2009 ANNUAL REPORT

Cover Photo and above © Giles Winstanley / pelagicon.com Contents

ARC Centre of excellence for coral reef studies 09 ANNUAL REPORT 2 4 16

Vision 2 Director’s Report 4 Research 16 Aims 2 Management Structure 6 Researcher Profile: Overview 3 Governance 7 Professor Peter Mumby 33 Hon Virginia Chadwick 9 Graduate Training 34 Membership 10 Media and Public Outreach 44 Program Leaders 12 Business Leaders 15 47 56 66

International Coral Reef Publications 56 Performance Measures 66 Symposium 2012 47 Recognition of Excellence by Financial Statement 70 Symposium 2010 49 Centre Members 64 Acknowledgements 72 National Benefit Case Study 1 50 National Benefit Case Study 2 53

2009 annual report 1 Vision Global leadership in the provision of scientific knowledge necessary for sustaining the ecosystem goods and services of the world’s coral reefs.

Aims The aims of the ARC Centre of Excellence for Coral Reef Studies are:

Research The Centre’s research is world-best, innovative, and highly relevant to coral reef management and policy.

Research Training and Professional Education The Centre attracts and trains outstanding coral reef scientists at all stages of career, to build human capacity and expertise in coral reef science world-wide.

End-user and Community Linkages Transfer and exchange of knowledge, technologies and research outcomes by the Centre to end-users, industry and the wider community promotes co-operation and improves the management of coral reefs.

National and International Linkages The ARC Centre, through its networks and activities nationally and internationally, represents a global hub for coral reef science collaborations.

Management and Governance Centre management is collaborative, co-operative, multi-institutional, communicative and continuously improving.

Commercial Activities Commercial activities and research contracts undertaken by the ARC Centre extend knowledge transfer, nationally and globally.

2 ARC Centre of Excellence for Coral Reef Studies © Giles Winstanley / pelagicon.com

Overview The ARC Centre of Excellence for Coral Reef Studies was established in July 2005 under the ARC Centres of Excellence Program. Headquartered at James Cook University, the ARC Centre partnership includes the Australian Institute of Marine Science, the Australian National University, the Great Barrier Reef Marine Park Authority, the University of Queensland, and the University of Western Australia which formally joined the Centre in 2009. The Centre has collaborative links to 345 institutions in 52 countries.

Major research themes include adaptation to climate change, understanding and managing biodiversity, marine reserves, fisheries biology, genomics, conservation planning, social studies and governance and policy – in short, the basic and applied science that underpins the sustainable delivery of goods and services from the world’s coral reefs.

2009 annual report 3 Director’s Report

Welcome to our 2009 annual report. A key Guinea and the Solomon Islands. Our website outcome for the year has been our commitment features a new list of links to 134 of the Centre’s to organize and host the next International publications featuring science undertaken within Coral Reef Symposium (ICRS) in Australia. the Coral Triangle (www.coralcoe.org.au/events/ Almost 3000 delegates attended the 11th ICRS ctiworkshop/pubscticountry10.pdf). In May, in Fort Lauderdale, Florida, in 2008. The ICRS we provided expertise and advice at the World is the world’s largest and premier forum for Ocean Conference in Manado, Indonesia, where the dissemination and discussion of coral reef the six Coral Triangle nations launched an accord science, management and conservation. The for sustainable management of coral reefs ARC Centre made a major contribution to the across the region. During the year, the Centre 11th symposium, presenting 124 talks and provided briefings in Townsville on Coral Triangle posters during the 5-day event. We look forward research and on our capacity-building activities to co-hosting the 12th ICRS with James Cook to the Ambassadors and Consular Generals of University in the tropical city of Cairns in July Indonesia, Papua New Guinea, the Solomon 2012 (see p.47). Islands, Timor-Leste, and the USA.

The Centre’s publication output continued to We’ve had a very busy year providing advice grow rapidly this year, doubling since 2006. Our and services to governments, agencies and Non 224 publications in 2009 were co-authored by Government Organisations (NGOs) around the colleagues from 345 institutions in 52 countries, world. In February, Deputy Director Malcolm reflecting our extensive activities around the McCulloch and I joined colleagues from National world. Among this year’s publications is a Academies of Australia and nine other countries provocative multi-national study on planetary to write an Inter-Academy statement on ocean tipping points published in Nature, and a Policy acidification. The statement, timed in advance Forum article in Science magazine on missing of the Copenhagen United Nations Framework institutions for coping with trans-boundary issues Convention on Climate Change (UNFCCC) such as climate change and oceanic fisheries negotiations, summarizes the current state of the (see p.24). These trans-disciplinary studies will science, and is aimed at policy-makers. Deputy- be developed further by research programs 5, 6 Director Ove Hoegh-Guldberg was involved in and 7 in 2010. A new ISI Web of Science analysis Intergovernmental Panel on Climate Change of journal publications and citations identifies our (IPCC) workshops in Venice and Geneva, and ARC Centre of Excellence as the premier climate provided UNFCCC briefings in Barcelona and change research institution in Australia, with Canberra. In September, I delivered a plenary James Cook University ranked 2nd in the world talk in Stockholm, at an international conference for citation impact (p.54). of environmental policy-makers, held under the auspices of the Swedish Presidency of the The ARC Centre’s fieldwork in 2009 was European Union. In Australia, Centre members undertaken in 23 tropical countries, with a major drafted sections of the national Climate Change ongoing focus in the Coral Triangle region to the Research Plan for marine biodiversity and north of Australia. The Centre expended over resources. The Plan provides a framework to $3 million this past year to support fieldwork guide research funding decisions for developing in the Philippines, Indonesia, Papua New effective adaptation strategies. In November,

4 ARC Centre of Excellence for Coral Reef Studies the Centre was a major contributor to a underwater images to the global launch The membership of our Centre’s briefing on emission reduction targets, of a new ocean version of Google Earth Advisory Board will change in early 2010, provided to Australian Members of – which is designed to enable internet coinciding with the retirement from the Parliament and Senators, in Parliament users worldwide to explore more fully Board of Professors Mandy Thomas, House, Canberra. The Centre’s research the two thirds of the planet covered by Chris Cocklin and Max Lu (respectively, program summaries on pp.16-32 provide water. The Centre’s media coverage has the Deputy- and Pro-Vice Chancellors many more examples of similar activities continued to grow rapidly during 2009 – for Research at the Australian National in many countries throughout 2009. well over two thousand stories featuring University, James Cook University, the Centre’s research activities were and University of Queensland). I’d like Outreach activities during the year published or broadcast around the world to thank them all very much for their included our annual symposium, further in the past year (p.44). marvelous support. Sadly, one of our website development, and extensive inaugural Board members, the Hon. media uptake. This year’s 2-day The Centre welcomed a new node Virginia Chadwick died in 2009. A great symposium, entitled Securing Coral Reef in 2009, the University of Western champion for the Great Barrier Reef, Futures – linking ecosystems, societies Australia, following Deputy Director Virginia led the Great Barrier Reef Marine and economies was held in Brisbane in Malcolm McCulloch’s move there Park Authority from 1999-2007. In August, and was eloquently launched by Virginia’s honour we have established from Canberra to take up a prestigious Her Excellency, Ms Penelope Wensley, the The Virginia Chadwick Awards”, in Western Australian Premier’s Fellowship. “ the Governor of Queensland. Video recognition each year of five outstanding We’ve retained our node at the recordings of 35 talks, including a public publications written by ARC Centre of Australian National University, and forum, are posted at www.coralcoe.org.au Excellence graduate students. Please recruited Chris Fulton as a new Chief /events/symposium09/program.html. read our tribute to Virginia on p.9. Investigator. Membership of the Centre In October, members of the Centre met with Israeli marine scientists affiliated has been further enhanced by the award Lastly, I’d like to express my gratitude with the Inter-University Institute for of five prestigious ARC Fellowships to our many other friends around Marine Sciences, at a joint workshop during 2009 – two ARC Australian the world for their contributions to a hosted in Eilat by Professor Yossi Loya. Postdoctoral Fellowships (Natalie Ban, fourth outstanding year, especially my Our next coral reef symposium will be Nick Graham), two Future Fellowships University colleagues, the Centre’s held in the Shine Dome in Canberra on (Glenn Almany, Andrew Baird) and an Advisory Board, and our partners from 7th-8th October, 2010, in conjunction ARC Laureate Fellowship (Peter Mumby, the Australian Institute for Marine with the Australian Academy of Science see p.33). At the end of 2009, the Science, The Nature Conservancy, WWF and The Royal Society – as part of The Centre’s membership stands at 21 Chief and the Great Barrier Reef Marine Park Royal Society’s 350th anniversary and Partner Investigators, 36 full-time Authority. I am especially grateful to the (see p.49). Research Fellows and 159 graduate Centre’s administrative team – Jenny students (from 39 countries, see pp.34- Lappin, David Yellowlees, Olga Bazaka, Interest in the Centre’s website reflects 43). A further highlight of 2009 has been Monica Gaffney, Janet Swanson and our growing interaction with the broader the launch of the Centre’s new Programs Eliza Glasson – for their unseen support community, with 4.5 million hits in 7, Policy development, institutions that underpins the Centre’s performance. 2009 compared to 680,000 in 2006. In and governance of coral reefs, and 8, February, researchers from the Centre Genomics and metagenomics of coral Terry Hughes contributed scientific information and reefs (pp.28-32). Director

2009 annual report 5 Management Structure

Centre Advisory Board

Scientific Management Centre Director Business Team Committee Professor Terry Hughes Assistant Director David Yellowlees Chief Operations Officer Jennifer Lappin Finance Manager & Student Coordinator Olga Bazaka Office Manager Monica Gaffney Administrative Officer Janet Swanson Conference Coordinator Eliza Glasson

Program 1 Program 2 Program 3 Program 4

Evolutionary Understanding Marine Genetic, and and Managing Reserves and Molecular and Environmental Coral Reef Connectivity Physiological Change Biodiversity Garry Russ Processes Malcolm McCulloch Sean Connolly Ove Hoegh- Guldberg

Program 5 Program 6 Program 7 Program 8

Resilience of Conservation Policy Genomics and Linked Social- Planning for a Development, Metagenomics Ecological Sustainable Institutions and of Coral Reefs Systems Future Governance of David Miller Coral Reefs Terry Hughes Bob Pressey Simon Foale

6 ARC Centre of Excellence for Coral Reef Studies Governance

The Centre’s governance structures increasing international engagement. The Professor Max Lu involve stakeholders in planning Centre Director and Chief Operations Deputy Vice Chancellor (Research) and management processes. The Officer provide the operational and University of Queensland chart opposite illustrates the current management link between the Advisory governance structure and relationships. Board and the Centre. The Board met Professor Mandy Thomas Programs 7 and 8 commenced during formally in Canberra in April 2009. Pro Vice-Chancellor 2009 and the Centre’s governance Australian National University structures were revised to incorporate In 2009, the ARC Centre of Excellence these two new research programs. Review Panel recommended that the Dr Ian Poiner Centre vary the representation of its Chief Executive Officer James Cook University is the Advisory Board to match the Centre’s Australian Institute of Marine Science administering organisation with demonstrably strong global research the Centre Director, Terry Hughes activities and international linkages. In Andrew Skeat reporting to Professor Chris Cocklin, conjunction with this change to Advisory General Manager the Deputy Vice-Chancellor (Research Board membership, the Review Panel Great Barrier Reef Marine Park Authority and Innovation). The Centre’s Chief also recommended that the terms of Investigators are located in three reference for the Board be revised to Honourable Virginia Chadwick Faculties at JCU, and at the Australian take account of the Centre’s international former Chair National University, the University profile and its focus on sustainable Great Barrier Reef Marine Park Authority of Queensland and the University of management of coral reefs. In response Western Australia which joined the to this, the terms of reference of the Professor Terry Hughes Centre this year. Partner Investigators Advisory Board have been updated, ARC Centre Director are based at the Australian Institute of and several new members have been and Federation Fellow Marine Science, the Great Barrier Reef recruited for next year. The first meeting Marine Park Authority, and in overseas of the new board will be in March 2010. institutions. Day-to-day operations are managed by the Chief Operations We have been privileged to have Scientific Management Officer, Jenny Lappin, in consultation access to the expertise and experience Committee with the Centre Director and Assistant of our departing university Board Director, David Yellowlees. The Centre members and would like to thank Ongoing operational management of Director oversees the Centre’s research Professors Chris Cocklin, Max Lu the Centre and planning for its scientific programs together with the two deputy and Mandy Thomas for their advice research program is the responsibility of directors, Ove Hoegh-Guldberg (UQ) and and contribution to the Centre. the Scientific Management Committee Malcolm McCulloch (UWA). (SMC). The SMC is chaired by an In 2009, the Advisory Board’s eminent Israeli researcher, Professor membership was: Yossi Loya. Other members are the leaders of each of the Centre’s eight Centre Advisory Board Dennis Trewin (Chair) Research Programs, and the Director former Australian Statistician of the Knowledge Management Group The ARC Centre’s Advisory Board from the Great Barrier Reef Marine provides vision and strategic advice Park Authority, the Centre’s principal and facilitates improved linkages Professor Chris Cocklin Deputy Vice-Chancellor end-user in Australia. Priorities for between the Centre and the private each meeting include reviewing and sector, government agencies, research (Research and Innovation) James Cook University expanding the objectives and operations institutions and the wider community. for the Centre’s research programs, From 2010 the focus of the Board will developing international collaborations be more global, reflecting the Centre’s and engagements, recruiting high-

2009 annual report 7 Governance

quality postdoctoral fellows, planning Scientific Management Committee Professor Ove Hoegh-Guldberg professional development programs, Members are: Leader, Research Program 4 undertaking an effective communications University of Queensland strategy and reviewing processes for Professor Yossi Loya (Chair) engaging with the Centre’s many end- Professor of Marine Biology Professor Terry Hughes users around the world. The Committee The Raynor Chair for Environmental Leader, Research Program 5 met 3 times in 2009, in February Conservation Research James Cook University (videoconference), April (Townsville) and Tel Aviv University October (Israel). Israel Professor Bob Pressey Leader, Research Program 6 Priorities for the SMC in 2009 included Dr David Wachenfeld James Cook University responding to the ARC review, continuing Director, Knowledge Management Group to expand the Centre’s international Great Barrier Reef Marine Park Authority Dr Simon Foale engagement, particularly in the Coral Leader, Research Program 7 Triangle region, developing the Centre’s Professor Malcolm McCulloch James Cook University outreach program and responding Leader, Research Program 1 to the Australian Government’s new University of Western Australia Professor David Miller research fellowship initiatives. The Leader, Research Program 8 trans-disciplinary nature of the Centre’s Professor Sean Connolly James Cook University research was further developed during Leader, Research Program 2 2009 with the establishment of two James Cook University new research programs: Program 7: Policy development, institutions Professor Garry Russ and governance of coral reefs (see Leader, Research Program 3 p.28) and Program 8: Genomics and James Cook University metagenomics of coral reefs (see p.30).

