THE IMPACTS OF FINE SEDIMENTS AND VARIABLE FLOW REGIMES ON THE HABITAT AND SURVIVAL OF ATLANTIC SALMON (Salmo salar) EGGS

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1 THE IMPACTS OF FINE SEDIMENTS AND VARIABLE 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: Examining Board: Rick Cunjak, Ph.D., UNB Biology Fred Whoriskey, Ph.D., Atlantic Salmon Federation Katy 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

2 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! ii

3 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 was 80% (range 65-98%) and from was 95% (range %). Emergence survival was generally much more variable and ranged from 2 to 83% from and 47 to 85% in The percent fines measured in and 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 , 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. iii

4 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. iv

5 Table of Contents Dedication... ii Abstract...iii Acknowledgements... iv Table of Contents... v List of Tables...viii List of Figures... x CHAPTER 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 Relationship between fine sediments and the survival of incubating Atlantic salmon (Salmo salar) eggs in Catamaran Brook Abstract Introduction Study Site...20 Methods Results v

6 Egg-to-Fry Survival in Catamaran Brook, Eyed Survival, & Emergence Survival, & Intragravel Temperatures and Degree Days Fine Sediments Discussion Eyed Survival Emergence Survival Fines Incubation Basket Method References CHAPTER The effects of regulated stream flow on the survival of Atlantic salmon (Salmo salar) eggs in the Tobique River, New Brunswick Abstract Introduction Study Area Methods Results Egg survival Discharges 1998, 1999 and Temperatures and Degree Days Fine Sediments vi

7 Discussion Unregulated (control) River Regulated Rivers References: CHAPTER General Discussion Discussion Incubation Basket Method and Design Survival Studies References APPENDIX I Calculations of Dimensions of the Incubation Baskets Used in the Current Studies APPENDIX II Survival and Sediment Data for Individual Baskets from Catamaran Brook Study and APPENDIX III Survival Estimates from Individual Incubation Baskets in the Tobique River Study VITA vii

8 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 Table 2-1: Atlantic salmon egg survival (%) from Catamaran Brook, New Brunswick, and Data for were collected by personnel from the Department of Fisheries and Oceans and were not hatchery corrected. Baskets in column n 3 were not included in survival estimates. In , four baskets (2 Middle reach and 2 Lower reach) were removed at the hatch stage (not shown) Table 2-2: Survival (%) of Atlantic salmon eggs to the hatch stage in the Middle reach (site-1) and Lower reach, Catamaran Brook Table 2-3: Percent fines by weight (g) from incubation baskets buried in Catamaran Brook for the years Gorge ( ) three baskets removed from analysis at emergence stage due to significant change in habitat Table 2-4: Volume occupied by gravel/substrate in incubation baskets in and Volumes and percentages calculated based on the volume 2513cm 3 of the baskets. Numbers in brackets are baskets that were not included in calculation because of lost sediments Table 2-5: Percent volume of fines accumulated in baskets in Catamaran Brook in and Values calculated as percent volume of basket viii

9 ( cm 3 ). Gorge reach ( ) three baskets were removed from analysis at emergence stage due to a significant change in habitat 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 in rivers from the Tobique River basin, New Brunswick Table 3-3: Mean volume of fine sediments measured from different sites in the Tobique River basin, Percent fines calculated based on the volume occupied within the basket = cm ix

10 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) Figure 1-2: Characteristics of salmonid redds, showing how river water flows through the redd. Adapted from Peterson (1978) 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) Figure 2-1: Map of Catamaran Brook, including sites used in and Figure 2-2: Detailed description of incubation baskets used in and at Catamaran Brook 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) Figure 2-4: Diagram of an incubation basket buried in the streambed substrate Figure 2-5: Emergence basket in situ (A) schematic, (B) actual picture looking through water Figure 2-6: Annual survival of Atlantic salmon eggs to the eyed stage, by study reach in Catamaran Brook x

11 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 Figure 2-8: Daily emergence of Atlantic salmon alevins from all incubation baskets combined by reach in Catamaran Brook in (A) and (B) Figure 2-9: Mean survival including standard error bars at eyed, hatch and emergence stages in 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 Figure 2-10: Average daily intragravel temperatures by reach for (A) and (B) Figure 2-11: Accumulated degree-days by reach for Atlantic salmon eggs in Catamaran Brook in (A) and (B). Eyed refers to the day on which incubation baskets were removed from the streambed Figure 2-12: Regression of percent survival vs. percent volume of fines at the eyed and emergence stages in Catamaran Brook for and R 2 values shown 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 xi

12 Figure 3-2: Tobique River basin showing tributaries and sites used in each year of this study Figure 3-3: Incubation basket (s) used to study egg survival of Atlantic salmon eggs in the Tobique River Basin Figure 3-4: Mean survival (with standard error bars) of Atlantic salmon eggs to the eyed stage for the years 1999 and Graph shows effects of year and site on egg survival 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, n is the number of baskets used to determine the mean survival Figure 3-6: Mean daily discharges for regulated and unregulated rivers in 1998, 1999 and Gulquac River discharges represented by discharges measured in the 'unregulated' Grande Rivière. All discharges adjusted for the same drainage area of 193km 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 Figure 3-8: The average accumulated degree-days for each river (all sites combined) during incubation in 1998, 1999 and xii

13 1 CHAPTER 1 General Introduction

14 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.

15 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

16 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 km 2 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)

17 5 research project to evaluate the impacts of forestry activities on aquatic biota within Catamaran Brook, a 3 rd 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 and 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;

18 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 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.

19 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.

