Ethology and sensory physiology associated with social organisation in yellow-eyed mullet (Aldrichetta forsteri), kahawai (Arripis trutta), and snapper (Chrysophrys auratus) by Karen Lewanne Middlemiss Submitted as a thesis in fulfilment of the requirements for the degree of Doctor of Philosophy The School of Biological Sciences University of Canterbury, Christchurch, New Zealand 2017 This thesis is available for library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that no material has previously been submitted and approved for the award of a degree by this or any other University. (Signature) ……………………………………………………………………………… ‒ ii ‒ Acknowledgements In the words of arguably the greatest naturalist humankind has ever known, and who since childhood has inspired my love of the natural world, “I wish the world was twice as big and half of it unexplored” – David Attenborough. Me too! My journey to becoming a biologist began in my ‘youth-adjacent’ years whilst working for the Royal New Zealand Air Force. I was on a five-month secondment at Scott Base with Antarctica New Zealand providing logistical support to hundreds of New Zealand scientists doing some amazing research during the summer of 2005/06. One of those scientists would nine years later become my doctoral supervisor; Professor Bill Davison. Together with then PhD student Dr. Esme Robinson, who became a dear friend and mentor in my early academic career, we spent many hours drilling holes in the ice-covered McMurdo Sound to catch research fish. I would later watch with intrigue as experiments were conducted. Bill and Esme, I am forever grateful for those amazing experiences, because a seed was planted which marked a turning point in my life and career. Two years later, I began a new career path and enrolled in a BSc at Lincoln University, which led on to a MSc by Research at Exeter University in England, and ultimately my return home to New Zealand to enrol at the University of Canterbury for my doctorate, based in Nelson at The New Zealand Institute of Plant & Food Research (PFR). Anyone who has completed such a large undertaking as a doctoral degree knows it is a team effort and would not be possible without the involvement of many people. Firstly, Bill for your guidance, for transporting and entrusting lab equipment to me from uni, and for your dry sense of humour and relentless calm and exacting approach to the rigours of scientific research and writing (is that a sentence…? ). You are a wealth of fish physiology knowledge (among other things) and a man who can speak volumes with very few words. Thank you for everything and I’m proud to be one of your last PhD students! To Helen, Alistair, Suzy, Denham and Esme for heading my supervisory team at PFR. Thank you for all the opportunities this research has provided me with. You have an amazing and innovative team. I am also grateful for the funding I received through the Ministry of Business, Innovation and Employment scholarship (contract # C11X1203), as part of PRFs Wildfish 2030 project. That gave me the space to focus on the research and not on how to pay the bills as well. Denham, we managed to navigate our way through the maze and I thank you for all your help and persistence during the uphill times and for your vision in helping to elucidate the intricacies of fish behaviour. To the technical staff at PFR who provided assistance with animal husbandry, engineering of experimental equipment, biochemistry, statistical advice, manuscript reviews, and general support and encouragement for my research projects. Special mention to Therese for your friendship and support, and to Belinda, Benie, Steve, Scotty, Seb, Igor, Dan, Peter, Duncan, Andrew, Matt, Sharon, Annalise, Emma, Nick, Marcus, Josh, and Mark. You were all amazing! Also, a big thank you to PFR senior scientist Dr. Maren Wellenreuther who became a mentor, unofficial supervisor and good friend. I will always remember the kindness you showed to me in constantly checking on my progress in and out of working hours when it wasn’t required of you, and for the leadership you showed in offering to review my work and provide guidance and career advice, especially in postdoc matters and the development of future projects and ‒ iii ‒ funding applications. Thank you for the walks, talks, dinners and high tea breaks and for recognising and encouraging my strengths! Go Emirates Team NZ! A big thank you also to Jim Seager of SeaGIS, Australia, for your time and commitment to tailoring photogrammetry software solutions to my specific research needs, for providing training, and for always being available to answer questions no matter where on the globe you were! I have no doubt students around the world would