8 ARC Centre of Excellence for Coral Reef Studies Honourable Virginia Chadwick 1944 – 2009

Sadly, Virginia Chadwick died on 19th Great Barrier Reef - The Great Barrier meetings with thousands of people September 2009 after a long and Reef Marine Park Representative Areas in coastal Queensland. Over 10,500 determined battle with cancer. She Program (RAP). This program has been submissions were received as a result was a supporter of the ARC Centre the most comprehensive and innovative of phase 1 and a further 20,000 in phase from its inception, commencing with marine conservation and biodiversity 2. The result was the issue of the Great an enthusiastic letter of support for our program ever to occur in world Barrier Reef Marine Park Zoning Plan, initial application in 2004. As Chair of the marine conservation. The program will which has minimized, as far as possible, Great Barrier Reef Marine Park Authority significantly enhance the resilience of the impacts on users of the Marine Park, (GBRMPA), she became an Advisory Great Barrier Reef (GBR) in the face of while maximizing the level of biodiversity Board member of the ARC Centre on mounting environmental pressures, and protection. Because of the level of co- its establishment in mid 2005 and was will assist industry, particularly tourism operation from local communities, the a major contributor to the strategic and fisheries, to achieve increased levels GBRMPA has been able to access local direction of the Centre. She remained as of environmental sustainability and knowledge, and significantly reduce a Board member following her retirement financial security. impacts on existing users. and relocation to NSW. Her insight into how the ARC Centre could contribute The Great Barrier Reef Marine Park The success of this very sizeable to management of coral reefs and to Zoning Plan, the statutory instrument consultation process, and the timely policy was invaluable in the Centre’s giving effect to the Representative tabling of the Zoning Plan in December success. Her significant contribution was Areas Program, was tabled in Federal 2003, was due substantially to the recognized by James Cook University Parliament on 3 December 2003, and outstanding professional and personal by the award of an Honorary Doctorate, passed through all legislative stages contribution made by Virginia. which she received in a ceremony in during early 2004. The Zoning Plan took Townsville on 28th March 2009. Her effect on 1 July 2004. These works have made a very counsel and support will be sorely significant contribution to fostering missed within the ARC Centre. In Under Virginia Chadwick’s direction and international awareness of sophisticated Virginia’s honour the Centre of Excellence leadership, officers of the GBRMPA environmental conservation initiatives, has established “The Virginia Chadwick convened panels of independent natural and have served to enhance Australia’s Awards”, in recognition each year of five and social scientists. Their aim was to international marine conservation outstanding publications written by ARC develop planning principles on how to reputation. The RAP initiative has been Centre of Excellence graduate students. best protect the reef, while minimising recognized by nine major awards - three impacts for those who depend on the international and six national - and set Virginia Chadwick served the people reef for their livelihood. After arranging a new global benchmark for marine of Queensland and Australia with for peer review of the principles, Virginia conservation. This outcome would not distinction through her contribution to directed a major program of bioregional have been possible without Virginia’s conserving the marine environment, as mapping for the GBR, using the best drive and vision. Chair and CEO of the Great Barrier Reef scientific advice, and ground-breaking Marine Park Authority (1999 – 2007). applied spatial data technology. Before moving to Townsville, she had a distinguished political career in New In 2002, Virginia Chadwick and her South Wales, including a term as the team directed and conducted the most State’s Education Minister. extensive community consultation process ever conducted in Australia. The Upon taking up the position, Virginia first phase of community consultation led The Authority in a visionary plan to with stakeholders and local communities enhance the level of protection for the in Queensland involved hundreds of

2009 annual report 9 membership

Researchers Dr Simon Dunn Dr Johnathan Kool Research Fellow Research Fellow Professor Terry Hughes University of Queensland James Cook University Centre Director and ARC Federation Fellow, Program 5 leader Dr Toby Elmhirst Dr Bill Leggat James Cook University Research Fellow Chief Investigator James Cook University James Cook University Dr Tracy Ainsworth ARC Australian Postdoctoral Fellow Dr Kathryn Ferguson Dr Janice Lough James Cook University ARC Australian Postdoctoral Fellow Partner Investigator James Cook University Australian Institute of Marine Science Dr Glenn Almany Dr Pedro Fidelman Dr Jennie Mallela ARC Future Fellow Research Fellow Research Fellow James Cook University James Cook University Australian National University Dr Kenneth Anthony Dr Simon Foale Dr Laurence McCook Chief Investigator Research Fellow and Program 7 Leader Partner Investigator University of Queensland James Cook University Great Barrier Reef Marine Park Authority Dr Andrew Baird Professor Carl Folke Dr Mark McCormick ARC Future Fellow Partner Investigator Chief Investigator James Cook University Stockholm University James Cook University Dr Natalie Ban Dr Sylvain Forêt Professor Malcolm McCulloch ARC Australian Postdoctoral Fellow Research Fellow Deputy Director, Western Australia James Cook University James Cook University Premier’s Fellow and Program 1 Leader University of Western Australia Dr Line Bay Dr Christopher Fulton Queensland Smart State Fellow Chief Investigator Dr Mark Meekan James Cook University Australian National University Partner Investigator Australian Institute of Marine Science Professor David Bellwood Dr Nick Graham Chief Investigator ARC Australian Postdoctoral Fellow Professor David Miller James Cook University and Queensland Smart Futures Fellow Chief Investigator and Program 8 Leader Dr Joshua Cinner James Cook University James Cook University ARC Australian Postdoctoral Fellow Dr Lauretta Grasso Professor Philip Munday James Cook University Research Associate ARC Queen Elizabeth II Fellow Professor Sean Connolly James Cook University James Cook University ARC Australian Professorial Fellow Professor Ove Hoegh-Guldberg Professor John Pandolfi and Program 2 leader Deputy Director, Queensland Smart Chief Investigator James Cook University State Premier’s Fellow University of Queensland Debora De Freitas and Program 4 Leader University of Queensland Dr Serge Planes Research Associate Partner Investigator James Cook University Professor Geoffrey Jones University of Perpignan Dr Guillermo Diaz-Pulido Chief Investigator James Cook University Dr Morgan Pratchett Research Fellow ARC Australian Research Fellow University of Queensland Professor Ronald Karlson James Cook University Partner Investigator Dr Maria Dornelas University of Delaware Professor Bob Pressey Research Fellow Research Fellow and Program 6 Leader James Cook University Professor Michael Kingsford James Cook University Chief Investigator Associate Professor Sophie Dove James Cook University Professor Garry Russ Chief Investigator Chief Investigator and Program 3 Leader University of Queensland James Cook University

10 ARC Centre of Excellence for Coral Reef Studies Professor Robert Steneck Professor Yossi Loya Maya Srinivasan Partner Investigator Tel Aviv University, Israel James Cook University University of Maine Dr Tim Lynam Jenn Tanner Dr Madeleine van Oppen CSIRO James Cook University Partner Investigator Australian Institute of Marine Science Dr Laurence McCook Annameike Van Den Heuvel Great Barrier Reef Marine Park Authority University of Queensland Dr Benjamin Walther Research Fellow Dr Madeleine van Oppen Sharon Wismer Australian National University Australian Institute of Marine Science James Cook University Dr David Williamson Professor John Tanzer Research Fellow Environmental Pathways and Solutions James Cook University Dr David Wachenfeld Business Team Great Barrier Reef Marine Park Authority Professor Bette Willis Jennifer Lappin Chief Investigator Chief Operations Officer James Cook University James Cook University Professor David Yellowlees Graduate Students David Yellowlees Chief Investigator Assistant Director James Cook University (see page 34) James Cook University Olga Bazaka Finance Manager and Resident International Technical Staff Graduate Coordinator James Cook University Scholars Lewis Anderson James Cook University Lianne Cook Dr Tatjana Good Project Officer Swiss National Foundation, Switzerland Mary Boyle University of Queensland James Cook University Dr Cristina Linares Monica Gaffney University of Barcelona, Spain Paul Costello Office Manager and KPI Officer Professor Yossi Loya James Cook University James Cook University Tel Aviv University, Israel Maria Gomez Eliza Glasson Dr Aurélie Moya University of Queensland ICRS Conference Coordinator James Cook University Marie Curie Fellow Mizue Hisano University of Nice, France James Cook University Janet Swanson Administrative Assistant Dr Lucie Penin Paulina Kaniewska Marie Curie Fellow University of Queensland James Cook University University of Perpignan, France Richard Krege Australian National University Jessica Maddams Adjunct Researchers James Cook University Dr Alison Green James Moore The Nature Conservancy James Cook University Dr Alexander Kerr Graham Mortimer University of Guam, USA Australian National University Professor Janice Lough Nela Rosic Australian Institute of Marine Science University of Queensland

2009 annual report 11 program leaders

Professor Malcolm McCulloch Professor Malcolm McCulloch is one of the Centre’s two Deputy Directors and Leader of Program 1: Evolutionary and Environmental Change. He is a Professor in the School of Earth and Environment at the University of Western Australia, Perth, and a newly appointed Western Australian Premier’s Fellow (2009-2013). His research interests focus on the modern part of the geologic record using isotopic and trace element geochemical methods to determine how climate and anthropogenic processes have influenced both past and present marine environments with particular emphasis on coral reefs. Malcolm has received a number of prestigious awards, including Fellowships of the Australian Academy of Science (2004), the Geological Society of Australia (2007), the Geochemical Society (2008) and the American Geophysical Union (2002). In 2009 he was awarded the Jaeger Medal in Earth Sciences by the Australian Academy of Science. Malcolm holds an Honorary Doctorate from Curtin University, and he is an ISI Highly Cited Researcher. His 240 scientific papers have been published in leading international journals including 23 articles in Science or Nature.

Professor Sean Connolly ARC Professorial Fellow Sean Connolly, from James Cook University, is Leader of Program 2: Understanding and Managing Coral Reef Biodiversity. Sean combines mathematical and statistical modelling with fieldwork and laboratory experiments to study the dynamics of biological turnover at all scales, including population dynamics, species interactions and biodiversity, and macroevolution. He received his doctorate in 1999 from Stanford University in California, USA, for research on the ecology of rocky shores. In 1999-2000, he was a postdoctoral research fellow at the University of Arizona, USA, where he examined global dynamics of marine biodiversity in the fossil record. In 2000, he was recruited to JCU to develop and lead a research program in ecological modelling applied to coral reefs. Sean has 38 publications in leading international journals, including 5 in Science or Nature, and he has supervised 22 Postgraduate and Honours students since 2001. He currently holds an Australian Professorial Fellowship from the Australian Research Council, and was most recently honoured by the award of the 2009 Fenner Medal of the Australian Academy of Science, for pioneering new approaches to understanding biodiversity.

Professor Garry Russ Professor Garry Russ, from the School of Marine and Tropical Biology at James Cook University, is Leader of Program 3: Marine Reserves and Reef Connectivity. Garry studies the biology of reef fish of commercial and recreational fishing significance (mostly serranids, lutjanids and lethrinids). A major area of his applied research involves population and community dynamics of reef fish of commercial significance. In the Coral Triangle region and Australia, he is undertaking long-term (25 year) monitoring of reef fish populations inside and outside marine reserves. Russ received his PhD from the University of Melbourne in 1981. Subsequently he was awarded an ARC Queen’s Fellowship at the Australian Institute of Marine Science. Garry moved to JCU from the University of Sydney in 1988 where he is currently a Professor in Marine Biology. Garry has published over 65 papers in international journals. In 1999, he received a prestigious Pew Fellowship in Marine Conservation jointly with his long-time colleague Dr. Angel Alcala. In 2007, he was awarded recognition for his contributions to management of the Great Barrier Reef, by the Great Barrier Reef Marine Park Authority.

