Trophic ecology of euryhaline and coastal elasmobranchs in northern Australia Sharon Louise Every A thesis submitted for the degree of Doctor of Philosophy at Charles Darwin University and The Australian National University 12th of May 2017 © Copyright by Sharon Louise Every All Rights Reserved Plate 1 South Alligator River 2014 ii Plate 2 Speartooth Shark Glyphis glyphis Declaration by Author This work contains no material which has been accepted for the award of any other degree or diploma in any university or other tertiary institution and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. I give consent to this copy of my thesis, when deposited in the Libraries of my two Universities, being made available for loan and photocopying online via the Universities open access repositories. I have received copyright permissions from the Journal of Experimental Marine Biology and Ecology and Marine Ecology Progress Series to use my publications in this thesis. Sharon Every 12th of May 2017 iii Acknowledgements Thank you to the Bininj and Mungguy people for allowing me to conduct this research on their traditional country. I would like to thank my principal supervisor, Associate Professor David Crook who guided the formation of key ecological questions, provided expertise in aquatic and fish ecology, kept me on track and provided critical support and guidance throughout my candidature. Also to my co-supervisors; Associate Professor Christopher Fulton who helped direct me to consider key areas of ecological theory, and what general philosophy I was trying to address in this thesis as well as statistical assistance and ensuring that my writing was succinct, Dr. Heidi Pethybridge for her guidance within the laboratory and introducing me to biotracer techniques, Dr. Peter Kyne for teaching me fieldwork practice, and the ecology and biology of elasmobranchs. I thank all my supervisors for the timely feedback, encouragement and assistance. Thanks must also go to Professor Karen Edyvane and Dr. Emile Ens for assisting at the beginning of my PhD. Thank you to Dr. David Parry who accepted my scholarship to North Australia Marine Research Association, then to Dr. Edward Butler, the current director of NAMRA who has assisted and mentored me throughout my PhD candidature. By being a part of NAMRA I was fortunate to be made welcome as a part of the Australian Institute of Marine Science (AIMS) and the Arafura Timor Research Facility. I thank all my colleagues, particularly Dr. Claire Streten for providing invaluable advice and feedback. iv To Dr. Thor Saunders and Northern Territory Fisheries for their expertise and equipment, particularly to Grant Johnson for assisting in the field and his guidance in the collection of elasmobranchs. I also appreciate all the people that assisted in the field including Mark Grubert, Duncan Buckle, Roy Tipagola, Kirsty McAllister and Crew of Solander RV, Dominic Valdez and Francisco Zillamarin and volunteers. I thank the Commonwealth Scientific Industrial Research Organization (CSIRO) for allowing me the use of Dr. Peter Nichols lipid laboratories. Dr. Nichols also provided invaluable assistance with lipid analysis along with Dr. Peter Mansuer. I also wish to thank my relatives for allowing me to stay in their homes in Hobart whilst working at CSIRO. I would like to thank my late father Capt. Mark Every and mother Lesley who sparked and encouraged my interested in marine life by taking my brother and I snorkelling and diving and allowing us free rein at the beach to explore rock pools. I also thank my mother for her continuous support throughout my PhD candidature. v Table of Contents Declaration by author ......................................................................................... iii Acknowledgements ......................................................................................... iv Table of Contents ............................................................................................... vi Abbreviations .................................................................................................... viii List of Figures ......................................................................................................xi List of Tables ...................................................................................................... xiii Abstract ............................................................................................................ 1 1 General Introduction ...................................................................................... 3 1.1 Trophic ecology ....................................................................................................................................3 1.1.1 Food webs............................................................................................................................................... 3 1.2 Trophic cascades and keystone species .....................................................................................5 1.3 Ecological Niche....................................................................................................................................6 1.4 Trophic ecology of cartilaginous fishes ......................................................................................8 1.5 Trophic specialisation ..................................................................................................................... 10 1.6 Measuring trophic niche and resource overlap ................................................................... 12 1.6.1 Stable carbon and nitrogen isotopes as trophic indicators .......................................... 13 1.6.2 Stable isotope analysis of elasmobranchs ............................................................................. 15 1.6.3 Fatty acids as food web tracers ................................................................................................. 17 1.6.4 Fatty acids in elasmobranchs ..................................................................................................... 19 1.7 Study Site: South Alligator River ................................................................................................ 20 1.8 Thesis Outline & Aims ..................................................................................................................... 28 2 Comparison of fin and muscle tissues for analysis of signature fatty acids in tropical euryhaline sharks .................................................................................. 32 2.1 Abstract ................................................................................................................................................. 33 2.2 Introduction ........................................................................................................................................ 34 2.3 Methods ................................................................................................................................................ 36 2.3.1 Ethics statement ............................................................................................................................... 36 2.3.2 Tissue sampling and preparation ............................................................................................. 37 2.1.1 Lipid and fatty acid extraction ................................................................................................... 38 2.3.3 Statistical analyses .......................................................................................................................... 39 2.4 Results ................................................................................................................................................... 40 2.4.1 Intraspecific tissue differences ................................................................................................... 42 2.4.2 Interspecific differences ................................................................................................................. 48 2.5 Discussion ............................................................................................................................................ 50 2.6 Conclusion ........................................................................................................................................... 55 2.7 Acknowledgments ............................................................................................................................ 57 3 Niche metrics suggest euryhaline and coastal elasmobranchs provide trophic connections among marine and freshwater biomes in northern Australia .......... 58 3.1 Abstract ................................................................................................................................................. 59 3.2 Introduction ........................................................................................................................................ 60 3.3 Methods ................................................................................................................................................ 64 3.3.1 Site description, sample collection and preparation ....................................................... 64 3.3.2 Stable isotopes ..................................................................................................................................