society 117: 1-21.

Chaput, G. 1998. Status of wild Atlantic salmon (Salmo salar) stocks in the Maritime

Provinces. Canadian Stock Assessment Secretariat Research Document 98/153:

30p.

Cunjak, R.A., D. Caissie, and N. El-Jabi. 1990. The Catamaran Brook Habitat Research

Project: description and general design of study. Canadian Technical Report of

Fisheries and Aquatic Sciences 1751: 14p.

Crisp, D.T. 1988. Prediction, from temperature, of eyeing, hatching and 'swim-up' times

for salmonid embryos. Freshwater Biology 19: 41-48.

Crisp, D.T. and P.A. Carling. 1989. Observations on siting, dimensions and structure of

salmonid redds. Journal of Fish Biology 34: 119-134.

Cunjak, R.A., D. Caissie, and N. EI-Jabi. 1990. The Catamaran Brook Habitat Research



9

Cunjak, R.A., D. Guignion,, R.B. Angus, and R. MacFarlane. 2002. Survival of eggs and

alevins of Atlantic salmon and brook trout in relation to fine sediment deposition,

pp. 82-91 In D.K. Cairns (ed.). Effects of land use practices on fish, shellfish, and

their habitats on Prince Edward Island. Canadian Technical Report of Fisheries

and Aquatic Sciences 2408: 157p.

Cushman, R.M. 1985. Review of ecological effects of rapidly varying flows downstream

from hydroelectric facilities. North American Journal of Fisheries Management 5:

330-339.

DFO. 1998. Atlantic salmon, southwest New Brunswick outer-Fundy SFA 23.

Department of Fisheries and Oceans Science Stock Status Report D3 13: 6p.

Fleming, I.A. 1996. Reproductive strategies of Atlantic salmon: ecology and evolution.

Reviews in Fish Biology and Fisheries 6: 379-416.

Gibson, R.J. 1993. The Atlantic salmon in fresh water: spawning, rearing and production.


Gunnes, K. 1979. Survival and development of Atlantic salmon eggs and fry at three

different temperatures. Aquaculture 16: 211-218.

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.

Kane, T.R. 1988. Relationship of temperature and time of initial feeding of Atlantic

salmon. Progressive Fish Culturist 50: 93-97.

10

Kocik, J.F. and W.W. Taylor. 1987. Effect of fall and winter instream flow on year-

class strength of Pacific salmon evolutionarily adapted to early fry outmigration:

A Great Lakes Perspective. American Fisheries Society Symposium 1: 430-440.

MacKenzie, C. and J.R. Moring. 1988. Estimating survival of Atlantic salmon during the

intragravel period. North American Journal of Fisheries Management 8: 45-49.

Maret, T.R., T.A. Burton, G.W. Harvvey and W.H. Clark. 1993. Field testing of new

monitoring protocols to assess brown trout spawning habitat in an Idaho stream.

North American Journal of Fisheries Management 13: 567-580.

Pauwels, S.J. and T.A. Haines. 1994. Survival, hatching, and emergence success of

Atlantic salmon eggs planted in three Maine streams. North American Journal of

Fisheries Management 14: 125-130.

Peterson, R.H. 1978. Physical characteristics of Atlantic salmon spawning gravel in some

New Brunswick streams. Fisheries and Marine Service Technical Report 785:

28p.

Phillips, R.W., and K.V. Koski. 1969. A fry trap method for estimating salmonid survival

from egg deposition to fry emergence. Journal of the Fisheries Research Board of

Canada 26: 133-141.

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.

Rubin, J. F. 1995. Estimating the success of natural spawning of salmonids in streams.

Journal of Fish Biology 46: 603-622.

Scott, W.B. and E.J. Crossman. 1998. Freshwater fishes of Canada. 2nd Ed. Galt House

Publications, Ltd. Ontario, Canada. 966p.

11

Snucins, E.J., R.A. Curry and J.M. Gunn. 1992. Brook trout (Salvelinus fontinalis)

embryo habitat and timing of alevin emergence in a lake and stream. Canadian

Journal of Zoology 70: 423-427.

Vignes, J.C., and M. Heland. 1995. Comportement alimentaire au cours du changement

d'habitat lié a l'émergence chez le saumon Atlantique, Salmo salar L., et la truite

commune, Salmo trutta L., en conditions semi-naturelles. Bulletin Français de la

Pêche et de la Pisciculture 337-339: 207-214.

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

salmon: A river by river assessment. 184p.

12

Table 1-1: Approximate number of accumulated degree-days for different stages of

development in incubating Atlantic salmon embryos. All values are to

median eyed, hatch and swim-up (emergence) stages and were based on

hatchery experiments.

Mean Eyed Hatch Emergence SourceTemperature

(°C)

3.4 - 5.3 214 - 265 371 - 557 513 - 816 Crisp, 19888.0 - 12.0 208 - 228 453 - 504 742 - 791 Gunnes, 1979

280 434 650 - 813 Vignes and Heland, 1995

13

Figure 1-1: Life cycle of Atlantic salmon (Salmo salar). Pictures courtesy of

Mactaquac Fish Culture Station (Department of Fisheries and Oceans) and

Peter Hardie (DFO, Moncton).

Adult

Eggs

Alevin

Fry

Parr

Smolt

INT

RA

GR

AVE

L P

ER

IOD

14

Figure 1-2: Characteristics of salmonid redds, showing how river water flows through

the redd. Adapted from Peterson (1978).

15

Figure 1-3: The Miramichi River Basin (shaded area) within the Province of New

Brunswick. Location of the Catamaran Brook study area is also shown.

Catamaran BrookMiramichi RiverBasin

Hydroelectric Dam

0 50 100

kilometers

16

Figure 1-4: The Tobique River Basin (shaded area) within the Province of New

Brunswick, showing different hydroelectric facilities (i.e., dams).

Tobique River Basin

Hydroelectric Dam

0 50 100

kilometers

17

CHAPTER 2

Relationship between fine sediments and the survival of incubating Atlantic salmon

(Salmo salar) eggs in Catamaran Brook

18

Abstract

Using incubation baskets, the effects of fine sediments (<2mm) from forestry activities

on the intragravel survival of Atlantic salmon (Salmo salar) eggs was evaluated in situ, in

different reaches in Catamaran Brook, New Brunswick. The results of egg survival

studies from 1994-1997 and 1998-2000 are reported. Survival was typically higher to the

eyed stage (mean=89%) than to emergence (mean=54%) in all years, but emergence

survival remained high in comparison with other studies. When measured by weight, the

composition of fines was <13% of the gravel matrix. A new way of expressing fines as

the percent volume of available space in an egg incubation basket (i.e., a simulated redd)

was also introduced. The mean percent fines calculated in this manner was not >35%.

No relationship between fines and survival at either stage was determined, except for a

negative linear relationship in 1998-99 at emergence. Nevertheless, it was suggested that

the amount of fines in Catamaran Brook in 1998-99 and 1999-00 did not contribute to a

decrease in survival of eggs, rather, any decreases were attributed to significant natural

events (e.g. ice scour).

19

Introduction

The earliest stages of the Atlantic salmon life cycle are spent in the intragravel

environment. Several environmental factors are important for the survival of incubating

salmon eggs. Temperature, dissolved oxygen, fine sediments and water flows have been

shown to influence survival of salmon eggs during incubation (Chapman, 1988; Bjornn

and Reiser, 1991; Gibson, 1993). Such aspects of the environment are the result of

natural circumstances, but can be influenced by human activities as well. For example,

agriculture, forestry and hydroelectric activities in the river basin can affect the survival

of incubating salmonid eggs and other stream biota through the introduction of fine

sediments to streams (Chapman and MacLeod, 1987; Meehan, 1991).

Everest et al. (1987) cited a number of studies detailing how forestry activities can lead to

increased fines in streams. Scrivener and Brownlee (1989) found that survival to

emergence of coho (Oncorhynchus kisutch) and chum salmon (Oncorhynchus keta) in

Vancouver Island streams decreased by almost 50% following logging, and mean

survival and fry size were related to sediment composition. Similarly, an inverse

relationship between survival to emergence and percent fines was determined for brook

trout (Salvelinus fontinalis) eggs (Hausle and Coble, 1976) and for coho salmon and

steelhead trout (Oncorhynchus mykiss) eggs in situ (Tappel and Bjornn, 1983). Others

have shown similar relationships of fines and emergence survival in laboratory and

artificial channel experiments (Hall and Haley, 1986; Reiser and White, 1988; Argent and

Flebbe, 1999).

20

Using a simple and rather inexpensive method such as an “incubation box”, the success

of the intragravel stages of salmonids can be measured in relation to various

environmental factors. Researchers have planted incubation boxes with salmonid eggs in

streams or in a laboratory channel, and used them to monitor the success of the

developing eggs during incubation (Harshbarger and Porter, 1979, 1982; Scrivener, 1988;

MacCrimmon et al., 1989; Bardonnet and Gaudin, 1990; Bardonnet et al., 1993; Rubin,

1995). Such studies have been conducted in streams in France, Sweden, Scotland, United

States and Canada. They have also been used to study a variety of salmonid species such

as Atlantic salmon (Salmo salar), brown trout (S. trutta), brook trout, grayling

(Thymallus thymallus) and all five species of Pacific salmon (Oncorhynchus spp.).

The present study was conducted in Catamaran Brook, New Brunswick, the site of a long

term multidisciplinary study investigating the impacts of timber harvest in a small stream

catchment (Cunjak et al., 1990). It was hypothesized that the influence of fine sediments

within the stream would affect egg incubation conditions thereby limiting survival of

Atlantic salmon eggs. The objective was to determine if the amount of fines originating

from nearby timber harvest ‘blocks’ and road (re-) construction in the Catamaran Brook

basin influenced survival of salmon eggs relative to areas removed from forestry impacts.

Study Site

Catamaran Brook (46° 52.7’ N, 66° 06.0’ W) is a third-order tributary (52 km2) of the

21

Little Southwest Miramichi River in central New Brunswick (Figure 2-1). In 1996 and

1997, 7% of the Catamaran Brook basin was harvested as part of the Catamaran Brook

Habitat Research Project. Three different reaches representing different potential impacts

from forestry activities were studied (Figure 2-1):

Middle Reach - upstream of harvest blocks and therefore represented a 'natural'

control site for incubating eggs in baskets; impact believed

minimal. Two sites (site 1 and 2). Site-2 potentially impacted by

bridge (re-) construction in 1999-00.

Gorge Reach - adjacent to harvest blocks and tributaries (GT-2 and GT-3)

through the cut-blocks, immediate impacts possible. Two sites -

site 3 and 4 (1998-99), one site - site 4 (1999-00).

Lower Reach - downstream and far removed from any timber harvest areas;

possible impacts from forestry predicted to be minimal.

Wild Atlantic salmon migrate into Catamaran Brook from mid-October to early

November to spawn. Where possible, the study sites were selected in known spawning

locations in Catamaran Brook (P. Hardie, Department of Fisheries and Oceans (DFO),

pers. comm.) and located at the heads of riffles where salmon would typically spawn

(Gibson, 1993; Fleming, 1996).

Methods

Data from 1994-97 from incubation studies conducted in Catamaran Brook by DFO

personnel was included here. The methods used were similar to that described hereafter.

22

Atlantic salmon eggs and milt were obtained from one pair of ripe wild adult fish (i.e.,

one female and one male) in both 1998-99 and 1999-00. Only a single pair of adults was

spawned in order to minimize the variability from inter-family genetic differences. The

salmon were captured when entering the brook to spawn, using a fish counting fence

located at the mouth of Catamaran Brook. The fish were confirmed to be ready to spawn

by gently squeezing the abdomen to determine if eggs or milt could be extruded. In both

years, the fish being used were held in the stream in a wood/metal cage (2.5m X 1.0m X

1.5m) for one to two days, until spawning took place. Flow through the cage in the

stream was not altered.

An artificial “dry fertilization” technique, commonly used in fish hatcheries, was used

when spawning the fish (M. Hambrook, Miramichi Fish Hatchery, pers. comm.). The

fish were anaesthetized with MS-222 and the required number of eggs and milt was

removed from the salmon and mixed in a dry stainless steel bowl. About half of the eggs

from the adult females and a portion of the males' sperm were removed in both years.

The fish were then placed in a tub full of fresh stream water to recover, and later released

into the stream.

Fertilized eggs were separated into batches of 100 eggs. Each batch was submersed in a

500ml jar filled with stream water for safe transport to the sites where they were planted

in incubation baskets modified from Bardonnet and Gaudin (1990). The method

consisted of planting the fertilized salmon eggs in gravel-filled incubation baskets and

23

burying the baskets in the stream. The incubation baskets were made of 10cm (diameter)

ABS pipe and 2mm Nytex plastic mesh. Each basket was 32cm long with 3 windows

(10cm X 15.5cm) of plastic mesh and had a volume of 2513cm3 (Figure 2-2). The pore

size of the mesh (2mm) windows only allowed particles <2mm in diameter into the

basket and permitted an evaluation of the fines (<2mm) that accumulated during

incubation. Garrett and Bennett (1996) suggested this mesh size would prevent alevin

escapement, while being big enough to allow fine sediment intrusion representative of

that in nature.

At the study sites, pits approximately 1m2 in area and deep enough for the baskets were

excavated and arranged as in Figure 2-3. The upstream pits at each site were dug first to

avoid introducing sediments to baskets immediately downstream. A plastic funnel and

tubing was placed in the center of the baskets and sieved gravel (2 - 10cm) from the

respective study site was placed in each basket. The gravel in the baskets at installation

occupied approximately 50% of the available volume within the baskets (mean volume of

gravel (2 - 10cm) = 1284cm3). It was important to include a variety of gravel sizes within

the baskets upon installation, in order to separate eggs and to more closely represent the

natural intragravel environment of incubating salmon eggs (Rubin, 1995). Not including

gravel-size particles would lead to the accumulation of fines in an unnatural manner;

larger-than-normal voids within the basket would cause the incubation baskets to act as a

sediment “sink” (Harbarger and Porter, 1979; Mackenzie and Moring, 1988). Each

basket was then seeded with one batch of salmon eggs (n = 100), by pouring the eggs into

the funnel while simultaneously removing the funnel and tubing apparatus from the

24

basket. This allowed better distribution of eggs within the gravel matrix of the incubation

baskets and lessened the probability of eggs being damaged during installation. The

incubation baskets were buried at a 45° angle oriented downstream and covered with

sieved gravel so that eggs were roughly 20-30 cm deep (Figure 2-4). The time elapsed

from fertilization of eggs until planting of baskets within the gravel was <12 hours. This

was important to minimize mortality of eggs due to handling, since eggs become highly

fragile approximately 48 hours after fertilization (Piper et al., 1982; Rubin, 1995).

Baskets were left over the winter to evaluate incubation success to three stages of

development: eyed stage, hatch/alevin and emergence.

Where possible, two sites per reach were studied. Each site was limited to five or six

incubation baskets so that all of the baskets with eggs were buried within the shortest

time possible and a greater coverage of the spawning habitat within each study reach was

possible. In 1998-99, ten incubation baskets (five baskets X two sites) in both the Middle

and Gorge reaches and five baskets in the Lower reach (site 5) were buried in the

streambed. The same sites in each reach were also used in 1999-00, with the exception of

site 3 in the Gorge reach, which was omitted because a debris jam located just

downstream, backed up water past the site. This resulted in a drastic change in habitat

and the site was no longer representative of where salmon would spawn. Also in 1999-

00, one basket was added to the Middle reach at site 1 (n=11 baskets total in the Middle

reach) and the Lower reach (n=6 baskets total), while five baskets were buried in the

Gorge reach (site 4).

25

In both years, two baskets per site were removed in early April to evaluate eyed egg

survival. In 1999-00 (only), two baskets) from both the Middle reach at site 1 and the

Lower reach were removed in early-May (hatch stage) to document survival between the

eyed and emergence stages. Lastly, alevin emergence into a smaller 'emergence basket'

(Figure 2-5) attached to all remaining baskets in late-May/early-June in both years

allowed an accurate account of survival to emergence, relative to the number of eggs

originally planted in each basket.