12 ARC Centre of Excellence for Coral Reef Studies Professor Ove Hoegh-Guldberg Professor Ove Hoegh-Guldberg is one of two Deputy Directors of the ARC Centre and Leader of Program 4: Genetic, molecular and physiological processes. He is also the Director of the new Global Change Institute at the University of Queensland. His research interests span a broad range of topics including marine biology, physiology, biochemistry and molecular biology of plant-animal symbioses, co-evolution, coral bleaching, ocean acidification and climate change.I n 1999, he was awarded the University of NSW Eureka Prize for Scientific Research, for “research by an Australian scientist under 40”. Ove is Co-Chair of the Global Environment Facility/World Bank Working Group on Coral Bleaching and Related Ecological Disturbances, one of three expert groups within the Intergovernmental Oceanographic Commission and World Bank Coastal Program’s Global Coral Reef Targeted Research and Capacity Building Project that includes members from the ARC Centre. He has published over 160 papers, including 15 in Science or Nature. He is well known as an advocate for coral reefs and their future fate in the face of rapid climate change, and maintains an active blog, which regularly features the ARC Centre’s research. In 2008 Ove was awarded the prestigious Queensland Premier’s Smart State Fellowship (2008-2013).

Professor Terry Hughes Professor Terry Hughes is the Director of the ARC Centre of Excellence and Leader of Program 5: Resilience of linked social-ecological systems. He received his PhD in 1984 from Johns Hopkins University in Baltimore, USA and was an NSF Postdoctoral Fellow at the University of California, Santa Barbara before moving to Australia and James Cook University in 1990. Terry was elected a Fellow of the Australian Academy of Science in 2001 in recognition of “a career which has significantly advanced the world’s store of scientific knowledge”. He has been awarded two Federation Fellowships by the Australian Research Council, from 2002-2012, and is a Fellow of the Beijer Institute for Ecological Economics, in Stockholm. In 2007 he was awarded the Sherman Eureka prize for Environmental Research. He is a member of the ARC Advisory Council and Board Member of the Resilience Alliance and the Beijer Institute. Terry has broad research interests in ecology, marine biology and the social-ecological dynamics of coral reefs. As Centre Director, he provides academic leadership and is responsible for the strategic development of the Centre. He is an ISI Highly Cited Researcher, ranked #1 in Australia for citations in Ecology & Evolution. In 2008, he was awarded the prestigious quadrennial Darwin Medal by the International Society for Reef Studies.

Professor Bob Pressey Professor Bob Pressey was recruited by JCU in late 2007 to establish and lead the ARC Centre’s new Program 6: Conservation planning for a sustainable future. Bob’s research includes aspects of spatial data sets on biodiversity, geographic information systems, spatial modeling of species and human activities, software development, explicit frameworks for deciding on the location and timing of conservation investments, and the socio-economic issues involved in implementing conservation action. Prior to moving to JCU he was a professorial research fellow at the University of Queensland. Before that, he worked as a research scientist for the New South Wales National Parks and Wildlife Service for almost 20 years. During that time, he developed and applied leading- edge techniques in conservation planning, influenced policy and conservation practice, and began a long series of international collaborations. Along with Malcolm McCulloch and Terry Hughes he is one of three ISI Highly Cited Researchers in the ARC Centre and serves on the editorial boards of the leading conservation biology journals. Bob was awarded The Royal Botanic Gardens’ Eureka Prize for Biodiversity Research, in 2002 and the inaugural (2008) Australian Ecology Research Award from the Ecological Society of Australia. His most recent recognition (2009) was the title of James Cook University Distinguished Professor for excellence in scholarly activities.

2009 annual report 13 program leaders

Dr Simon Foale Senior Research Fellow Simon Foale leads the ARC Centre’s Program 7: Policy development, institutions and governance of coral reefs. He joined the Centre in late 2006, after a postdoctoral fellowship at the Australian National University’s Resource Management in Asia Pacific Program. Simon is a marine biologist who, since his PhD. was awarded in 1998 at the University of Melbourne, has been increasingly engaging with the social sciences in an attempt to address pressing fishery management issues in the Pacific, particularly in theS olomon Islands and Papua New Guinea. Simon has very broad applied experience in the Pacific, having worked for non-government conservation organisations, mining companies, regional agencies, governments and aid agencies. He publishes in a wide range of journals spanning the natural and social sciences. Simon’s current research examines political, social and economic aspects of fishery use and management in Melanesia, with a particular emphasis on developing locally relevant and culturally appropriate educational resources for improving coral reef fishery management.

Professor David Miller Professor David Miller is Leader of Program 8: Genomics and metagenomics of coral reefs. David studies the molecular biology of corals and other “simple” marine animals. His research interests span a broad range of topics from marine biology to genomics, and include the biochemistry and molecular biology of coral symbioses, the evolution of developmental mechanisms (“evo-devo”), immune system evolution, and the molecular bases of coral responses to stressors such as disease, ocean acidification and climate change. David obtained his PhD in genetics and biochemistry from the University of Kent (UK). He subsequently undertook post-doctoral research at the University of Bristol (UK) and then the University of Adelaide. David moved to James Cook University from Adelaide in 1984 and is currently a Professor in molecular genetics and genomics. David’s main claim to fame is the discovery that “simple” animals such as corals have genomes as complex as those of man and other vertebrates, and in highlighting the role of gene loss in shaping animal genomes. He plays a leading role in a number of genome projects on various lower animals, including the first coral genome project and the first all-Australian whole genome project, and is a regular commentator on animal genome evolution for a number of high profile journals.

14 ARC Centre of Excellence for Coral Reef Studies BUSINESS leaders

Professor David Yellowlees Professor David Yellowlees is the Assistant Director of the ARC Centre of Excellence and a Chief Investigator in Programs 4 and 8. Trained as a biochemist, he has undertaken extensive research on the symbiosis between coral reef organisms, particularly in corals and tridacnid clams since the mid 1980s. His major interests have centred on the metabolic relationship between the symbiotic partners. His research on the acquisition of inorganic carbon, its photosynthetic fixation and the transfer of this to the animal host forms the basis of much of our understanding of these organisms at the metabolic level. David has published over 80 papers in international journals. He has had a long career at James Cook University commencing in the Department of Chemistry and Biochemistry in 1971. After resigning as Head of the School of Pharmacy and Molecular Sciences at the beginning of 2007, he joined the staff of the Centre in a part time capacity as its Assistant Director. He now applies many of these skills learned as Head of School to assisting with the running of the Centre.

Jenny Lappin Jenny Lappin is the Chief Operations Officer of the ARC Centre of Excellence. Jenny has a Bachelor of Commerce degree from the University of Queensland and is a member of the Australian Society of Certified Practicing Accountants. She has over 20 years of senior management experience with responsibilities for strategic planning, finance management, human resources, communications, business process engineering, change management and policy development. Starting work as an accountant in Townsville she progressed her career in Sydney, Melbourne and London before returning to Australia. She started as an academic in the Department of Commerce at James Cook University in 1988, moving to general financial management positions soon after.F ollowing various leadership positions in finance, research, foreign aid projects and as an executive officer at JCU, she moved in October 2005 to the Centre of Excellence to oversee, with the Centre Director, its establishment. She enjoys the diversity and challenges of a rapidly growing and vibrant research Centre of Excellence.

2009 annual report 15 RESEARCH

Program 1: Evolutionary and Environmental Change

Researchers challenges, researchers in Program 1 have influenced coral reefs and reef ƒƒ Malcolm McCulloch have combined resources to develop growth on the Great Barrier Reef, as well Program Leader and apply novel geochemical methods, as in Tobago in the Southern Caribbean. ƒƒ Sean Connolly Research Fellow historical records and ecological studies In 2009, she commenced a new study to identify and understand changes in on the effects of runoff into the key ƒƒ Ove Hoegh-Guldberg biodiversity and ecosystem function, tourist areas of Dunk Island and Mission Research Fellow over a range of timeframes. In a major Beach located in the central Great Barrier ƒƒ Terry Hughes Research Fellow new development, in mid-2009 a new Reef between Cairns and Townsville. ƒƒ Jennie Mallela Research Fellow node of the Centre was established ƒƒ Michael Kingsford at the University of Western Australia, A major research program is yielding following the award of the WA Premier’s exciting insights into the long-term ƒƒ Janice Lough Fellowship to Malcolm McCulloch. This history of nearshore Great Barrier ƒƒ John Pandolfi expansion will allow us to significantly Reef and Moreton Bay (south east ƒƒ Robert Steneck expand on the Centre’s existing activities Queensland) coral reef communities. ƒƒ Benjamin Walther Research Fellow on the west coast (in Programs 1, 2, 3 Led by John Pandolfi, the research and 6). uses precise chronological measures Understanding how coral reefs are and paleoecological analysis to show responding to the ongoing effects of In 2009, McCulloch and colleagues dramatic shifts in nearshore coral both climate and environmental changes published their initial findings of the long- communities that can be attributed to is the major objective being addressed term influence of ocean acidification European colonization of Queensland. by Program 1. A multi-faceted approach on Arlington Reef, an oceanic coral The work is providing reef managers with is being followed, not only using direct reef system offshore from the Great a new perspective on what was natural observations from modern reefs but Barrier Reef. This study is using novel on the Great Barrier Reef prior to modern also examining how reefs have evolved geochemical tools based on boron human influences. and changed over timescales ranging isotopic variations in long-lived coral from a few decades and years to many cores. Results indicate that the long- John Pandolfi and Malcolm McCulloch thousands of years. This research is term pre-industrial variation of seawater are continuing their ongoing of growing importance because it is pH in this region is partially related to paleontological and geochemical studies now becoming increasingly clear that the decadal–interdecadal variability of of the regional dynamics of biodiversity contemporary changes are occurring atmospheric and oceanic anomalies in coral reefs under differing past at a faster pace than anticipated due to in the Pacific.I mportantly, from the climates. One major focus is the fossil the combination of local environmental 1940s to the present-day, there is a reefs that grew along the Western impacts and changes in climate and general overall trend of increasing ocean Australian coastline ~125,000 years ocean chemistry, the latter from rapidly acidification, with pH decreasing by ago during the last interglacial period,

rising levels of atmospheric CO2. Even if about 0.2–0.3 pH units. Boron and carbon when global temperatures were several the most optimistic outcome is achieved isotopes indicate that the increasing degrees warmer and sea levels were up from global cooperation on greenhouse trend towards ocean acidification over to 4 to 5 metres higher. These studies gas emissions, and increases in global the past 60 years in this region is clearly suggest that coral reefs can adapt, given temperatures are kept at < 2oC, levels the result of enhanced dissolution of CO2 sufficient time, to the effects of a global of atmospheric CO2 will almost certainly derived mainly from fossil fuel burning. warming ocean, and that they migrated exceed 450 ppm in the coming decades. southwards into sub-tropical areas when Research Fellow Jennie Mallela is using the temperature increased. However, Global warming and ocean acidification novel geochemical techniques based history may not repeat itself under the are already changing the physiology, on direct measurements of phosphorus current anthropogenic climate change ecology and geology of coral reefs, in concentration in coral skeletons to regime due to the added complexity of ways that are still poorly understood. assess how both land-based runoff (e.g. ocean acidification. In order to meet these growing nutrients) together with climate change

16 ARC Centre of Excellence for Coral Reef Studies Photo by John Pandolfi

Media Release 7000 year old corals of Moreton Bay tell their story

The 7000-year-old coral communities of Moreton Bay The scientific symposium Securing Coral Reef Futures are telling a curious tale, expanding when sea-levels rise will take place on August 6 and 7 at the Brisbane Customs or water quality improves, then declining when current House. It will be followed by the Public Forum on the circulation becomes more restricted. future of the coral reefs worldwide at 6.00pm, Friday 7 August at the Brisbane Convention and Exhibition Centre. Intriguing new insights into the behaviour of corals and Media are welcome to attend both. fish under changing climatic conditions will be presented by leading marine researchers at a public forum in Brisbane “Coral reef scientists and managers are worried about this coming Friday. the future, and with good reason,” Prof. Hughes says. “The world is on a conveyor belt driven by population Professor John Pandolfi from the University of growth, rising consumption and climate change - yet most Queensland and ARC Centre of Excellence for Coral governments and agencies are focused on maintaining the Reef Studies and his team have been dating the corals of status quo, while many conservation groups would like Moreton Bay and finding they have undergone surges of to return to a pristine past. In a rapidly changing world, growth, probably triggered by subtle changes in sea level standing still or going backwards is simply not an option. and water conditions. The trick is to actively steer forward to a sustainable future “We’ve found coral communities up to 7000 years old that recognizes the importance of healthy ecosystems for showing these curious growth episodes – the last one human well-being.” started about 400 years ago. When coral reef growth slows At the symposium eminent environmental scientists or stops in the Bay, it appears to correspond with a decline will release an international communiqué on the future of in the current circulation and an increase in turbidity.” coral reefs and the human communities which depend on The team has also found clear evidence of changes in the them under climate change. A media conference will be types of corals in the Bay from the delicate staghorns to held at 10.40am on Thursday, August 6, at The Customs more massive forms, coinciding with European settlement House Reid Room, where CoECRS head Professor Terry and possibly resulting from declining water quality as Hughes, Professor John Quiggin (UQ) and Dr Josh Cinner nearby catchments were altered. (JCU) will be available to answer questions. These and many other aspects of the future of Australia’s corals will be explored at a scientific symposium and Communiqué at www.coralcoe.org.au/news_stories/ public forum in Brisbane this week. brisstatement.html

