ResearchOnline@JCU This file is part of the following reference: Leahy, Susannah Marie (2016) Habitat determinants of Chaetodon butterflyfish and fishery-targeted coral reef fish assemblages in the central Philippines. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/46299/ 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/46299/ Habitat determinants of Chaetodon butterflyfish and fishery-targeted coral reef fish assemblages in the central Philippines Thesis submitted by Susannah Marie Leahy (BSc, MAppSci) on 8 February 2016 for the degree of Doctor of Philosophy in the College of Marine and Environmental Sciences, the Centre for Tropical and Environmental Sustainability Science, and the Centre of Excellence for Coral Reef Studies James Cook University Cairns, Queensland, Australia This page is intentionally left blank. ii Acknowledgements I would first like to thank my supervisors: Garry Russ, Rene Abesamis, and Mike Kingsford. Garry, for his guidance and advice, and for his trust in me. Rene, for teaching me how to function in the Philippines. Mike, for being such a source of wisdom when I felt out of my depth. I would also like to thank the organisations who funded my work, including the Graduate Research School at James Cook University for a Postgraduate Research Scholarship and for two research grants, as well as the Australian Society for Fish Biology for the Michael Hall Student Innovation Award. A big thank you to Garry as well for being so incredibly generous with his funding from the Australian Research Council Centre of Excellence for Coral Reef Studies. A number of people facilitated my work and provided support at key times in my PhD. At Silliman University, Claro Renato Jadloc was the most helpful and supportive friend and colleague I could have asked for. I would also like to thank Angel Alcala, Ma’am Emily, Ma’am Janet, Abner Bucol, Jasper Maypa, and Brian Stockwell for their friendship and support. Antonio Yocor and Christopher Sanson were my heroes during my fieldwork and deserve a big thank you, as do Dioscoro Inocencio, Zacharias Generoso, Rey Santero, Mac Mac, Roland Tuble and his family, and the many boat captains and crew members who made my work possible. A particular thank you to Mercy Quisto and Monet Raymundo, who welcomed me into their home and treated me like family. I would also like to thank the resource managers, administrators, and fisherfolk who permitted me to access their coral reefs and who trusted me to do good work. In particular, thank you to the staff at the Environmental and Rural Development Program iii in Dumaguete and to their colleagues at the municipals halls of Dauin, Zamboanguita, and Siaton. Thank you to the barangay captains, fisherfolk associations, and bantay dagat of barangays Looc, Bantayan, Bulak, Lipayo, Masaplod Sur, Maayongtubig, Apo Island, Basak, Guinsuan, Latason, Kabkab, Bonbonon, Salag, and Cabangahan, and most especially to those at Piapi, Poblacion I, Poblacion III, Masaplod Norte, Lutoban, Andulay, and Bonbonon, who gave me such a warm welcome and were so supportive of my work. Back home, I would like to thank Rhondda Jones and Justin Rizzari for encouraging me to explore a whole new world of statistics, and Gordon Bailey, Andrew Gray-Spence, and Joel Millwood for making sure I had the hardware and software to make it happen. Thank you to my friends on the Townsville and Cairns campuses, who put up with so much of my grief, and to my kayaking mates, who got me out of my head and onto the river when I needed it most. And of course, a special thank you to Bronwyn Masters for putting up with so much, and for being my rock. I wouldn’t have made it without you. iv Statement on the contribution of others The research presented in this thesis was primarily funded by an Australian Research Council grant to Prof. Garry Russ, and was further supported by two JCU Graduate Research School grants and an Australian Society for Fish Biology Michael Hall Student Innovation award to Susannah Leahy. The long-term monitoring reported in Chapter 4 was supported by funding to Prof. Garry Russ from the UNEP-NRMC Philippines (1983), the Great Barrier Reef Marine Park Authority (1985), a Pew Fellowship (1999-2000), an ARC Discovery grant (2002-2004) and funding from the ARC Centre of Excellence in Coral Reef Studies (2006-2013). This thesis was primarily supervised by Prof. Garry Russ, who supported the development of each component project and provided guidance and editorial support on all thesis chapters. This thesis was also supervised by Dr. Rene Abesamis, who provided guidance on the logistics of conducting research in the Philippines, and some editorial support of Chapters 2, 3, and 5. Prof. Michael Kingsford also supervised this thesis, and provided some statistical and professional advice. The Silliman University Angelo King Center for