echo the same sentiment when I say that without you, I would have spent so much more time extracting data from footage instead of on data analysis. I’ve had the great pleasure of working with so many amazing PFR people, but a highlight has been sharing an office with David, a fellow PhD candidate. Your ever bubbly personality and broad view of the world made the past three years even more memorable. We enjoyed endless philosophical debates about subjects as broad as Schrödinger’s Cat, or the latest publication in Science Daily, and many long Fridays were made easier with funny you-tube clips (bad lip reading…). I’d hate to think how much tea we got through over the past three years! Thank you for your friendship, for the epic fishing trip with Seb to catch my experimental kahawai, for giving me an education in genetics and coding, for being interested in the synergies between both our projects, which helped to deepen my understanding, and for always being up for a light refreshment with the team on a Friday. Friends for life! To my family and friends. Outside of the academic arena, you all played such an important role in this journey, and probably unknowingly. It can’t have always been easy listening to my research ramblings! To my extended family, Garrick and Anne, I am deeply grateful for your love, encouragement and the interest you have shown in my endeavours not just in the past three years, but for over half a lifetime. To all of you who have supported me professionally and personally, I am truly grateful. It cannot go unmentioned that I also had the loyal support of my loyal four-legged companion Biddy who at times had to wait very patiently for walks while I was lost in thought! Lastly, to my late Mum and best friend Lois. I wish you had been here for this moment, because no one would be more proud of this achievement than you. The courage, love of the natural world, inner-strength, and self-motivation you passed on to me helped make this possible. Pinned to the wall above my desk throughout my studies was the congratulations card you gave me on attaining my first degree shortly before we said goodbye; you wrote “never stop learning”. This is for the both of us Mum. ‒ iv ‒ Table of Contents CO-AUTHORSHIP FORM………...………………………...……...…....… II ACKNOWLEDGEMENTS…...…...…...…...…...…...…...…...…...…...….. III TABLE OF CONTENTS…………………………………………….……......V LIST OF ABBREVIATIONS………………………...……..……….............. X 1 GENERAL INTRODUCTION…………………………………………….1 1.1. THEORETICAL BACKGROUND…………………..……………………………...2 1.2. SPECIES ECOLOGY AND STUDY SITE…………………………………..……11 1.2.1. Yellow-eyed mullet (Aldrichetta forsteri) …………………………………….11 1.2.2. Snapper (Chrysophrys auratus)………………………………………………12 1.2.3. Kahawai (Arripis trutta)…………………...…………………………………14 1.2.4. Study site……………………………………………………………………...15 1.3. RESEARCH OBJECTIVES………………………………………………………...16 2 PHOTOGRAMMETRY METHODOLOGY…………………………...20 2.1. THEORETICAL BACKGROUND…..………………………………………..……21 2.2. EQUIPMENT………………………………………………………………………..21 2.2.1. Stereo-video camera configuration and measurement software…....………...21 2.2.2. Sonar configuration and measurement software……………………………..24 2.2.3. Tank setup ……………………………………………………………………25 2.3. CALIBRATION VERIFICATION SYNTHETIC TARGETS……………….……..26 2.3.1. Sonar …………………………………………………………………………27 2.3.2. Stereo-video camera………………………………………………………….27 2.4. FISH LENGTH MEASUREMENT ACCURACY………………………………….29 2.5. SPECIES IDENTIFICATION FROM SONAR IMAGERY………………………..31 3 MIXED SPECIES FISH ASSEMBLAGES……………………………...32 3.1. ABSTRACT……………..………………………………………………………….33 ‒ v ‒ 3.2. INTRODUCTION………………………….………………………………………..34 3.3. MATERIALS AND METHODS………………………….………………………...37 3.3.1. Experimental animals……………………………………..…………….……37 3.3.2. Experimental tank setup ………………………………………….…..………38 3.3.3. Behavioural manipulations ………………………………………..…………39 3.3.4. Behavioural measurements……………………………………………..…….40 3.3.5. Statistical analysis……………………………………………………………41 3.4. RESULTS ………………………….…………………………………..……………42 3.4.1. Qualitative behavioural observations………………………………………..42 3.4.2. Quantitative analysis of school structure………………………………….…43 3.5. DISCUSSION …………………………………………………………...………….50 3.5.1. Qualitative interspecific behaviours………………………………………….50 3.5.2. Quantitative analysis of school structure………………………………..……52 3.5.3. Estuarine context…………………………….………………….……………55 3.6. SUMMARY……………………….………………………………………………...57 3.7. ETHICS APPROVAL ………………….…………………………………………...57 4 EFFECTS OF GROUP SIZE ON SCHOOL STRUCTURE………………58 4.1. ABSTRACT……………..……………………………………………….………….59 4.2. INTRODUCTION…………………………………………….……………………..59 4.3. MATERIALS AND METHODS……………………………….…………………...62 4.3.1. Experimental animals…………………………………………………...……62 4.3.2. Experimental tank