When baskets were removed from the substrate, the contents were immediately placed in

plastic bags (to minimize sediment loss) and transported to the University of New

Brunswick in Fredericton, where each was thoroughly rinsed and examined for the

presence of eggs and alevins. When all eggs or alevin samples were recovered, the

substrate samples were then retained in plastic sample bags and frozen until further

examination of accumulated sediment composition. Samples were thawed, and water

poured off the top of the sample without losing sediment. Samples were then emptied

into aluminium pans and oven dried for 12 to 24 hours at 60°C. When completely dried,

samples were sieved into the following sediment classes: >2mm (2000 only), 1mm,

0.5mm, 0.25mm, 0.125mm, 0.063mm and silt (<0.063mm), and each class was weighed

to the nearest 0.01g. In order to determine the percentage of fine sediments by weight for

1998-99, calculations were based on the mean weight of gravel >2mm from the 1999-00

baskets: 3372.16 ± 155.81g. In 1999-00 each sediment class was also measured for

volume (cm3), by volume displacement. This was not done in 1998-99. Instead,

regressions of the volume versus the weight of accumulated fines from each sediment

26

class in 1999-00 were used to calculate the volume of gravel in 1998-99. So, percent

fines by weight and volume were determined for both years.

In many previous studies, the amount of fines was expressed as a percentage based solely

on the weight of the gravel. However, egg survival depends highly on the intragravel

flow, porosity and permeability of the intragravel environment (Bjornn and Reiser, 1991,

Garrett and Bennett, 1996). The interstitial spaces within the gravel are therefore key

components of suitable incubation habitat, so it was deemed appropriate to also evaluate

the amount of fines in terms of the available space within the redd (basket), by using the

following equation:

Where Volfi and Volbsk are the volume of fines (<2mm) and the volume of the incubation

basket, respectively; Volsub is the volume of the initial substrate placed in the basket and

Volegg is the volume of eggs (n=100) placed in each basket. It is believed that this

provides a better measure of the amount of space available to the eggs within the

substrate matrix and subsequently what percentage of that space was eliminated due to

accumulated fines.

During the first year of this study (1998-99), eggs were reared in incubation baskets at the

Miramichi Fish Hatchery to evaluate potential effects of the baskets on the survival of

eggs to emergence. These eggs had an excellent survival of 98%. Therefore, it was

established that the baskets had no adverse effects on the incubating eggs. In 1999-00,

Volfi

Volbsk - (Volsub + Volegg)*100

27

only hatching trays were used to raise eggs at the hatchery, resulting in a 96% (288/300

eggs) mean survival of eggs.

The hatchery eggs served as controls to account for egg viability and success of

fertilization from the pair of wild salmon spawned. Based on the survival percentages

obtained in the hatchery both years, it was concluded that fertilization success was high

and the fertilization methods used did not negatively affect survival. The results of the

hatchery-raised eggs were also used to correct for the survival of eggs in baskets in the

stream during 1998-99 and 1999-00, but not for the studies conducted by the DFO at

Catamaran Brook from 1994-97. Survival percentage (S) of eggs in baskets was

calculated using the following formula (from Cunjak et al., 2002):

S = [n/(i-m)] x 100

where n = number of live eggs/alevin/fry counted from retrieved baskets; i = initial

number of eggs placed in the basket (i.e., 100 eggs); and m = number of dead eggs (out of

100) from the hatchery control.

In 1999-00 fertilization success was confirmed three days after planting by retaining one

batch of 50 eggs at the hatchery for three days. After three days, the eggs were cleared in

Stockard’s solution and observed under a microscope to determine presence of an embryo

(T. Benfey, UNB, pers. comm.; Gaudemar et al., 2000). Using this method, fertilization

success was determined earlier than in 1998-99 and prevented the chances of discovering

too late (i.e., in March) that the eggs may not have been viable or were not fertilized. In

fact, 47 of 50 eggs showed presence of an embryo (early stages), so fertilization in 1999-

28

00 was successful.

Intragravel water temperatures were monitored at all sites in both years of the study. A

Vemco minilog 12-TR thermometer (PVC cylinder, 22mm diameter x 95mm length) was

placed at the bottom of one basket in each study site. Hourly temperatures were recorded

for the entire length of the incubation period to determine accumulated degree-days and

to estimate the rate of development of eggs.

All statistical analyses were performed using SAS/STAT® software (SAS Institute Inc.,

1999). Analysis of variance (ANOVA) tests for the least squares adjusted means of log-

transformed survival data were based on the equation:

which was derived from the model for the instantaneous mortality rate described by

Ricker (1975). The effects of year and reach and their interaction effect on survival were

tested. A similar ANOVA was used to determine differences in fine sediment deposition

between years and reaches in Catamaran Brook. A linear regression model (α = 0.05) of

survival (log-transformed) and fines was used to evaluate the effect of fines on survival at

both the eyed and emergence stages.

reach*year*βαNNln

o

t +=

29

Results

All raw data for survival and sediments are reported in Appendix II.

Egg-to-Fry Survival in Catamaran Brook, 1994 - 1997

Overall mean survival to the eyed stage in Catamaran Brook was > 74% during the 3

years of preliminary investigations (Table 2-1). Baskets that were displaced or exposed

above the substrate by stream scouring were not included in the survival estimates. A

slight interaction effect (p=0.05) of year and reach was found for survival to the eyed

stage (Figure 2-6). The lowest eyed survival in any reach for the three years was in 1996-

97 (65%, n=1), but it should be noted that fertilization success was not accounted for as

hatchery controls were not used in the studies from 1994-97.

Survival to emergence each year was lower than to the eyed stage and ranged from 34 to

82% (n=3) in 1994-95, 2 to 83% (n=10) in 1995-96 and 11 to 61% (n=14) in 1996-97

(Table 2-1). In 1995-96, survival to emergence was lowest in the Gorge reach (6%, n=2).

An interaction effect between year and reach on survival to emergence (p=0.005) was

witnessed and was undoubtedly the result of differences between the Lower reach in

1995-96 and 1999-00 (Figure 2-7). During the late winter of 1995-96, many baskets

(n=11) were lost or exposed due to ice-related scour. The exposure of baskets above the

substrate may have subjected the eggs to freezing temperatures that could explain the 0%

survival in those baskets. No such disturbance affected baskets in other years (Table 2-

1).

30

Eyed Survival, 1998-99 & 1999-00

During the studies in 1998-99 and 1999-00, ice scour was not a problem and only 1

basket in the Gorge reach (1999-00) was completely displaced from its original position.

The basket was reburied when it was found on May 31, 2000. The basket was probably

displaced when a debris jam upstream of the site dislodged during the snowmelt freshet.

In April, the debris jam was intact and all of the incubation baskets were present in the

gravel when baskets were removed from the Gorge reach in 1999-00 to evaluate survival

to the eyed stage. The displaced basket was not included in the survival estimates for the

Gorge reach that year.

Eyed survival of eggs in baskets in the stream was very high in both years for all reaches

within Catamaran Brook. The survival of eggs to the eyed stage in 1998-99 ranged from

77 to 100%, with an overall mean survival of 93% for the entire brook (Table 2-1).

Survival to the eyed stage in 1999-00 was from 88 to 100%, yielding an overall mean for

the entire brook of 97%. In both years the mean survival of eggs to the eyed stage was

highest in the Middle reach and decreased downstream to the Gorge and Lower reaches

(Figure 2-6). However, no significant differences in survival to the eyed stage were

observed between reaches in 1998-99 (ANOVA, p=0.07) or 1999-00 (ANOVA, p=0.74).

Emergence Survival, 1998-99 & 1999-00

Mean survival to emergence was 66% and 63% in 1998-99 and 1999-00 respectively, and

did not differ among reaches in either year (Table 2-1; p=0.86 for 1998-99 and p=0.07 for

31

1999-00). Overall, emergence survival in both years declined 27% (1998-99) and 29%

(1999-00) from survival to the eyed stage. In 1998-99, one basket in the Lower reach

showed a very low survival (21%) compared with the other baskets at the same site. A

large mass of fungus was observed around a cluster of dead eggs in the basket after it was

retrieved, and it was believed this might have caused the lower survival in the basket that

year and was thus removed from the analysis.

Daily emergence in 1998-99 took place from June 04 to July 02 (Figure 2-8). Emergence

peaked from June 08-12, the Lower reach being earliest (June 07/99) followed by the

Gorge (June 10/99) and Middle (June 11/99) reaches. In 1999-00, peak emergence

occurred between June 17 and 19 about a week later than in 1998-99 and was similar

among reaches (Figure 2-8).

Mean survival at the hatch stage in the Middle reach (site 1) and Lower reach in 1999-00

was 82% and 76%, respectively (Table 2-2). Though mean survival decreased from the

eyed, hatch and emergence stages at both sites (Figure 2-9), when tested, survival did not

differ significantly among the three stages (p = 0.08). This could be the result of the

small sample sizes at each site coupled with the large range of survival in the Lower

reach (8% to 72%).

Intragravel Temperatures and Degree Days

Intragravel temperatures were monitored hourly during incubation in both years (Figure

2-10). Temperatures in the Gorge and Lower reaches remained below 1.0°C from

32

November 14, 1998 to April 04, 1999. During this time temperatures in the Middle reach

were on average 0.77 and 0.82°C warmer than the Gorge and Lower reaches respectively.

Intragravel temperatures in the Middle reach are, especially at site 2 are largely affected

by ground-water infiltration, which is typically warmer during winter months (D. Caissie,

DFO, pers. comm.). In 1999-00, however, temperatures among reaches were similar

throughout incubation, remaining below 1.0°C from December 18, 1999 to April 06,

2000 (Figure 2-10).

The intragravel differences in temperature in 1998-99 led to degree-days accumulating

much faster in the Middle reach compared with the Gorge and Lower reaches (Figure 2-

11). The same was not observed in 1999-00. The amount of accumulated degree-days

realized when baskets were removed at the eyed stage in both years was <200 degree-

days. In comparison to studies elsewhere, the rate of development in Catamaran Brook

was faster (see Table 1-1, Chapter 1).

Fine Sediments

Weight

In 1998-99, the percentage of fines (by weight) in the incubation baskets was highest in

the Gorge reach and lowest in the Middle reach, for both the eyed and emergence stages

(Table 2-3). The mean amount of fines nearly doubled in the Gorge and Lower reaches

in 1999-00 compared with 1998-99. In 1999-00, the Lower reach accumulated the

highest percentage of fines in baskets, while the Middle reach again had the lowest

percentage of accumulated fines. Fines never comprised >12.7% (on average) of the

33

gravel matrix within the incubation baskets in the two years from 1998-2000.

Volume

In neither year were any baskets saturated with substrate particles (i.e., 100% volume

occupied) after being retrieved in the spring. The largest mean volume occupied (by

gravel and fines) within baskets, at any life stage, was 64% at emergence in 1999-00

(Table 2-4). This would translate into 36% space available to eggs within the basket after

fine sediments had accumulated.

In 1998-99 the highest percent volume of fines occurred in the Gorge reach and the

lowest was measured in the Middle reach for the eyed and emergence stages (Table 2-5).

The only significant difference found in percent fines at the eyed stage existed between

the Middle and Gorge reach (p = 0.004).

Generally more sediment accumulated in the incubation baskets in 1999-00 than in 1998-

99 in all reaches (Table 2-5). At the eyed stage in 1999-00, the percent volume of fines

in the Middle reach baskets (n=4) were significantly lower than in the Gorge (p<0.0001)

and Lower reach (p<0.0001). When the percent volume of fines at the emergence stage

in 1999-00 was evaluated, it was necessary to separate the two sites in the Middle reach.

Tests showed the percent volume of fines at the Middle reach site 1 (above bridge) was

significantly less than at the Middle reach site 2 (p=0.004), Gorge (p=0.02) and Lower

reaches (p=0.002, Table 2-5). The increase in fine sediments at the Middle reach (site 2)

was suggestive of a point source impact from the reconstructed bridge crossing just

34

upstream of the site.

Regression analyses of survival versus percent fines showed no significant relationship at

the eyed stage in either 1998-99 (R2=0.02, p=0.69) or 1999-00 (R2=0.07, p=0.51, Figure

2-12). Percent volume of fines was inversely related to the survival of eggs to emergence

in 1998-99 (R2=0.72, p=0.004, Figure 2-12). However, this was not observed in 1999-00

(R2=0.008, p=0.81, Figure 2-12) although the amount of sediments increased in 1999-00.

Discussion

The primary objective of this study was to determine if the amount of fine sediments

associated with forestry activities and deposited in Catamaran Brook adversely affected

survival of Atlantic salmon eggs during incubation.

Eyed Survival

Eyed survival each year from 1994-1997 was high, except in 1995-96 in the Gorge reach.

A mid winter break-up of ice that year (Cunjak et al., 1998) was believed to have had an

impact on the survival of eggs as a result of scouring and completely exposing most of

the incubation baskets above the substrate (R. Cunjak and P. Hardie, pers. comm.). This

was obvious in 1995-96 (see Table 2-1) and the decreased egg survival was possibly due

to the exposure of incubating eggs to freezing conditions. In addition, the evidence of

scouring suggested in-stream flows in the Gorge reach were altered (e.g. increased flow)

and the physical disturbance this created to the streambed resulted in the low egg

35

survivals as well as the lost or displaced baskets. It has been reported elsewhere that the

impact of such disturbances on fish habitat is often more pronounced in areas relative to

timber harvest - like the Gorge reach (Chamberlain et al., 1991).

Mean eyed survival was >83% (77 - 100%) in all stream reaches in 1998-99 and 1999-00.

These results indicated that eyed survival during 1998-99 and 1999-000 was not

negatively affected by adverse environmental conditions or land-use activities, and was

generally as high or higher than survival estimates found in other studies. For instance,

Mackenzie and Moring (1988) reported 89% survival to the eyed stage for Atlantic

salmon eggs from Whitlock-Vibert boxes planted in Northern Stream in Maine. Pauwels

and Haines (1994) showed survival to the eyed stage ranged from 10 to 65% for Atlantic

salmon in three other Maine rivers. Studies of other salmonids suggested survival to the

eyed stage was also high (>67%) barring extreme events that affected intragravel

permeability, dissolved O2 concentrations and fine sediment accumulation (Argent and

Flebbe, 1999; Greenburgh, 1992; and Rubin 1995), or scouring events such as those seen

in 1995-96.

Emergence Survival

The overall mean emergence survival was lowest in 1995-96 (43%) and 1996-97 (39%)

and exceeded 58% in other years (1994-95, 1998-99 and 1999-00). Emergence survival

overall was generally more variable than survival to the eyed stage and also varied

substantially between microhabitats (i.e. redds) within a given reach. In 1995-96 for

example, emergence survival from baskets apparently not affected by scour was between

36

2% and 83%, yet other baskets in the same reaches were lost or displaced due to the mid-

winter thaw (see above) and were not included in survival estimates. Variability

however, was not only limited to years with significant events like the 1995-96 mid-

winter thaw. In 1999-00, survival from two baskets in the Lower reach was 8% and 72%

(Table 2-1). It was not certain what caused the lower survival in the one basket. None of

the variables measured (e.g. fines) appeared different between the baskets and eggs were

well separated in the baskets when they were retrieved, suggesting other unmeasured

factors played a role in the poor survival in the one basket. Bardonnet and Baglinière

(2000) suggested that the "high variability between replicates" (baskets in this case) could

be associated with significant changes in dissolved O2 as a result of different 'paths' of

intragravel flow within each basket or redd. This may have been the case here, since

dissolved O2 and flow were not measured in this study. Therefore, a more detailed study

to measure other additional variables (e.g., micro-hydraulics) that affect survival at a

microhabitat level would be needed to help explain the variability observed in egg

incubation studies, especially at the emergence stage.

