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  • This file is part of the following reference:

    Gainsford, Ashton (2016) A multi-disciplinary evaluation

    of the hybrid anemonefish Amphiprion leucokranos:

    behaviour shaping evolutionary outcomes of hybridization.

    PhD thesis, James Cook University.

    Access to this file is available from:


    The author has certified to JCU that they have made a reasonable effort to gain

    permission and acknowledge the owner of any third party copyright material

    included in this document. If you believe that this is not the case, please contact

    [email protected]

    [email protected]

    http://dx.doi.org/10.4225/28/58c62be6f0a34 mailto:[email protected]





    Thesis submitted by

    Ashton Gainsford (BSc Hons)

    In November 2016

    For the degree of Doctor of Philosophy

    College of Science and Engineering

    James Cook University

    Townsville, Queensland, Australia

  • i


    A number of collaborators and colleagues have contributed in various ways to this thesis and the subsequent manuscripts which are published, submitted or in preparation for submission. A summary of these contributions are listed below.

    Nature of Assistance Contribution Co-contributors

    Intellectual support Project design Dr. L. van Herwerden (JCU) & Prof. G.P. Jones (JCU, ARC CoE)

    Proposal writing Dr. L. van Herwerden (JCU) & Prof. G.P. Jones (JCU, ARC CoE)

    Data analysis support Chapter 2: S.R. Montanari ([email protected]) & Dr. M. van der Meer (JCU)

    Statistical support Chapter 5: Prof Emer. R. Jones (JCU)

    Editorial assistance Chapters 2-4: Dr. L. van Herwerden (JCU), Prof. G.P. Jones (JCU, ARC CoE); Chapter 4: Dr. J-P. Hobbs (CU); Chapter 4-5: H. Epstein ([email protected], ARC CoE)

    Data collection Fieldwork assistance Dr. M. Lal (JCU), K. Thomas Brown (USP), T. Millitz (JCU), Dr. J-P. Hobbs (CU), H. Campbell, Dr. L. Bostrom-Einarsson (JCU, ARC CoE), Dr. H.B. Harrison (JCU, ARC CoE), T. Bowling, & Dr. M.C. Bonin (ARC CoE)

    Laboratory assistance F.M. Heindler (JCU) & H. Epstein ([email protected], ARC CoE)

    Diving & boating support

    L. Choquette & Solomon Dive Adventures, Mahonia Na Dari, Kimbe Bay & (NIMRF, Kavieng)

    Histology S. Reilly (JCU)

    Otolith sectioning Dr. D. Lou (Tropical Fish Ageing)

    Financial assistance Research funding Prof. G.P. Jones (JCU, ARC CoE), Dr. J-P. Hobbs (CU), & Dr. L. van Herwerden (JCU)

    The research presented and reported in this thesis was conducted in compliance with the National Health and Medical Research Council (NHMRC) Australian Code of Practice for the Care and Use of Animals for Scientific Purposes, 7th Edition, 2004 and the Qld Animal Care and Protection Act, 2001. The proposed research study received animal ethics approval from the JCU Animal Ethics Committee Approval Number A1633 and A1791.

  • ii


    “Solitude is a human presumption. Every quiet step is thunder to beetle life underfoot, a tug of impalpable thread on the web pulling mate to mate and predator to prey, a beginning or an end. Every choice is a world made new for the chosen.” – Barbara Kingsolver

    The journey to completing my dissertation was not travelled alone and I will be forever

    grateful to my family, friends and colleagues who have shared in this experience. Each small

    kindness contributed to me finishing, which sometimes felt beyond reach. Many favours, words of

    encouragement, insights, late night phone calls, blind faith and understanding were shared without

    question. You’re all lovely and wonderful and I will never forget it.

    A few special mentions – Carol and Brian Gainsford, your generosity inspires me and I am

    proud beyond measure to be your daughter. Thank you for always encouraging curiosity and

    adventure, even though it has put considerable distance between us. You have given me spirit and

    strength, and a family with unconditional love. Thank you for your unwavering support every step

    of the way.