20 8 References Bardonnet, A. and P. Gaudin Diel pattern of emergence in grayling (Thymallus thymallus Linnaeus, 1759). Canadian Journal of Zoology 68: Bardonnet, A., P. Gaudin, and E. Thorpe 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: Chapman, D.W Critical review of variables used to define effects of fines in redds of large salmonids. Transactions of the American Fisheries Society 117: Chaput, G 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 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 Prediction, from temperature, of eyeing, hatching and 'swim-up' times for salmonid embryos. Freshwater Biology 19: Crisp, D.T. and P.A. Carling Observations on siting, dimensions and structure of salmonid redds. Journal of Fish Biology 34: Cunjak, R.A., D. Caissie, and N. EI-Jabi The Catamaran Brook Habitat Research Project: description and general design of study. Canadian Technical Report of Fisheries and Aquatic Sciences 1751: 14p.

21 9 Cunjak, R.A., D. Guignion,, R.B. Angus, and R. MacFarlane Survival of eggs and alevins of Atlantic salmon and brook trout in relation to fine sediment deposition, pp 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 Review of ecological effects of rapidly varying flows downstream from hydroelectric facilities. North American Journal of Fisheries Management 5: DFO Atlantic salmon, southwest New Brunswick outer-fundy SFA 23. Department of Fisheries and Oceans Science Stock Status Report D3 13: 6p. Fleming, I.A Reproductive strategies of Atlantic salmon: ecology and evolution. Reviews in Fish Biology and Fisheries 6: Gibson, R.J The Atlantic salmon in fresh water: spawning, rearing and production. Reviews in Fish Biology and Fisheries 3: Gunnes, K Survival and development of Atlantic salmon eggs and fry at three different temperatures. Aquaculture 16: Johnston, T.A Downstream movements of young-of-the-year fishes in Catamaran Brook and the Little Southwest Miramichi River, New Brunswick. Journal of Fish Biology 51: Kane, T.R Relationship of temperature and time of initial feeding of Atlantic salmon. Progressive Fish Culturist 50:

22 10 Kocik, J.F. and W.W. Taylor Effect of fall and winter instream flow on yearclass strength of Pacific salmon evolutionarily adapted to early fry outmigration: A Great Lakes Perspective. American Fisheries Society Symposium 1: MacKenzie, C. and J.R. Moring Estimating survival of Atlantic salmon during the intragravel period. North American Journal of Fisheries Management 8: Maret, T.R., T.A. Burton, G.W. Harvvey and W.H. Clark Field testing of new monitoring protocols to assess brown trout spawning habitat in an Idaho stream. North American Journal of Fisheries Management 13: Pauwels, S.J. and T.A. Haines Survival, hatching, and emergence success of Atlantic salmon eggs planted in three Maine streams. North American Journal of Fisheries Management 14: Peterson, R.H 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 A fry trap method for estimating salmonid survival from egg deposition to fry emergence. Journal of the Fisheries Research Board of Canada 26: Randall, R.G Emergence, population densities, and growth of salmon and trout fry in two New Brunswick streams. Canadian Journal of Zoology 60: Rubin, J. F Estimating the success of natural spawning of salmonids in streams. Journal of Fish Biology 46: Scott, W.B. and E.J. Crossman Freshwater fishes of Canada. 2 nd Ed. Galt House Publications, Ltd. Ontario, Canada. 966p.

23 11 Snucins, E.J., R.A. Curry and J.M. Gunn Brook trout (Salvelinus fontinalis) embryo habitat and timing of alevin emergence in a lake and stream. Canadian Journal of Zoology 70: Vignes, J.C., and M. Heland 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 : World Wildlife Fund (WWF) Henning Røed, editor. The status of wild Atlantic salmon: A river by river assessment. 184p.

24 12 Mean Eyed Hatch Emergence Source Temperature ( C) Crisp, Gunnes, Vignes and Heland, 1995 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.

25 13 Smolt Parr Adult Fry INTRAGRAVEL PERIOD Eggs Alevin 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).

26 14 Figure 1-2: Characteristics of salmonid redds, showing how river water flows through the redd. Adapted from Peterson (1978).

27 15 Miramichi River Basin Catamaran Brook Hydroelectric Dam kilometers 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.

28 16 Tobique River Basin Hydroelectric Dam kilometers Figure 1-4: The Tobique River Basin (shaded area) within the Province of New Brunswick, showing different hydroelectric facilities (i.e., dams).

29 17 CHAPTER 2 Relationship between fine sediments and the survival of incubating Atlantic salmon (Salmo salar) eggs in Catamaran Brook

30 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 and 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 at emergence. Nevertheless, it was suggested that the amount of fines in Catamaran Brook in and did not contribute to a decrease in survival of eggs, rather, any decreases were attributed to significant natural events (e.g. ice scour).

31 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).

32 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 ( N, W) is a third-order tributary (52 km 2 ) of the

33 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 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 ( ), one site - site 4 ( ). 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 from incubation studies conducted in Catamaran Brook by DFO personnel was included here. The methods used were similar to that described hereafter.

34 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 and 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

35 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 2513cm 3 (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 1m 2 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) = 1284cm 3 ). 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

36 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 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 , 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 , 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 , 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).

37 25 In both years, two baskets per site were removed in early April to evaluate eyed egg survival. In (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 , calculations were based on the mean weight of gravel >2mm from the baskets: ± g. In each sediment class was also measured for volume (cm 3 ), by volume displacement. This was not done in Instead, regressions of the volume versus the weight of accumulated fines from each sediment

38 26 class in were used to calculate the volume of gravel in 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: Vol fi Vol bsk - (Vol sub + Vol egg ) *100 Where Vol fi and Vol bsk are the volume of fines (<2mm) and the volume of the incubation basket, respectively; Vol sub is the volume of the initial substrate placed in the basket and Vol egg 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 ( ), 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 ,

39 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 and , but not for the studies conducted by the DFO at Catamaran Brook from 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 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 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-

40 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 logtransformed survival data were based on the equation: N t ln = α + β * year* reach N o 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.