Emergence survival for Atlantic salmon in other studies was lower than that found here.

Elson (1957) reported only 6-8% survival to emergence for Atlantic salmon in the Pollett

River, New Brunswick, based on collections of underyearlings vs. potential egg

deposition. Peterson (1978) found similarly low values (0-13%) in the St. Croix River,

New Brunswick. Cunjak and Therrien (1998), Maret et al. (1993) and Scrivener (1988)

showed slightly higher values of 30.7% (Catamaran Brook, 6 years data), 18 to 83%

(mean=48%, control sites) and 3-99% for Atlantic salmon, brown trout and chum salmon

37

(Oncorhynchus keta), respectively. As such, survival of Atlantic salmon eggs to

emergence in Catamaran Brook was at the very least comparable to other similar studies

of salmonids.

The development of Atlantic salmon eggs in 1998-99 and 1999-00 based on the

accumulation of degree-days (DD) suggested that eggs in Catamaran Brook developed

much faster than elsewhere. In other studies, the DD ranges for each stage were 200-300

for eyed, 400-500 for hatch and >500 for emergence (Gunnes, 1979; Crisp, 1988; Vignes

and Heland, 1995). In Catamaran Brook, the ranges were 50-160 to eyed and <500 at the

start of emergence. These values however, must be interpreted with some caution. The

periods of eyed and emergence stages can last for several weeks and the DD values

within those ranges may also vary considerably. For example, by the end of emergence

in Catamaran Brook, the DD were typically near 900 DD in 1998-99 and 1999-00.

Fines

Fine sediments decrease egg survival most notably by depriving eggs of oxygen,

reducing the ability to remove wastes due to decreased intragravel permeability and in

some cases “burying” or “entombing” alevins (MacNeil and Ahnell, 1964; Chapman,

1988; Young et al., 1990; Rubin, 1995). It has been suggested that sand content of >20%

(by weight) in spawning substrates would result in decreased egg survival (Peterson,

1978; Bjornn and Reiser, 1991; Lisle and Eads, 1991).

The intragravel permeability is a function of porosity - the ratio of space to the volume of

38

the redd (Bjornn and Reiser, 1991) - and in reports where fines are a percentage based on

the gravel matrix alone (e.g. by weight), the amount of interstitial space was not

accounted for. In this study the percent volume of fines took into account both substrate

and the interstitial spaces within the gravel. This provided a more thorough

representation of the intragravel environment and considering the importance of the

interstitial spaces (i.e. porosity) percent fines calculated in this manner should be

investigated further. The relation of percent volume of fines to intragravel permeability

should also be examined. I am not aware of other studies that have determined percent

fines in this way, so direct comparisons with other studies were not possible.

The mean accumulated fines in 1998-99 and 1999-00 were not more than 12.7% (by

weight) or 34.9% (by 'new' volume) and were below the critical sediment values

suggested above. At no point in either year were baskets saturated with gravel or fine

sediments. This was a reflection of the near pristine nature (i.e., low amounts of fines) of

the substrate matrix within Catamaran Brook, an excellent environment in which salmon

eggs can incubate. The composition of fines within the incubation baskets in 1998-99

and 1999-00 also reflected the substrate composition found in other studies at Catamaran

Brook. For example, St. Hilaire et al. (1997) showed sediments <4mm ranged from 11 to

23% (by weight) and fines <2mm were generally <15% of the gravel matrix (D. Caissie,

DFO, pers. comm.).

Reiser and White (1988) determined that eggs were highly susceptible to fines early in

development based on the eggs' increased O2 demands. Presumably, then, any increases

39

in fines that altered survival would have been obvious at the eyed stage in either 1998-99

or 1999-00, but eyed survival in both years was high (77 – 100%) and showed no

significant relationship when plotted against fines (Figure 2-12). Fines also did not

negatively affect survival to emergence, even though a significant relationship was

detected in 1998-99 (Figure 2-12). The fines measured that year were considerably less

than in 1999-00, yet the overall, mean emergence survival rate remained relatively

unchanged (66% in 1998-99 and 63% in 1999-00). In 1999-00, there was evidence of a

potential point-source impact from a bridge crossing in the Middle reach. The bridge was

reconstructed during the previous fall (1999) and it was believed that run-off from the

area of the bridge, lead to a three-fold increase in fines downstream at site-2 when

compared to site-1 located immediately upstream of the bridge (Figure 2-1). The

difference in fines at the two sites in the Middle reach did not translate into a difference

in survival however.

Incubation Basket Method

Two important aspects of incubation baskets give them a greater advantage over other

methods used to evaluate survival of salmonid eggs during incubation (e.g. capping

redds). First, knowing the number of eggs in the incubation baskets when they are buried

in the gravel allows a more accurate evaluation of egg survival. Rubin (1995) suggested

an egg density within the baskets of 30 eggs/108cm3, and Scrivener (1988) suggested 30

eggs/capsule be maintained in order to negate effects caused by egg density. The egg to

basket ratios (100 eggs/2513cm3) used here were well below these recommended

40

densities and based on their calculations each of the baskets used in this study could

contain ~700 eggs. This would be useful in studies where larger egg densities are

preferred (e.g. stock enhancement). Second, the incubation basket is multipurpose.

Researchers can use it to measure and relate survival of eggs to fine sediments or, in

combination with other tools (e.g., minilog thermometer), can use the baskets to help

measure and relate survival to numerous environmental variables such as temperature,

flow, dissolved oxygen and intragravel permeability.

The incubation basket method has some shortcomings, however. For instance, the 2.5cm

opening from the incubation basket to the emergence basket could have prevented some

fry from escaping into the emergence basket immediately upon exiting the gravel (R.

Cunjak, UNB, pers. comm.). This was not observed in any of the study years here. A

larger opening to the emergence basket may still be preferred in future constructions of

the baskets to avoid this possibility. Also, because the baskets are buried rather than

anchored in the gravel, they are more susceptible to loss or displacement by high flows

(e.g. in 1995-96). The basket design may actually promote further scouring around the

baskets once they become partially exposed (D. Caissie, DFO - Moncton, pers. comm.).

This may be of particular concern for resource managers using incubation baskets for

stock enhancement purposes, but it does reflect streambed disturbance, which could

provide researchers with evidence of the conditions for the intragravel environment

during the winter months.

Each year it was attempted to provide an evaluation of egg survival from the best

41

possible representation of each of the three key reaches for Atlantic salmon habitat in

Catamaran Brook. But, in order to minimize handling mortality, the process of spawning

eggs to basket burial took place within one day. This meant that sites usually only

contained five to six baskets (depending on the year) and thereby limited the results to

two baskets at the eyed stage and two to three baskets at emergence. Statistically, this

made the calculation of differences among variables between reaches somewhat difficult

and error was likely greater due to the small sample sizes. Nevertheless, it was important

to evaluate survival at both eyed and emergence stages to accurately establish a timeline

of changes in survival. In future studies, it may be more beneficial to concentrate the

number of baskets at fewer locations, thereby allowing researchers to minimize handling

mortality (i.e. remain within 24-48h. window after fertilization) and provide an increased

number of replicates at each study site.

No effects of accumulated fine sediments on Atlantic salmon egg survival in Catamaran

Brook were observed in this study. Survival of eggs in years following clear-cut logging

was >63% to emergence and the amount of fines was low (<12.7% by weight and

<34.9% by volume). The combination of limiting clear-cutting to 7% of the Catamaran

Brook basin and the imposed 20-30m buffer strips appears to have worked effectively in

reducing any impacts from forestry activities. However, in 1999-00 it was believed that a

significant increase in fines at the Middle reach (site-2) was directly related run-off from

a newly reconstructed bridge crossing located just upstream. Still, this did not have an

effect on survival and therefore Catamaran Brook remains an excellent environment

where Atlantic salmon can deposit their eggs. With annual fall runs averaging 165 adults

42

(1990-1996) to this stream (Cunjak and Therrien, 1998), it should be considered a

valuable tributary of the Miramichi River system.

43

References

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Meehan, W.R. [editor]. Influences of forest and rangeland management on

salmonid fishes and their habitats. American Fisheries Society Special Publication

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Chamberlain, T.H., R.D. Harr, and F.H. Everest. 1991. Timber harvesting, silviculture,

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Chapman, D.W., and K.P. MacLeod. 1987. Development of criteria for fine sediment in

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2-73, Final Report, Boise, Idaho. 279p.



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season of parr discontent”? Canadian Journal of Fisheries and Aquatic Sciences

55 (Supplement 1): 161-180.

Cunjak, R.A., and J. Therrien. 1998. Inter-stage survival of wild juvenile Atlantic salmon,

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Cunjak, R.A., D. Guignion,, R.B. Angus, and R. MacFarlane. 2002. Survival of eggs and

alevins of Atlantic salmon and brook trout in relation to fine sediment deposition,

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their habitats on Prince Edward Island. Canadian Technical Report of Fisheries

and Aquatic Sciences 2408: 157p.

45

Elson, P.F. 1957. Number of salmon needed to maintain stocks. Canadian Fish Culturist

21: 19-23.

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1987. Fine sediment and salmonid production: a paradox. In: E.O. Salo, Cundy,

T.W. [editors]. Streamside management: forestry and fishery interactions.

University of Washington, Institute of Forest Resources, Contribution No. 57:

471p.



Garrett, J.W., and D.H. Bennett. 1996. Evaluation of fine sediment intrusion into

Whitlock-Vibert boxes. North American Journal of Fisheries Management 16:

448-452.

de Gaudemar, B., S.L. Schroder, and E.P. Beall. 2000. Nest placement and egg

distribution in Atlantic salmon redds. Environmental Biology of Fishes 57: 37-47.



Greenburg, L.A. 1992. Field survival of brown trout eggs in a perforated incubation

container. North American Journal of Fisheries Management 12: 833-835.



Hall, T.J., and R.K. Haley. 1986. A laboratory study of the effects of fine sediments on

survival of three species of Pacific salmon from eyed egg to fry emergence.

46

National Council of the Paper Industry for Air and Stream Improvement –

Technical Bulletin No. 482: 28p.

Hamor, T., and E.T. Garside. 1976. Developmental rates of embryos of Atlantic salmon,

Salmo salar L., in response to various levels of temperature, dissolved oxygen,

and water exchange. Canadian Journal of Zoology 54: 1912-1917.

Harshbarger, T.J., and P.E. Porter. 1979. Survival of brown trout eggs: two planting

techniques compared. The Progressive Fish-Culturist 41(4): 206-209.

Harshbarger, T.J., and P.E. Porter. 1982. Embryo survival and fry emergence from two

methods of planting brown trout eggs. North American Journal of Fisheries

Management 2: 84-89.

Hausle, A., and D. Coble. 1976. Influence of sand in redds on survival and emergence

of brook trout (Salvelinus fontinalis). Transactions of the American Fisheries

Society 105: 57-63.

Lisle, T.E., and R.E. Eads. 1991. Methods to measure sedimentation of spawning gravels.

Res. Note PSW-411. Berkeley, CA: Pacific Southwest Research Station, Forest

Service, USDA; 7p.

MacCrimmon, H.R., B.L. Gots, and L.D. Witzel. 1989. Simple apparatus for assessing

embryo survival and alevin emergence of stream salmonids. Aquaculture and


MacKenzie, C., and J.R. Moring. 1988. Estimating survival of Atlantic salmon during the


47

Maret, T.R., T.A. Burton, G.W. Harvey, and W.H. Clark. 1993. Field testing of new

monitoring protocols to assess brown trout spawning habitat in an Idaho stream.

North American Journal of Fisheries Management 13: 567-580.

McNeil, W.J., and W.H. Ahnel. 1964. Success of pink salmon spawning relative to size

of spawning bed materials. U.S. Fish and Wildlife Service Special Scientific

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Meehan, W.R., editor. 1991. Influences of forest and rangeland management on salmonid

fishes and their habitats. American Fisheries Society Special Publication 19:

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Pauwels, S.J., and T.A. Haines. 1994. Survival, hatching, and emergence success of

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Piper, R.G., I.B. McElwain, L.E. Orme, J.P. McCraren, L.G. Fowler, and J.R. Leonard.

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Reiser, D.W., and R.G. White. 1988. Effects of two sediment size-classes on survival of

steelhead and chinook salmon eggs. North American Journal of Fisheries




48

SAS Institute Inc., 1999. The SAS System for Windows, version 8. SAS Institute Inc.,

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Scrivener, J.C. 1988. Two devices to assess incubation survival and emergence of

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Scrivener, J.C., and M.J. Brownlee. 1988. Effects of forest harvesting on spawning gravel

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St-Hilaire, A., D. Caissie, R.A. Cunjak, and G. Bourgeois. 1997. Spatial and temporal

characterization of suspended sediments and substrate composition in Catamaran

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Tappel, P.D., and T.C. Bjornn. 1983. A new method of relating size of spawning gravel

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3: 123-135.




Pêche et de la Pisiculture 337-339: 207-214.

Young, M.K., W.A. Hubert, and T.A. Wesche. 1990. Fines in redds of large salmonids.

Transactions of the American Fisheries Society 119: 156-162.

49

Table 2-1: Atlantic salmon egg survival (%) from Catamaran Brook, New

Brunswick, 1994-1997 and 1998-2000. Data for 1994-1997 were

collected by personnel from the Department of Fisheries and Oceans and

were not hatchery corrected. Baskets in column n3 were not included in

survival estimates. In 1999-2000, four baskets (2 Middle reach and 2

Lower reach) were removed at the hatch stage (not shown).

Year Reach n1 n2 Mean Eyed n2 Mean Emergence n3

Survival (range) Survival (range)

1994-95 Middle 4 1 87 3 58 (34-82) 0

1995-96 Middle 9 1 87 6 39 (15-83) 2Gorge 8 0 - 2 6 (2-18) 6Lower 6 1 98 2 66 (64-68) 3

Total/Mean 23 2 93 10 43 (2-83) 11

1996-97 Middle 6 1 70 5 48 (27-61) 0Gorge 6 1 65 5 30 (11-49) 0Lower 7 2 80 (75-86) 4 26 (15-46) 1

Total/Mean 19 4 74 (65-80) 14 39 (11-61) 1

1998-99 Middle 10 4 97 (97-98) 6 71 (55-85) 0Gorge 10 4 93 (83-100) 3 60 (47-74) 3*Lower 6 2 83 (77-92) 3 59 (50-66) 1**

Total/Mean 26 10 93 (77-100) 12 66 (47-85) 4

1999-00 Middle 11 4 98 (95-100) 5 69 (46-83) 0Gorge 5 2 96 (93-100) 2 67 (63-72) 1Lower 6 2 93 (88-100) 2 24 (8-72) 0

Total/Mean 22 8 97 (88-100) 9 63 (8-83) 1

n 1 - number of baskets installed; n 2 - number of baskets retrieved; n 3 - total number of baskets lost or exposed

Middle - minimal impacts of forestry (potential impacts of bridge at site-2);Gorge - immediate impacts from harvest blocks;Lower - downstream, far removed from forestry activity

* baskets retrieved at the emergence stage but removed from analysis due to change in habitat at Gorge reach, site-3** most eggs in basket clumped together in one mass from poor installation of eggs; not included in survival estimate

50

Table 2-2: Survival (%) of Atlantic salmon eggs to the hatch stage in the Middle

reach (site-1) and Lower reach, Catamaran Brook 1999-00.

Date Reach n Mean Survival Range

Middle 2 82 77 - 861999-00 Lower 2 76 72 - 80

Total/Mean 4 79 72 - 86n - number of baskets retrieved

51

Table 2-3: Percent fines by weight (g) from incubation baskets buried in Catamaran

Brook for the years 1998-2000. Gorge (1998-99) three baskets removed

from analysis at emergence stage due to significant change in habitat.

