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Drivers of Coral Reef Composition, Cryptic Marine Biodiversity, and Coral Health Along the North Coast of Timor-Leste

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Drivers of Coral Reef Composition, Cryptic Marine Biodiversity, and Coral Health Along the North Coast of Timor-Leste Drivers of coral reef composition, cryptic marine biodiversity, and coral health along the north coast of Timor-Leste Catherine Jung Shim Kim Bachelor of Science 0000-0002-8558-6500 Photo: C. Kim A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2021 School of Biological Sciences Coral Reef Ecosystems Laboratory Abstract Coral reefs are among the most biodiverse ecosystems on the planet. Almost a third of tropical reefs lie in the Coral Triangle (CT), the epicenter of marine biodiversity, and are substantially threatened by human activity. Timor-Leste became independent in 2002 and is the newest of six nations in the CT, which include Indonesia, Malaysia, the Philippines, Papua New Guinea, and the Solomon Islands. It is important to establish a baseline for the current composition and state of coral reefs. For this thesis, the following specific objectives related to the coral reefs along the north coast of Timor-Leste were addressed: (1) assess coral reef variability based on kilometer-scale phototransects and explore environmental drivers of differences; (2) explore how the diversity of marine cryptic invertebrates varies at local scales over the same regions; and (3) quantify the condition of corals (coral health) using coral disease surveys and measurements of water quality and temperature in the capital area of Dili, taken before and after the global bleaching event in 2016. The benthic structure of outer reef slope communities along the north coast was analyzed using kilometer-scale phototransects (each 1.5-2 km) collected from the 2014 XL Catlin Seaview Survey. Chapter 2 analyzed over 20,000 benthic photos using machine learning techniques, which revealed significant coral cover in Timor-Leste ranging from 5.4 to 33.0%, comparable to coral cover in other regions of the Indo-Pacific and CT. Wave exposure, distance to nearest river, and human population density were explored as potential drivers of benthic composition. A linear mixed-effects model tested the same covariates plus the ratio of branching to massive corals (i.e., structural complexity) on total coral cover. All parameters significantly explained benthic composition while there was a significant positive effect from wave exposure on coral cover that interacted with structural complexity where the effect was greatest on more complex reefs. This was due to the low incidence of storms and the comparatively protected north coast. Marine cryptic invertebrate biodiversity was explored in Chapter 3 using Autonomous Reef Monitoring Structures (ARMS) and genetic DNA barcoding of brachyuran crabs for outer reef slope sites in Timor-Leste. This was accomplished in collaboration with the US National Oceanic and Atmospheric Administration and the Smithsonian Institution National Museum of Natural History. Three size fractions (i.e., two meiofaunal and one sessile) from the ARMS were DNA metabarcoded. The results indicated several interesting trends that corroborate the biogeographic pattern of maximal diversity in the CT. For example, rarefaction curves of i crabs and metabarcodes did not reach asymptotes meaning greater sampling would likely uncover more species. There was a high degree of unique operational taxonomic units (37% for brachyuran crabs) and diversity was greater than other Indo-Pacific sites as expected. The metabarcoding resulted in 19% unclassified operational taxonomic units, indicating the cryptic biodiversity of reefs is under-sampled with biodiversity being much more than previously quantified. The relationship between cryptofaunal diversity and coral cover was inconclusive. However, there was further evidence that rubble habitats promote the greatest diversity of coral reef cryptofauna. Reef condition in Timor-Leste was the focus of Chapter 4. The condition of four reefs was surveyed in November 2015 and July 2017. Temperature and nutrient data were also collected in 2015. Both surveys revealed disease prevalence was low, but had higher levels of compromised health (e.g., algal overgrowth). Interestingly, the isotope signature of nitrogen along the north coast did not match that expected for coastal pollution (8-30‰) but did match that expected from oceanic sources (2-6‰). Heat stress during the 2016-2017 global bleaching event was also quantified in Timor-Leste. Surveys before and after the event did not indicate high bleaching mortality as predicted by the Coral Reef Watch Timor- Leste (CRWTL) satellite sea surface temperature. CRWTL was significantly higher (> 1˚C) than in situ temperature during the austral summer. Both the temperature and nutrient data indicate seasonal oceanographic processes such as upwelling influence shallow reefs along the north coast. As local and global conditions change along the coastline of developing nations such as Timor-Leste, understanding the condition of reefs becomes critical. This thesis undertook the largest survey of coral reefs in the history of Timor-Leste. This study revealed rich coral reefs relatively high in biodiversity that are comparatively protected from climate change- induced ocean warming. The findings emphasize Timor-Leste’s significance as one of 50 coral reef world regions that are relatively less vulnerable to recent climate change impacts from a systematic global analysis. As such, immediate conservation priorities for Timor- Leste should focus on addressing localized anthropogenic pressures including sedimentation and overfishing. The balance between communities, ecosystems, and sustainable economies, must be further investigated using the wealth of Traditional Knowledge such as tara bandu customary law to build strong and resilient socio-ecological systems. All of this must be seen in the context of strong, intergovernmental action that is needed to address global climate change. ii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co- authors for any jointly authored works included in the thesis. iii Publications included in this thesis No publications included. Submitted manuscripts included in this thesis Kim CJS, Roelfsema C, Dove S, Hoegh-Guldberg O. (in review) The condition of coral reefs in Timor-Leste before and after the 2016-2017 marine heatwave. Oceans-1001163. doi:10.1101/2020.11.03.364323 Other publications during candidature Nolan MKB, Kim CJS, Hoegh-Guldberg O, Beger M. (in review). The benefits of heterogeneity in spatial planning within coral reef environments. BIOCON-D-20-00446 Rodriguez-Ramirez A, González-Rivero M, Beijbom O, Bailhache C, Bongaerts P, Brown K, Bryant DEP, Dalton P, Dove S, Ganase A, Kennedy EV, Kim CJS… (2020) A contemporary baseline record of the world’s coral reefs. Scientific Data. 7(1): 355. doi: 10.1038/s41597- 020-00698-6 Kennedy EV, Vercelloni J, Neal B, Ambariyanto, Bryant D, Ganase A, Gartell P, Brown K, Kim CJS… (2020) Coral Reef Community Changes in Karimunjawa National Park, Indonesia: Assessing the Efficacy of Management in the Face of Local and Global Stressors. J of Mar Sci Eng. 8(760): 27. doi:10.3390/jmse8100760 González-Rivero M, Beijbom O, Rodriguez-Ramirez A, Bryant DEP, Ganase A, Gonzalez- Marrero, Herrera- Reveles A, Kennedy EV, Kim CJS… (2020). Monitoring of Coral Reefs Using Artificial Intelligence: A Feasible and Cost-Effective Approach. Remote Sensing. 12(3): 489. doi: 10.3390/rs12030489 Kim CJS. (2016). Coral Health and Disease in Timor-Leste. Report for the Global Change Institute, The University of Queensland, St. Lucia, QLD, Australia. iv Conference abstracts: Kim CJS, Timmers M, Ransome E, Dove S, Hoegh-Guldberg O, Meyer C (2017). Biodiversity of Coral Reef Cryptofauna in Relation to Coral Reef Habitat. PEP talk. Australian Marine Science Association Conference, Darwin, Australia. Kim CJS, Rodriguez-Ramirez A, Dove S, Hoegh-Guldberg O. (2017) Drivers of kilometer- scale coral reef benthic composition in Timor-Leste. Presentation. Australian Marine Science Association Conference, Darwin, Australia. Kim CJS, Roelfsema C, Dove
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