41 29 Results All raw data for survival and sediments are reported in Appendix II. Egg-to-Fry Survival in Catamaran Brook, 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 (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 Survival to emergence each year was lower than to the eyed stage and ranged from 34 to 82% (n=3) in , 2 to 83% (n=10) in and 11 to 61% (n=14) in (Table 2-1). In , 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 and (Figure 2-7). During the late winter of , 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).

42 30 Eyed Survival, & During the studies in and , ice scour was not a problem and only 1 basket in the Gorge reach ( ) was completely displaced from its original position. The basket was reburied when it was found on May 31, 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 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 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 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 (ANOVA, p=0.07) or (ANOVA, p=0.74). Emergence Survival, & Mean survival to emergence was 66% and 63% in and respectively, and did not differ among reaches in either year (Table 2-1; p=0.86 for and p=0.07 for

43 ). Overall, emergence survival in both years declined 27% ( ) and 29% ( ) from survival to the eyed stage. In , 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 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 , peak emergence occurred between June 17 and 19 about a week later than in and was similar among reaches (Figure 2-8). Mean survival at the hatch stage in the Middle reach (site 1) and Lower reach in 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

44 32 November 14, 1998 to April 04, 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 , 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 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 The amount of accumulated degree-days realized when baskets were removed at the eyed stage in both years was <200 degreedays. In comparison to studies elsewhere, the rate of development in Catamaran Brook was faster (see Table 1-1, Chapter 1). Fine Sediments Weight In , 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 compared with In , 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

45 33 gravel matrix within the incubation baskets in the two years from 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 (Table 2-4). This would translate into 36% space available to eggs within the basket after fine sediments had accumulated. In 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 than in in all reaches (Table 2-5). At the eyed stage in , 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 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

46 34 upstream of the site. Regression analyses of survival versus percent fines showed no significant relationship at the eyed stage in either (R 2 =0.02, p=0.69) or (R 2 =0.07, p=0.51, Figure 2-12). Percent volume of fines was inversely related to the survival of eggs to emergence in (R 2 =0.72, p=0.004, Figure 2-12). However, this was not observed in (R 2 =0.008, p=0.81, Figure 2-12) although the amount of sediments increased in 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 was high, except in 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 (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

47 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 and These results indicated that eyed survival during and 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 O 2 concentrations and fine sediment accumulation (Argent and Flebbe, 1999; Greenburgh, 1992; and Rubin 1995), or scouring events such as those seen in Emergence Survival The overall mean emergence survival was lowest in (43%) and (39%) and exceeded 58% in other years ( , and ). 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 for example, emergence survival from baskets apparently not affected by scour was between

48 36 2% and 83%, yet other baskets in the same reaches were lost or displaced due to the midwinter thaw (see above) and were not included in survival estimates. Variability however, was not only limited to years with significant events like the midwinter thaw. In , 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 O 2 as a result of different 'paths' of intragravel flow within each basket or redd. This may have been the case here, since dissolved O 2 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

49 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 and 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 for eyed, for hatch and >500 for emergence (Gunnes, 1979; Crisp, 1988; Vignes and Heland, 1995). In Catamaran Brook, the ranges were 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 and 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

50 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 and 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 and 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 O 2 demands. Presumably, then, any increases

51 39 in fines that altered survival would have been obvious at the eyed stage in either or , 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 (Figure 2-12). The fines measured that year were considerably less than in , yet the overall, mean emergence survival rate remained relatively unchanged (66% in and 63% in ). In , 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/108cm 3, 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/2513cm 3 ) used here were well below these recommended

52 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 ). 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

53 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 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

54 42 ( ) to this stream (Cunjak and Therrien, 1998), it should be considered a valuable tributary of the Miramichi River system.

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56 44 Chapman, D.W., and K.P. MacLeod Development of criteria for fine sediment in the Northern Rockies Ecoregion. Don Chapman Consultants, Work Assignment 2-73, Final Report, Boise, Idaho. 279p. Crisp, D.T Prediction, from temperature, of eyeing, hatching and 'swim-up' times for salmonid embryos. Freshwater Biology 19: Cunjak, R.A., D. Caissie, and N. EI-Jabi The Catamaran Brook Habitat Research Project: description and general design of study. Canadian Technical Report of Fisheries and Aquatic Sciences 1751: 14p. Cunjak, R.A Addressing forestry impacts in the Catamaran Brook basin: an overview of the pre-logging phase. In: Chadwick, E.M.P. [editor] Water, science, and the public: the Miramichi ecosystem. Canadian Special Publication of Fisheries and Aquatic Sciences 123: 300p. Cunjak, R.A. T.D. Prowse, and D.L. Parrish Atlantic salmon in winter: the season of parr discontent? Canadian Journal of Fisheries and Aquatic Sciences 55 (Supplement 1): Cunjak, R.A., and J. Therrien Inter-stage survival of wild juvenile Atlantic salmon, Salmo salar L. Fisheries Management and Ecology 5: Cunjak, R.A., D. Guignion,, R.B. Angus, and R. MacFarlane Survival of eggs and alevins of Atlantic salmon and brook trout in relation to fine sediment deposition, pp 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.