2009 annual report 17 RESEARCH

Program 2: Understanding and Managing Coral Reef Biodiversity

Researchers example, Phil Munday, Geoff Jones Program 2 researchers also continue to ƒƒ Sean Connolly Program Leader and their graduate students published interact with Commonwealth agencies ƒƒ Glenn Almany Research Fellow several papers in 2009 detailing the and other relevant parties on the effects of ocean acidification on coral proposed re-zoning of the Coral Sea. ƒƒ Andrew Baird Research Fellow reef fish larvae and juveniles, including ƒƒ David Bellwood impairment of their abilities to home in Program 2 researchers were granted ƒƒ Guillermo Diaz-Pulido on reef habitat, and to identify and avoid numerous awards and honours in Research Fellow predators (see p.55). Toby Elmhirst, Sean 2009. Program Leader Sean Connolly ƒƒ Maria Dornelas Research Fellow Connolly and Terry Hughes developed received the Fenner Medal from the mathematical models of ecosystem Australian Academy of Science; this ƒƒ Toby Elmhirst Research Fellow dynamics, which predict that the supply award recognizes outstanding research ƒƒ Chris Fulton of new coral juveniles to overfished in biology by a scientist under the age of ƒƒ Nick Graham Research Fellow reefs from nearby protected areas 40. Andrew Baird was awarded an ARC does not enhance their resilience to Future Fellowship, and Nick Graham ƒƒ Terry Hughes Research Fellow collapsing into seaweed-dominated received an Australian Postdoctoral ƒƒ Geoffrey Jones states. However, spill-over of larvae can Fellowship and a Queensland Smart ƒƒ Ronald Karlson facilitate the reversal of those collapses Futures Fellowship. In addition, Joana ƒƒ Philip Munday Research Fellow back to coral-dominated states. This Figueredo (PhD, University of Lisbon) has study highlights the importance of good been awarded a postdoctoral fellowship ƒƒ John Pandolfi management outside no-take areas for from the Portuguese Fundação para a ƒƒ Lucie Penin Visiting Research Fellow preventing coral reef collapse, but also Ciência e a Tecnologia, and will be joining ƒƒ Morgan Pratchett Research Fellow shows how no-take areas can provide Program 2 as a Visiting Research Fellow ƒƒ Robert Steneck an insurance policy in the event that in 2010. John Pandolfi was appointed collapses do occur. New work by John Vice-President of the Australian Coral Pandolfi and colleagues investigating Reef Society, the world’s oldest Coral reef biodiversity underpins the ecological baselines over centennial professional association of coral reef critically important functions and services time scales on the Great Barrier Reef scientists. Program 2 researchers, with performed by reef ecosystems, such shows convincing evidence for human- other Centre colleagues, received ARC as sustaining the productivity of fish induced shifts in species composition infrastructure funding to establish the stocks on which many tropical nations associated with European colonization. Marine Climate Change Experimental depend for their food security and This work provides the first key evidence Facility at JCU, which will be used to future development. Program 2 aims for shifting baselines on the Great Barrier substantially enhance the ARC Centre’s to understand the mechanisms and Reef, and will aid managers in setting capacity for further study of the effect of processes that maintain coral reef appropriate management goals. global warming and ocean acidification biodiversity, using a combination of on reef organisms. mathematical modelling and field studies. Program 2 researchers also made This multi-disciplinary approach informs numerous important contributions in In addition to the award of new ARC knowledge-based management of 2009 to coral reef policy issues at State, research fellowships to Andrew biodiversity resulting in environmental, Commonwealth, and international Baird and Nick Graham, a new Chief social, and economic benefits to tropical levels. Future Fellow Glenn Almany is Investigator, Chris Fulton from the maritime nations. working with The Nature Conservancy Australian National University, also and local communities in Papua New joined the ARC Centre in 2009. Chris Program 2 research in 2009 provided Guinea to establish new Marine Park has already forged strong links with several key breakthroughs in Areas for managing overfishing and the colleagues in Program 2, and adds an understanding how coral reefs respond effects of climate change. Nick Graham extensive record of research into the to overfishing and climate change, is providing advice to the Great Barrier effects of flow on organism performance and importantly how management Reef Foundation on the development to the Centre’s portfolio of expertise. can mediate those responses. For of indicators of coral reef resilience.

18 ARC Centre of Excellence for Coral Reef Studies Photo by Simon Foale

Media Release Corals raise hopes for survival

Hope that some of the world’s corals may be able to Dr Penin said the Tiahura Outer Reef Sector of Moorea escape destruction under climate change has emerged from had been closely studied for four decades by scientists, a study by an international team of scientists working in and the corals’ responses to natural disturbances were French Polynesia in the Pacific. The researchers found that now well understood. The five major disturbances had corals off Moorea, in the central Pacific, have rebounded on reduced coral cover at the time from over 50% of the area five occasions despite sustaining heavy damage from four to as little as 22% while, in the early nineties sea weeds bleaching events and one cyclone in the past 18 years. known as turf algae had taken over more than half of the area in the wake of cyclone and bleaching. However key In particular, they were able to recover even after the coral species were able to re-colonise the reef in subsequent reef had been swamped by weeds, says team member years. Dr Lucie Penin of the ARC Centre of Excellence for Coral Reef Studies, James Cook University and the Université “Our results support the idea that a rapid recovery de Perpignan. from a weed-dominated reef to a coral dominated one is possible – but it will depend on what other pressures “We conclude from this that coral reefs may not the corals are facing,” Dr Penin says. “It also shows that a completely disappear as a result of climate change – as fast recovery, in just a decade, is possible under the right some people fear they might,” she says. (In the Earth’s conditions.” past history corals have become either nearly or totally extinct on five separate occasions, and some researchers However since the study was completed the Tiahura reef warn that conditions under global warming may prove has come under a new threat – Crown of Thorns starfish similar to those previous events.) have mounted a severe attack on the corals, slashing coral cover to as little as two per cent in some areas. However, Dr Penin notes that the corals studied lie on the outer reef slope of an island that is not heavily “We are keeping a very close eye on this outbreak. Right populated, and that the main human impact on them is now the reef is in a very bad condition, but there are signs fishing. “The lack of human pressure on the reef makes of recovery and we are hoping it will come back from it more resilient,” she says. “This research suggests that, this as it has from the damage caused by bleaching and if left alone, coral reefs have the possibility to recover and cyclones,” she says. re-grow.” Researcher Loïc Thibaut, James Cook University and Adjeroud, M, Michonneau, F, Edmunds, P, Chancerelle, Y, Université Pierre et Marie Curie adds “One of the salient de Loma, T, Penin, L, Thibaut, L, Vidal-Dupiol, J, Salvat, features of this reef is that the fish community, and in B and Galzin, R (2009). Recurrent disturbances, recovery particular herbivorous fishes have remained at high levels trajectories, and resilience of coral assemblages on a of abundance throughout the study. This might well South Central Pacific reef. Coral Reefs 28(3): 775-780 explain why the coral community recovered so quickly despite the catastrophic events it had to face.” 6 July 2009

2009 annual report 19 RESEARCH

Program 3: Marine Reserves and Reef Connectivity

Researchers recommendations for the design of assessment of the current extent, ƒƒ Garry Russ Program Leader marine protected area networks (e.g., conservation efficacy and gaps in size and spacing) to protect connectivity. coverage of Marine Protected Areas ƒƒ Glenn Almany Research Fellow These papers formed the core output (MPAs), using a newly compiled GIS ƒƒ Andrew Baird Research Fellow from an international workshop entitled database with records for more than ƒƒ David Bellwood “Connectivity and population resilience – 1000 marine reserves. The analysis sustaining coral reefs during the coming shows that the current extent and ƒƒ Sean Connolly Research Fellow century” co-hosted in Townsville in distribution of MPAs does not adequately ƒƒ Nick Graham Research Fellow 2008 by the ARC Centre and Global represent biodiversity in the Philippines. ƒƒ Terry Hughes Research Fellow Environment Fund. At present, only 2.8% of coral reef area in the Philippines is protected within ƒƒ Geoffrey Jones Program 3 continues to lead the world no-take zones, and 88% of MPAs are ƒƒ Michael Kingsford in the development and application of smaller than 1km2. However, spacing techniques for tagging and tracking distances between MPAs are such ƒƒ Laurence McCook marine larvae. Geoff Jones and that larval connectivity between sites ƒƒ Mark McCormick colleagues used larval tagging and is likely, providing opportunities to ƒƒ Mark Meekan genetic studies to reveal the export of develop regional-scale MPA networks. larvae from marine reserves in Papua The results indicate that, even if ƒƒ Philip Munday Research Fellow New Guinea. They showed that larval adopted universally, community-based ƒƒ John Pandolfi dispersal connected fish populations in a MPAs will not be sufficient to meet network of marine protected areas over national goals. A dual approach to MPA ƒƒ Serge Planes scales of 30km. This ground-breaking implementation was recommended, ƒƒ Morgan Pratchett Research Fellow research was published in 2009 in whereby continued efforts to increase ƒƒ David Williamson Research Fellow Proceedings of the National Academy of the number of community-based MPAs Science. This year, for the first time, we are supplemented by the designation ƒƒ Bette Willis also applied these novel larval tracking of additional large no-take areas with a techniques, combined with detailed larval conservation focus. Networks of marine reserves (no-take dispersal modeling, to Australia’s iconic areas) are used to manage biodiversity Great Barrier Reef Marine Park. Many of the research projects within and fisheries. Zoning for multiple levels Program 3 are designed to actively of use and protection, including no-take Program 3 continues to make engage with local stakeholders. For areas, has become one of the principal breakthroughs in understanding of larval example, work on the Great Barrier mechanisms for management of marine biology. Mark McCormick and colleagues Reef in 2009 required assistance from resources in Australia and around the completed a synthesis of how the several recreational fishing groups, world. Program 3 focuses on how physiological state of parents (particularly including the major recreational fishing marine reserves enhance biodiversity mothers) during gametogenesis body in Queensland, SUNFISH. In the and fisheries management. A major affects offspring success. This novel Philippines, Garry Russ’s long-standing issue is the level of larval dispersal and research shows that successful colleague, Angel Alcala, continues to connectivity within and between marine recruitment to the next generation of work closely with Philippine fishing reserve networks. Program 3 focuses on breeding fish is strongly influenced communities to set up marine reserves. the optimal design of reserve networks by parental condition. Phil Munday In PNG and the Solomon Islands, Future for coral reef conservation and fisheries and colleagues showed that ocean Fellow Glenn Almany and others work management; and on the consequences acidification impairs the innate ability closely with The Nature Conservancy to of shifts in connectivity, due to climate of fish larvae to avoid their predators. test and design new Marine Protected change and other processes that affect If acidification continues unabated, Area networks. stock-recruitment relationships. the impairment of sensory ability will reduce population sustainability of many Research on the design and In 2009, Program 3 researchers, marine fish species, with potentially implementation of marine reserve together with colleagues from France profound consequences for marine networks, as outlined above for the and the USA, published a set of six biodiversity, fisheries sustainability and Great Barrier Reef, Papua New Guinea, articles in a Special Theme section of connectivity patterns of populations the Solomon Islands and the Philippines, the journal Coral Reefs. The papers and networks of marine reserves. represents a significant contribution by reviewed and synthesized information Program 3 to the scientific knowledge on biological connectivity on coral In the Philippines, Garry Russ and underpinning the Coral Triangle Initiative reefs, while also providing updated colleagues undertook a national-scale (see also p.26, 28, 50).

20 ARC Centre of Excellence for Coral Reef Studies Photo by Ashley Frisch Media Release Proof that marine parks work

New evidence supports the growing view that a network In another first, the team has demonstrated the power of marine reserves is more effective for maintaining a of parental DNA analysis for measuring the health and diversity of fish and other marine species than a single, viability of fish populations in marine protected areas. isolated park or no-fishing area. Because orange clownfish live in sea anemones and An international research team has found that networks because the locations of all the anemone clumps around of marine protected areas (MPAs) can play a big role in Kimbe Island were known, the team was able to collect protecting threatened coral reef fish and other marine DNA from 506 adult clownfish living around the island – species from local extinction. In a world-first experiment, which they believe to be its entire population. the researchers used DNA fingerprinting to show that They then tested juvenile fish which had recently baby orange clownfish have remarkable homing abilities, returned from the open sea and settled on the reef in order with many finding their way back to home reefs after to establish their parentage, finding that about 40 per cent being swept out to sea as hatchlings. were locally-bred while the remainder had come from In the process they discovered some baby clownfish had other reefs. travelled to reefs as much as 35 kilometres distant from “This level of recruitment to the home reef was the reef where they were spawned – a spectacular feat remarkably stable over time. It shows both the value considering they were only a few millimetres in length. of having a protected area to maintain the local fish The research was carried out in Kimbe Bay, New Britain population – and also the importance of having a network in Papua New Guinea, a region of relatively pristine coral of protected areas within a range that allows them to reefs where it is proposed to set up a network of marine replenish one another’s fish populations,” Professor Jones reserves. says. “Using their parent’s DNA to identify where they had “Given the mounting evidence worldwide that come from, we have been able to show that about 40 per populations of many small reef fish are under threat, we cent of baby clownfish that settle in a marine reserve are think parental DNA analysis offers a new tool to help those that have returned home. In addition, the parents protect them.” within one marine reserve can explain up to 10 per cent of the baby fish settling in reserves 20-30km away”, says Prof Geoff Jones of the ARC Centre of Excellence for Coral Reef Studies. Planes, S, Jones, GP and Thorrold, SR (2009). Larval dispersal connects fish populations in a network of “This shows not only how effective a marine protected marine protected areas. Proceedings of the National area can be for conserving the breeding stock on a Academy of Sciences 106(14): 5693-5697. particular reef – but also how important it is to have a network of protected reefs at the right distance which can 25 March 2009 help to re-stock one another.”

