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ResearchOnline@JCU This file is part of the following work: Morais Araujo, Renato (2020) The productivity of coral reef fishes. PhD Thesis, James Cook University. Access to this file is available from: https://doi.org/10.25903/c2h5%2Df063 Copyright © 2020 Renato Morais Araujo. The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owners of any third party copyright material included in this document. If you believe that this is not the case, please email [email protected] The productivity of coral reef fishes Renato Morais Araujo February 2020 For the Degree of Doctor of Philosophy College of Science and Engineering ARC Centre of Excellence for Coral Reef Studies James Cook University Dedico esta tese ao Vovô Manoel, avô, pai, herói ii Acknowledgements I thank my supervisor, David Bellwood, for continued guidance, counselling, and unconditional availability and support throughout the thesis; for those long hours of brain-draining, incredibly insightful meetings, and for not minding my artful representations of him in presentations. Thanks also to Sean Connolly for his disproportional contribution to the theoretical development of this thesis, which happened in the context of a particularly challenging chapter. Thanks to all who kindly helped me during field work: Pauline Narvaez, Victor Huertas, Ale Siqueira, Chris Hemingson, Sterling Tebbett, Rob Streit, Joshua Phua, Sam Shu Quin and Sabrina Inderbitzi. Special thanks to ‘my’ rusty chain field crew, Pauline, Victor and Ale, for taking over big responsibilities while I eternally counted 68,656 big or small fish. You tamed Quaddie and marinated chains (just enough rustiness), spending days at depths deeper than the height of a (short) person. That happened despite broken ears, fingers, cameras and unplanned alarms. Thank you very much. Thanks to my academic mentors, Sergio Floeter and Cadu Ferreira, who, since 2007 (back in the Holocene), taught me to think geographically and energetically. The opportunities you provided me opened doors I did not think existed. Conversations with Michel Kulbicki and Howard Choat, back in 2015, were instrumental in my will to pursue the merging of fish demography and visual surveys to investigate coral reef production. Howard also provided great many insights over coffee during my candidature. Murray Logan pointed the way to the newly accessible Bayesian world and influenced much of the analytical reasoning of this thesis. Thank you to the Centre of Mediocrity for Coral Reef Studies folks: Ale SiQueira, Arun Oakley- Cogan, Chris Hemingson, François Latrille, Mike Mihalitsis, Rob Streit, Victor Huertas, Sterling Tebbett. Our adventures, from the Tin Box to the ATSIP, including French Polynesia, Canberra, Sydney, Brisbane, Finch Hatton, and, obviously, fossicking in the desertic Richmond, will never be forgotten. Many of this thesis’ concepts and solutions were triggered by coffee break conversations on workdays (sometimes coffee days on work breaks). Thanks also to Bellwood Lab people, past and present: Orpha Bellwood, Martial Depczynski, Simon Brandl, Chris Fulton, Roberta Bonaldo, Michael Marnane. Martial Depczynski’s work was the foundation stone on which this thesis developed. iii Fieldwork for this thesis was made possible by a Lizard Island Doctoral Fellowship provided by the Lizard Island Reef Research Foundation, with the support of the Australian Museum Lizard Island Research Station. Special thanks to Anne Hogget, Lyle Vail, Marianne and John Dwyer for making Lizard Island the best place on Earth to do coral reef research. Staff at JCU and the Centre of Excellence for Coral Reef Studies supported aspects of my candidature, particularly Janet Swanson, Vivian Doherty, Greg Suosaari, Glenn Ewels, Claire Meade, Prof. Garry Russ, Prof. Andy Hoey, Tammy Walsh, Rick Abom and Liz Tynan. Also, special thanks to the amazing staff of the Damai II for all the field support. Friends from Lavras, Floripa, Townsville and elsewhere have endured my absolute incapacity to read, respond to or send messages. Thank you for persisting (I hope). Also, to my French family, who have received me with open arms, tolerated repeated mumblings of a very narrow vocabulary, and still want to see me back: merci beaucoup. I will always be grateful to my family. My grandpa Manoel and my grandma Zulma were much more than grandparents, they offered me infinite love and the best childhood I could ask. They were role models for life and will forever live in my heart. This thesis is dedicated to my grandpa, who sadly passed away during this thesis, but who will remain my eternal inspiration. My mom Débora, my dad Fábio and my brother Fabinho have provided enormous support throughout my life, and have coped with excessively long