Population structure of a predatory demersal fish (Argyrosomus japonicus, Sciaenidae) determined with natural tags and satellite telemetry Thomas Chaffey Barnes Presented for the degree of Doctor of Philosophy School of Biological Sciences the University of Adelaide, South Australia September 2015 Declaration I certify that this work contains no material which has been accepted for the award of any other degree or diploma in my name, 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. In addition, I certify that no part of this work will, in the future, be used in a submission in my name, for any other degree or diploma in any university or other tertiary institution without the prior approval of the University of Adelaide and where applicable, any partner institution responsible for the joint-award of this degree. I give consent to this copy of my thesis when deposited in the University Library, being made available for loan and photocopying, subject to the provisions of the Copyright Act 1968. The author acknowledges that copyright of published works contained within this thesis resides with the copyright holder(s) of those works. I also give permission for the digital version of my thesis to be made available on the web, via the University’s digital research repository, the Library Search and also through web search engines, unless permission has been granted by the University to restrict access for a period of time. Thomas Chaffey Barnes September 2015 Cover image: Every anglers dream – photo courtesy of Michael Hammer 2 Contents Declaration .......................................................................................................................................... 2 Acknowledgements ............................................................................................................................. 5 Abstract ............................................................................................................................................... 6 Chapter 1: General introduction ......................................................................................................... 9 Background ..................................................................................................................................... 9 The natural tags ............................................................................................................................ 10 Molecular genetics ........................................................................................................................ 10 Otolith chemistry .......................................................................................................................... 11 Otolith shape ................................................................................................................................. 13 Satellite telemetry ......................................................................................................................... 13 Holistic approach to population structure .................................................................................... 14 Study species ................................................................................................................................. 16 Mulloway ...................................................................................................................................... 16 Mulloway biology .......................................................................................................................... 17 Aims of thesis ................................................................................................................................ 18 Chapter 2a: Statement of authorship ............................................................................................... 20 Chapter 2a: Development of 15 microsatellite loci from mulloway, Argyrosomus japonicus (Pisces: Sciaenidae) using next generation sequencing and an assessment of their cross amplification in other sciaenids ................................................................................................................................ 23 Chapter 2b: Statement of authorship ............................................................................................... 28 Chapter 2b: Population structure in a wide-ranging coastal teleost (Argyrosomus japonicus, Sciaenidae) reflects marine biogeography across southern Australia ............................................ 31 Chapter 3: Statement of authorship ................................................................................................. 47 Chapter 3: Integrating molecular, geochemical and morphological methods for a robust investigation into population structure .......................................................................................... 50 Abstract ......................................................................................................................................... 52 Introduction .................................................................................................................................. 53 Methods ........................................................................................................................................ 57 Results ........................................................................................................................................... 63 Discussion ...................................................................................................................................... 69 References .................................................................................................................................... 74 Acknowledgements ....................................................................................................................... 77 Chapter 4: Statement of authorship ................................................................................................. 78 3 Chapter 4: Combined effects of extrinsic and intrinsic factors on otolith chemistry: implications for environmental reconstructions ....................................................................................................... 80 Chapter 5: Statement of authorship ................................................................................................. 89 Chapter 5: Movement of an exploited demersal fish species (Argyrosomus japonicus - sciaenidae) around marine parks inferred from satellite telemetry .................................................................. 91 Abstract ......................................................................................................................................... 93 Introduction .................................................................................................................................. 94 Materials and Methods ................................................................................................................. 97 Results ......................................................................................................................................... 103 Discussion .................................................................................................................................... 110 References .................................................................................................................................. 116 Acknowledgements ..................................................................................................................... 123 Chapter 6 – General Discussion ...................................................................................................... 124 The molecular ‘natural’ tag differentiates mulloway populations.............................................. 124 A holistic approach to population structuring ............................................................................ 126 Controlled testing of the otolith ‘natural’ chemical tag .............................................................. 127 An ‘electronic’ tag provides population and conservation information ..................................... 129 Integration of the outcomes from all the experimental chapters .............................................. 130 Future research directions .......................................................................................................... 130 Conclusions ................................................................................................................................. 132 References .................................................................................................................................. 133 Appendix: Permission from publishers to reproduce Chapters 2a, 2b and 4 ................................. 141 4 Acknowledgements Firstly I would like to thank my supervisors, Bronwyn Gillanders, Chris Izzo and (initially) Travis Elsdon. Their ability to teach and patience is appreciated. Besides skills in marine research I also picked up more general skills from them, which I will thankfully take with me into the next phase of my life. The people and facilities at the research institutions and other departments and corporations that made this thesis possible are acknowledged, namely