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Biogeography and the Evolution of Coral Reef Fish Species

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Biogeography and the Evolution of Coral Reef Fish Species ResearchOnline@JCU This file is part of the following reference: Hodge, Jennifer Reneé (2014) Biogeography and the evolution of coral reef fish species. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/42130/ 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] and quote http://researchonline.jcu.edu.au/42130/ Biogeography and the evolution of coral reef fish species Thesis submitted by Jennifer Reneé Hodge (MappSc), James Cook University, Australia April 2014 for the degree of Doctor of Philosophy in Marine Biology School of Marine and Tropical Biology, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia i Statement of Access I, the undersigned, author of this thesis, understand that James Cook University will make this thesis available for the use within the University Library and, via the Australian Digital Thesis Network, for use elsewhere. I understand that as unpublished work a thesis has significant protection under Copyright Act and; I do not wish to put any further restriction on access to this thesis. Jennifer Hodge __________________________________ ___________________ Signature Date ii Statement of Sources I declare that this thesis is my own work and has not been submitted in any form for another degree or diploma at my university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text and a list of references is given. Jennifer Hodge __________________________________ ___________________ Signature Date iii Electronic Copy Declaration I, the undersigned and author of this work, declare that the electronic copy of this thesis provided to James Cook University Library is an accurate copy of the print thesis submitted, within the limits of technology available. Jennifer Hodge __________________________________ ___________________ Signature Date iv Statement on the Contribution of Others This thesis includes some collaborative work with my supervisors, Professor David Bellwood and Dr. Lynne van Herwerden, and their former PhD candidate Charmaine Read. While undertaking these collaborations, I was responsible for the project concept and design, data collection, analysis and interpretation, and the final synthesis of results into a form suitable for publication. My supervisors provided intellectual guidance, equipment, access to their sample collections, financial support, and editorial assistance. My collaborator, Charmaine Read, performed laboratory analysis and provided the resultant molecular sequence data I analysed in the first two data chapters of this thesis. These chapters form collaborative publications and all authors contributed to earlier drafts of the papers. Financial support for the project was provided by the Australian Research Council Centre of Excellence for Coral Reef Studies. Tuition and stipend support were provided by an Australian Postgraduate Award and the James Cook University Graduate Research Scheme. Financial support for conference travel was provided by the Australian Research Council Centre of Excellence for Coral Reef Studies, the Australian National Network in Marine Science (ANNiMS), James Cook University Graduate Research Scheme, and the Australian Biological Resources Study (ABRS) Student Travel Bursary Program. v Acknowledgements Firstly, I would like to thank my supervisors, David Bellwood and Lynne van Herwerden. Lynne, thank you for having the courage to accept me as your student despite my minimal background in molecular biology. Thank you for guiding me through the forest of seemingly endless phylogenetic trees early on and for believing that I was capable of finding my way out with a thesis in hand. Your encouragement and support throughout has kept me motivated, and your thoughtful discussions and suggestions have enhanced my work. David, thank you for your honesty, high expectations and inspiring discussions. Your supervision has continually improved my work and my future potential as a research scientist. Thank you both for mentoring me over the past four years. You have each played an integral role in my professional development, and for that I am truly grateful. I would especially like to thank Peter Cowman for his supportive guidance. Pete, your patient advice and consultation have helped me immensely. There are many people who have provided support and helpful direction throughout my candidature. Thank you to Jenn Tanner, Chris Goatley, Howard Choat, Blanche Danastas, Danielle Dixson, Andrew Hoey, John Horne, Charlotte Johansson, Jess Maddams, Melanie Trapon and Justin Welsh. I appreciate your friendly conversation and assistance. A special thank you is extended to Simon Brandl for prying me away from my computer and insisting I introduce him to a tiger shark. Thank you to all of those who lived in the TBOD for accepting me into your lab and letting me share your