absences. My uncle Luís Cesar unveiled the world for me and lovingly provided me with opportunities that eventually brought me here. Muito obrigado a vocês por tudo, sempre. Finally, Lizard Island gave me more than fish data: to my partner Pauline, thank you for enduring stressful deadlines, and for sharing a life, good and bad times, love, plans and dreams with me. iv Statement of the Contribution of Others This thesis was supported by funds provided to me by the Lizard Island Reef Research Foundation (Lizard Island Doctoral Fellowship) and the Graduate Research School, James Cook University (HDR Competitive Research Training Grant), as well as funds provided to David Bellwood by the Australian Research Council (ARC Discovery, ARC Centre of Excellence and ARC Laureate Fellowship). Part of the fieldwork was also supported by an invitation from the Ocean Geographic Society to integrate the Elysium Heart of the Coral Triangle Expedition. During the course of my degree, I was supported by a James Cook University Postgraduate Research Scholarship. This thesis was conducted under the supervision of David Bellwood, and all chapters benefited from his conceptual guidance and editorial assistance. In Chapter 5, Martial Depczynski, Christopher Fulton, Michael Marnane, Pauline Narvaez and Victor Huertas participated in the data collection and data analysis, and Simon Brandl participated in the data analysis and conceptual development. All co- authors provided editorial assistance. Chapter 6 was conducted under the shared supervision of David Bellwood and Sean Connolly. Sean Connolly contributed conceptual guidance, data analysis advice and editorial assistance. All work reported in this thesis has been conducted in accordance with Great Barrier Reef Marine Park Authorization Permit number G17/38142.1 to David Bellwood, and JCU Animal Ethics Committee Approval A2375 to myself. v Abstract Coral reefs are undergoing profound climate-driven structural and functional changes. These changes are expected to affect the fish and fisheries production that provide food for millions of people. However, the energetic processes that lead from solar energy to fish production on coral reefs are still poorly understood. This raises the Question: will coral reefs maintain their capacity to provide this critically important ecosystem service? Answering this question will reQuire innovative strategies to measure food production potential on reefs and to identify the impacts of ecosystem change. In this thesis, I first developed a framework for quantifying reef fish productivity from common field survey data and life-history traits. Combining this framework with detailed reef fish surveys, I then addressed three key ecological questions: What are the main trophic pathways fuelling reef fish productivity? What are the effects of coral loss, reduced topographic complexity and overfishing on productivity? And, what are the potential causal mechanisms underpinning potential productivity changes? Growth is a fundamental process of life, but little is known about what drives reef fish growth at macroecological scales. Given the practical challenges of collecting growth data for all 6,000+ reef fish species, universal relationships would be useful for predicting growth trajectories. My first objective was, therefore, to evaluate the drivers of reef fish growth across large spatial and environmental gradients and across a range of morphological and behavioural traits. I compiled, filtered and standardised a dataset of almost 2,000 Von Bertalanffy Growth Model curves from 588 reef fish species. These were used to test the influence of environmental variables and species traits on growth, while also accounting for phylogenetic structure. Body size was found to be the main driver of reef fish growth curves, followed by temperature. Alongside diet and reef dependence, these provided the basis for a machine learning model that predicted reef fish growth trajectories with high accuracy and precision. Although there is increasing interest in the productivity of coral reef fisheries, there are currently no standardised methods to explore assemblage-level reef fish production. My second objective was, therefore, to develop a robust and easily applicable framework to quantify fish productivity in high- diversity systems, such as coral reefs. I started by integrating the model developed to predict growth trajectories into an existing approach to estimate individual and species-level somatic growth, and then vi expanding this approach by incorporating mortality in the growth functions. This resulted in a framework that yielded fisheries-independent fish productivity from routinely-collected fish survey data. A step by step guide
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