57 45 Elson, P.F Number of salmon needed to maintain stocks. Canadian Fish Culturist 21: Everest, F.H., R.I. Beschta, J.C. Scrivener, K.V. Koski, J.R. Sedell, C.J. Cederhoolm Fine sediment and salmonid production: a paradox. In: E.O. Salo, Cundy, T.W. [editors]. Streamside management: forestry and fishery interactions. University of Washington, Institute of Forest Resources, Contribution No. 57: 471p. Fleming, I.A Reproductive strategies of Atlantic salmon: ecology and evolution. Reviews in Fish Biology and Fisheries 6: Garrett, J.W., and D.H. Bennett Evaluation of fine sediment intrusion into Whitlock-Vibert boxes. North American Journal of Fisheries Management 16: de Gaudemar, B., S.L. Schroder, and E.P. Beall Nest placement and egg distribution in Atlantic salmon redds. Environmental Biology of Fishes 57: Gibson, R.J The Atlantic salmon in fresh water: spawning, rearing and production. Reviews in Fish Biology and Fisheries 3: Greenburg, L.A Field survival of brown trout eggs in a perforated incubation container. North American Journal of Fisheries Management 12: Gunnes, K Survival and development of Atlantic salmon eggs and fry at three different temperatures. Aquaculture 16: Hall, T.J., and R.K. Haley A laboratory study of the effects of fine sediments on survival of three species of Pacific salmon from eyed egg to fry emergence.

58 46 National Council of the Paper Industry for Air and Stream Improvement Technical Bulletin No. 482: 28p. Hamor, T., and E.T. Garside Developmental rates of embryos of Atlantic salmon, Salmo salar L., in response to various levels of temperature, dissolved oxygen, and water exchange. Canadian Journal of Zoology 54: Harshbarger, T.J., and P.E. Porter Survival of brown trout eggs: two planting techniques compared. The Progressive Fish-Culturist 41(4): Harshbarger, T.J., and P.E. Porter Embryo survival and fry emergence from two methods of planting brown trout eggs. North American Journal of Fisheries Management 2: Hausle, A., and D. Coble Influence of sand in redds on survival and emergence of brook trout (Salvelinus fontinalis). Transactions of the American Fisheries Society 105: Lisle, T.E., and R.E. Eads Methods to measure sedimentation of spawning gravels. Res. Note PSW-411. Berkeley, CA: Pacific Southwest Research Station, Forest Service, USDA; 7p. MacCrimmon, H.R., B.L. Gots, and L.D. Witzel Simple apparatus for assessing embryo survival and alevin emergence of stream salmonids. Aquaculture and Fisheries Management 20: MacKenzie, C., and J.R. Moring Estimating survival of Atlantic salmon during the intragravel period. North American Journal of Fisheries Management 8:

59 47 Maret, T.R., T.A. Burton, G.W. Harvey, and W.H. Clark Field testing of new monitoring protocols to assess brown trout spawning habitat in an Idaho stream. North American Journal of Fisheries Management 13: McNeil, W.J., and W.H. Ahnel Success of pink salmon spawning relative to size of spawning bed materials. U.S. Fish and Wildlife Service Special Scientific Report 469: 15p. Meehan, W.R., editor Influences of forest and rangeland management on salmonid fishes and their habitats. American Fisheries Society Special Publication 19: 751p. Pauwels, S.J., and T.A. Haines Survival, hatching, and emergence success of Atlantic salmon eggs planted in three Maine streams. North American Journal of Fisheries Management 14: Peterson, R.H Physical characteristics of Atlantic salmon spawning gravel in some New Brunswick streams. Fisheries and Marine Service Technical Report 785: 28p. Piper, R.G., I.B. McElwain, L.E. Orme, J.P. McCraren, L.G. Fowler, and J.R. Leonard Fish Hatchery Management. American Fisheries Society, Bethesda, Maryland, U.S.A. 517p. Reiser, D.W., and R.G. White Effects of two sediment size-classes on survival of steelhead and chinook salmon eggs. North American Journal of Fisheries Management 8: Rubin, J. F Estimating the success of natural spawning of salmonids in streams. Journal of Fish Biology 46:

60 48 SAS Institute Inc., The SAS System for Windows, version 8. SAS Institute Inc., Cary, NC, USA. Scrivener, J.C Two devices to assess incubation survival and emergence of salmonid fry in an estuary streambed. North American Journal of Fisheries Management 8: Scrivener, J.C., and M.J. Brownlee Effects of forest harvesting on spawning gravel and incubation survival of chum (Oncorhynchus keta) and coho salmon (O. kisutch) in Carnation Creek, British Columbia. Canadian Journal of Fisheries and Aquatic Sciences 46: St-Hilaire, A., D. Caissie, R.A. Cunjak, and G. Bourgeois Spatial and temporal characterization of suspended sediments and substrate composition in Catamaran Brook, New Brunswick. Canadian Technical Report of Fisheries and Aquatic Sciences 2165: 31p. Tappel, P.D., and T.C. Bjornn A new method of relating size of spawning gravel to salmonid embryo survival. North American Journal of Fisheries Management 3: Vignes, J.C., and M. Heland 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 : Young, M.K., W.A. Hubert, and T.A. Wesche Fines in redds of large salmonids. Transactions of the American Fisheries Society 119:

61 49 Year Reach n 1 n 2 Mean Eyed n 2 Mean Emergence n 3 Survival (range) Survival (range) Middle (34-82) Middle (15-83) 2 Gorge (2-18) 6 Lower (64-68) 3 Total/Mean (2-83) Middle (27-61) 0 Gorge (11-49) 0 Lower (75-86) 4 26 (15-46) 1 Total/Mean (65-80) (11-61) Middle (97-98) 6 71 (55-85) 0 Gorge (83-100) 3 60 (47-74) 3* Lower (77-92) 3 59 (50-66) 1** Total/Mean (77-100) (47-85) Middle (95-100) 5 69 (46-83) 0 Gorge (93-100) 2 67 (63-72) 1 Lower (88-100) 2 24 (8-72) 0 Total/Mean (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 Table 2-1: Atlantic salmon egg survival (%) from Catamaran Brook, New Brunswick, and Data for were collected by personnel from the Department of Fisheries and Oceans and were not hatchery corrected. Baskets in column n 3 were not included in survival estimates. In , four baskets (2 Middle reach and 2 Lower reach) were removed at the hatch stage (not shown).