2009 annual report 21 RESEARCH

Program 4: Genetic, Molecular and Physiological Processes

Researchers host and zooxanthellae, have now the 2009 study by Mia Hoogenboom ƒƒ Ove Hoegh-Guldberg shown that it can take up to 3 years which showed that, contrary to Program Leader to establish adult patterns of algal conventional thinking, the optimal light ƒƒ Tracy Ainsworth Research Fellow endosymbioses. This is a remarkable regimes for coral growth and energetics finding, with important implications for are below the maximum observed light ƒƒ Ken Anthony how reefs recover from recurrent bouts levels of coral reefs. ƒƒ Line Bay Research Fellow of bleaching. Along with the work of ƒƒ Guillermo Diaz-Pulido PhD students David Abrego and Jos Simon Dunn, Sophie Dove, Bill Leggat Research Fellow Mieog, these studies have revealed and Tracy Ainsworth have been exploring ƒƒ Sophie Dove fresh insights into the complexity of the involvement of cell death pathways the symbiosis between these partners. in thermal stress and breakdown of ƒƒ Simon Dunn Research Fellow Interestingly, they have shown more the symbiosis between corals and ƒƒ Bill Leggat clearly than any previous studies their dinoflagellates. This has led to the ƒƒ David Miller that the fitness of this relationship is identification of a series of key genes ƒƒ Madeleine van Oppen influenced by interactions between the that control the fate of cells affected by symbiont type and the environment. rapid changes in sea temperature. ƒƒ Bette Willis ƒƒ David Yellowlees The impact of climate change on the Research into causative agents of coral symbiotic association is a major focus diseases by Program 4 researchers is Program 4 researchers continued in 2009 of all researchers in Program 4, across adding to the toolbox available to reef to investigate the relationships between both the UQ and JCU/AIMS nodes, managers. A study by PhD student Yui the coral animal and their symbiotic with a wide range of important research Sato is the first to describe the seasonal microalgae, and microbial associates – questions being addressed. PhD student dynamics of an outbreak of black band both as beneficial partners and disease Rachael Middlebrook demonstrated that disease on the Great Barrier Reef, which agents. A major focus within the Program heating rate is an important parameter highlights the increasing susceptibility has been determining the impact when determining thermal susceptibility of corals to rising sea temperatures. that environmental factors – including of corals. The shuffling or switching of Early successional changes in bacterial global climate change – have on these symbionts (the “adaptive bleaching” communities that facilitate development relationships, and particularly on an array hypothesis) came under scrutiny when of black band disease were identified and of projects that address the mechanisms PhD student Michael Stat and co- will aid in early detection of the disease. of coral bleaching triggered by thermal workers found no evidence for switching A complementary study of the natural stress. These studies greatly increase in ten coral species 12 months after a bacterial communities in corals, by Tracy our knowledge of these symbioses, thermal stress event on the Great Barrier Ainsworth showed that they too are providing a broader understanding of Reef. Gene expression studies, led by significantly altered during thermal stress. how and why corals respond in certain Queensland Smart State Fellow Line Landmark studies by PhD student Meir ways to different stressors. Bay, have revealed evidence of major Sussman identified Vibrio coralliilyticus as phenotypic plasticity in gene expression a causative agent of white syndromes, Eugenia Sampayo in the Hoegh-Guldberg levels in response to environmental a group of damaging Indo-Pacific and Dove laboratories have analysed change. Line and co-workers’ ongoing coral diseases, and showed that eight ecologically distinct Symbiodinium studies are exploring the genetic basis photoinactivation of algal endosymbionts spp and showed that there was a strong of trait variation, to assess the potential by zinc-metalloproteases contributes correlation between phylogenetically for adaptation by corals in response to to its virulence. These studies lay the independent lineages and ecological climate change and to potentially find groundwork for developing assays that and physiological attributes. The Willis genetic markers associated with the will provide important management tools and van Oppen laboratories, in studying tolerance of corals to climate change. for detecting future disease outbreaks. the relationship between the coral Also of relevance to global warming was

22 ARC Centre of Excellence for Coral Reef Studies Photo by Ove Hoegh-Guldberg

Media Release Reef boom beats doom

Marine scientists say they are astonished at the “Coral reefs globally are increasingly being damaged spectacular recovery of certain coral reefs in Australia’s by mass bleaching and climate change, and their capacity Great Barrier Reef Marine Park from a devastating coral for recovery from that damage is critical to their future,” bleaching event in 2006. explains Prof. Ove Hoegh-Guldberg. “Our study suggests that managing local stresses that affect reefs such as That year high sea temperatures caused massive overfishing and declining water quality can have a big and severe coral bleaching in the Keppel Islands, in the influence on the trajectory of reefs under rapid global southern part of the Great Barrier Reef. The damaged reefs change.” were quickly smothered by a single species of seaweed – an event that can spell the total loss of the corals. “Clearly, we need to urgently deal with the problem of rising carbon dioxide in the atmosphere, but managing However, a lucky combination of rare circumstances reefs to reduce the impact of local factors can buy important meant the reefs were able to achieve a spectacular recovery, time while we do this,” he says. with abundant corals re-established in a single year. Dr Guillermo Diaz-Pulido explains that “Three factors were Understanding the different mechanisms of resilience critical. The first was exceptionally high re-growth of is critical for reef management under climate change. fragments of surviving coral tissue. The second was an “Diversity in processes may well be critical to the overall unusual seasonal dieback in the seaweeds, and the third resilience and persistence of coral reef ecosystems globally,” was the presence of a highly competitive coral species, Dr Laurence McCook, from the Great Barrier Reef Marine which was able to outgrow the seaweed.” Park Authority, says. “It is rare to see reports of reefs that bounce back from “This combination of circumstances provided a lucky mass coral bleaching or other human impacts in less than escape for the coral reefs in Keppel Islands, but is also a decade or two,” said Dr Diaz-Pulido. “But this also all a clear warning for the Great Barrier Reef. As climate happened in the context of a well-protected marine area change and other human impacts intensify, we need to and moderately good water quality,” he adds. do everything we possibly can to protect the resilience of coral reefs,” he adds. “The exceptional aspect was that corals recovered by rapidly regrowing from surviving tissue. Recovery of corals is usually thought to depend on sexual reproduction Diaz-Pulido, G, McCook, LJ, Dove, S, Berkelmans, R, Roff, and the settlement and growth of new corals arriving from G, Kline, DI, Weeks, S, Evans, RD, Williamson, DH other reefs. This study demonstrates that for fast-growing and Hoegh-Guldberg, O (2009). Doom and boom on coral species asexual reproduction is a vital component of a resilient reef: climate change, algal overgrowth and reef resilience” says Dr Sophie Dove. coral recovery. PLoS ONE 4(4): e5239 22 April 2009

2009 annual report 23 RESEARCH

Program 5: Resilience of Linked Social-Ecological Systems

Researchers with the co-evolution of an emerging in fertilisers, use of fresh water, the ƒƒ Terry Hughes Program Leader system of governance. The next meeting clearing of land, ozone depletion, aerosol ƒƒ Andrew Baird Research Fellow will be held in June 2010 in the Baltic pollution of the atmosphere and chemical Sea, addressing the challenges of trans- contamination. These two studies ƒƒ David Bellwood boundary governance in the ocean. reflect the ARC Centre’s ongoing links ƒƒ Joshua Cinner Research Fellow to the Resilience Alliance, the Beijer ƒƒ Toby Elmhirst Research Fellow In June, Terry Hughes joined the Institute for Ecological Economics, ƒƒ Kathryn Ferguson Research Fellow inaugural Science Committee responsible and the Stockholm Resilience Centre. for developing a 10-year global research Other major publications during the year ƒƒ Pedro Fidelman Research Fellow project of ICSU, the International included a cutting-edge theme section ƒƒ Simon Foale Research Fellow Council for Science. The project, entitled in the journal Coral Reefs, on larval ƒƒ Carl Folke Program on Ecosystem Change and connectivity and ecological resilience ƒƒ Nick Graham Research Fellow Society (PECS), will focus on both (see Program 3 summary), compiled and human development and sustainability edited by Geoff Jones, Garry Russ, Peter ƒƒ Laurence McCook of natural resources at regional to global Sale and Bob Steneck. ƒƒ John Pandolfi scales. PECS aims to link science and ƒƒ Bob Pressey Research Fellow environmental management to society, Senior Fellow Simon Foale was ƒƒ Robert Steneck policy and human well-being. The PECS contracted by The Nature Conservancy Science Committee will meet twice a (TNC) to review the extent to which year in Paris to develop a social-ecological TNC have applied the ecosystem Program 5 focuses on the interface research agenda that is closely aligned approach to fisheries in their Melanesian between people, economies and coral to the ARC Centre’s Programs 5, 6 and projects. ARC Australian Postdoctoral reef ecosystems. Our objective is to 7. PECS is co-sponsored by UNESCO, Fellow Josh Cinner and colleagues undertake research and develop new and will complement existing global undertook a regional analysis of the tools that improve the governance environmental change programs and role of socioeconomic development and management of natural systems international partnerships. in sustaining coral reefs in the Indian and enhance their capacity to sustain Ocean. The study, published in Current human and natural capital. Program Two of the ARC’s high-profile articles in Biology, was also presented by Josh 5’s multi-disciplinary research 2009, published in Science and Nature, at the 2009 meeting of the American combines expertise on coral reef are at the interface of Programs 5 and 7. Association for the Advancement of biology, management, governance, The first argues that coping with global Science, in Chicago. Research Fellow economics and the social sciences. changes requires new institutions and Toby Elmhirst and colleagues presented a global system of governance that is the results of a novel modelling study In February, Program 5 leader Terry currently missing. Energy, food and in the December issue of Coral Reefs, Hughes and Rodrigo Bustamante from water crises, climate change, declining which examines the reliance of highly- CSIRO, co-hosted the latest of the world fisheries, emerging diseases and protected areas on larval input from the ARC Centre’s series of international antibiotic resistance are all examples surrounding seascape. Most research in working group meetings on marine of intertwined global challenges that large scale connectivity has emphasized social-ecological systems, focussing are outpacing the capacity of existing spill-over from no-take areas. Toby’s work this time on the Galapagos Islands. The institutions (see p.29). The Nature paper predicts that the ecological resilience group examined how climate change, proposes ten earth-system boundaries of no-take areas can be undermined by tourism, global markets, migration, and which should not be exceeded to avoid degradation at larger scales, requiring a introduced pests have all changed the crossing dangerous tipping points. These seascape approach to marine resource nature and scale of the social-ecological include the rate of species extinction, management beyond the conventional dynamics of the Galapagos archipelago, the amount of nitrogen and phosphorus focus on networks of no-take areas.

24 ARC Centre of Excellence for Coral Reef Studies Photo by Simon Foale Media Release Gear bans “can help save reefs”

An international team of scientists led by Dr Josh Cinner “Spear guns target a high proportion of species that help of the ARC Centre of Excellence for Coral Reef Studies has maintain the resilience of coral reefs, but also can result in proposed that bans on fishing gear - like spear guns, fish a surprising amount of damage to the corals themselves. traps, beach seine nets, and gill nets – could aid in the When a fish is shot with a spear gun, it often hides in the recovery of reefs and fish populations hard hit by coral reef, so some fishermen break the corals in their attempts bleaching events. to get it.” Dr Cinner says. Research carried out in Kenya and Papua New Guinea But in developing countries, spear guns can be the has shown that certain types of gear are more damaging fishing tool most used by the poorest fishers because they to corals, to coral-dependent fish and to the key species of are cheap to make and the yield can be high, so they are an fish that are needed to help reefs recover from bleaching important source of income for poor fishers. or storm damage. “You can’t simply impose an arbitrary ban on their “This is creating a double jeopardy for both the corals use – you need to consider issues like compensation, and certain types of reef fish. They are already on the edge other fishing options, or alternative livelihoods for the because of the overfishing – and the additional impact affected fishers,” says co-author Dr. Shaun Wilson of the caused by a bleaching event can push them over” Dr Western Australian Department of Environment and Cinner explains. The result can be an accelerated decline Conservation. “One key issue may be educating fishers of the reef, its fish populations and their ability to sustain about the importance of reef habitat and the species that local people. help to maintain reef quality – and the need to be selective in what they shoot. This would mean fishers could still use “From an ecological perspective, the best response to this cheap and effective fishing tool without necessarily bleaching is to close reefs to fishing entirely. But that is not damaging habitat and reef resilience.” feasible everywhere and is a particularly hard sell among the impoverished fishers in developing countries” says co- author Dr. Tim McClanahan of the Wildlife Conservation Cinner, JE, McClanahan, TR, Graham, NAJ, Pratchett, MS, Society. “In areas where fishery closures are impractical, Wilson, SK and Raina, J-B (2009). Gear-based fisheries managers don’t have many options and haven’t been able management as a potential adaptive response to climate to do much but watch the reef die and often not recover.” change and coral mortality. Journal of Applied Ecology 46: The team investigated the effects of five main types of 724-732 gear on different types of fish: spear guns, traps, hook and 18 June 2009 line, beach seine nets and gill nets.