1998-99 1999-00

Reach n Mean (range) n Mean (range)

Middle 4 2.1 (1.6 - 2.5) 4 2.0 (1.6 - 2.5)Eyed Gorge 4 3.8 (3.0 - 5.3) 2 7.2 (7.2 - 7.3)

Lower 1* 2.9 (-) 2 8.8 (8.2 - 9.4)

Hatch Middle - n/a 2 5.3 (4.4 - 6.1)Lower - n/a 2 11.4 (10.9 - 12.0)

Middle 5* 3.6 (2.5 - 5.5) 2a 2.6 (2.2 - 3.0)Emergence 3b 11.1 (9.9 - 12.5)

Gorge 3 6.8 (4.1-9.6) 2 11.6 (10.5 - 12.4)Lower 2 4.2 (4.0 - 4.4) 2 12.7 (10.8 - 14.6)

* one sediment sample lost after retrieval of baskets. a and b are the Middle reach (site-1) and Middle reach (site-2), respectively.

52

Table 2-4: Volume occupied by gravel/substrate in incubation baskets in 1998-99 and

1999-00. Volumes and percentages calculated based on the volume

2513cm3 of the baskets. Numbers in brackets are baskets that were not

included in calculation because of lost sediments.

Year Stage Number of Volume of Volume of Total Volume Percent Volume Percent VolumeBaskets Gravel (>2mm) Fines (<2mm) (Gravel & Fines) of Basket of Basket

(cm3) (cm3) Occupied AvailableEyed 9(1) 1284a 118 1403 56 44Emergence 13(3) 1284a 186 1471 59 41Eyed 8 1273 165 1437 57 43

1999-00 Hatch 4 1303 266 1568 62 38Emergence 9(1) 1287 331 1618 64 36

a determined based on the average from the gravel >2mm in 1999-00

1998-99

53

Table 2-5: Percent volume of fines accumulated in baskets in Catamaran Brook in

1998-99 and 1999-00. Values calculated as percent volume of basket

(2513.27cm3). Gorge reach (1998-99) three baskets were removed from

analysis at emergence stage due to a significant change in habitat.

1998-99 1999-00

Reach n Mean (range) n Mean (range)

Middle 4 7.2 (5.9 - 8.3) 4 6.1 (4.6 - 7.2)Eyed Gorge 4 12.4 (9.4 - 17.1) 2 19.4 (18.7 - 20.1)

Lower 1* 9.0 2 22.1 (20.7 - 23.5)

Hatch Middle - n/a 2 15.4 (15.1 - 15.7)Lower - n/a 2 28.7 (26.3 - 31.1)

Middle 5 11.2 (7.8 - 16.4) 2a 10.6 (8.4 - 12.9)Emergence 3b 31.2 (28.0 - 34.2)

Gorge 3 17.1 (12.4 - 27.5) 2 31.2 (26.4 - 35.9)Lower 2 11.6 (10.8 - 12.3) 2 34.9 (27.7 - 42.0)

* one sediment sample lost after retrieval of baskets. a and b are the Middle reach (site-1) and Middle reach (site-2), respectively.

54

Figure 2-1: Map of Catamaran Brook, including sites used in 1998-99 and 1999-2000.

Stud

y Si

te

Site

2

Site

1Si

te 3

(199

9 on

ly)

Site

4

Site

5

Mid

dle

Rea

chG

orge

Rea

ch

Low

er R

each

55

Figure 2-2: Detailed description of incubation baskets used in 1998-99 and 1999-00 at

Catamaran Brook.

56

Figure 2-3: Conceptual illustration of the arrangement of incubation baskets in the

streambed at different reaches in Catamaran Brook, as they pertain to

different forestry impacts (e.g. timber harvest block).

FLOW

Forest

Timber Harvest Block

Riparian Buffer

(with riparian buffer)

IncubationBaskets

57

Figure 2-4: Diagram of an incubation basket buried in the streambed substrate.

58

A

B

Figure 2-5: Emergence basket in situ (A) schematic, (B) actual picture looking

through water.

59

Figure 2-6: Annual survival of Atlantic salmon eggs to the eyed stage, by study reach

in Catamaran Brook.

0

20

40

60

80

100

120

Middle Gorge Lower

Reach (upstream downstream)

% S

urvi

val

1994-95 1995-96 1996-97 1998-99 1999-00

60

Figure 2-7: Annual emergence survival of Atlantic salmon eggs, by reach in

Catamaran Brook. Graph shows interaction effect of year and reach on

egg survival to emergence.

0

10

20

30

40

50

60

70

80

90

100

Middle Gorge Lower

Reach

% S

urvi

val

1995 1996 1997 1999 2000

61

Figure 2-8: Daily emergence of Atlantic salmon alevins from all incubation baskets

combined by reach in Catamaran Brook in 1998-99 (A) and 1999-00 (B).

0

20

40

60

80

100

120

4-Ju

n-99

5-Ju

n-99

6-Ju

n-99

7-Ju

n-99

8-Ju

n-99

9-Ju

n-99

10-J

un-9

9

11-J

un-9

9

12-J

un-9

9

13-J

un-9

9

14-J

un-9

9

15-J

un-9

9

16-J

un-9

9

17-J

un-9

9

18-J

un-9

9

19-J

un-9

9

20-J

un-9

9

21-J

un-9

9

22-J

un-9

9

23-J

un-9

9

24-J

un-9

9

25-J

un-9

9

26-J

un-9

9

27-J

un-9

9

28-J

un-9

9

29-J

un-9

9

30-J

un-9

9

1-Ju

l-99

2-Ju

l-99

Date

Num

ber

of sa

lmon

Middle Gorge Lower

A

0

20

40

60

80

100

120

2-Ju

n-00

3-Ju

n-00

4-Ju

n-00

5-Ju

n-00

6-Ju

n-00

7-Ju

n-00

8-Ju

n-00

9-Ju

n-00

10-J

un-0

011

-Jun

-00

12-J

un-0

013

-Jun

-00

14-J

un-0

015

-Jun

-00

16-J

un-0

017

-Jun

-00

18-J

un-0

019

-Jun

-00

20-J

un-0

021

-Jun

-00

22-J

un-0

023

-Jun

-00

24-J

un-0

025

-Jun

-00

26-J

un-0

027

-Jun

-00

28-J

un-0

029

-Jun

-00

30-J

un-0

01-

Jul-0

02-

Jul-0

03-

Jul-0

04-

Jul-0

05-

Jul-0

06-

Jul-0

07-

Jul-0

0

Date

Num

ber

of sa

lmon

Middle Gorge LowerB

62

Figure 2-9: Mean survival including standard error bars at eyed, hatch and emergence

stages in 1999-00. Survival between stages in the Middle reach (site-1)

and Lower reach were not statistically different (p=0.17 (Middle) and

p=0.27 (Lower)). Mean percent volume of fines at each stage also shown.

0

20

40

60

80

100

120

Eyed Hatch Emergence

Developmental Stage

Perc

ent S

urvi

val

0.0

10.0

20.0

30.0

40.0

50.0

60.0

70.0

80.0

90.0

100.0

110.0

120.0

% F

ines

(by

volu

me)

Middle (S%) Lower (S%) Middle (Fines) Lower (Fines)

63

A

B

Figure 2-10: Average daily intragravel temperatures by reach for 1998-99 (A) and

1999-00 (B).

0.00

2.00

4.00

6.00

8.00

10.00

12.00

14.00

16.00

18.00

20.00

22.00

24.00

03-N

ov-98

17-N

ov-98

01-D

ec-98

15-D

ec-98

29-D

ec-98

12-Ja

n-99

26-Ja

n-99

09-F

eb-99

23-F

eb-99

09-M

ar-99

23-M

ar-99

06-A

pr-99

20-A

pr-99

04-M

ay-99

18-M

ay-99

01-Ju

n-99

15-Ju

n-99

Date

Tem

pera

ture

(°C

)

Middle Reach Gorge Reach Lower Reach

0.00

2.00

4.00

6.00

8.00

10.00

12.00

14.00

16.00

18.00

20.00

22.00

24.00

02-N

ov-99

16-N

ov-99

30-N

ov-99

14-D

ec-99

28-D

ec-99

11-Ja

n-00

25-Ja

n-00

08-F

eb-00

22-F

eb-00

07-M

ar-00

21-M

ar-00

04-A

pr-00

18-A

pr-00

02-M

ay-00

16-M

ay-00

30-M

ay-00

13-Ju

n-00

27-Ju

n-00

Date

Tem

pera

ture

(°C

)

Middle Reach Gorge Reach Lower Reach

64

A

B

Figure 2-11: Accumulated degree-days by reach for Atlantic salmon eggs in Catamaran

Brook in 1998-99 (A) and 1999-00 (B). “Eyed” refers to the day on which

incubation baskets were removed from the streambed.

0

200

400

600

800

1000

1200

03-N

ov-9

8

10-N

ov-9

8

17-N

ov-9

8

24-N

ov-9

8

01-D

ec-9

8

08-D

ec-9

8

15-D

ec-9

8

22-D

ec-9

8

29-D

ec-9

8

05-J

an-9

9

12-J

an-9

9

19-J

an-9

9

26-J

an-9

9

02-F

eb-9

9

09-F

eb-9

9

16-F

eb-9

9

23-F

eb-9

9

02-M

ar-9

9

09-M

ar-9

9

16-M

ar-9

9

23-M

ar-9

9

30-M

ar-9

9

06-A

pr-9

9

13-A

pr-9

9

20-A

pr-9

9

27-A

pr-9

9

04-M

ay-9

9

11-M

ay-9

9

18-M

ay-9

9

25-M

ay-9

9

01-J

un-9

9

08-J

un-9

9

15-J

un-9

9

22-J

un-9

9

29-J

un-9

9

D ate

Deg

ree

Day

s

M iddle Reach G orge R each L ow er R each

Planted E yed

Start ofEmergence

0

200

400

600

800

1000

1200

02-N

ov-9

909

-Nov

-99

16-N

ov-9

923

-Nov

-99

30-N

ov-9

907

-Dec

-99

14-D

ec-9

921

-Dec

-99

28-D

ec-9

904

-Jan

-00

11-J

an-0

018

-Jan

-00

25-J

an-0

001

-Feb

-00

08-F

eb-0

015

-Feb

-00

22-F

eb-0

029

-Feb

-00

07-M

ar-0

014

-Mar

-00

21-M

ar-0

028

-Mar

-00

04-A

pr-0

011

-Apr

-00

18-A

pr-0

025

-Apr

-00

02-M

ay-0

009

-May

-00

16-M

ay-0

023

-May

-00

30-M

ay-0

0

06-J

un-0

013

-Jun

-00

20-J

un-0

027

-Jun

-00

04-J

ul-0

0

D ate

Deg

ree

Day

s

M iddle Reach G orge R each L ow er R each

Planted eggs Eyed

Start ofEmergence

65

Figure 2-12: Regression of percent survival vs. percent volume of fines at the eyed and

emergence stages in Catamaran Brook for 1998-99 and 1999-00. R2

values shown.

R2 = 0.02R2 = 0.07

R2 = 0.008

R2 = 0.73

0.0

20.0

40.0

60.0

80.0

100.0

120.0

0.00 5.00 10.00 15.00 20.00 25.00 30.00 35.00 40.00 45.00

Percent Fines (by volume)

Perc

ent S

urvi

val

Eyed 1998-99 Eyed 1999-00 Emergence 1998-99 Emergence 1999-00

66

CHAPTER 3

The effects of regulated stream flow on the survival of Atlantic salmon (Salmo salar)

eggs in the Tobique River, New Brunswick

67

Abstract

The effects of variable stream flows on the habitat and survival of Atlantic salmon

(Salmo salar) eggs were determined for different tributaries regulated by hydroelectric

dams and one unregulated river in the Tobique River basin, New Brunswick. Using

incubation baskets seeded with a known quantity of eggs, mean eyed and hatch survival

from 1998-2000 in the regulated rivers ranged from 31%-79% and 9%-37%, respectively.

Survival was usually much higher in the unregulated (control) river. The regulated rivers

showed more evidence of streambed scour; had higher and more variable winter

discharges; intragravel water temperatures were warmer during incubation and also

exhibited warmer, spring-like temperatures more than a month earlier than in the

unregulated river in all years. These differences in the intragravel environment had a

direct effect on the development of eggs and likely helped contribute to the low survivals

at both life stages in the regulated rivers.

68

Introduction

Atlantic salmon (Salmo salar) in eastern Canadian rivers generally spawn in the months

of October and November and their eggs remain buried in the gravel for 6-8 months until

they emerge from the gravel as fry (Scott and Crossman, 1998).

This form of reproduction (i.e., burying eggs in the gravel) has evolved over time as a

way of enhancing the recruitment of salmonids in streams (Fleming, 1996). However,

during the winter months while eggs are incubating they may be exposed to various

factors such as stream-bed scour due to high flow events (Montgomery et. al., 1996) and

ice (Cunjak et. al., 1998) that can limit their survival (Cunjak, 1990). The severity of

physical factors governs the stream environment (Cunjak, 1990) and the effects on

incubating eggs can be even greater because eggs are immobile during this time (Kocik

and Taylor, 1987). As such, the survival of incubating salmon eggs depends almost

exclusively on the surrounding environment and therefore incubation habitat plays a

critical role in the life cycle of salmonids and other fishes (Kocik and Taylor, 1987;

Humphries and Lake, 2000).

Activities associated with generating hydroelectric power modify the natural flow regime

of rivers and can be the leading cause of habitat degradation in some rivers, ultimately

leading to reduced numbers of fish (Bain and Travnichek, 1996). In New Brunswick,

Canada, dams used to generate hydroelectric power significantly influence the St. John

River (Carr, 2001). The construction and activities associated with hydroelectric

69

development have contributed to the decline in the Atlantic salmon population returning

to the river and its tributaries. Humphries and Lake (2000) proposed that dams affect fish

populations during reproduction (e.g. limiting access to available spawning habitat

because of low flows or by dam obstruction) and during recruitment (e.g., inadvertently

damaging eggs by scouring substrate during water releases from impoundments).

Three dams (Mactaquac, Beechwood and Tobique-Narrows) have effectively eliminated

natural upstream migration on the main stem of the St. John River (Figure 3-1). The

available salmon spawning habitat above the Mactaquac dam (the first dam that upstream

migrating salmon encounter in the St. John River) is roughly 13.5 million square metres,

more than half of which (7, 900, 000 m2) is located in the Tobique River drainage

(Marshall et al., 1998). It is accepted that salmon production in the upper St. John River

occurs mostly in the Tobique River basin (Washburn and Gillis, 1996). As a result, the

Department of Fisheries and Oceans (DFO) transports adult salmon above these dams

(Ruggles and Watt, 1975) in efforts to allow salmon to spawn naturally in the available

tributaries further upstream. However, some of the tributaries within the Tobique River

basin are also regulated by headwater storage reservoirs. Most notably, dams located at

the outflow of Trousers, Long and Serpentine Lakes regulate the flows of the Dee, Don

and Serpentine Rivers, respectively (Figure 3-1). These storage reservoirs store spring

runoff and generally discharge at low flow periods during the year, often throughout

winter (Washburn and Gillis, 1996). The discharges are often irregular and the timing

and magnitude of flows resulting from these discharges may greatly influence the habitat

and therefore the survival of incubating salmon eggs.

70

The population of Atlantic salmon returning to the St. John River has declined

substantially (Marshal, 1998), and egg deposition estimates in the river and its tributaries

since 1986 have not met conservation requirements (Chaput, 1998). In addition,

electrofishing surveys have encountered low numbers of juvenile salmon in the regulated

Dee, Don and Serpentine rivers (R. Jones, DFO, pers. comm.). This has prompted local

conservation and protection groups to question the survival of incubating salmon eggs in

these regulated headwater streams.

The goal of this research was to investigate the potential effects of regulated flow regimes

on the survival of incubating salmon eggs. Using incubation baskets seeded with a

known quantity of fertilized Atlantic salmon eggs, it was possible to monitor survival of

eggs during the incubation period in various rivers impacted by hydroelectric activities

(two rivers in 1998, 2000 and three rivers in 1999) relative to an unregulated (control)

river.

