Spatial Ecology of Fish in Toronto Harbour in Response to Aquatic Habitat Enhancement by Maxime A. N. Veilleux B.Sc., University of Guelph, 2012 A thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Master of Science in Biology Carleton University Ottawa, Ontario © 2014, Maxime A. N. Veilleux Abstract Every year billions of dollars are being spent on rehabilitation activities in hopes of improving the state of degraded ecosystems. In this thesis, I considered the practical aspects of acoustic telemetry for studying habitat enhancement and investigated the effectiveness of habitat enhancement initiatives in Toronto Harbour by comparing fish habitat use of six species in two enhanced slips to two non-enhanced slips. During spring, Northern pike were found to spend more time in the enhanced slips compared to the non- enhanced slips. All other species did not spend significantly different amounts of times across the slips. When Largemouth bass and Northern pike were experimentally displaced in the enhanced slips, they left within 29 hours suggesting that the enhanced habitats did not provide substantial direct benefits to adult fish in this study. Overall, telemetry studies with good experimental designs are considered valid tools for management. ii Acknowledgements I would like to thank my supervisor Steven Cooke, my co-supervisor Susan Doka, and my mentors Nick Lapointe, and Jon Midwood for their help, guidance, support and patience. I would also like to thank my collaborators (Andrew Rous, Tyler Peat, Bodgan Hlevca, Mathew Wells, and Liset Cruz-Font) for helping with the overall Toronto Harbour project development. I would like to extend my sincerest appreciation to many employees from the Toronto and Region Conservation Authorities (TRCA) (Adam Weir, Pete Shuttleworth, Brian Graham, Rosss Davidson, Rick Portiss, and Emily Morton) and volunteers from the Fish Ecology and Conservation Physiology Laboratory (Robert Lennox, Tanya Prystay, Graham Raby, and Andrew Weatherhead) for assistance in the field. Finally, I would like to thank my family and friends for the continuous support and encouragement. iii Co-Authorship Chapter 2: Tracking Fish to Inform Habitat Management and Rehabilitation: A Case Study of the Toronto Harbour Area of Concern M.A.N. Veilleux, J.D. Midwood, A. Rous, S.E. Doka, N.W.R. Lapointe, A. Weir, M. Wells, and S.J. Cooke While the study is my own, the research was undertaken as part of a collaborative effort, and each co-author played a valuable role in its completion. The project was conceived by Veilleux, Midwood, Lapointe, and Cooke. Field work was completed by Veilleux, Lapointe, Midwood, Rous, and Weir. All writing was conducted by Veilleux. All co-authors provided comments and feedback on the manuscript. The manuscript is in preparation for submission to a peer-reviewed journal. Chapter 3: Spatial ecology of adult fish relative to habitat enhancement activities in an urban freshwater harbour: a multi-species acoustic telemetry study M.A.N. Veilleux, J.D. Midwood, S.E. Doka, N.W.R. Lapointe, A. Weir, R. Portiss, M. Wells, and S.J. Cooke While the study is my own, the research was undertaken as part of a collaborative effort, and each co-author played a valuable role in its completion. The project was conceived by Veilleux, Midwood, Lapointe, and Cooke. Field work was completed by Veilleux, Lapointe, Midwood, Rous, and Weir. All data analysis was conducted by Veilleux. Data were interpreted by Veilleux, Midwood, and Cooke. All writing was conducted by Veilleux. All co-authors provided comments and feedback on the manuscript. The manuscript is in preparation for submission to a peer-reviewed journal. iv Table of Contents Abstract .............................................................................................................................. ii Acknowledgements .......................................................................................................... iii Co-Authorship .................................................................................................................. iv Chapter 2: Tracking Fish to Inform Habitat Management and Rehabilitation: A Case Study of the Toronto Harbour Area of Concern ................................................. iv Chapter 3: Spatial ecology of adult fish relative to habitat enhancement activities in an urban freshwater harbour: a multi-species acoustic telemetry study ................... iv Table of Contents .............................................................................................................. v List of Tables ................................................................................................................... vii List of Figures ................................................................................................................... ix Glossary ........................................................................................................................... xii Chapter 1: General Introduction .................................................................................... 1 1.1 Background Information ................................................................................................ 1 1.2 Research Objectives ....................................................................................................... 