2009 annual report 25 RESEARCH

Program 6: Conservation Planning for a Sustainable Future

Researchers to balance. A keynote presentation by postdoctoral fellows, Stacy Jupiter of ƒƒ Bob Pressey Program Leader Pressey at the inaugural Island Arks the Wildlife Conservation Society, to ƒƒ Glenn Almany Research Fellow symposium led to a major funding estimate the opportunity costs to local application to the Federal government in communities of establishing marine ƒƒ Natalie Ban Research Fellow collaboration with Derek Ball, Operations protected areas in inshore waters. ƒƒ Debora de Freitas Manager of Reef Catchments (Mackay In Papua New Guinea, Natalie Ban ƒƒ Tatjana Good Whitsundays) NRM. has developed her research project Visiting Research Fellow on patch dynamics and conservation ƒƒ Johnathan Kool Research Fellow Natalie Ban and Bob Pressey contributed planning within the Bismarck Sea and to two working groups of the Great the Great Barrier Reef. Natalie also led ƒƒ Laurence McCook Barrier Reef Foundation to discuss the a consultancy for the Pew Foundation importance of dynamics such as coral to estimate the management costs of Program 6, established in 2008, bleaching and pelagic productivity for complete no-take and partial no-take focuses on spatial solutions to resource planning multiple-use reef zones. This scenarios for the proposed Coral Sea management problems, involving the involvement led to Natalie’s successful Marine Reserve. design of conservation areas that are application for the Foundation’s inaugural managed to promote the persistence Bommies Award, shared with Eddie The Program had a busy and productive and sustainable use of natural resources, Game of The Nature Conservancy. 2009. As well as her award from the and implemented with local communities They will use the award funding to Great Barrier Reef Foundation, Natalie and other stakeholders. During 2009 our hold a scientific workshop on how received an Australian Postdoctoral number of PhD students grew to nine to incorporate patch dynamics into Fellowship from the ARC. Bob Pressey and further growth is planned for 2010, conservation planning for the Great and Helene Marsh were awarded an with the recruitment of two additional Barrier Reef region. Research Fellow, ARC Linkage grant entitled “Innovative Research Fellows. Johnathan Kool, who is co-funded by the systematic conservation planning for Australian Institute of Marine Science indigenous land and sea country: Torres The Great Barrier Reef and the Coral (AIMS), has begun work on the extensive Strait as a case study”. The grant will Triangle region are both a major focus CSIRO-AIMS seabed biodiversity data set fund a new Research Fellow for three of Program 6, and Bob Pressey and for the Great Barrier Reef. He is analysing years to combine Indigenous knowledge colleagues have already built close these data to help inform marine with software tools for participatory links with local governments, state classification and conservation objectives. planning of harvesting restrictions in governments, Australian government Torres Strait. departments, Natural Resource Program 6 has launched a number of Management (NRM) boards, international new projects in the Coral Triangle and Program 6 researchers and PhD conservation NGOs, International Union the south-west Pacific.F or instance, students attended national conferences for Conservation of Nature (IUCN - the in 2009 Johnathan Kool completed a in Alice Springs, Brisbane, Canberra, World Conservation Union) and the unique model of ocean circulation in Newcastle and the Whitsunday United Nations Environment Program. the Coral Triangle region. Johnathan Islands and international conferences During 2009, Pressey established new also leads a new project in the Solomon in China, the Czech Republic, Fiji, collaborative links with two NRM Boards Islands, in collaboration with The Nature Indonesia (two meetings), Portugal, in north Queensland. With Allan Dale, Conservancy, identifying marine and Tahiti, and the USA (two meetings). CEO of Terrain (Wet Tropics), the NRM terrestrial bioregions as a basis for a Attendance at these conferences Boards, and Debora de Freitas, Pressey gap analysis of protected areas and involved a total of 36 presentations, is designing a research project to provide identification of preliminary additional including three invited keynotes. managers of coastal catchments with protected areas that link catchments and the tools to make effective trade-offs inshore waters. In Fiji, Program 6 has between the many objectives they have initiated a project with one of our former

26 ARC Centre of Excellence for Coral Reef Studies The Great Barrier Reef as seen from space MODIS satellite image (http://visibleearth.nasa.gov) Photo courtesy NASA Media Release Rules proposed to save the world’s coral reefs

An international team of scientists has proposed a set of 3. aim to create networks of protected areas which (a) basic rules to help save the world’s imperiled coral reefs protect all the main types of reef creatures, processes from ultimate destruction. and connections, known and unknown; (b) achieve sufficient protection for each type of reef habitat Their proposal is being unveiled at the World Ocean type, and for the whole region; (c) achieve maximum Conference 2009 in Manado, Indonesia, where leaders of protection for all reef processes (d) contain several six regional governments plus Australia and the United examples of particular reef types to spread the risk; States are meeting to declare the largest-ever marine reserve in world history, the Coral Triangle Initiative. 4. protect whole reefs where possible; place buffer zones around core areas; “The catastrophic decline in the world’s coral reefs demands urgent management responses on two fronts,” 5. allow for reef species to spread over a range of say the researchers from the ARC Centre of Excellence distances, especially 20–30 km; and for Coral Reef Studies, The Australian Museum, Woods 6. use a range of conservation approaches, including Hole Oceanographic Institution, James Cook University, marine protected areas. University of Perpignan, the United Nations University and The Nature Conservancy. The rules are designed to operate in a range of situations, including where detailed scientific knowledge of local These are the “...reduction of immediate direct threats coral reefs and their species is sparse, the team says in a such as climate change, over-fishing and water pollution, review article in the journal Coral Reefs. and actions to protect or enhance the resilience of reef ecosystems in the face of existing and unavoidable future “The Coral Triangle Initiative is one of the most important threats,” they say. marine conservation measures ever undertaken anywhere in the world and the first to span several countries. It The key to saving threatened coral ecosystems is to involves Indonesia, the Philippines, Malaysia, Papua maintain the links (connectivity) between reefs allowing New Guinea, East Timor and the Solomon islands, and larvae to flow between them and re-stock depleted areas, is as much about nation building and food security as it the team led by Pew Fellow Dr Laurence McCook of is about reef conservation” says Professor Terry Hughes, Australia’s Great Barrier Reef Marine Park Authority Director of the CoECRS, attending the Coral Triangle argues. meeting today in Manado, Indonesia. The researchers propose six ‘rules of thumb’ for keeping coral ecosystems viable, based on the results of research carried out in the Philippines, Australia, and Papua New McCook, L, Almany, G, Berumen, M, Day, J, Green, A, Guinea. Jones, G, Leis, J, Planes, S, Russ, G, Sale, P and Thorrold, S (2009). Management under uncertainty: Guide-lines These rules are: for incorporating connectivity into the protection of 1. allow margins of error in extent and nature of coral reefs. Coral Reefs 28(2): 353-366. protection, as insurance against unforeseen threats; 11 May 2009 2. spread risks among areas;

2009 annual report 27 RESEARCH

Program 7: Policy Development, Institutions and Governance of Coral Reefs

Researchers on governance and marine systems in resources for improving coral reef fishery ƒƒ Simon Foale Program Leader Kenya and she is currently a research management. During the latter half of ƒƒ Joshua Cinner Research Fellow fellow at WorldFish in Malaysia. Mike 2009, Simon consolidated a productive is an anthropologist currently at the working relationship with key personnel ƒƒ Pedro Fidelman Research Fellow Australian National University working in the Curriculum Development Centre of ƒƒ John Pandolfi on social equity and marine resource the Department of Education in Solomon ƒƒ Terry Hughes Research Fellow regulation in the Philippines. These Islands. This work with Education two new recruits will provide a greater Departments on high school science Program 7, launched in 2009 and led by geographic spread of expertise and curricula addresses the need for training Senior Research Fellow Simon Foale, projects in Program 7. in the biology and ecology of over-fishing addresses the multi-faceted challenges and reef ecosystem degradation and is of improving coral reef governance. Other research fellows with a role in essential for the future leaders of the Because it is people, rather than fish or Program 7 include Josh Cinner and community. Other aspects of this three coral that must be managed, this multi- Pedro Fidelman. In 2009 Josh held a year research project address the social, disciplinary research program covers workshop on fisheries co-management political and economic aspects of coral cultural, political, historical, and economic in La Reunion, gave a keynote talk on reef fishery governance at various levels. aspects of coral reef management at governance at the Western Indian Ocean multiple scales. While Program 7’s Marine Science Association (WIOMSA) In July and August the Centre completed activities include a focus on the Great Conference, participated in a WIOMSA a long-term consultancy with the Barrier Reef, they are global in scope research priority-setting round table AusAID-funded Community Sector (see press release). In 2009, most of on climate change and gave talks at a Program in Solomon Islands – a program the Program’s projects were directed number of research institutions in the led by Simon Foale, which has provided at the rapidly evolving coastal resource USA with governance or policy-related valuable research material on community- management and governance challenges themes. Pedro presented a paper at the based sustainable development and in the Indo-Pacific region, in particular Earth System Governance Project (part capacity building. In October, Simon and in Melanesia and the Coral Triangle. of the International Human Dimensions colleagues at the Australian Institute of Program 7 addresses the global political Programme on Global Environmental Marine Science organised a workshop and economic drivers of resource-use at Change) on the institutional dimensions addressing the challenge of developing several scales, and aims to understand of environmental governance, and sustainable livelihoods in the Indo-Pacific the cultural, social and political was admitted as a fellow of the region as part of the Global Environment dimensions of coral reef tenure systems Earth Systems Governance Project. Facility’s International Waters conference and resource use, both contemporary He also commenced collaborations in Cairns. and historical. Program 7 is already with the Stockholm Resilience involved in capacity-building activities in Centre on research into governance In 2010, Program 7 researchers will host many countries, working with NGOs and of large marine ecosystems, and three working groups, on sustainable national governments. with CSIRO and the University of artisanal fisheries (led byS imon Foale Georgia, USA on the institutional in collaboration with WorldFish, in This new program is rapidly ramping dimensions of climate change. Townsville), trans-boundary governance up with the recruitment late in 2009 in the sea (Terry Hughes, in Stockholm), of two additional post-doctoral fellows In the Solomon Islands and Papua and on legal frameworks for incorporating Louisa Evans and Mike Fabinyi, who will New Guinea, Program 7 is undertaking ecological knowledge (John Pandolfi, in commence in May 2010. Louisa’s Ph.D. social and ecological research on Washington DC). at the University of East Anglia focussed how to develop locally relevant and culturally appropriate educational

28 ARC Centre of Excellence for Coral Reef Studies Photo by Simon Foale Media Release Missing institutions for dealing with global crises

The world faces a compounding series of crises driven grow biofuels or the emergence of pandemic flu through by human activity, which existing governments and lack of appropriate animal husbandry protocols. institutions are increasingly powerless to cope with, a “Knowing what to do is not enough,” says Dr Walker. group of eminent environmental scientists and economists “Institutional reforms are needed to bring about changes has warned. In today’s issue of the leading international in human behaviour, to increase local appreciation of journal Science, the researchers say that nations alone are shared global concerns and to correct the sort of failures of unable to resolve the sorts of planet-wide challenges now collective action that cause global-scale problems.” arising. “We are not advocating that countries give up their Pointing to global action on ozone depletion (the sovereignty,” adds co-author Professor Terry Hughes, Montreal Protocol), high seas fisheries and antibiotic Director of the ARC Centre of Excellence for Coral Reef drug resistance as examples, they call for a new order of Studies. “We are instead proposing a much stronger focus cooperative international institutions capable of dealing on regional and worldwide cooperation, helped by better- with issues like climate change – and enforcing compliance designed multi-national institutions. The threat of climate where necessary. change to coral reefs, for example, has to be tackled at “Energy, food and water crises, climate disruption, a global scale. Local and national efforts are already declining fisheries, ocean acidification, emerging diseases failing.” and increasing antibiotic resistance are examples of serious, “The major powers must be willing to enforce an intertwined global-scale challenges spawned by the agreement – but legitimacy will depend on acceptance by accelerating scale of human activity,” say the researchers, numerous and diverse countries, and non-governmental who come from Australia, Sweden, the United States, actors such as civil society and business,” they add. India, Greece and The Netherlands. “To address common threats and harness common “These issues are outpacing the development of opportunities, we need greater interaction amongst institutions to deal with them and their many interactive existing institutions, and new institutions, to help construct effects. The core of the problem is inducing cooperation in and maintain a global-scale social contract,” the scientists situations where individuals and nations will collectively conclude. gain if all cooperate, but each faces the temptation to free- ride on the cooperation of others.” “There are few institutional structures to achieve co- Walker, B, Barrett, S, Polasky, S, Galaz, V, Folke, C, operation globally on the sort of scales now essential to Engstrom, G, Ackerman, F, Arrow, K, Carpenter, S, avoid very serious consequences”, warns lead author Dr Chopra, K, Daily, G, Ehrlich, P, Hughes, T, Kautsky, N, Brian Walker of Australia’s CSIRO. Levin, S, Maler, K-G, Shogren, J, Vincent, J, Xepapadeas, T and de Zeeuw, A (2009). Looming global-scale failures While there are signs of emerging global action on issues and missing institutions. Science 325(5946): 1345-1346 such as climate change, there is widespread inaction on others, such as the destruction of the world’s forests to 11 September 2009