62 50 Date Reach n Mean Survival Range Middle Lower n - number of baskets retrieved Total/Mean Table 2-2: Survival (%) of Atlantic salmon eggs to the hatch stage in the Middle reach (site-1) and Lower reach, Catamaran Brook

63 Reach n Mean (range) n Mean (range) Middle ( ) ( ) Eyed Gorge ( ) ( ) Lower 1* 2.9 (-) ( ) Hatch Middle - n/a ( ) Lower - n/a ( ) Middle 5* 3.6 ( ) 2 a 2.6 ( ) Emergence 3 b 11.1 ( ) Gorge ( ) ( ) Lower ( ) ( ) * one sediment sample lost after retrieval of baskets. a and b are the Middle reach (site-1) and Middle reach (site-2), respectively. Table 2-3: Percent fines by weight (g) from incubation baskets buried in Catamaran Brook for the years Gorge ( ) three baskets removed from analysis at emergence stage due to significant change in habitat.

64 52 Year Stage Number of Volume of Volume of Total Volume Percent Volume Percent Volume Baskets Gravel (>2mm) Fines (<2mm) (Gravel & Fines) of Basket of Basket (cm 3 ) (cm 3 ) Occupied Available Eyed 9(1) 1284 a Emergence 13(3) 1284 a Eyed Hatch Emergence 9(1) a determined based on the average from the gravel >2mm in Table 2-4: Volume occupied by gravel/substrate in incubation baskets in and Volumes and percentages calculated based on the volume 2513cm 3 of the baskets. Numbers in brackets are baskets that were not included in calculation because of lost sediments.

65 Reach n Mean (range) n Mean (range) Middle ( ) ( ) Eyed Gorge ( ) ( ) Lower 1* ( ) Hatch Middle - n/a ( ) Lower - n/a ( ) Middle ( ) 2 a 10.6 ( ) Emergence 3 b 31.2 ( ) Gorge ( ) ( ) Lower ( ) ( ) * one sediment sample lost after retrieval of baskets. a and b are the Middle reach (site-1) and Middle reach (site-2), respectively. Table 2-5: Percent volume of fines accumulated in baskets in Catamaran Brook in and Values calculated as percent volume of basket ( cm 3 ). Gorge reach ( ) three baskets were removed from analysis at emergence stage due to a significant change in habitat.

66 54 Study Site Middle Reach Site 2 Site 1 Lower Reach Gorge Reach Site 4 Site 3 (1999 only) Site 5 Figure 2-1: Map of Catamaran Brook, including sites used in and

67 55 Figure 2-2: Detailed description of incubation baskets used in and at Catamaran Brook.

68 56 Forest Timber Harvest Block (with riparian buffer) FLOW Riparian Buffer Incubation Baskets 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).

69 57 Figure 2-4: Diagram of an incubation basket buried in the streambed substrate.

70 58 A B Figure 2-5: Emergence basket in situ (A) schematic, (B) actual picture looking through water.

71 % Survival Middle Gorge Lower Reach (upstream downstream) Figure 2-6: Annual survival of Atlantic salmon eggs to the eyed stage, by study reach in Catamaran Brook.

72 60 % Survival Middle Gorge Lower Reach 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.

73 Number of salmon Jun-99 5-Jun-99 6-Jun-99 7-Jun-99 8-Jun-99 9-Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun-99 1-Jul-99 2-Jul-99 A 120 Date Middle Gorge Lower Number of salmon Jun-00 3-Jun-00 4-Jun-00 5-Jun-00 6-Jun-00 7-Jun-00 8-Jun-00 9-Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun Jun-00 1-Jul-00 2-Jul-00 3-Jul-00 4-Jul-00 5-Jul-00 6-Jul-00 7-Jul-00 B Date Middle Gorge Lower Figure 2-8: Daily emergence of Atlantic salmon alevins from all incubation baskets combined by reach in Catamaran Brook in (A) and (B).

74 Percent Survival % Fines (by volume) 0 Eyed Hatch Emergence Developmental Stage 0.0 Middle (S%) Lower (S%) Middle (Fines) Lower (Fines) Figure 2-9: Mean survival including standard error bars at eyed, hatch and emergence stages in 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.

75 Temperature ( C) Nov Nov Dec Dec Dec Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun-99 Date A Middle Reach Gorge Reach Lower Reach Temperature ( C) Nov Nov Nov Dec Dec Jan Jan Feb Feb Mar Mar Apr Apr May May May Jun Jun-00 Date B Middle Reach Gorge Reach Lower Reach Figure 2-10: Average daily intragravel temperatures by reach for (A) and (B).

76 Start of Emergence Degree Days 600 Planted Eyed Nov Nov Nov Nov Dec Dec Dec Dec Dec Jan Jan Jan Jan Feb Feb Feb Feb Mar Mar Mar Mar Mar Apr Apr Apr Apr May May May May Jun Jun Jun Jun Jun-99 Date A Middle Reach Gorge Reach Lower Reach 1200 Start of Emergence Degree Days 600 Planted eggs Eyed Nov Nov Nov Nov Nov Dec Dec Dec Dec Jan Jan Jan Jan Feb Feb Feb Feb Feb Mar Mar Mar Mar Apr Apr Apr Apr May May May May May Jun Jun Jun Jun Jul-00 Date B Middle Reach Gorge Reach Lower Reach Figure 2-11: Accumulated degree-days by reach for Atlantic salmon eggs in Catamaran Brook in (A) and (B). Eyed refers to the day on which incubation baskets were removed from the streambed.