Study Area

The study area was located in northwestern New Brunswick, Canada (Figure 3-2). In all

three years at least three rivers (the Dee, Don and Gulquac) were evaluated; in 1999 a

fourth river, the Serpentine River, was also studied. All of the rivers are affected by

hydroelectric activity, except the Gulquac River, which served as an unregulated

(control) river. All of the rivers are tributaries of the Tobique River which is a major

71

branch of the St. John River, the largest river in Atlantic Canada (Smith, 1969).

Methods

In all years of the study, fertilized eggs from a single pairing of adults were obtained

from the Mactaquac Fish Culture Station, Fredericton, New Brunswick. Because of the

relatively long distance between the fish culture station and where the eggs were to be

planted, it was impossible to fertilize and plant the eggs in the stream on the same day.

Instead, fertilized eggs were transported and held overnight in separate 1L jars filled with

ambient fresh water (100 eggs/jar). Eggs were planted in-stream the next day (i.e., within

24 hours from when they were fertilized) so mortality of eggs from handling was

expected to be minimal. It has been shown that eggs become increasingly fragile 48

hours after fertilization (Piper et al., 1982).

Fertilized eggs were seeded in incubation baskets (100 eggs/basket) and the baskets

buried in the gravel on November 05, 1997, October 30, 1998, and October 28, 1999.

The incubation baskets used were constructed by the DFO from 10cm diameter ABS

plumbing pipe cut 38 cm long (each basket). Four windows (3.5cm x 18.0cm), equally

spaced, were cut from the pipe and the inside of the pipe lined with 2 mm plastic

screening that allowed water to flow through the baskets. Baskets were capped at either

end with the appropriate 10cm (diameter) plumbing clean-outs and plugs (Figure 3-3).

Each basket was filled with sieved (>2mm) gravel, seeded with eggs and buried in the

stream bottom at an angle of approximately 45° where they remained throughout the

72

winter. Eggs were placed in the baskets using a plastic funnel and long tubing which

allowed better separation of eggs within the baskets.

All baskets were planted at sites representative of where salmon would normally spawn,

i.e., in areas where suitable substrate (2-10cm in diameter) was observed and where the

gradient of the streambed declined, allowing water to percolate through the gravel

(Bjornn and Reiser, 1991). The areas chosen were usually at the heads of riffles

(Fleming, 1996; Gibson, 1993).

In 1998, two sites in the Dee River and one site in each of the Gulquac and Don Rivers

were studied. In 1999, two sites on each of the same rivers in addition to two sites on the

Serpentine River were evaluated (Figure 3-2). The Serpentine River was excluded from

the 2000 study due to logistical constraints. A summary of the sites and locations during

the three years is presented in Table 3-1.

In each year, it was proposed that two baskets would be removed from each site in late

March in order to evaluate survival to the eyed stage, and the remaining two baskets

would be removed in May to determine survival to hatch. This, however, was not always

possible because baskets were often scoured and displaced downstream leaving the eggs

inside exposed to the flow and in an environment unlike typical spawning gravel.

Consequently, any baskets that were displaced and/or exposed due to scouring were not

included in survival estimates. In 1998, removal of baskets in March was delayed until

May 09 as a large amount of ice covered baskets in the Gulquac River, whereas

73

discharges and high flows prevented retrieval of baskets in the Dee and Don River. In

1999, removal of baskets from the Serpentine River was delayed such that all baskets in

that river were left in place and evaluated for survival to the hatch stage only. Substantial

ice-cover (~130cm) was present at the Gulquac-DN site in late-March (1999) and made it

very difficult to retrieve baskets. The Gulquac-UP site was also covered by ice, but was

only half as thick and baskets were retrieved without any problem. Interestingly, none of

the regulated sites were ice-free at that time of the year. In 2000, all of the sites were free

of ice cover when the first baskets were removed in the spring (March), although large

amounts of ice were observed on the banks in the Gulquac River. Also in 1999, all

alevins removed from baskets collected on May 11/99 were measured for fork length (±

.01mm) because a noticeable difference in alevin size between the regulated and

unregulated river(s) was observed when counting these fish.

All remaining fertilized eggs from the spawning batch were reared at the Mactaquac Fish

Culture Station. The results of the hatchery-raised eggs were then used to correct for

percent survival of eggs in the wild (a measure of egg viability), using the same

correction formula used in Chapter 2. In 1998 and 1999, hatchery survival of eggs was

64% and 71%, respectively. In 2000, egg survival was considerably higher at 97%.

Discharge data was not directly available for the unregulated Gulquac River but the daily

discharges measured in the nearby Grande River (Figure 3-2) were used as a surrogate

(Environment Canada, 2002). The Grande River is an unregulated tributary of the St.

John River, with a similar drainage area to the Gulquac River and presumably its

74

discharge would have been similar to the Gulquac. Discharge data for the regulated

rivers was obtained from the New Brunswick Power Corporation, which monitors

discharges at the dams that regulate the affected rivers in this study. Prevailing

discharges were derived from the hypolimnion (i.e., the bottom) of the reservoir, which is

characteristically warmer during the winter months (Blachut, 1988, Cushman, 1985). All

drainage areas were measured from topographic maps (scale 1: 250 000).

Intragravel temperatures throughout incubation were also recorded with Vemco minilog

thermometers placed in the bottom of one of the 4 baskets at each site in 1998 and 1999.

In 2000, minilog thermometers were placed in 5cm ABS pipe drilled randomly with holes

to allow flow through the pipe. The apparatus with thermometer was buried to a depth

(20-30cm) similar to the depth of the eggs buried in the incubation baskets in the gravel.

The rate of embryo development was then determined for eggs in each of the rivers/sites

used in all years.

When removed, all baskets were immediately placed in thick plastic bags with water and

transported to the University of New Brunswick where each basket was thoroughly

examined for eggs or alevins the same day. Sediment samples from each basket were

frozen and later examined for accumulated fine sediments (<2mm) by oven drying the

sediments to remove all water and dry sieving through the following size fractions: 1mm,

0.5mm, 0.25mm, 0.125mm, 0.063mm and silt. Each size fraction was weighed to the

nearest 0.01g in both years and in 2000 all gravel and sediments within the basket were

also measured for volume by displacement.

75

Results

Egg survival

Survival estimates from individual incubation baskets are reported in Appendix III.

Eyed survival 1999 & 2000

Mean survival of eggs to the eyed stage was significantly different between the two sites

in the unregulated Gulquac River in 1999 (p=0.002) and 2000 (p=0.01, Figure 3-4).

Survival in the Gulquac-UP site was 84% and 85% in 1999 and 2000, respectively, but

was less than half that value in the Gulquac-DN site in both years (30% in 1999, 39% in

2000, Table 3-2). Mean egg survival in the regulated rivers was 69% (1999) and 74%

(2000) in the Dee River (n=3, sites combined each year), and 31% (n=1, 1999) and 43%

(n=2, 2000) in the Don River (Table 3-2). Eyed egg survival in 2000 did not differ from

survival at the same sites in 1999 (p=0.32, Figure 3-4) but results did suggest a

significant site effect on survival (p=0.004).

Hatch Survival 1998, 1999 & 2000

Incubation baskets from the Gulquac-DN site in 1999 and 2000 were lost before retrieval

at hatch and therefore could not be used in comparisons with the regulated rivers. The

loss or displacement of baskets due to scour by ice and/or high flows was also evident in

the regulated rivers (Table 3-2) and all affected baskets were subsequently removed from

analyses of survival.

76

Each year from 1998-2000, the unregulated Gulquac River (Gulquac-UP site) had the

highest mean survival to hatch: 52% in 1998, 35% in 1999 and 75% in 2000 (Figure 3-5).

Comparisons with the regulated rivers showed survival was lowest in the Dee-DN site in

1998 (5.0%), the Don-UP site in 1999 (8.5%) and the Don-DN site (15%) in 2000 (Table

3-2). Survival from the eyed stage to hatch decreased by >50% in all regulated sites in

1999 and 2000, and in the Gulquac-UP site in 1999. Site location contributed

significantly to hatch survival from 1998-2000 (p=0.01), but no year effect on survival

was evident (p=0.10).

The length of alevins collected in the regulated rivers in 1999 was significantly larger

than those removed from the Gulquac River (p<0.0001). Mean lengths in the Dee and

Don rivers were 23.81mm (SD=0.21) and 23.68mm (SD=0.31), respectively, compared

with 16.88mm (SD=0.32) for alevins from the Gulquac River.

Discharges 1998, 1999 and 2000

Estimated discharge in the unregulated Gulquac River during the winter months (e.g.

Dec. - Mar.) rarely exceeded 5.0m3/sec in 1998, 1999 or 2000 (Figure 3-6). By

comparison, discharge in the regulated rivers during the same period were often three to

eight times the discharges measured for the same drainage area in the unregulated river.

77

The mean daily discharges from each of the dams that regulates the Dee, Don and

Serpentine (1999) rivers varied incrementally with periods of constant flow interrupted

by abrupt, extreme changes within a day (Figure 3-6). This stepwise pattern of

discharges was most obvious in 1999 and in all years contributed to a sustained, elevated

flow during the winter months in each of the regulated rivers.

The greatest discharges were from the Trousers Lake dam (Dee River) and in 1998 (Dee

River only) and 1999 the peak discharges during the winter were greater than the

maximum discharges measured in the spring freshet in the unregulated river. Discharges

from each of the dams, in all years, was reduced to near 0 m3/sec by the end of March

(Figure 3-6) in order to refill reservoir capacity; about the same time the discharges in the

unregulated river began to increase, due to runoff from the spring snowmelt. Virtually no

low-flow conditions existed in the regulated rivers during incubation in the study years.

Temperatures and Degree Days

Mean intragravel temperatures from the regulated rivers were higher than in the

unregulated Gulquac River in 1998, 1999 and 2000, most notably during the winter

period from December to March (Figure 3-7). In each of the regulated rivers, the

temperatures were always highest in the upstream most sites, nearest the dam (separate

data for each site not shown). In 1998, minilog thermometers were not installed until

mid-December, more than a month after the incubation baskets were buried in the gravel,

but temperatures were clearly higher in the regulated Dee River than in the Gulquac

78

River (Figure 3-7). In 1999, the Dee and Don rivers had mean temperatures (all sites

combined) of 1.9°C and 2.0°C, respectively, during incubation, compared with mean

temperatures of 1.0°C in the Gulquac River and 1.3°C in the Serpentine River. The mean

intragravel temperature in the Gulquac River in 2000 (1.5°C) was higher than in 1999.

The average temperatures in the Dee and Don rivers (2.1°C, for both) remained similar to

1999, despite warmer temperatures that persisted until mid-December at the beginning of

the incubation period (Figure 3-7).

In all years, intragravel temperatures in the regulated rivers began to increase a month

earlier than in the unregulated Gulquac River. The combination of an earlier increase in

temperature and the warmer intragravel temperatures throughout the winter in the

regulated rivers promoted a faster rate of development for the Atlantic salmon eggs

incubating in these rivers (Figure 3-8). The amount of accumulated degree-days in each

year was higher in the Dee, Don and Serpentine (1999) rivers. By the time baskets were

removed at the hatch stage, eggs in the Dee and Don rivers had accumulated >350 degree

days and 250 degree-days in the Serpentine River (1999); in the Gulquac River the

degree days to hatch were <200 in 1999 and <300 in 2000 (Figure 3-8). A noticeable

difference in alevin size (length) was observed in 1999 (see Hatch Survival section) but

not in 2000, which would be expected based on the number of degree-days accumulated

to hatch.

79

Fine Sediments

The mean volume of fines by site was never higher than 27.5% (Table 3-3). The Dee-UP

site had the least accumulated fines in any year at the eyed stage (2.7-3.1%) and also at

the hatch stage (3.0-4.2%), except for 1998 in which the Dee-DN site had the least fines

(mean=1.1%). This was a reflection of the close proximity of the Dee-UP site to the

hydroelectric dam in the Dee River. Interestingly, the percent fines measured in the

Gulquac-UP site were usually higher than in any of the regulated rivers at hatch. This

might suggest that the elevated discharges throughout the winter in the regulated systems,

combined with the nearness of the sites to the respective dams - especially in the Dee and

Don rivers - provides an intragravel environment with few fine sediments (<2mm) in the

upper reaches of these rivers.

Discussion

The present study investigated the survival of Atlantic salmon eggs in different rivers

regulated by hydroelectric dams, and in one unregulated (control) river in the Tobique

River basin. It was hypothesized that the increased discharges from the dams during

incubation in the winter months affected egg survival in the regulated rivers.

In each year of the present study there was a high degree of variability in survival of eggs

among replicates (baskets) and among sites within all rivers, including the unregulated

(control) Gulquac River. Bardonnet and Baglinière (2000) suggested this was not

80

unusual for incubation basket type studies and could be the result of different flow

patterns within individual baskets. In this study however, evidence of scour from ice and

high flows during the winter resulted in the loss or displacement of baskets at sites where

other baskets remained unaffected and suggests scour is a regular determinant of survival

of eggs on a microhabitat scale. Moreover, the timing of when baskets were affected by

scour (i.e. many were affected before the eyed stage when eggs are most sensitive)

indicates it was the result of the high discharges from the dams throughout the winter

rather than from increased flows due to spring run-off or ice. For instance, the discharges

during the winter in the unregulated river were stable (<5.0m3/sec) until after baskets

were retrieved at the eyed stage (late-March), with some exception in 1998 (Figure 3-6),

and little ice-cover in the regulated rivers was observed during incubation in all years.

Overall, survival in all rivers at both life stages in 1998 and 1999 was less than in 2000.

The survival estimates calculated in this study included the hatchery controls and

therefore should have corrected for any decreases in survival due to poor egg viability.

Nevertheless, it shows the importance of using hatchery controls in egg survival

estimates, and concurs with suggestions made by previous authors to include controls in

egg survival calculations (Peterson, 1978; Rubin, 1995); without which egg survival may

be misrepresented.

Unregulated (control) River

Ironically, the Gulquac River displayed both the highest and lowest eyed survivals of all

81

the rivers in 1999 and 2000. The consistent low survival and the loss of remaining

baskets by the hatch stage in the Gulquac-DN site were unexpected, but may in part be

due to ice build-up at the site. Such events have resulted in the freezing of eggs,

dewatered redds, or diverted/ blocked intragravel flow, elsewhere (Blachut, 1988;

Bradford, 1994; Reiser et al., 1979; Reiser, 1981). Evidence that the incubating eggs

were periodically subjected to freezing and perhaps a dewatered intragravel environment

during incubation, was based on observations made when retrieving baskets at both the

eyed and hatch stages. Significant ice-cover (~130cm) at the Gulquac-DN site in 1999

and the presence of large amounts of ice on the banks and newly deposited, loose

substrate in 2000, suggested significant ice was present at the site before the baskets were

retrieved and resulted in the lower eyed survival in both years.

The loss of baskets by the hatch stage was potentially the result of ice-related scour in

1999, but the absence of ice well before the baskets were retrieved in 2000 would imply

that high flows as a result of spring run-off, rather than ice, removed baskets that year. It

was obvious that a large amount of gravel had been deposited at the Gulquac-DN site by

May (2000), so much so, that extensive digging at the site was done to determine if the

baskets might have been buried rather than scoured and displaced downstream. No

baskets were found, and it was concluded that they had likely been removed due to high

flows. Lapointe et al. (2000) pointed out that significant scour events could be followed

by equally significant fill of the substrate at affected sites, such that the streambed may

appear relatively unchanged. This may have been the situation here. The presence of

unstable (loose) substrate at the Gulquac-DN site was indicative of a site exposed to

82

significant disturbance.

In contrast, the Gulquac-UP site yielded the highest survivals at both stages in all three

years of the study. Gravel at the Gulquac-UP site was relatively more stable and

undisturbed when the baskets were retrieved in the spring, and no baskets were ever lost

at this site in any of the years. This site was more indicative of a salmon spawning zone

in an unregulated river, displaying the "head of riffle" habitat characteristics where

salmon would normally spawn (Fleming, 1996; Gibson, 1993). The Gulquac-DN site on

the other hand, was more representative of a shallow, "flat" type habitat.