2009 annual report 29 CENTRES OF EXCELLENCE

RESEARCH Australia’s Cenfirst full t r e s genome project Program 8: Genomics and Metagenomics of Coral Reefs gets green light Researchers resource, making Acropora millepora enabled the collection of material for ƒƒ David Miller Program Leader the coral of choice for molecular and cell characterisation of the viral component ƒƒ Tracy Ainsworth Research Fellow biology research by most scientists in the associated with the coral Acropora coral research community. millepora. The analyses of the virome, ƒƒ Line Bay Research Fellow along with screening the coral genome ƒƒ Simon Dunn Research Fellow In Program 8’s first year, David Miller and for genes of viral origin, is underway.  One of the corals that form the backbone of the ƒƒ Sylvain Forêt Research Fellow his group have made significant progress Great Barrier Reef will be the first animal to have its ƒƒ Lauretta Grasso Research Fellow with a novel, comprehensive analysis of Other research highlights in 2009 genes fully explored in Australia. the coral transcriptome. This project has included major advances towards the ƒƒ Ove Hoegh-Guldberg The program to sequence the entire genome, or genetic been assisted by the recruitment of Dr establishment of stable cell lines from information, of Acropora millepora—a branching coral ƒƒ Bill Leggat Sylvain Forêt, a bioinformatician and the coral (Alejandro Reyes-Bermudez) and whose ‘staghorn’ shape and beautiful colours are familiar ƒ first postdoctoral fellow in the Program, the identification of more members of ƒ Aurélie Moya to millions of visitors to the Great Barrier Reef—marks a Visiting Research Fellow co-funded by the Australian Institute of a unique group of genes that encode major milestone in Australian biotechnology: it will be the Continued from page 6… Marine Science. Sylvain collaborated key components of the organic matrix ƒƒ Madeleine van Oppen first animal genome to be fully sequenced and assembled previously with the Miller group on the of corals (Reyes-Bermudez & Zhiyi Lin). “This gene mapping project has both practical and scientific in Australia. For more information contact Professor Terry Hughes at coral transcriptome project while on the David Miller analysed the homeobox significance. It will help us to understand how corals build The establishment of Program 8 in 2009 staff at ANU and is now a key participant gene repertoire in the genome of The staghorn coral may look like a simple animal, but its [email protected] or on + 61 7 4781 4000. recognises the growing importance reefs, and why they fail to do so when they are under stress. in the A. millepora genome assembly Schistosoma japonicum, while Sylvain genome is surprisingly large and complex. In fact, Acropora of genomics in coral reef research “It will enable us to predict, with much greater confidence, team. The first iteration of the genome Forêt was a member of the team that and the Centre’s growing expertise millepora has around 20 000 genes—about the same number assembly has been completed and the analysed the genomes of three Nasonia how corals are likely to respond to changes in the oceans such and leadership in this field. The new as a human. Why such apparently simple animals as corals team members are looking forward to species. Both resulted in authorship of as warming, acidification, the spread of coral diseases, and research program is based around should require as many genes as humans is still unclear; but it the second run which will be available in Nature papers. various forms of pollution.” the structure and function of the was this coral which provided the first hints of how genetically the second quarter of 2010. complex simple animals can be. The mapping of the coral genome is a joint undertaking by genomes of corals, their dinoflagellate PhD student Marcelo Kitahara was symbionts and associated bacterial the ARC Centre of Excellence for Coral Reef Studies and Program 8 researchers are also an invited participant at the FAO While they don’t much resemble humans, corals lie deep and viral communities, known as the Australian Genome Research Facility, in collaboration engaged in unravelling the unique workshop on the identification of on the ancestral tree of all animals and share many of our Coral in the Soloman Islands. Photo courtesy of Dr Simon Foale the ”holobiome”. The long-term aim with the ANU, The Walter and Eliza Hall Institute, and nature of the transcriptome of the deep-sea species, held in Rome in genes, says Professor David Miller, head of the Genomics of Program 8, in association with The University of Queensland. coral’s photosynthetic dinoflagellate December. He subsequently prepared Program at the Australian Research Council (ARC) Centre “Corals are among the simplest animals and may reflect the Program 4, is to understand how symbionts. In addition to obtaining the Global List of Cold Water Corals of Excellence for Coral Reef Studies, based at James ancestral animal condition and reveal important features of “This is a fabulous example of a multi-nodal collaboration the “holobiome” functions under a more comprehensive coverage to be used as the basis for a series of among many players, creating a new world-class research normal and stressed conditions. Cook University. genome evolution”, says Professor Miller. of the transcriptome, they have identification guides that will be the program in coral reef genomics”, says Centre Director and “Acropora millepora is already the The project is expected to provide significant insights into provided an interesting insight into the global reference on the subject. Marcelo ARC Federation Fellow, Professor Terry Hughes. The major research highlight of 2009 evolution of these organisms through was also an invited participant at a best-characterised coral at the the mechanisms that underlie the evolution of life on Earth, was the selection of the coral Acropora The sequencing project builds on earlier collaborations characterisation of the light-harvesting 5-day workshop entitled Systematics molecular level and has yielded including the genetic branch leading to the higher animals millepora as the first animal to undergo between the ANU and James Cook University, sponsored gene complement of the dinoflagellate and evolution of scleractinian corals important insights into the and humans. whole genome sequencing and by the ARC Special Research Centre for the Molecular symbionts. The research of PhD at the National Museum of Natural evolution of all animals”, explains As to why a coral has been chosen as the first Australian assembly by an all-Australian team. Rapid Genetics of Development under the Directorship of student, Lynda Boldt, in Bill Leggat’s History of the Smithsonian Institution Professor Miller who, together with advances in sequencing technology and animal to be gene-mapped by Australian scientists, Professor group has shown this to be the most in Washington DC, held in June. The Dr Eldon Ball of the Australian Professor Robert Saint. the new ground-breaking partnership Miller explains: “Corals have iconic significance for Australia. complex repertoire of such proteins workshop was sponsored and funded National University (ANU), will Future plans for the Centre include mapping the genome between the ARC Centre, The Australian We have the best-preserved coral reef system in the world and identified in any organism to date. by the Encyclopaedia of Life (EOL), with of the coral’s symbiotic partner, the dinoflagellate Genome Research Facility and Illumina lead the Acropora millepora genome the Great Barrier Reef is a cornerstone of a $6 billion a year additional support from the Treatise on Symbiodinium—a primitive marine plant, with its associated Inc, (see opposite) has made this project sequencing program. tourism industry. As reefs elsewhere in the world decline, this Research on the virome was greatly Invertebrate Palaeontology (TIP). possible. A key factor in the decision Professor David Miller. value will grow if we can keep our reefs healthy and intact.” microbes. Symbiodinium is essential for coral growth because assisted by the visit of Rebecca Vega- Photo courtesy of the ARC was the extensive transcriptome data it carries out photosynthesis and provides the coral with Thurber (Florida International University) Centre of Excellence for Coral Continued on page 7… accumulated by David Miller at James Reef Studies carbohydrates and energy. and two of her group from the US during Cook University and his collaborators at the 2009 coral spawning period on the A bacterial community is also important for the health of the Australian National University. These Great Barrier Reef. This collaboration “ As the world’s largest reef and one of the most important the coral animal. Only by understanding all community data have proven to be an invaluable interactions, and how they change under conditions of Great Barrier Reef corals. Photos courtesy of the ARC Centre of marine ecosystems on earth, the Great Barrier Reef is one stress, will we be able to understand how the entire coral Excellence for Coral Reef Studies organism functions. of Australia’s greatest natural assets and national icons.”

30 ARC Centre of Excellence for Coral Reef Studies Discovery • Spring 2009 • Page 6 Discovery • Spring 2009 • Page 7

Discovery5.indd 6-7 9/03/10 9:27 AM Article in Discovery Newsletter: Spring 2009 reproduced with thanks to the Australian Research Council CENTRES OF EXCELLENCE

Australia’s Cenfirst full t r e s genome project gets green light

 One of the corals that form the backbone of the Great Barrier Reef will be the first animal to have its genes fully explored in Australia. The program to sequence the entire genome, or genetic information, of Acropora millepora—a branching coral whose ‘staghorn’ shape and beautiful colours are familiar to millions of visitors to the Great Barrier Reef—marks a major milestone in Australian biotechnology: it will be the Continued from page 6… first animal genome to be fully sequenced and assembled “This gene mapping project has both practical and scientific in Australia. For more information contact Professor Terry Hughes at significance. It will help us to understand how corals build [email protected] or on + 61 7 4781 4000. The staghorn coral may look like a simple animal, but its reefs, and why they fail to do so when they are under stress. genome is surprisingly large and complex. In fact, Acropora “It will enable us to predict, with much greater confidence, has around 20 000 genes—about the same number millepora how corals are likely to respond to changes in the oceans such as a human. Why such apparently simple animals as corals as warming, acidification, the spread of coral diseases, and should require as many genes as humans is still unclear; but it various forms of pollution.” was this coral which provided the first hints of how genetically complex simple animals can be. The mapping of the coral genome is a joint undertaking by the ARC Centre of Excellence for Coral Reef Studies and While they don’t much resemble humans, corals lie deep the Australian Genome Research Facility, in collaboration on the ancestral tree of all animals and share many of our Coral in the Soloman Islands. Photo courtesy of Dr Simon Foale with the ANU, The Walter and Eliza Hall Institute, and genes, says Professor David Miller, head of the Genomics The University of Queensland. Program at the Australian Research Council (ARC) Centre “Corals are among the simplest animals and may reflect the of Excellence for Coral Reef Studies, based at James ancestral animal condition and reveal important features of “This is a fabulous example of a multi-nodal collaboration Cook University. genome evolution”, says Professor Miller. among many players, creating a new world-class research program in coral reef genomics”, says Centre Director and “ is already the The project is expected to provide significant insights into Acropora millepora ARC Federation Fellow, Professor Terry Hughes. best-characterised coral at the the mechanisms that underlie the evolution of life on Earth, molecular level and has yielded including the genetic branch leading to the higher animals The sequencing project builds on earlier collaborations important insights into the and humans. between the ANU and James Cook University, sponsored by the ARC Special Research Centre for the Molecular evolution of all animals”, explains As to why a coral has been chosen as the first Australian Genetics of Development under the Directorship of Professor Miller who, together with animal to be gene-mapped by Australian scientists, Professor Professor Robert Saint. Dr Eldon Ball of the Australian Miller explains: “Corals have iconic significance for Australia. National University (ANU), will We have the best-preserved coral reef system in the world and Future plans for the Centre include mapping the genome lead the Acropora millepora genome the Great Barrier Reef is a cornerstone of a $6 billion a year of the coral’s symbiotic partner, the dinoflagellate sequencing program. tourism industry. As reefs elsewhere in the world decline, this Symbiodinium—a primitive marine plant, with its associated Professor David Miller. value will grow if we can keep our reefs healthy and intact.” microbes. Symbiodinium is essential for coral growth because Photo courtesy of the ARC it carries out photosynthesis and provides the coral with Centre of Excellence for Coral Continued on page 7… Reef Studies carbohydrates and energy. A bacterial community is also important for the health of “ As the world’s largest reef and one of the most important the coral animal. Only by understanding all community interactions, and how they change under conditions of Great Barrier Reef corals. Photos courtesy of the ARC Centre of marine ecosystems on earth, the Great Barrier Reef is one stress, will we be able to understand how the entire coral Excellence for Coral Reef Studies organism functions. of Australia’s greatest natural assets and national icons.”