    Yvette, Dean and Chiara-Lee – you are the craziest, kindest and most spirited bunch of

    bloody drongos anyone could ever hope to call family. Thank you for reminding me to see humour

    in each and every moment and for sharing in my trials and triumphs. You are my best friends.

    Mary – you taught me how to catch a fish and a hell of a lot about research in the field for

    which I will be forever grateful; thanks for all the epic adventures and laughs along the way. Hannah

    – your enthusiasm for my research, challenging conversations, tireless assistance in the lab and

    editing in the final weeks of this long journey are appreciated beyond words. Lisa, Gigi, Emma and

    Margaux – you are one solid group of fearless, strong ladies. Your friendship has picked me up and

    empowered me to keep moving forward. Thank you for always celebrating each other’s successes,

    big and small – your joy is powerful and contagious.

  • iii

    To my supervisors, Lynne and Geoff, I cannot thank you enough for the time and effort

    you have invested in developing me as a researcher, whilst also juggling your own demanding lives

    and many responsibilities. Lynne, you took me under your wing with blind faith, you have

    challenged my thinking and ability, and offered me many opportunities to increase my skills and

    responsibilities in academia. Thank you for your time, guidance and friendship.

    Formally, I would also like to acknowledge and thank the following institutions and

    funding bodies for financial support of my research and professional development: Sea World

    Research and Rescue Foundation Inc., the College of Marine and Environmental Sciences and

    Australian Research Council Centre of Excellence for Coral Reef Studies, and the Comparative

    Genomics Centre at James Cook University, and the Australian Coral Reef Society. Finally, I was

    generously supported by an Australian Postgraduate Award for three and a half years with full

    tuition waiver while completing my dissertation, as well as a living stipend through the Graduate

    Research Scheme (JCU) to complete my dissertation writing, for which I am beyond grateful.

  • iv


    Hybridization is an evolutionarily significant and common occurrence in nature.

    Interspecific breeding between closely related taxa challenges established phylogenies and

    questions what constitutes a species; where hybridization may drive rapid evolution of taxa and

    provide a source of evolutionary novelty to ecosystems. Despite the enhanced study of

    hybridization in recent time, a clear understanding of the mechanisms which initiate and maintain

    hybridization remains limited. Hybrid zones are ideal for testing theoretical questions regarding

    speciation and elucidating patterns of variation among species. For many taxa, reproductive success

    is skewed towards large, socially dominant individuals within groups, and reproductive traits and

    mating systems are expected to influence the outcomes of hybridization and gene exchange between

    hybridizing species. In this thesis, I addressed how ecology and behaviour contribute to

    maintenance and persistence of the Amphiprion leucokranos hybrid zone. This research employed

    a combination of ecological, phylogenetic and population genetic assays, as well as an observational

    study and behavioural experiment to test key concepts of the importance of hybridization to

    evolution of species.

    A suite of 42 novel and published microsatellite markers were developed and tested in

    Chapter 2 to facilitate investigation into the relatedness of taxa within the hybrid zone. The

    influence of ecology and behaviour on the outcomes of hybridization were tested in Chapter 3,

    addressing how habitat use and relative size differences of parent species and hybrids drive patterns

    of gene exchange. Findings confirmed A. leucokranos to be the hybrid of closely related

    A. chrysopterus and A. sandaracinos, and subsequently verified that behavioural isolation, habitat

    use and species-specific size differences dictates the direction and degree of back-crossing and

    subsequent introgression. Hybridization took place exclusively with A. chrysopterus in the

    dominant female rank and the smaller A. sandaracinos in the sub-dominant male rank, based on

    mtDNA cytochrome b and multiple nDNA microsatellite loci. Overlap in habitat, depth and host

    anemone use was found, with hybrids intermediate to parents and co-habitation in over 25% of

    anemones sampled. Hybrids, intermediate in body size, colour and pattern, were classified 55% of

  • v

    the time as morphologically first generation hybrids relative to parents, whereas 45% of hybrids

    were more like A. sandaracinos, suggesting back-crossing. Unidirectional introgression of

    A. chrysopterus mtDNA into A. sandaracinos via hybrid back-crosses was found, wi