77 R 2 = 0.02 R 2 = 0.07 Percent Survival 60.0 R 2 = 0.73 R 2 = Percent Fines (by volume) Eyed Eyed Emergence Emergence Figure 2-12: Regression of percent survival vs. percent volume of fines at the eyed and emergence stages in Catamaran Brook for and R 2 values shown.

78 66 CHAPTER 3 The effects of regulated stream flow on the survival of Atlantic salmon (Salmo salar) eggs in the Tobique River, New Brunswick

79 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 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.

80 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

81 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 m 2 ) 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.

82 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

83 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, 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

84 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

85 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

86 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: ). 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 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.

87 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.

88 76 Each year from , 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 Site location contributed significantly to hatch survival from (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 5.0m 3 /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.

89 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 m 3 /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

90 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 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.

91 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 ( %) and also at the hatch stage ( %), 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

92 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 (<5.0m 3 /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 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

93 81 the rivers in 1999 and 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

94 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 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 ( ) was also much less than in the Gulquac-UP site. Furthermore, the magnitude by which

95 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

96 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

97 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 degreedays 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

98 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).

99 87 References: Bain, M.B. amd V.T. Travnichek 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.] 2 nd International Symposium on Habitat Hydraulics. Ecohydraulics B: B543-B552. Bardonnet, A. and J. Baglinière Freshwater habitat of Atlantic salmon (Salmon salar). Canadian Journal of Fisheries and Aquatic Sciences 57: Beschta, R.L., R.E. Bilby, G.W. Brown, L.B. Holtby, and T.D. Hofstra Stream Temperature and Aquatic Habitat: Fisheries and Forestry Interactions. In Salo, E.O. and T.W. Cundy [ed.]. Streamside Management: Forestry and Fishery Interactions: Bjornn, T.C., and D.W. Reiser 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. Blachut, S.P The winter hydrologic regime of the Nechako River, British Columbia. Canadian Manuscript Report of Fisheries and Aquatic Sciences No. 1964: 145p. Bradford, M.J Trends in the abundance of chinook salmon (Oncorhynchus tshawytscha) of the Nechako River, British Columbia. Canadian Journal of Fisheries and Aquatic Sciences 51:

100 88 Brännäs, E First access to territorial space and exposure to strong predation pressure: a conflict in early emerging Atlantic salmon (Salmon salar L.) fry. Evolutionary Ecology 9: Brannon, E. L Mechanisms stabilizing salmonid fry emergence timing. In H. D. Smith, L. Margolis, and C. C. Wood [ed.]. Sockeye salmon (Oncorhynchus nerka) Population Biology and Future Management. Canadian Special Publication of Fisheries and Aquatic Sciences 96: Carr, J A review of downstream movements of juvenile Atlantic salmon (Salmo salar) in the dam-impacted St. John River drainage. Canadian Manuscript Report of Fisheries and Aquatic Sciences 2573: 76p. Chaput, G Status of wild Atlantic salmon (Salmo salar) stocks in the Maritime Provinces. Canadian Stock Assessment Secretariat Research Document 98/153: 30p. Crisp, D.T Prediction, from temperature, of eyeing, hatching and 'swim-up' times for salmonid embryos. Freshwater Biology 19: Crisp, D.T Water temperature in a stream gravel bed and implications for salmonid incubation. Freshwater Biology 23: Cunjak, R.A Factors Affecting the Winter Survival of Juvenile Atlantic Salmon. In Collected Papers on Fish Habitat with Emphasis on Salmonids. Canadian Atlantic Fisheries Scientific Advisory Committee Research Document 90/77: 423p.

101 89 Cunjak, R.C Winter habitat of selected stream fishes and potential impacts from land-use activity. Canadian Journal of Fisheries and Aquatic Sciences 53 (Supplement 1): Cunjak, R.C., T.D. Powers, and D.L. Parrish Atlantic salmon (Salmo salar) in winter: the season of parr discontent? Canadian Journal of Fisheries and Aquatic Science 55 (Supplement 1): Cushman, R. M Review of ecological effects of rapidly varying flows downstream from hydroelectric facilities. North American Journal of Fisheries Management 5: Danie, D.S., J.G. Trial, and J.G. Stanley Species profiles: life histories and environmental requirements of coastal fish and invertebrates (North Atlantic) - Atlantic Salmon. U.S. Fish and Wildlife Service FWS/OBS-82/ U.S. Army Corps of Engineers, TR EL p. Environment Canada HYDAT CD, version Climate and Water Products Division, Downsview, Ontario. [downloaded: 19 June 2002]. Available from: Fleming, I.A Reproductive strategies of Atlantic salmon: ecology and evolution. Reviews in Fish Biology and Fisheries 6: Gibson, R.J The Atlantic salmon in fresh water: spawning, rearing and production. Reviews in Fish Biology and Fisheries 3: Gunnes, K Survival and development of Atlantic salmon eggs and fry at three different temperatures. Aquaculture 16:

102 90 Humphries, P. and P.S. Lake Fish larvae and the management of regulated rivers. Regulated Rivers: Research & Management 16: Kane, T.R Relationship of temperature and time of initial feeding of Atlantic salmon. Progressive Fish Culturist 50: Kocik, J.F. and W.W. Taylor Effect of fall and winter instream flow on yearclass strength of Pacific salmon evolutionarily adapted to early fry outmigration: A Great Lakes perspective. American Fisheries Society Symposium 1: Lapointe, M. et. al Modelling the probability of salmonid egg pocket scour due to floods. Canadian Journal of Fisheries and Aquatic Sciences 57: MacKenzie, C, and J.R. Moring Estimating survival of Atlantic salmon during the intragravel period. North American Journal of Fisheries Management 8: Marshall, L., C.J. Harvie, and R. Jones Status of Atlantic salmon stocks of southwest New Brunswick, Canadian Stock Assessment Secretariat Research Document 98/30: 60p. Montgomery, D. R, J.M. Buffington, N.P. Peterson, D. Schuett-Hames, and T.P. Quinn 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: Nathanailides, C., O. Lopez-Albors, and N.C. Stickland Influence of prehatch temperature on the development of muscle cellularity in posthatch Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 52:

103 91 Ojanguren, A.F., F.G. Reyes-Gavilán and R.R Muñox Effects of temperature on growth and efficiency of yolk utilisation in eggs and pre-feeding larval stages of Atlantic salmon. Aquaculture International 7: Peterson, R.H., Spinney, H.C.E. and Sreeharan, A Development of Atlantic salmon (Salmo salar) eggs and alevins under varied temperature regimes. Journal of the Fisheries Research Board of Canada 34: Peterson, R.H Physical characteristics of Atlantic salmon spawning gravel in some New Brunswick streams. Fisheries and Marine Service Technical Report 785: 28p. Piper, R.G., I.B. McElwain, L.E. Orme, J.P. McCraren, L.G. Fowler, and J.R. Leonard Fish Hatchery Management. American Fisheries Society, Bethesda, Maryland, U.S.A. 517p. Reiser, D.W. and T.A. Wesche In situ freezing as a cause of mortality in brown trout eggs. The Progressive Fish Culturist 41: Reiser, D.W Effects of streamflow reduction, flow fluctuation and flow cessation on salmonid egg incubation and fry quality. Ph.D. thesis, University of Idaho. 236p. Rubin, J. F Estimating the success of natural spawning of salmonids in streams. Journal of Fish Biology 46: Ruggles, C.P. and W.D. Watt Ecological changes due to hydroelectric development on the St. John River. Journal of the Fisheries Research Board of Canada 32:

104 92 Scott, W. B. and E. J. Crossman Freshwater Fishes of Canada. Galt House Publications, Ltd., Ontario, Canada. 966p. Siler, E.R., J.B. Wallace, and S.L. Eggert Long-term effects of resource limitation on stream invertebrate drift. Canadian Journal of Fisheries and Aquatic Sciences 58: Smith, K.E.H Compendium, St. John River System, New Brunswick. Department of the Environment, Fisheries Service, Halifax, Nova Scotia. 238p. Symons, P.E.K Territorial behavior of juvenile Atlantic salmon reduces predation by brook trout. Canadian Journal of Zoology 52: Vignes, J.C., and M. Heland 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 : Washburn and Gillis Associates Limited Assessment of Atlantic salmon smolt recruitment in the St. John River, Final Report prepared for Salen Inc., Edmunston, New Brunswick.

105 93 River Site* Location Comments Dee UP Below Trousers Lake Moved upstream in 2000 because more representative of salmon spawning area, salmon redds 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 Gulquac UP Above Bridge Moved upstream (~200m) in 1999 due to significant ice build-up experienced at former site in Gulquac DN Below Dingee Added in 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 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).

106 94 Eyed Survival p-value* Hatch Survival Baskets p-value* Year River Location n 1 n 2 Mean Survival n 2 Mean Survival Lost/ (range) (range) Exposed Gulquac UP (47-58) Dee UP (14-30) 0 - DN (0-16) Don UP (12-38) 2 - Gulquac UP (83-86) (23-54) 0 - DN (25-37) n/a Dee UP (75-77) (9-21) 0 - DN ( - ) - 0 n/a 3 - Don UP ( - ) (8-9) 1 - DN 4 0 n/a - 0 n/a 4 - Serpentine UP (7-41) 0 - DN (6-34) 0 - Gulquac UP (76-95) (73-77) 0 - DN (32-48) n/a Dee UP (56-93) (22-62) 0 - DN ( - ) (10-24) n/a 0 n/a 4 - Don UP 4 0 n/a - 0 n/a 4 - DN (37-50) (9-24) n/a - 0 n/a 4 - * p-values for comparisons with Gulquac-UP site; only values significant at 0.05 shown n 1 - number of baskets installed in the fall n 2 - number of baskets retrieved at stage Table 3-2: Mean egg survival in incubation baskets from in rivers from the Tobique River basin, New Brunswick.

107 95 Eyed Stage Hatch Stage Baskets Year River Location n 1 n 2 Mean Percent Volume of Fines n 2 Mean Percent Volume of Fines Lost/Exposed Gulquac UP 4 - n/a ( ) Dee UP 4 - n/a 3 a 4.9 ( ) 0 DN 4 - n/a 3 a 1.1 ( ) 0 Don UP 4 - n/a ( ) 2 Gulquac UP ( ) ( ) 0 DN 4 2 b n/a 0 n/a Dee UP ( ) 1 c 3.0 ( - ) 1 DN ( - ) 0 n/a 3 Don UP ( ) 1 DN 4 0 n/a 0 n/a 4 Serpentine UP 4 0 n/a ( ) 0 DN 4 0 n/a ( ) 0 Gulquac UP ( ) ( ) 0 DN ( ) 0 n/a Dee UP ( ) ( ) 0 DN ( - ) ( ) n/a 0 n/a 4 Don UP 4 0 n/a 0 n/a 4 DN ( ) ( ) n/a 0 n/a 4 a substrate analysis not performed on one basket b difficulty retrieving baskets, fines lost; no sediment analysis recorded c sediment sample dropped while processing; analysis not performed Table 3-3: Mean volume of fine sediments measured from different sites in the Tobique River basin, Percent fines calculated based on the volume occupied within the basket = cm 3.