space. Thank you Colin Wen for ‘fixing’ my Dell laptop in the first few months of my candidature. Without your unintentional removal of an essential partition I would not have been forced to find a new laptop. Following that, I would like to thank my MacBook Pro for introducing me to the world of seamless computing and for making this thesis and the bulk of vi my research possible. Thank you to those people who support and maintain the CIPRES super computing facility and to those who have developed the open source databases and computer programs that have afforded me the ability to access and analyse data, and find information on how to do so freely. Thank you to G. Bernardi and K. Ma for sharing their data that had not yet become publicly available. I am also grateful to the organisers and participants of the Adelaide Phylogenetics Workshop 2010 and the Bodega Bay Phylogenetics Workshop 2011, hosted by UC Davis, for playing a vital role in developing my theoretical knowledge of the field and my ability to appropriately address the questions I sought to incorporate in my research. In particular, I would like to thank P. Wainwright, T. Heath, T. Near and J. O’Donnell for helpful discussions during the Bodega workshop and for their continued correspondence afterwards. This research and thesis were made possible through generous financial support. I thank the Commonwealth government of Australia for providing me with an Australian Postgraduate Award. I am appreciative of funds received from the James Cook University Internal Research Awards, the Graduate Research Scheme, and the Australian Research Council Centre of Excellence for Coral Reef Studies. I am grateful for the receipt of additional funds for conference travel provided by the Australian Research Council Centre of Excellence for Coral Reef Studies, the Australian National Network in Marine Science (ANNiMS), the Australian Biological Resources Study (ABRS) Student Travel Bursary Program, and the James Cook University Graduate Research Scheme. A special thank you to O. Bellwood, D. Bellwood, Y. Everingham, J. Sheaves and L. van Herwerden for employing me as a tutor during my candidature. The training and experience I gained as a result are invaluable. I thank the dedicated staff of the School of Marine and Tropical Biology and the Graduate Research School for logistical support and the helpful answers they have provided. Special thanks to J. Wilson, D. Ford, S. Francis, K. Wood, and J. Bull for their assistance. Thank you to the staff of Orpheus Island and Lizard Island Research Stations for facilitating sample collection, and to F. Welsh and N. Konow for the provision of additional tissue samples. A very vii special thank you to C. Read for all of the hard work you performed in the lab and for allowing me to work with the resultant data. I would like to extend a warm thank you to my friends and family in Australia and abroad for their unwavering support and encouragement. Thank you to my parents for instilling in me the belief that I can achieve anything I set my mind to. Thank you for supporting me even when I set my mind to things in far away places, and when I come to visit indefinitely. Thank you to my parents-in-law for your love and support, and for the gift of our espresso machine – I am not sure this thesis would have come into being without it. Thank you to Andrea and Steve, Lucy and Stef, Matt, Lockie, Melanie, Brittany and Jade for your true friendship and shared drinks. Thank you to Monica and Dave for letting me science with you; you showed me how it should be done. Thank you to the RBT for giving me a hobby and a festive break from research once a month. To my husband Stephen, your patience, kindness and encouragement have seen me through all of the highs and lows of this journey. Thank you for understanding me and for always being able to make me laugh. Thank you for supporting me and for believing in me even when I did not believe in myself. Thank you for loving me. Now let’s go on another adventure! viii Abstract This thesis examines the evolution of coral reef fish species, specifically the chronology and geography of extant species divergence, and the evolutionary processes that have shaped contemporary patterns of biodiversity. The evolutionary histories of species belonging to multiple genera from four common coral reef fish families: the Chaetodontidae (butterflyfishes), Labridae (wrasses), Pomacanthidae (angelfishes), and Epinephelidae (groupers) were reconstructed based on molecular data. Resultant phylogenies were temporally calibrated using palaeontological data. The reconstructed chronograms were combined with detailed distributional data to determine how closely related species are geographically distributed, and to explore the processes responsible for contemporary patterns of reef fish diversity. First, the diversification of endemic species was explored by considering a case study of the wrasse genus Anampses.
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