Regulated Rivers

In the regulated rivers, eyed egg survival was low compared with other studies of

Atlantic salmon. For instance, MacKenzie and Moring (1988) showed survival to the

eyed stage for Atlantic salmon in Maine Rivers averaged 89%. In Catamaran Brook,

New Brunswick, survival from similar incubation basket experiments ranged from 77%

to 100% from 1998-2000. Of the regulated rivers examined in this study, only eyed

survival in the Dee River (58% - 79%) was similar to the high survival estimates

observed in the unregulated Gulquac-UP site. Survival to the eyed stage in the remaining

regulated river sites was considerably lower (25% - 50%).

Like survival at the eyed stage in the regulated river sites, hatch survival (1998-2000)

was also much less than in the Gulquac-UP site. Furthermore, the magnitude by which

83

survival decreased from the eyed to hatch stages was much greater in the regulated rivers.

However, these low survival estimates in the regulated rivers cannot be explained by the

loss of eggs due to scouring since these data were collected from baskets which were

believed to have been unaffected by scour (i.e. not moved). Therefore, factors other than

scour contributed to the low survival estimates in the regulated rivers.

The accumulation of fines was measured in this study, but the small amounts obtained

here would suggest that they did not negatively influence egg survival. The largest mean

volume of fines recorded in the 3 years was 27.5% in the Gulquac River and the

regulated rivers consistently showed fewer fines at both life stages. By comparison, the

percent volume of fines in Catamaran Brook (1999 and 2000) were <28.7% up to the

hatch stage (see Chapter 2). If increased fines had negatively affected survival in this

study, then presumably survival should have been greater, at least in the regulated rivers

where fines were less. This was not the case however, and fines were not considered to

have contributed to the low survivals obtained in these studies.

The evidence of warmer intragravel temperatures measured in the regulated rivers in all

three years (Figure 3-7) no doubt contributed to the increased rate of development for the

incubating embryo's in the incubation baskets (Figure 3-8) and were certainly influenced

by the discharges from the dams during the winter. This was most obvious in 1999 when

alevins measured in the Gulquac River were significantly (p<0.0001) smaller (less

advanced) than alevins measured in the Dee and Don rivers. From this it can be inferred

that salmon would emerge earlier in the regulated rivers and would likely have

84

consequences for the recruitment of Atlantic salmon in the affected rivers.

Brännäs (1995) showed that in the presence of predators (e.g., brown trout), early

emergence of fry in simulated redds resulted in decreased survival after emergence.

Similarly, brook trout that are present (R. Jones, DFO, Pers. comm.) in the study rivers,

may prey on newly emerged fry who have not yet established their territory (Symons,

1974), thus resulting in reduced fry survival. Also, fry rely on benthic invertebrate drift

for food (Bardonnet and Baglinière, 2000; Danie et al, 1984). If fry were to emerge when

the ground surrounding the river was still snow covered or frozen then it is likely that

detritus to the stream would be lacking and the invertebrate abundance decreased (Siler et

al., 2001). Therefore, early emerging fry may find themselves in an environment where

rations are limited, thereby decreasing the likelihood for survival. However, in order to

strengthen and confirm such suggestions, it is recommended follow-up studies (e.g.

emergence sampling and electrofishing surveys) of both emerging and juvenile Atlantic

salmon be carried out.

Intragravel temperature is intricately related to egg incubation (Beschta et. al., 1987;

Brannon, 1987; Crisp, 1990, Kane, 1988, and Peterson, 1978) and can affect the

physiological development of embryos (Nathanailides et al., 1995). It has also been

shown that early stages of development in Atlantic salmon (i.e. pre-hatch) are critically

stenothemal meaning significant changes in temperature of more than a few degrees

during incubation can be lethal to the development and survival of eggs (Ojanguren et al.,

1999; Peterson et al., 1977). The low survival at the eyed and hatch stages, combined

85

with the variable intragravel temperatures during the winter and the fact that temperatures

increased more than a month earlier (i.e. in February) in the regulated rivers would

support this hypothesis. What's more, the temperatures in the unregulated Gulquac River

generally remained stable from December until April and only increased steadily

thereafter (coinciding with the increased natural discharges; Figure 3-6 and 3-7).

In summary, the evidence supports the hypothesis that variable flows in the regulated

rivers in this study had an adverse effect on stream survival of incubating salmon eggs.

Overall, egg survival at both the eyed and hatch stages was lower in the regulated streams

when compared to the unregulated Gulquac River, the difference being clearer at the

hatch stage. In all cases, survival was largely affected by scour from high flows and ice,

as witnessed by the large number of baskets lost or displaced each year.

It also appeared that variable flows during the winter, which led to differences in

temperature (both warm temperatures and an earlier seasonal increase in the spring) in

the regulated rivers, negatively affected intragravel survival of incubating eggs. An

advancement of embryo development was witnessed based on the accumulated degree-

days and almost certainly led to earlier fry emergence (especially in 1999) in the rivers

with regulated flow. Ultimately, a reduction in the number of fry produced and the

overall salmonid recruitment within the regulated rivers was possible, but needed to be

confirmed through additional surveys of emergent and juvenile Atlantic salmon in the

study years. Regardless, the timing of emergence that has evolved over time to enhance

salmonid survival (Cunjak, 1996; Fleming, 1996; Bardonnet and Baglinière, 2000) has

86

been put in jeopardy. Lastly, the changes in intragravel temperature, which occurred

earlier in the spring in the regulated rivers, appear to have resulted in the reduction of egg

survival (both eyed and hatch). This supports the findings of other researchers who

suggested temperature, especially during pre-hatch, largely affects the physiological

development of embryos and therefore egg survival (Nathanailides et al., 1995;

Ojanguren et al., 1999; Peterson et al., 1977).

87

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downstream from hydroelectric facilities. North American Journal of Fisheries


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http://www.msc-smc.ec.gc.ca/climate/hydat/.







http://www.msc-smc.ec.gc.ca/climate/hydat/

90

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Regulated Rivers: Research & Management 16: 421-432.

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salmon. Progressive Fish Culturist 50: 93-97.



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675-680.

91

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Maryland, U.S.A. 517p.

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trout eggs. The Progressive Fish Culturist 41: 58-60.

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on salmonid egg incubation and fry quality. Ph.D. thesis, University of Idaho.

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Ruggles, C.P. and W.D. Watt. 1975. Ecological changes due to hydroelectric

development on the St. John River. Journal of the Fisheries Research Board of

Canada 32: 161-170.

92

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

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by brook trout. Canadian Journal of Zoology 52: 677-679.




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recruitment in the St. John River, Final Report prepared for Salen Inc.,

Edmunston, New Brunswick.

93

Table 3-1: Summary of site locations and changes made throughout the course of the

egg incubation studies in the Tobique River, fall (1997) – spring (2000).

River Site* Location Comments

Dee UP Below Trousers Lake Moved upstream in 2000 because more representative of salmon spawning area, salmonredds observed near 'new' 2000 site location. Sites not treated differently in analyses.

Dee DN Above Forks Same all 3 years of study.

Don UP Above Britt Brook Same all 3 years of study.

Don DN Above Forks Added in 1999.

Gulquac UP Above Bridge Moved upstream (~200m) in 1999 due to significant ice build-up experienced at former site in 1998.Gulquac DN Below Dingee Added in 1999. Downstream of Gulquac-UP.

Serpentine UP Anvil Brook 1999 only.Serpentine DN Hazelton Landing 1999 only.

* -UP and -DN designations indicate upstream and downstream, respectively

94

Table 3-2: Mean egg survival in incubation baskets from 1998-2000 in rivers from

the Tobique River basin, New Brunswick.

Eyed Survival p-value* Hatch Survival Baskets p-value*Year River Location n1 n2 Mean Survival n2 Mean Survival Lost/

(range) (range) Exposed

Gulquac UP 4 - - - 2 52 (47 - 58) 2 -

Dee UP 4 - - - 4 20 (14 - 30) 0 -DN 4 - - - 4 5 (0 - 16) 0 0.002

Don UP 4 - - - 2 21 (12 - 38) 2 -

Gulquac UP 4 2 84 (83 - 86) - 2 35 (23 - 54) 0 -DN 4 2 30 (25 - 37) 0.002 0 n/a 2 -

Dee UP 4 2 76 (75 - 77) - 2 13 (9 - 21) 0 -DN 4 1 58 ( - ) - 0 n/a 3 -

Don UP 4 1 31 ( - ) 0.008 2 9 (8 - 9) 1 -DN 4 0 n/a - 0 n/a 4 -

Serpentine UP 4 - - - 4 22 (7 - 41) 0 -DN 4 - - - 4 18 (6 - 34) 0 -

Gulquac UP 4 2 85 (76 - 95) - 2 75 (73 - 77) 0 -DN 4 2 39 (32 - 48) 0.01 0 n/a 2 -

Dee UP 4 2 72 (56 - 93) - 2 37 (22 - 62) 0 -DN 4 1 79 ( - ) - 2 16 (10 - 24) 1 0.0300 4 0 n/a 0 n/a 4 -

Don UP 4 0 n/a - 0 n/a 4 -DN 4 2 43 (37 - 50) 0.02 2 15 (9 - 24) 0 0.0300 4 0 n/a - 0 n/a 4 -

* p-values for comparisons with Gulquac-UP site; only values significant at 0.05 shownn1 - number of baskets installed in the falln2 - number of baskets retrieved at stage

1998

1999

2000

95

Table 3-3: Mean volume of fine sediments measured from different sites in the

Tobique River basin, 1998-2000. Percent fines calculated based on the

volume occupied within the basket = 2984.51cm3.

Eyed Stage Hatch Stage BasketsYear River Location n1 n2 Mean Percent Volume of Fines n2 Mean Percent Volume of Fines Lost/Exposed

Gulquac UP 4 - n/a 2 6.0 (5.8 - 6.2) 2

Dee UP 4 - n/a 3a 4.9 (4.4 - 5.4) 0DN 4 - n/a 3a 1.1 (1.0 - 1.3) 0

Don UP 4 - n/a 2 4.8 (1.4 - 8.1) 2

Gulquac UP 4 2 2.9 (2.4 - 3.3) 2 21.3 (9.5 - 33.1) 0DN 4 2b n/a 0 n/a 2

Dee UP 4 2 2.7 (2.6 - 2.7) 1c 3.0 ( - ) 1DN 4 1 20.7 ( - ) 0 n/a 3

Don UP 4 1 10.3 2 23.2 (23.0 - 23.4) 1DN 4 0 n/a 0 n/a 4

Serpentine UP 4 0 n/a 4 16.2 (13.9 - 19.5) 0DN 4 0 n/a 4 12.3 (9.1 - 14.1) 0

Gulquac UP 4 2 4.5 (2.9 - 6.0) 2 27.5 ( 25.4 - 29.5) 0DN 4 2 18.4 (17.9 - 18.8) 0 n/a 2

Dee UP 4 2 3.1 (2.7 - 3.4) 2 4.2 (3.5 - 4.9) 0DN 4 1 14.7 ( - ) 2 10.8 ( 9.7 - 11.8) 100 4 0 n/a 0 n/a 4

Don UP 4 0 n/a 0 n/a 4DN 4 2 6.0 (4.8 - 7.2) 2 15.9 (8.9 - 22.9) 000 4 0 n/a 0 n/a 4

a substrate analysis not performed on one basketb difficulty retrieving baskets, fines lost; no sediment analysis recordedc sediment sample dropped while processing; analysis not performed

1998

1999

2000

96

Figure 3-1: Map of St. John River in New Brunswick, Canada, showing the major

dam obstructions on the mainstem of the river and the three dams of

interest in this study.

Tobique River Basin

Hydroelectric Dam

0 50 100

kilometers

97

Figure 3-2: Tobique River basin showing tributaries and sites used in each year of this

study.

0 12.5 25

kilometers

Gulquac Lake

Trousers Lake

Long Lake

Serpentine Lake

Gulquac-UPGulquac-DN

Dee-UP

Dee-DN

Don-DN

Don-UP

Serpentine-UP

Serpentine-DNGrande Rivièr

e

New

Bru

nsw

ick,

Can

ada/

Mai

ne, U

SA B

orde

r

Incubation Basket SiteHydroelectric Dam

98

Figure 3-3: Incubation basket (s) used to study egg survival of Atlantic salmon eggs in

the Tobique River Basin.

99

Figure 3-4: Mean survival (with standard error bars) of Atlantic salmon eggs to the

eyed stage for the years 1999 and 2000. Graph shows effects of year and

site on egg survival.

0

10

20

30

40

50

60

70

80

90

100

Dee-UP Dee-DN Don-UP Don-DN Gulquac-UP Gulquac-DN

Site

Perc

ent S

urvi

val

1999 (thin error bars) 2000 (thick error bars)

100

Figure 3-5: Mean survival (with standard error bars) to the hatch stage of Atlantic

salmon eggs incubated in egg baskets in 4 rivers tributary to the Tobique

River, 1999-2000. n is the number of baskets used to determine the mean

survival.

0

10

20

30

40

50

60

70

80

90

100

Dee-UP Dee-DN Don-UP Don-DN Gulquac-UP Gulquac-DN Serpentine-UP

Serpentine-DN

Sites

Perc

ent S

urvi

val

1998 (dashed error bars) 1999 (thin error bars) 2000 (thick error bars)

101

Figure 3-6: Mean daily discharges for regulated and unregulated rivers in 1998, 1999

and 2000. Gulquac River discharges represented by discharges measured

in the 'unregulated' Grande Rivière. All discharges adjusted for the same

drainage area of 193km2.

Dis

char

ge (m

/sec

)3

1998

1999

2000

102

Figure 3-7: Mean daily intragravel temperatures measured during incubation in the

regulated Dee, Don and Serpentine (1999) rivers and the unregulated

Gulquac River in 1998, 1999 and 2000.

1999

2000

Date

Gulquac Dee Don Serpentine

Dai

ly In

trag

rave

l Wat

er T

empe

ratu

res (

°C)

1998

103

Figure 3-8: The average accumulated degree-days for each river (all sites combined)

during incubation in 1998, 1999 and 2000.

1999

2000

Acc

umul

ated

Deg

ree-

days

1998

104

CHAPTER 4

General Discussion

105

Discussion

The overall objective of this study was to determine the effects of different human-made

impacts on the survival of Atlantic salmon (Salmo salar) eggs in some New Brunswick

rivers. Forestry activities and hydroelectric dams are common in and near many of the

streams within the Province and thus presented an environment where human

disturbances on salmonid egg survival and habitat could be evaluated.

In Chapter 2, conducted in Catamaran Brook, the effects of fine sediments on survival of

incubating salmon eggs were evaluated. In Chapter 3, different streams within the

Tobique River Basin were studied to assess the impacts of variable flow regimes on the

survival of salmon eggs. As an aside, both studies showed the application of incubation

baskets as a method for monitoring egg survival during the intragravel period.

Incubation Basket Method and Design

The incubation baskets used in these studies were a modification of those used by

Bardonnet et al. (1993). Essentially, the baskets in this study were much more rigid with

the addition of 10cm ABS pipe and caps on either end of the basket (see Appendix I).

The design allowed the attachment of emergence baskets so that survival of incubating

eggs could be monitored throughout the entire incubation period (Catamaran Brook study

only). Survival of eggs was not affected by the baskets and it was believed that this

basket provided an accurate measurement of accumulated fine sediments (<2mm). Lisle

106

and Eads (1991) pointed out limitations to using similar methods to determine the

composition of fines within the streambed gravel matrix. The authors suggested that a

proportion of fines would be lost through the screening when the baskets were removed.

Although some loss of fines was inevitable when baskets were removed, it was believed

to have been reduced with the new basket design because the cap on the bottom of the

basket would have prevented this.