6 Chapter 2: Tracking Fish to Inform Habitat Management and Rehabilitation: A Project Implementation Case Study of the Toronto Harbour Area of Concern ........ 8 2.1 Abstract .......................................................................................................................... 8 2.2 Introduction .................................................................................................................... 9 2.3 Background................................................................................................................... 10 2.4 Site Information ............................................................................................................ 11 2.5 Choice of Species ......................................................................................................... 12 2.6 Fish tagging .................................................................................................................. 15 2.7 Receiver Configuration & Fine-Scale Positioning ....................................................... 18 2.8 Receiver Deployments and Retrievals .......................................................................... 21 v 2.9 Range Testing ............................................................................................................... 25 2.10 Database Management .................................................................................................. 27 2.11 Conclusions .................................................................................................................. 29 2.12 Tables ........................................................................................................................... 33 2.13 Figures .......................................................................................................................... 36 Chapter 3: Spatial ecology of adult fish relative to habitat enhancement activities in an urban freshwater harbour: a multi-species acoustic telemetry study .................. 41 3.1 Abstract ........................................................................................................................ 41 3.2 Introduction .................................................................................................................. 42 3.3 Methods ........................................................................................................................ 46 3.3.1 Field Site/ Receiver Arrays ...................................................................................... 46 3.3.2 Fish Collection ......................................................................................................... 47 3.3.3 Surgical Procedures .................................................................................................. 48 3.3.4 Statistical Analysis ................................................................................................... 49 3.4 Results .......................................................................................................................... 50 3.5 Discussion..................................................................................................................... 55 3.6 Tables ........................................................................................................................... 65 3.7 Figures .......................................................................................................................... 70 Chapter 4: General Discussion ...................................................................................... 79 4.1 Findings and Implications ............................................................................................ 79 4.2 Conclusions .................................................................................................................. 81 4.3 Future Directions .......................................................................................................... 81 Literature Cited .............................................................................................................. 84 vi List of Tables Table 2-1 Challenges associated with acoustic telemetry studies in nearshore temperate freshwater systems such as Toronto Harbour, Lake Ontario, ON, CAN. ......................... 33 Table 2-2 Details of fish sedations using a portable electroanesthesia system (PES) (Smith-Root, Inc., Vancouver, WA). Electrode positions were determined based on the size of the fish (efforts were made to reduce the distance between electrodes for each individual). ........................................................................................................................ 34 Table 2-3 Pros and cons of various acoustic receiver station models............................... 35 Table 3-1 Physical characteristics of the four waterfront slips in Toronto Harbour. Temperature data originate from Hobo (Onset Computer Corporation, Bourner, MA) temperature data loggers. .................................................................................................. 65 Table 3-2 Slip presence, time spent (hours) before leaving the release slip, total time spent (hours) during spring and summer, and number of days until return to capture location of displaced Largemouth bass and Northern pike in the four slips after being released in either Spadina or Peter on 7-8 May 2013. ...................................................... 