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
Project: description and general design of study. Canadian Technical Report of
Fisheries and Aquatic Sciences 1751: 14p.
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.
Reviews in Fish Biology and Fisheries 3: 39-73.
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
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48
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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
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, and Y. Côté
[ed.] 2nd International Symposium on Habitat Hydraulics. Ecohydraulics B:
B543-B552.
Bardonnet, A. and J. Baglinière. 2000. Freshwater habitat of Atlantic salmon (Salmon
salar). Canadian Journal of Fisheries and Aquatic Sciences 57: 497-506.
Beschta, R.L., R.E. Bilby, G.W. Brown, L.B. Holtby, and T.D. Hofstra. 1987. Stream
Temperature and Aquatic Habitat: Fisheries and Forestry Interactions. In Salo,
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89
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land-use activity. Canadian Journal of Fisheries and Aquatic Sciences 53
(Supplement 1): 267-282.
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 (Supplement 1): 161-180.
Cushman, R. M. 1985. Review of ecological effects of rapidly varying flows
downstream from hydroelectric facilities. North American Journal of Fisheries
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environmental requirements of coastal fish and invertebrates (North Atlantic) -
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Division, Downsview, Ontario. [downloaded: 19 June 2002]. Available from:
http://www.msc-smc.ec.gc.ca/climate/hydat/.
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Reviews in Fish Biology and Fisheries 6: 379-416.
Gibson, R.J. 1993. The Atlantic salmon in fresh water: spawning, rearing and production.
Reviews in Fish Biology and Fisheries 3: 39-73.
Gunnes, K. 1979. Survival and development of Atlantic salmon eggs and fry at three
different temperatures. Aquaculture 16: 211-218.
90
Humphries, P. and P.S. Lake. 2000. Fish larvae and the management of regulated rivers.
Regulated Rivers: Research & Management 16: 421-432.
Kane, T.R. 1988. Relationship of temperature and time of initial feeding of Atlantic
salmon. Progressive Fish Culturist 50: 93-97.
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.
Lapointe, M. et. al. 2000. Modelling the probability of salmonid egg pocket scour due to
floods. Canadian Journal of Fisheries and Aquatic Sciences 57: 1120-1130.
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.
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1996. Stream-bed scour, egg burial depths and the influence of salmonid
spawning on bed surface mobility and embryo survival. Canadian Journal of
Fisheries and Aquatic Sciences 53: 1061-1070.
Nathanailides, C., O. Lopez-Albors, and N.C. Stickland. 1995. Influence of prehatch
temperature on the development of muscle cellularity in posthatch Atlantic
salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 52:
675-680.
91
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.
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1982. Fish Hatchery Management. American Fisheries Society, Bethesda,
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.
236p.
Rubin, J. F. 1995. Estimating the success of natural spawning of salmonids in streams.
Journal of Fish Biology 46: 603-622.
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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
Publications, Ltd., Ontario, Canada. 966p.
Siler, E.R., J.B. Wallace, and S.L. Eggert. 2001. Long-term effects of resource limitation
on stream invertebrate drift. Canadian Journal of Fisheries and Aquatic Sciences
58: 1624-1637.
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Department of the Environment, Fisheries Service, Halifax, Nova Scotia. 238p.
Symons, P.E.K. 1974. Territorial behavior of juvenile Atlantic salmon reduces predation
by brook trout. Canadian Journal of Zoology 52: 677-679.
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 Pisiculture 337-339: 207-214.
Washburn and Gillis Associates Limited. 1996. Assessment of Atlantic salmon smolt
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., 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.
Bardonnet, A., J.-L. Baglinière. 2000. Freshwater habitat of Atlantic salmon (Salmo
salar). Canadian Journal of Fisheries and Aquatic Sciences 57: 497-506.
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.
Bjornn, T.C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. In:
Meehan, W.R. [editor]. Influences of forest and rangeland management on
salmonid fishes and their habitats. American Fisheries Society Special Publication
19: 751p.
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.
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.
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.
Reviews in Fish Biology and Fisheries 3: 39-73.
Humphries, P. and P.S. Lake. 2000. Fish larvae and the management of regulated rivers.
Regulated Rivers: Research & Management 16: 421-432.
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.
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
Fisheries and Aquatic Sciences 53: 1061-1070.
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.
Rubin, J. F. 1995. Estimating the success of natural spawning of salmonids in streams.
Journal of Fish Biology 46: 603-622.
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