108 96 Tobique River Basin Hydroelectric Dam kilometers 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.

109 97 Grande Rivière Serpentine-DN Serpentine-UP Dee-DN Don-DN Don-UP Serpentine Lake New Brunswick, Canada/Maine, USA Border Gulquac-DN Gulquac-UP Dee-UP Long Lake Trousers Lake Gulquac Lake Incubation Basket Site Hydroelectric Dam kilometers Figure 3-2: Tobique River basin showing tributaries and sites used in each year of this study.

110 98 Figure 3-3: Incubation basket (s) used to study egg survival of Atlantic salmon eggs in the Tobique River Basin.

111 Percent Survival Dee-UP Dee-DN Don-UP Don-DN Gulquac-UP Gulquac-DN Site 1999 (thin error bars) 2000 (thick error bars) Figure 3-4: Mean survival (with standard error bars) of Atlantic salmon eggs to the eyed stage for the years 1999 and Graph shows effects of year and site on egg survival.

112 Percent Survival Dee-UP Dee-DN Don-UP Don-DN Gulquac-UP Gulquac-DN Serpentine- UP Sites Serpentine- DN 1998 (dashed error bars) 1999 (thin error bars) 2000 (thick error bars) 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, n is the number of baskets used to determine the mean survival.

113 Discharge (m /sec) 2000 Figure 3-6: Mean daily discharges for regulated and unregulated rivers in 1998, 1999 and Gulquac River discharges represented by discharges measured in the 'unregulated' Grande Rivière. All discharges adjusted for the same drainage area of 193km 2.

114 Daily Intragravel Water Temperatures ( C) Date Gulquac Dee Don Serpentine 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.

115 Accumulated Degree-days Figure 3-8: The average accumulated degree-days for each river (all sites combined) during incubation in 1998, 1999 and 2000.

116 104 CHAPTER 4 General Discussion

117 105 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

118 106 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.).

119 107 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;

120 108 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.

121 109 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

122 110 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 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

123 111 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!

124 112 References Bain, M.B. amd V.T. Travnichek 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.] 2 nd International Symposium on Habitat Hydraulics. Ecohydraulics B: B543- B552. Bardonnet, A., P. Gaudin, and E. Thorpe 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: Bardonnet, A., J.-L. Baglinière Freshwater habitat of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 57: Bley, P.W., and J.R. Moring 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 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 Critical review of variables used to define effects of fines in redds of large salmonids. Transactions of the American Fisheries Society 117: 1-21.

125 113 Cunjak, R.C., T.D. Powers, and D.L. Parrish Atlantic salmon (Salmo salar) in winter: the season of parr discontent? Canadian Journal of Fisheries and Aquatic Science 55(Suppl. 1): Fleming, I.A Reproductive strategies of Atlantic salmon: ecology and evolution. Reviews in Fish Biology and Fisheries 6: Gibson, R.J The Atlantic salmon in fresh water: spawning, rearing and production. Reviews in Fish Biology and Fisheries 3: Humphries, P. and P.S. Lake Fish larvae and the management of regulated rivers. Regulated Rivers: Research & Management 16: Kocik, J.F. and W.W. Taylor Effect of fall and winter instream flow on yearclass strength of Pacific salmon evolutionarily adapted to early fry outmigration: A Great Lakes perspective. American Fisheries Society Symposium 1: Lisle, T.E., and R.E. Eads Methods to measure sedimentation of spawning gravels. Res. Note PSW-411. Berkeley, CA: Pacific Southwest Research Station, Forest Service, USDA: 7p. Lowney, C.L Stream temperature variation in regulated rivers: Evidence for a spatial pattern in daily minimum and maximum magnitudes. Water Resources Research 36: Montgomery, D. R. J.M. Buffington, N.P. Peterson, D.S. Schuett-Hames and T.P. Quinn 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:

126 114 Ojanguren, A.F., F.G. Reyes-Gavilán and R.R Muñox Effects of temperature on growth and efficiency of yolk utilisation in eggs and pre-feeding larval stages of Atlantic salmon. Aquaculture International 7: Peterson, R.H., Spinney, H.C.E. and Sreeharan, A Development of Atlantic salmon (Salmo salar) eggs and alevins under varied temperature regimes. Journal of the Fisheries Research Board of Canada 34: Peterson, R.H Physical Characteristics of Atlantic salmon spawning gravel in some New Brunswick streams. Fisheries and Marine Service Technical Report 785: 28p. Rubin, J. F Estimating the success of natural spawning of salmonids in streams. Journal of Fish Biology 46:

127 115 APPENDIX I Calculations of Dimensions of the Incubation Baskets Used in the Current Studies

128 116 Large Window (LW) Baskets: Volume (cylinder) = πr 2 x h = π(5cm) 2 x 32cm = cm 3 (Surface) Area = [2 x circles] + [area of rectangle]* = [2 x (πr 2 )] + [height x length**] = [157.08] + [ ] = cm 2 * Imagine the basket as 2 circles and a rectangle, to calculate area i.e. ** Where length, is calculated as πd, the circumference of a circle Window Area = length x width = 10cm x 15.5cm = 155cm 2 (multiplied by 3, for 3 windows per basket) = 465cm 2 Percent of surface (i.e. mesh) exposed: (465cm 2 / cm 2 ) x 100 = 40% of basket are exposed to gravel Small Window (SW) Baskets: Volume = cm 3 (Surface) Area = cm 2 Window Area = 252cm 2 Percent mesh = 19% Mesh Baskets: Volume (cylinder) = cm 3 Percent of surface exposed = 90%