Research and Environmental Management (SUAKCREM) provided office and laboratory space and logistical assistance during periods of fieldwork in the Philippines. The Kingsford Otolith Laboratory at JCU Townsville provided space laboratory space and equipment to process otoliths (Chapter 3). All data reported in this thesis were collected by Susannah Leahy, with the exception of: v (1) otolith increment numbers and widths (Chapter 3), which were collected by a commercial professional otolith ageing entity (Tropical Fish Ageing, Townsville) headed by Dr. Dongchun Lou; (2) long-term fish and benthic monitoring data (Chapter 4), which were collected by Prof. Garry Russ from 1983 to 2014; (3) remotely sensed imagery (Chapter 5), which was collected by the WorldView- 2 satellite, which is owned and operated by DigitalGlobe. Imagery was purchased from the Australian WorldView-2 imagery provider GeoImage Pty. Ltd., with some basic pre-processing steps already completed. Co-authors on current and future publications arising from this thesis made intellectual contributions to the manuscripts, in the form of guidance at the experimental design stage and the editing stage. Non-authors who provided important support for the thesis data chapters are: Prof. Rhondda Jones, Dr. Justin Rizzari, and Mr Mason Campbell, who acted as statistical “sounding boards” throughout the thesis; anonymous reviewers at Marine and Freshwater Research (Chapter 2) and Coral Reefs (Chapter 3), who provided helpful comments on earlier versions of the data chapter manuscripts; and Claro Renato Jadloc, who facilitated all of my fieldwork in the Philippines. I am the primary author of three of the four publications arising from this thesis (Chapters 2, 3, and 5), as I conceived of each research question, designed the experimental approach, implemented the work, collected the data, carried out the statistical analyses, and wrote the manuscripts. I am the second author of the publication arising from Chapter 4, although the first author (G.R. Russ) and I have contributed equally to that manuscript. G.R. Russ designed the experimental approach in 1983, was awarded funding for the work, collected the data used in Chapter 4 over the course of 31 years of monitoring the study sites, and edited the manuscript produced from this data vi chapter. I carried out the statistical analyses on the dataset and prepared the manuscript for the chapter. All of the research presented and reported in this thesis was conducted within the guidelines of the James Cook University Animal Ethics Committee (approval number A1803). vii List of publications arising from this thesis Leahy, S. M., G. R. Russ, and R. A. Abesamis. 2015. Primacy of bottom-up effects on a butterflyfish assemblage. Marine and Freshwater Research, 10.1071/MF15012 Leahy, S. M., G. R. Russ, and R. A. Abesamis. 2015. Pelagic larval duration and settlement size of a reef fish are spatially consistent, but post-settlement growth varies at the reef scale. Coral Reefs 34:1283-1296, 10.1007/s00338-015-1330-y Russ, G. R., and S. M. Leahy (in review). Rates and degrees of decline and recovery of corals and Chaetodon butterflyfish on Philippine coral reefs. Environmental Biology of Fishes Leahy, S. M., G. R. Russ, and R. A. Abesamis (in prep). Quality over quantity: habitat condition is a stronger driver of fish biomass on coral reefs than habitat spatial extent and connectedness. Ecology viii General Abstract Habitat availability and suitability are key factors determining the local abundance of a species and the structure of species assemblages. Nowhere is this more evident than in coral reef systems, where the availability, condition, and complexity of scleractinian corals are major determinants of the abundance, growth, and survival of both specialist and generalist coral reef fishes. Unfortunately, these shallow water habitats are also extremely vulnerable to destructive natural events such as cyclones, as well as anthropogenic environmental disturbances such as reduced water quality, overfishing and destructive fishing, and increased temperatures and reduced ocean pH associated with climate change. The deterioration of shallow water habitats is particularly pronounced in poor, developing nations such as those in the Coral Triangle, where marine biodiversity is high, but so are human population density and reliance on resource extraction. No-take marine reserves (NTMRs) are used throughout the region to reduce human impacts on coastal areas, and produce benefits for conservation, fisheries, or even both. This thesis aims to determine the habitat characteristics that drive the abundance, species richness, growth rates, and assemblage structure of coral reef fishes in order to inform placement of NTMRs, and to identify potential environmental stressors that may require more complex management strategies.