66 Table 3-3 Total number, mean length (mm), minimum and maximum lengths of fish, and type of acoustic transmitter in Toronto Harbour by year tagged. T=temperature sensor, P=pressure sensor. ............................................................................................................ 67 Table 3-4 Details of fish sedations using a portable electroanesthesia system (PES) (Smith-Root, Inc., Vancouver, WA). Electrode positions were determined based on the size of the fish (efforts were made to reduce the distance between electrodes for each individual). Brown bullhead and Yellow perch were sedated with a 60 ppm clove oil bath. ................................................................................................................................... 68 vii Table 3-5 Species richness among four waterfront slips across four seasons (total of 6 species: Largemouth bass, Northern pike, Common carp, Walleye, Brown bullhead, and Yellow perch).................................................................................................................... 69 viii List of Figures Figure 2-1 Map of acoustic telemetry study in Toronto Harbour from 2010-2014. ......... 36 Figure 2-2 a) Custom-built cement station with embedded polyvinyl chloride PVC pipe and b) station covered with biofouling. ............................................................................ 37 Figure 2-3 Probability of five receivers located in the Spadina slip to detect two V13-1x range-test tags (Vemco, 7 second delay) positioned at 10 nearby locations (5 bottom and 5 subsurface) for 10 minutes each. Each box on the figure represents the probability of detection of 10 different range-test tag locations from September 11, 2012. Each range- test tag emitted approximately 595 signals during each 10-minute period. ..................... 38 Figure 2-4 Probability of eight receivers located at the Outer Harbour channel to detect a V13-1x range-test tag (Vemco, 7 second delay) positioned at eight nearby locations for 30 minutes each. Each point on the figure represents the proportion of converted signals on a receiver (i.e., 8 range-test tag locations x 8 receivers). Data were obtained on October 25, 2011. The range-test tag emitted approximately 257 signals during each 30- minute period. ................................................................................................................... 39 Figure 2-5 Probability of a receiver located in Spadina slip (i.e., Spadina 1) to detect a stationary V13-1x synctag (Vemco, 500-700 second delay) from November 12, 2012 to November 13, 2013. Each box represents the average daily number of synctag detections for a particular month. The expected maximum number of synctag transmissions per day is 144. Outliers represent days where receivers were pulled out of the water for data downloads. ........................................................................................................................ 40 Figure 3-1 Map of Toronto Harbour acoustic telemetry array with insets of the meso- scale 2D positioning acoustic telemetry array in four waterfront slips. ........................... 70 ix Figure 3-2 Mean time fish spent per slip visit (minutes) in four waterfront boat slips during four seasons. No Yellow perch or Brown bullhead were detected in the slips. Bars represent standard error..................................................................................................... 71 Figure 3-3 Mean total time (hours) fish spent in four waterfront boat slips during four seasons. No Yellow perch or Brown bullhead were detected in the slips. Bars represent standard error. ................................................................................................................... 72 Figure 3-4 Kernel density estimates of Largemouth bass in four boat slips located in Toronto Harbour, ON, during four seasons (low KDEs are shown in light colours and high KDEs are shown in dark colours). Sample sizes from left to right: Spadina = 0, 0, 0, 0; Peter = 0, 0, 0, 0; Jarvis = 0, 0, 0; Parliament = 0, 0, 1. No meso-scale data available in Jarvis and Parliament after June 2013. ............................................................................. 73 Figure 3-5 Kernel density estimates of Northern pike in four boat slips located in Toronto Harbour, ON, during four seasons (low KDEs are shown in light colours and high KDEs are shown in dark colours). Sample sizes from left to right: Spadina = 8, 6, 13, 6; Peter = 6, 7, 13, 4; Jarvis = 0, 1, 5; Parliament = 0, 0, 2. No meso-scale data available in Jarvis and Parliament after June 2013. ........................................................................................ 74 Figure 3-6 Kernel density estimates of Common carp in four boat slips located in Toronto Harbour, ON, during four seasons (low KDEs are shown in light colours and high KDEs are shown in dark colours). Sample sizes from left to right: Spadina = 3, 0, 2, 6; Peter = 2, 0, 2, 5; Jarvis = 0, 0, 1; Parliament = 3, 0, 3. No meso-scale data available in Jarvis and Parliament after June 2013................................................................................................ 75 Figure 3-7 Kernel density estimates of Walleye in four boat slips located in Toronto Harbour, ON, during four seasons (low KDEs are shown in light colours and high KDEs x