The basket design coupled with a minilog thermometer provided further information to

the researcher with respect to the intragravel environment within which the eggs

incubated. With modern technology, it is very likely that other parameters (e.g.

permeability, and intragravel dissolved oxygen) could be monitored more closely

throughout incubation, thus providing more in-depth information to aquatic researchers

about the environment of the species they study.

One drawback of the baskets might be that once the baskets are lost or exposed due to

scour, it nullifies the measurement of egg survival in the intragravel environment. One

might argue that this would more appropriately indicate 0% survival, assuming that scour

would have also removed eggs incubating at similar burial depths in naturally occurring

redds. However, once initially becoming exposed, the baskets may have exaggerated

scouring due to a change in flow dynamics around the newly exposed basket. This idea

is not unlike what occurs around newly placed bridge piers (D. Caissie, DFO, pers.

comm.).

107

There was some question that the size of the opening (2.5cm) to the emergence baskets

might alter emergence timing because fry would not enter the emergence basket

immediately (R. Cunjak, UNB, pers. comm.). Survival to emergence was only monitored

in the Catamaran Brook study (Chapter 2), but stranding of fry in the incubation basket

was not observed in any of the years. Ideally, a bigger opening would be preferred in

future studies to eliminate any potential that this might occur.

Survival Studies

Egg-to-fry survival of salmonids has been studied extensively for many decades,

particularly by researchers in western North America (Peterson, 1978). Their results

have determined that many human-made disturbances, in particular clear-cut logging and

road development, as well as the construction and activities associated with hydroelectric

dams, have negatively affected Pacific salmon (Oncorhynchus sp.) populations. In terms

of Atlantic salmon, many egg-to-fry survival studies have been conducted, but most

relied on estimates from potential egg deposition, based on fecundity and the number of

returning spawners (Bley and Moring, 1988). Recently, in the past 20 years or so, more

in-depth evaluations were conducted, and studies using incubation type boxes provided

additional information about the early life stages of Atlantic salmon. Egg-to-fry survival

of salmon has ranged anywhere from 0% to 80% (Table 1 in Bley and Moring, 1988),

and is highly dependant on the conditions within the intragravel environment. Fine

sediments, temperature, dissolved oxygen and permeability of spawning gravels, to name

a few, have all been linked to egg survival (Chapmann, 1988; Gibson, 1993; Rubin, 1995;

108

Fleming, 1996 and Bardonnet and Baglinière, 2001).

In Chapter 2, fine sediments showed no negative effects on the survival and habitat of

Atlantic salmon eggs in Catamaran Brook. Egg survival to both the eyed and emergence

stages was high, and accumulated fines (<2mm) were much lower than the 20% (by

weight) threshold that some researchers have indicated leads to decreased egg survival

(Bjornn and Reiser, 1991). Fines in this study were calculated as the percentage of

interstitial space which they occupied within the redd (i.e., basket). This was a new

approach to expressing fines, and took into account both space and substrate within the

intragravel environment. Further studies to evaluate this new method of calculating the

percentage of fines are recommended, but are limited to incubation basket studies,

because a standard volume (e.g., volume of the basket) is needed in order to account for

the volume of spaces within the gravel.

The Catamaran Brook study provided a good sense of the egg-to-fry survival within

Catamaran Brook. Overall, the harvesting practices within the basin (about 7% of the

basin was harvested in 1996) appears to have been effective at minimizing the

introduction of fines to the stream. But the evidence of a point-source impact from a

newly renovated bridge crossing in the Middle reach - site 2 (2000) shows the importance

of continually monitoring the effects to streams when such forestry practices are

occurring nearby.

109

In Chapter 3, the effects of variable flow regimes on salmonid habitat and egg survival

was witnessed. Variable flows as a result of hydroelectric activities can affect fish

populations in many ways (Bain and Travnichek, 1996, and Humphries and Lake, 2000),

but can be particularly harmful to the survival of incubating eggs which cannot avoid the

consequences of such activities (Kocik and Taylor, 1987). The survival of eggs in the

regulated rivers was considerably less than in the unregulated (control) river. However,

the latter also showed signs of disturbance, each year losing 2 baskets from the furthest

site downstream. It was concluded that the Gulquac-DN site was not representative of

where salmon would typically spawn. More importantly though, was that the loss of

baskets at the site was the result of natural disturbances from spring freshets and ice,

which disturb stream substrate and the aquatic biota therein (Montgomery et. al., 1996,

and Cunjak et. al., 1998). These results also provided additional evidence of factors that

affect the variability often seen in egg incubation studies.

Similar disturbances also affected survival in the regulated rivers. The disturbance from

scour in the regulated rivers, however, was most likely the result of the high discharges

from the dams rather than ice. It was believed that very little ice, if any, covered the

areas for an extended period during incubation where the baskets were buried in these

rivers. As well, the warmer temperature regimes during incubation in the regulated rivers

originated from the discharges from the bottom portions of each respective reservoir.

The warmer temperatures increased the rate of embryo development in the regulated

rivers and were believed to eventually result in earlier fry emergence, although it was not

proven since the study concluded at the hatch stage. Also, the increase in temperatures

110

by late-February in the regulated rivers probably contributed to the low survivals at the

eyed and hatch stages, due to the sensitivity of the pre-hatch stages to temperature

changes (Ojanguren et al., 1999; Peterson et al., 1977). Additionally, the effects from

discharges on aquatic biota are generally greater the closer they are to a dam (Bain and

Travnichek, 1996, and Lowney, 2000). The results in the Tobique River study concurred

with this, when the Dee and Don River sites (<10km from the dam) were compared with

the Serpentine River sites (>15 km) in 1999. The loss of baskets was greater and survival

was lower in the Dee and Don rivers. So with this in mind, one can also see that the

problems in the regulated rivers can be further complicated because salmon prefer to

spawn in the upper-most portions of streams; something Fleming (1996) points out, has

evolved as an integral part of the salmon’s life strategy for centuries.

Finally, studies of this nature have become very important in evaluating the entire

Atlantic salmon life cycle. Many of the streams in New Brunswick and the world for that

matter are affected by different human activities, and in one way or another their salmon

populations have probably suffered as a result. The status of Atlantic salmon populations

worldwide is dwindling and New Brunswick is no exception. However, much work is

being done to help conserve the species’ existence, and while much attention recently has

focussed on the marine survival of salmon, the fresh water aspect should not be forgotten

and aspects of it should still be pursued.

Both studies here have provided useful insight into the understanding of Atlantic salmon

egg survival in streams that are affected by different human disturbances. It is hoped that

111

these results will aid future researchers in their studies of egg-to-fry survival of

salmonids; that the efforts to help conserve this species are successful and that, at the

very least, the research here played a small part in that effort!

112

References

Bain, M.B. amd V.T. Travnichek. 1996. Assessing impacts and predicting resoration

benefits of flow alterations in rivers developed for hydroelectric power

production. In: Leclerc, M., H. Capra, S. Valentin, A. Boudreault, Y. Côté [ed.]

2nd International Symposium on Habitat Hydraulics. Ecohydraulics B: B543-

B552.




Bardonnet, A., J.-L. Baglinière. 2000. Freshwater habitat of Atlantic salmon (Salmo


Bley, P.W., and J.R. Moring. 1988. Freshwater and ocean survival of Atlantic salmon and

steelhead: a synopsis. U.S. Fish and Wildlife Service, Biological Report 88 (9):

22p.




19: 751p.



113

Cunjak, R.C., T.D. Powers, and D.L. Parrish. 1998. Atlantic salmon (Salmo salar) in

winter: “the season of parr discontent”? Canadian Journal of Fisheries and

Aquatic Science 55(Suppl. 1): 161-180.





Humphries, P. and P.S. Lake. 2000. Fish larvae and the management of regulated rivers.

Regulated Rivers: Research & Management 16: 421-432.



A Great Lakes perspective. American Fisheries Society Symposium 1: 430-440.

Lisle, T.E., and R.E. Eads. 1991. Methods to measure sedimentation of spawning gravels.

Res. Note PSW-411. Berkeley, CA: Pacific Southwest Research Station, Forest

Service, USDA: 7p.

Lowney, C.L. 2000. Stream temperature variation in regulated rivers: Evidence for a

spatial pattern in daily minimum and maximum magnitudes. Water Resources

Research 36: 2947-2955.

Montgomery, D. R. J.M. Buffington, N.P. Peterson, D.S. Schuett-Hames and T.P. Quinn.

1996. Stream-bed scour, egg burial depths and the influence of salmonid

spawning on bed surface mobility and embryo survival. Canadian Journal of


114

Ojanguren, A.F., F.G. Reyes-Gavilán and R.R Muñox. 1999. Effects of temperature on

growth and efficiency of yolk utilisation in eggs and pre-feeding larval stages of

Atlantic salmon. Aquaculture International 7: 81-87.

Peterson, R.H., Spinney, H.C.E. and Sreeharan, A. 1977. Development of Atlantic

salmon (Salmo salar) eggs and alevins under varied temperature regimes. Journal

of the Fisheries Research Board of Canada 34: 31-43.

Peterson, R.H. 1978. Physical Characteristics of Atlantic salmon spawning gravel in

some New Brunswick streams. Fisheries and Marine Service Technical Report

785: 28p.



115

APPENDIX I

Calculations of Dimensions of the Incubation Baskets Used in the Current Studies

116

Large Window (LW) Baskets:

Volume (cylinder) = πr2 x h= π(5cm)2 x 32cm= 2513.27cm3

(Surface) Area = [2 x circles] + [area of rectangle]*= [2 x (πr2)] + [height x length**]= [157.08] + [1005.31]= 1162.39cm2

* Imagine the basket as 2 circles and a rectangle, to calculate areai.e.

** Where length, is calculated as πd, the circumference of a circle

Window Area = length x width= 10cm x 15.5cm= 155cm2 (multiplied by 3, for 3 windows per basket)= 465cm2

Percent of surface (i.e. mesh) exposed:(465cm2/1162.39cm2) x 100 = 40% of basket are exposed to gravel

Small Window (SW) Baskets:

Volume = 2984.51cm3

(Surface) Area = 1350.89cm2

Window Area = 252cm2

Percent mesh = 19%

Mesh Baskets:

Volume (cylinder) = 5301.44cm3

Percent of surface exposed = 90%

117

APPENDIX II

Survival and Sediment Data for Individual Baskets from Catamaran Brook Study

1994-1997 and 1998-2000

118

1995Reach Site Basket Installed Eyed Hatch Emerged Dead Total Percent

Eggs Eggs SurvivalMiddle Down 3 100 - - 82 - 82 82Middle Down 4 100 - - 70 - 70 70Middle Down 5 100 86 1 0 8 95 87Middle Up1 1 85a - - 19 - 19 22Middle Up1 2 100 - - 34 - 34 34

1996Middle Down B1 100 - - 82 2 84 82Middle Down B2 100 - - 83 3 86 83Middle Down B3 100 - - 40 10 50 40Middle Up2 1 100 87 0 0 4 91 87Middle Up2 2 100 - - 0 49 49 0Middle Up2 3 100 - - 26 12 38 26Middle Up2 4 100 - - 15 31 46 15Middle Up2 5 100 - - 31 10 41 31Middle Up2 6b 100 61 0 0 13 74 61Gorge Down GA1 100 - - 2 46 48 2Gorge Down GA2 100 - - 18 42 60 18Gorge Down GA3 100 - - 0 43 43 0Gorge Down GA4b 100 64 0 0 16 80 64Gorge Up GB1c 100 - - - - - -Gorge Up GB2 100 - - 0 25 25 0Gorge Up GB3b 100 0 0 0 95 95 0Gorge Up GB4c 100 - - - - - -Lower - L1 100 - - 64 - 64 64Lower - L2 100 - - 68 - 68 68Lower - L3 100 98 0 0 1 99 98Lower - L4c 100 - - - - - -Lower - L5c 100 - - - - - -Lower - L6c 100 - - - - - -

1997Middle Down M1 125 - - 34 - 34 27Middle Down M2 125 - - 73 - 73 58Middle Down M3 125 - - 66 - 66 53Middle Down M4 125 - - 65 - 65 52Middle Down M5 125 - - 76 - 76 61Middle Down M6 125 34 53 0 10 97 70Gorge New G1 125 - - 57 - 57 46Gorge New G2 125 - - 48 - 48 38Gorge New G3 125 - - 61 - 61 49Gorge New G4 125 - - 14 - 14 11Gorge New G5 125 - - 34 - 34 27Gorge New G6 125 81 0 0 25 106 65Lower - L1 52 39 0 0 1 39 75Lower - L2 52 - - 8 - 8 15Lower - L3 52 - - 10 - 10 19Lower - L4c 52 - - - - - -Lower - L5 52 - - 18 - 18 35Lower - L6 125 - - 57 - 57 46Lower - L7 125 106 1 0 10 117 86

a estimation; eggs lost during installation; not used in survival estimatesb baskets exposed (i.e. nor gravel covering them when retrieved)c baskets lost

119

Eyed 1999Reach Site Basket Installed Eyed Hatch Emerged Dead Total Percent Corrected

Eggs Eggs Survival Survival

Middle 1 M2B1 100 95 - - 4 99 95 96.9Middle 1 M2B2 100 96 - - 3 99 96 98.0Middle 2 M1B1 100 95 - - 3 98 95 96.9Middle 2 M1B2 100 95 - - 3 98 95 96.9Gorge 3 G2B1 100 96 - - 4 100 96 98.0Gorge 3 G2B2 100 81 - - 17 98 81 82.7Gorge 4 G1B2 100 99 - - 1 100 99 100.0Gorge 4 G1B5 100 93 - - 6 99 93 94.9Lower 5 L1B2 100 75 - - 18 93 75 76.5Lower 5 OG2 100 90 - - 6 96 90 91.8

Emergence 1999Middle 1 M2B3 100 - - 83 1 84 83 84.7Middle 1 M2B4 100 - - 78 6 84 78 79.6Middle 1 M2B5 100 - - 73 0 73 73 74.5Middle 2 M1B3 100 - - 54 4 58 54 55.1Middle 2 M1B4 100 - - 65 6 71 65 66.3Middle 2 M1B5 100 - - 69 1 70 69 70.4Gorge 3 G2B3 100 - - 0 86 86 0 0.0Gorge 3 G2B4 100 - - 0 66 66 0 0.0Gorge 3 G2B5 100 - - 6 63 69 6 6.1Gorge 4 G1B1 100 - - 62 6 68 62 63.3Gorge 4 G1B3 100 - - 46 0 46 46 46.9Gorge 4 G1B4 100 - - 73 4 77 73 74.5Lower 5 L1B1 100 - - 61 0 61 61 62.2Lower 5 L1B3a 100 - - 21 3 24 21 21.4Lower 5 OG1 100 - - 65 0 65 65 66.3Lower 5 OG3 100 - - 49 0 49 49 50.0

Eyed 2000Middle 1 M2B2 100 97 - - 1 98 97 100.0Middle 1 Hatch 100 91 - - 7 98 91 95.0Middle 2 M1B1 100 94 - - 2 96 94 98.0Middle 2 M1B2 100 100 - - 0 100 100 100.0Gorge 4 G1B1 100 90 - - 1 91 90 93.0Gorge 4 G1B3 100 99 - - 0 99 99 100.0Lower 5 G2B1 100 96 - - 0 96 96 100.0Lower 5 G2B4 100 84 - - 6 90 84 88.0

Hatch 2000Middle 1 M2B1 100 - 83 - 8 91 83 86Middle 1 M2B3 100 - 74 - 13 87 74 77Lower 5 G2B3 100 - 77 - 6 83 77 80Lower 5 G2B_ 100 - 69 - 23 92 69 72

Emergence 2000Middle 1 M2B5 100 - - 75 0 75 75 78.0Middle 1 NN 100 - - 45 0 45 45 46.0Middle 2 NN 100 - - 67 0 67 67 68.0Middle 2 M1B4 100 - - 80 0 80 80 83.0Middle 2 M1B5 100 - - 76 0 76 76 77.0Gorge 4 G1B1b 100 - - 25 0 25 25 26.0Gorge 4 G1B2 100 - - 61 0 61 61 63.0Gorge 4 G1B5 100 - - 69 0 69 69 72.0Lower 5 G2B2 100 - - 69 0 69 69 72.0Lower 5 LSW 100 - - 8 0 8 8 8.0

a L1B3 - dead eggs encompassed in fungus.b G1B1 - Displaced downstream, not used in survival calculation.

120

Eyed 2000 Weight (gm)Reach Site Basket >2mm 1mm 0.5mm 0.25mm 0.125mm 0.063mm Silt Total >2mm 1mm 0.5mm 0.25mm 0.125mm 0.063mm Silt Total

Fines FinesMiddle 1 M2B2 2869.90 10.10 8.66 8.58 6.60 7.44 18.70 60.08 1200 9 8 11 11 13 30 82Middle 1 Hatch 3194.07 12.24 8.50 6.91 5.31 5.94 13.23 52.13 1240 11 9 6 7 7 18 58Middle 2 M1B1 3416.69 15.90 13.74 7.43 5.56 8.39 16.06 67.08 1270 12 10 7 8 16 27 80Middle 2 M1B2 3524.70 36.44 17.39 8.49 1.77 9.25 17.40 90.74 1340 24 13 8 2 12 26 84Gorge 4 G1B1 3522.35 64.44 121.47 37.28 12.71 13.65 22.49 272.04 1300 45 85 28 13 21 33 225Gorge 4 G1B3 3342.72 34.03 73.04 59.82 31.38 26.05 38.81 263.13 1300 24 55 44 30 33 56 242Lower 5 G2B1 3423.78 85.61 162.74 62.32 16.30 11.92 17.59 356.48 1260 62 118 49 16 17 30 292Lower 5 G2B4 3325.50 49.68 115.16 68.78 23.89 16.30 22.12 295.93 1270 35 85 53 24 22 36 255

Hatch 2000Middle 1 M2B1 3378.22 16.61 43.08 39.82 20.41 14.60 22.26 156.78 1340 14 41 40 26 22 40 183Middle 1 M2B3 3361.65 58.65 101.03 35.00 1.65 11.30 9.83 217.46 1290 42 75 31 3 18 15 184Lower 5 G2B_ 3278.54 99.07 181.41 61.90 19.08 14.16 24.62 400.24 1300 67 126 46 19 17 41 316Lower 5 G2B3 3444.85 94.82 222.10 89.85 23.36 17.85 22.45 470.43 1280 67 162 69 23 25 35 381

Emergence 2000Middle 1 M2B5 3387.6 11.8 15.98 14.02 12.55 10.64 10.3 75.31 1300 9 13 15 24 20 20 101Middle 1 NN 3145.3 15 26.9 16.79 12.64 12.64 14.7 98.67 1220 14 25 37 32 27 30 165Middle 2 NN 3277.9 63.4 149.9 63.34 31.61 23.8 26.3 358.4 1240 46 115 61 48 44 40 354Middle 2 M1B4 3558.5 133 177.7 62.01 26.27 20.11 21 439.9 1360 93 129 51 40 38 40 391Middle 2 M1B5 3385.8 144 208.6 68.05 23.69 18.96 19.8 483.5 1220 101 147 53 32 33 36 402Gorge 4 G1B1* 3538.1 51.3 80.82 39.98 15.6 8.9 8.8 205.4 1360 36 58 31 16 13 16 170Gorge 4 G1B2 3414.7 144 163.6 60.13 19.56 12.45 16.6 416.4 1280 103 117 46 17 16 24 323Gorge 4 G1B5 3457.8 146 175.3 88.94 35.06 21.82 22.9 490.4 1320 108 129 68 32 49 39 425Lower 5 G2B2 3528.8 158 283.1 96.71 24.57 17.02 22.6 602.2 1340 115 211 74 24 24 41 489Lower 5 LSW 3410.1 112 176.3 68.41 21.46 14.71 17.8 411 1300 79 127 52 21 22 32 333

Note: volume measured by displacementNote: * basket displaced; not used in caculations of survival or sediment

Volume (cm3 - measured)

Eyed 1999 Weight (gm) Volume (cm3 - calculated)Reach Site Basket 1mm 0.5mm 0.25mm 0.125mm 0.063mm Silt Total 1mm 0.5mm 0.25mm 0.125mm 0.063mm Silt Total

Fines FinesMiddle 1 M2B1 20.08 13.04 5.41 5.14 4.99 4.54 53.20 15 12 9 11 15 8 71Middle 1 M2B2 34.45 8.74 5.70 4.30 5.11 10.95 69.25 25 9 9 10 16 18 88Middle 2 M1B1 35.49 16.53 9.52 7.63 2.44 7.56 79.17 26 15 12 15 10 13 91Middle 2 M1B2 20.33 31.03 15.56 6.12 4.62 10.22 87.88 15 25 16 13 15 17 102Gorge 3 G2B1 39.43 11.61 9.38 17.36 9.80 15.26 102.84 29 11 12 30 26 25 133Gorge 3 G2B2 42.67 23.82 13.74 20.66 11.49 9.59 121.97 31 20 15 35 30 16 147Gorge 4 G1B2 56.47 28.56 11.31 5.65 3.98 6.41 112.38 41 24 13 12 13 11 114Gorge 4 G1B5 100.14 19.38 16.30 20.40 14.77 18.87 189.86 72 17 17 34 38 31 208Lower 5 L1B2 58.92 15.52 8.52 6.64 4.63 7.47 101.70 43 14 11 14 15 13 109Lower 5 OG2 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a

Emergence 1999Middle 1 M2B3 14.88 28.43 25.60 9.51 3.61 5.72 87.75 12 23 24 18 12 10 99Middle 1 M2B4 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/aMiddle 1 M2B5 32.99 34.95 11.04 4.92 2.47 4.73 91.10 24 28 13 11 10 8 95Middle 2 M1B3 65.22 64.29 26.37 20.96 7.61 13.67 198.12 47 49 25 35 21 23 200Middle 2 M1B4 29.21 12.46 16.72 20.29 10.17 15.70 104.55 22 12 17 34 27 26 138Middle 2 M1B5 32.26 67.58 36.31 10.01 3.67 6.84 156.67 24 52 32 19 13 12 150Gorge 3 G2B3 32.12 44.67 35.33 17.74 14.06 12.73 156.65 24 35 31 30 36 21 178Gorge 3 G2B4 31.33 28.56 39.02 45.09 28.65 41.12 213.77 23 24 34 71 69 66 287Gorge 3 G2B5 47.00 17.59 31.54 43.72 17.04 42.69 199.58 34 16 29 69 43 69 259Gorge 4 G1B1 77.51 64.44 47.03 19.01 14.48 19.63 242.10 56 49 40 32 37 32 246Gorge 4 G1B3 120.89 107.29 65.61 25.46 10.45 27.53 357.23 87 80 54 42 28 44 335Gorge 4 G1B4 66.61 28.69 19.08 10.85 8.99 9.44 143.66 48 24 19 20 25 16 151Lower 5 L1B1 77.60 33.40 13.80 7.50 3.10 4.20 139.60 56 27 15 15 11 8 132Lower 5 L1B3 78.40 38.70 17.50 8.70 4.00 9.00 156.30 56 31 18 17 13 15 150Lower 5 OG1 117.75 109.91 57.04 21.87 13.17 7.89 327.63 84 82 48 37 34 13 298Lower 5 OG3 115.10 96.14 54.10 34.62 14.61 26.44 341.01 82 72 46 56 37 43 335Notes: Volume calculated from regressions of weight vs. volume in 2000Notes: Percent fines = (volume of fines / volume of basket)*100Notes: n/a - sediment samples lost

121

APPENDIX III

Survival Estimates from Individual Incubation Baskets in the Tobique River Study

1998-2000

122

1997-1998 Eyed Survival Pre-Hatch SurvivalRiver Location Bsk. Live Eyed Alevin Dead Degree Percent Corrected Alevin Dead Degree Percent Corrected

Eggs Days Survival Survival Days Survival SurvivalRiver Dee UP A 107 0 *** *** *** *** *** 22 80 *** 21 30.1River Dee UP B 107 0 *** *** *** *** *** 14 69 *** 13 19.2River Dee UP D 104 1 *** *** *** *** *** 14 82 *** 14 21.4River Dee UP C 106 n/a *** *** *** *** *** 10 n/a *** 9 13.9River Dee DN A 107 0 *** *** *** *** *** 1 81 *** 1 1.4River Dee DN B 107 7 *** *** *** *** *** 5 55 *** 11 16.4River Dee DN C 107 0 *** *** *** *** *** 4 75 *** 4 5.5River Dee DN D 106 n/a *** *** *** *** *** 0 n/a *** 0 0.0River Don UP A 105 0 *** *** *** *** *** 13 67 *** 12 18.3River Don UP C 109 4 *** *** *** *** *** 25 45 *** 27 38.7River Don UP D 108 5 *** *** *** *** *** 23 58 *** 26 37.8River Don UP B 108 n/a *** *** *** *** *** 9 n/a *** 8 12.2Gulquac UP C 108 1 *** *** *** *** *** 34 33 *** 32 47.3Gulquac UP D 107 23 *** *** *** *** *** 19 32 *** 39 57.5Gulquac UP A *** *** *** *** *** *** *** *** *** *** *** LostGulquac UP B *** *** *** *** *** *** *** *** *** *** *** Lost

1998-1999River Dee UP 9 100 53 2 45 264 55 77.5 *** *** *** *** ***River Dee UP 11 100 53 0 47 264 53 74.6 *** *** *** *** ***River Dee UP 10 100 *** *** *** *** *** *** 15 81 429 15 21.1River Dee UP 12 98 *** *** *** *** *** *** 6 84 429 6 8.7River Dee DN 13 97 1 0 82 153 1 1.5 *** *** *** *** ***River Dee DN 16 100 41 0 58 153 41 57.7 *** *** *** *** ***River Dee DN 14 99 *** *** *** *** *** *** lost n/a n/a n/a n/aRiver Dee DN 15 100 *** *** *** *** *** *** lost n/a n/a n/a n/aRiver Don UP 22 100 29 0 71 152 29 40.8 *** *** *** *** ***River Don UP 23 100 22 0 78 152 22 31.0 *** *** *** *** ***River Don UP 21 100 *** *** *** *** *** *** 6 94 379 6 8.5River Don UP 24 99 *** *** *** *** *** *** 6 91 379 6 8.6River Don DN 17 100 28 0 72 n/a 28 39.4 *** *** n/a *** ***River Don DN 19 100 22 0 57 n/a 22 31.0 *** *** n/a *** ***River Don DN 18 100 *** *** *** *** *** *** 0 89 n/a 0 0.0River Don DN 20 100 *** *** *** *** *** *** lost n/a n/a n/a n/aGulquac UP 2 100 59 0 41 58 59 83.1 *** *** *** *** ***Gulquac UP 4 100 61 0 39 58 61 85.9 *** *** *** *** ***Gulquac UP 1 99 *** *** *** *** *** *** 38 55 188 38 54.3Gulquac UP 3 100 *** *** *** *** *** *** 16 79 188 16 22.5Gulquac DN 6 100 18 0 70 60 18 25.4 *** *** *** *** ***Gulquac DN 7 100 26 0 72 60 26 36.6 *** *** *** *** ***Gulquac DN 5 100 *** *** *** *** *** *** lost n/a 191 n/a n/aGulquac DN 8 100 *** *** *** *** *** *** lost n/a 191 n/a n/aSerpentine UP 25 99 n/a n/a n/a 103 n/a n/a 27 69 260 27 38.6Serpentine UP 26 99 n/a n/a n/a 103 n/a n/a 14 70 260 14 20.0Serpentine UP 27 100 n/a n/a n/a 103 n/a n/a 5 84 260 5 7.0Serpentine UP 28 100 n/a n/a n/a 103 n/a n/a 29 60 260 29 40.8Serpentine DN 29 99 n/a n/a n/a 81 n/a n/a 14 86 240 14 20.0Serpentine DN 30 100 n/a n/a n/a 81 n/a n/a 17 83 240 17 23.9Serpentine DN 31 99 n/a n/a n/a 81 n/a n/a 4 95 240 4 5.7Serpentine DN 32 99 n/a n/a n/a 81 n/a n/a 24 76 240 24 34.3

1999-2000River Dee UP 13 97 51 2 40 288 55 56.4 *** *** *** *** ***River Dee UP 12 97 86 1 13 288 90 92.6 *** *** *** *** ***River Dee UP 11 97 *** *** *** *** *** *** 21 58 488 22 22.3River Dee UP 14 96 *** *** *** *** *** *** 58 14 488 60 62.4River Dee DN 30 97 28 0 48 188 29 29.8 *** *** *** *** ***River Dee DN 32 99 76 0 13 188 77 79.2 *** *** *** *** ***River Dee DN 29 93 *** *** *** *** *** *** 9 62 371 10 10.0River Dee DN 31 98 *** *** *** *** *** *** 23 37 371 23 24.2River Dee 00 33 98 64 0 18 195 65 67.4 *** *** *** *** ***River Dee 00 35 100 45 1 37 195 46 47.4 *** *** *** *** ***River Dee 00 34 99 *** *** *** *** *** *** 33 39 389 33 34.4River Dee 00 36 100 *** *** *** *** *** *** lost n/a 389 n/a n/aRiver Don UP 22 98 41 1 30 183 43 44.2 *** *** *** *** ***River Don UP 23 99 73 0 22 183 74 76.0 *** *** *** *** ***River Don UP 24 93 35 0 26 183 38 38.9 *** *** *** *** ***River Don UP 21 99 *** *** *** *** *** *** lost n/a 425 ** n/aRiver Don DN 16 100 36 0 32 242 36 37.1 *** *** *** *** ***River Don DN 20 98 48 0 27 242 49 50.5 *** *** *** *** ***River Don DN 15 100 *** *** *** *** *** *** 9 62 445 9 9.3River Don DN 18 100 *** *** *** *** *** *** 23 37 445 23 23.7River Don 00 27 95 46 0 41 184 48 50.0 *** *** *** *** ***River Don 00 28 99 45 0 17 184 45 46.9 *** *** *** *** ***River Don 00 26 94 *** *** *** *** *** *** 49 51 395 52 53.8River Don 00 25 96 *** *** *** *** *** *** lost n/a 395 n/a n/aGulquac UP 5 95 70 0 23 123 74 76.1 *** *** *** *** ***Gulquac UP 2 97 89 0 5 123 92 94.7 *** *** *** *** ***Gulquac UP 3 99 *** *** *** *** *** *** 74 12 293 75 77.1Gulquac UP 6 98 *** *** *** *** *** *** 69 11 293 70 72.6Gulquac DN 8 96 30 0 43 147 31 32.3 *** *** *** *** ***Gulquac DN 9 99 46 0 38 147 46 47.9 *** *** *** *** ***Gulquac DN 7 100 *** *** *** *** *** *** lost n/a 325 n/a n/aGulquac DN 10 96 *** *** *** *** *** *** lost n/a 325 n/a n/aNote: shaded cells indicate baskets were exposed or lost and were not used in survival estimates.

VITA

Candidate: J. Jason Flanagan

University: University of New BrunswickBachelor of ScienceConferred - May 1997

Publications: N/A

Conference Presentations:

Canadian Conference for Fisheries Research 2000Fredericton, New BrunswickTitle: The impact of fine sediment deposition on survival of Atlantic salmon eggs

GSA Conference on Student Research 2000Wu Conference Center, University of New BrunswickTitle: Impact of sediment deposition on the survival of Atlantic salmon (Salmo

salar) eggs in Catamaran Brook

Miramichi River Environmental Assessment CommitteeAnnual Science Day Workshop 1999Miramichi, New BrunswickTitle: Impacts of sedimentation on Atlantic salmon in Catamaran Brook

Documents

THE IMPACTS OF FINE SEDIMENTS AND VARIABLE FLOW …