Discovery • Spring 2009 • Page 6 2009 annual report 31 Discovery • Spring 2009 • Page 7

Discovery5.indd 6-7 9/03/10 9:27 AM CENTRES OF EXCELLENCE

Australia’s Cenfirst full t r e s genome project gets green light

 One of the corals that form the backbone of the Great Barrier Reef will be the first animal to have its genes fully explored in Australia. The program to sequence the entire genome, or genetic information, of Acropora millepora—a branching coral whose ‘staghorn’ shape and beautiful colours are familiar to millions of visitors to the Great Barrier Reef—marks a major milestone in Australian biotechnology: it will be the Continued from page 6… first animal genome to be fully sequenced and assembled “This gene mapping project has both practical and scientific in Australia. For more information contact Professor Terry Hughes at significance. It will help us to understand how corals build [email protected] or on + 61 7 4781 4000. The staghorn coral may look like a simple animal, but its reefs, and why they fail to do so when they are under stress. genome is surprisingly large and complex. In fact, Acropora “It will enable us to predict, with much greater confidence, has around 20 000 genes—about the same number millepora how corals are likely to respond to changes in the oceans such as a human. Why such apparently simple animals as corals as warming, acidification, the spread of coral diseases, and should require as many genes as humans is still unclear; but it various forms of pollution.” was this coral which provided the first hints of how genetically complex simple animals can be. The mapping of the coral genome is a joint undertaking by the ARC Centre of Excellence for Coral Reef Studies and While they don’t much resemble humans, corals lie deep the Australian Genome Research Facility, in collaboration on the ancestral tree of all animals and share many of our Coral in the Soloman Islands. Photo courtesy of Dr Simon Foale with the ANU, The Walter and Eliza Hall Institute, and genes, says Professor David Miller, head of the Genomics The University of Queensland. Program at the Australian Research Council (ARC) Centre “Corals are among the simplest animals and may reflect the of Excellence for Coral Reef Studies, based at James ancestral animal condition and reveal important features of “This is a fabulous example of a multi-nodal collaboration Cook University. genome evolution”, says Professor Miller. among many players, creating a new world-class research program in coral reef genomics”, says Centre Director and “ is already the The project is expected to provide significant insights into Acropora millepora ARC Federation Fellow, Professor Terry Hughes. best-characterised coral at the the mechanisms that underlie the evolution of life on Earth, molecular level and has yielded including the genetic branch leading to the higher animals The sequencing project builds on earlier collaborations important insights into the and humans. between the ANU and James Cook University, sponsored by the ARC Special Research Centre for the Molecular evolution of all animals”, explains As to why a coral has been chosen as the first Australian Genetics of Development under the Directorship of Professor Miller who, together with animal to be gene-mapped by Australian scientists, Professor Professor Robert Saint. Dr Eldon Ball of the Australian Miller explains: “Corals have iconic significance for Australia. National University (ANU), will We have the best-preserved coral reef system in the world and Future plans for the Centre include mapping the genome lead the Acropora millepora genome the Great Barrier Reef is a cornerstone of a $6 billion a year of the coral’s symbiotic partner, the dinoflagellate sequencing program. tourism industry. As reefs elsewhere in the world decline, this Symbiodinium—a primitive marine plant, with its associated Professor David Miller. value will grow if we can keep our reefs healthy and intact.” microbes. Symbiodinium is essential for coral growth because Photo courtesy of the ARC it carries out photosynthesis and provides the coral with Centre of Excellence for Coral Continued on page 7… Reef Studies carbohydrates and energy. A bacterial community is also important for the health of “ As the world’s largest reef and one of the most important the coral animal. Only by understanding all community interactions, and how they change under conditions of Great Barrier Reef corals. Photos courtesy of the ARC Centre of marine ecosystems on earth, the Great Barrier Reef is one stress, will we be able to understand how the entire coral Excellence for Coral Reef Studies organism functions. of Australia’s greatest natural assets and national icons.”

Discovery • Spring 2009 • Page 6 32 ARC Centre of Excellence for Coral ReeDiscoveryf Studie s• Spring 2009 • Page 7

Discovery5.indd 6-7 9/03/10 9:27 AM CENTRES OF EXCELLENCE

Researcher Profile Australia’s Cenfirst full t r e s genome project gets green light

 One of the corals that form the backbone of the Great Barrier Reef will be the first animal to have its genes fully explored in Australia. The program to sequence the entire genome, or genetic information, of Acropora millepora—a branching coral whose ‘staghorn’ shape and beautiful colours are familiar to millions of visitors to the Great Barrier Reef—marks a major milestone in Australian biotechnology: it will be the Continued from page 6… first animal genome to be fully sequenced and assembled “This gene mapping project has both practical and scientific Professor Peter Mumby in Australia. For more information contact Professor Terry Hughes at significance. It will help us to understand how corals build [email protected] or on + 61 7 4781 4000. The staghorn coral may look like a simple animal, but its reefs, and why they fail to do so when they are under stress. genome is surprisingly large and complex. In fact, Acropora “It will enable us to predict, with much greater confidence, has around 20 000 genes—about the same number millepora how corals are likely to respond to changes in the oceans such as a human. Why such apparently simple animals as corals as warming, acidification, the spread of coral diseases, and should require as many genes as humans is still unclear; but it various forms of pollution.” The ARC Centre welcomes new used two post-doctoral fellowships to of parrotfish inside a well-managed was this coral which provided the first hints of how genetically member Professor Peter Mumby, who broaden his expertise into empirical reef reserve led to a reduction of macroalgae The mapping of the coral genome is a joint undertaking by complex simple animals can be. will be moving to Australia from the UK ecology and ecological modeling. Today, and concomitant increase in coral the ARC Centre of Excellence for Coral Reef Studies and While they don’t much resemble humans, corals lie deep in early 2010, following the award of a Peter uses remotely-sensed data to recruitment. Thus, while the reserve the Australian Genome Research Facility, in collaboration on the ancestral tree of all animals and share many of our Coral in the Soloman Islands. Photo courtesy of Dr Simon Foale prestigious Laureate Fellowship. Peter’s scale up ecological models so that they benefits fish directly, the resulting trophic with the ANU, The Walter and Eliza Hall Institute, and genes, says Professor David Miller, head of the Genomics award brings the number of senior are spatially-realistic and able to inform cascades also benefit the corals and The University of Queensland. fellows in the Centre to four – following conservation decisions directly. therefore help ensure the delivery of reef- Program at the Australian Research Council (ARC) Centre “Corals are among the simplest animals and may reflect the the earlier awards of a Federation based ecosystem services. of Excellence for Coral Reef Studies, based at James ancestral animal condition and reveal important features of “This is a fabulous example of a multi-nodal collaboration Fellowship (Terry Hughes, 2007-2012), Peter’s research has responded to the Cook University. genome evolution”, says Professor Miller. among many players, creating a new world-class research program in coral reef genomics”, says Centre Director and Queensland Premier’s Fellowship challenge of obtaining credible evidence Peter has recently developed “ is already the The project is expected to provide significant insights into Acropora millepora ARC Federation Fellow, Professor Terry Hughes. (Ove Hoegh-Guldberg, 2008-2012) and of human impacts at appropriate scales. mechanistic ecological models of coral best-characterised coral at the the mechanisms that underlie the evolution of life on Earth, Western Australian Premier’s Fellowship Using remote sensing and field survey, reefs that integrate reef dynamics, molecular level and has yielded including the genetic branch leading to the higher animals The sequencing project builds on earlier collaborations (Malcolm McCulloch, 2009-2013). In he designed a study across Belize conservation actions and disturbance, important insights into the and humans. between the ANU and James Cook University, sponsored 2009, the Centre also hosts nine other and Mexico that allowed his team including climate change. So far, the by the ARC Special Research Centre for the Molecular full-time ARC Fellows, ranging across the to test hypotheses on the effects of models have provided insight into the evolution of all animals”, explains As to why a coral has been chosen as the first Australian Genetics of Development under the Directorship of entire spectrum of career stages. mangroves on reef fish community consequences of conserving herbivorous Professor Miller who, together with animal to be gene-mapped by Australian scientists, Professor fishes, reducing nutrient runoff, Dr Eldon Ball of the Australian Professor Robert Saint. structure. An absence of mangroves Miller explains: “Corals have iconic significance for Australia. Before embarking on a research career, caused local extinction of the largest conserving mangroves, and restoring National University (ANU), will Future plans for the Centre include mapping the genome We have the best-preserved coral reef system in the world and Peter Mumby spent two years designing herbivorous fish in the Atlantic, and urchin populations. These results have lead the Acropora millepora genome of the coral’s symbiotic partner, the dinoflagellate the Great Barrier Reef is a cornerstone of a $6 billion a year marine reserves in Belize where he caused profound reductions in the influenced reef management policy and Symbiodinium—a primitive marine plant, with its associated sequencing program. tourism industry. As reefs elsewhere in the world decline, this experienced, first hand, the limited biomass of many fish species. led to new fisheries regulations. microbes. Symbiodinium is essential for coral growth because Professor David Miller. value will grow if we can keep our reefs healthy and intact.” scientific basis for such planning. This Photo courtesy of the ARC it carries out photosynthesis and provides the coral with Centre of Excellence for Coral Continued on page 7… experience was highly influential in Peter and colleagues have also studied Peter’s move to the University of Reef Studies carbohydrates and energy. defining and driving his research, which the impacts of marine reserves on Queensland early in 2010 will allow him A bacterial community is also important for the health of has been dedicated to conducting applied Caribbean reefs and discovered that to forge new collaborations in Australia. “ As the world’s largest reef and one of the most important the coral animal. Only by understanding all community science in support of the management of the direct effects of protecting fish can His work aligns closely with the ARC interactions, and how they change under conditions of coral reefs. In 1997, he obtained his PhD have profound indirect effects on the Centre’s Programs 2 and 6. Great Barrier Reef corals. Photos courtesy of the ARC Centre of in coral reef remote sensing and then ecosystem. For example, a recovery marine ecosystems on earth, the Great Barrier Reef is one stress, will we be able to understand how the entire coral Excellence for Coral Reef Studies organism functions. of Australia’s greatest natural assets and national icons.”

Discovery • Spring 2009 • Page 6 Discovery • Spring 2009 • Page 7 2009 annual report 33

Discovery5.indd 6-7 9/03/10 9:27 AM GRADUATE TRAINING

In 2009, one hundred and fifty nine Pty Ltd., who have for the past 15 years best student presentation. Yui Sato, graduate students were supervised by run workshops on communicating Rebecca Fox and Colin Wen also the ARC Centre’s senior researchers, science via the media. won student presentation prizes at making the Centre the world’s largest the meeting. provider of graduate training in coral The success of the ARC Centre’s ƒƒ Andrew Cole, Rebecca Lawton and reef science. This commitment to graduate program can be seen through Alexandra Carter received research postgraduate training entails a large the national and international recognition support from the PADI Foundation. investment in support of student the students attracted in 2009: ƒƒ Alexandra Carter received the research projects, conservatively costed GBRMPA Science for Management at 25% of our annual budget. In addition, ƒƒ Vanessa Adams was awarded the Sir Award for 2009. the Centre has a major early-career Keith Murdoch Fellowship of $25,000 development program. As part of this, from the American Australian ƒƒ Felipe Gusmao was awarded the we actively involve students through a Association. In addition she received Peter Holloway Oceanography Prize student committee. The Centre provides the Ecological Society of Australia for his presentation at the Australian intellectual, organisational and financial The Nature Conservancy Applied Marine Science Association help for student mentoring activities, Conservation Award for 2009. conference in Adelaide. student awards, inter-nodal supervision ƒƒ Darren Coker, Rebecca Lawton, ƒƒ Christopher Doropoulos was and visits by postgraduate students. Andrew Cole and Alexander Vail were awarded a Queensland Government The inaugural recipients of the “The all granted John Glover Travel Awards Smart State PhD Scholarship. Virginia Chadwick Awards”, are David by the Australian Society for Fish ƒƒ Rebecca Fox and Alicia Crawley were Abrego, Peter Cowman, Andrew Hoey, Biology. Darren also won an AIMS@ both awarded Lizard Island Doctoral Ruth Reef and Alejandro Reyes. The five JCU conference Travel Prize. Fellowships. prizes of $1000 are made each year for ƒƒ Stephanie Januchowski received outstanding publications written by ARC three grants for conference travel The Centre is indebted to the 2009 Centre of Excellence graduate students. and research, including $33,000 from Student Committee for their energy Biosecurity Queensland for research and input. They, along with student In 2009, the ARC Centre again organised associated with her PhD studies. co-ordinator, Olga Bazaka, make an and sponsored a National Mentoring invaluable contribution to the success Day for student delegates attending the ƒƒ Alexander Vail won the Michael Hall of the ARC Centre of Excellence. annual Australian Coral Reef Society Award for Student Innovation and Members of the committee during meeting. This year the mentoring day the Gilbert Whitley Memorial Student the year were Alicia Crawley (UQ), was held at the Novotel Hotel in Darwin Award (junior) at the Indo PacificF ish Anne Leitch (JCU/CSIRO), Juan Pablo at the end of September. The graduate Conference in Freemantle in June. D’Olivo (ANU), Paulina Cetina Heredia students who attended came from ƒƒ Andrew Cole was awarded the (JCU/AIMS), Rachael Middlebrook James Cook University, University of University Centenary Student Grant (UQ), Stephanie Januchowski Queensland, Victoria (NZ), Murdoch, for 2009 by the Wildlife Preservation (JCU) and Tom Brewer (JCU). Southern Cross, Sydney and NSW Society of Australia, universities. An exit survey of the ƒƒ Rebecca Fox was awarded the students revealed the success of the Australian Coral Reef Society’s Terry workshop with a rating of 3.89 from a Walker Prize for 2009. possible 4. In Brisbane, earlier in the ƒƒ At the annual Australian Coral Reef year at the Centre’s annual Symposium, Society Meeting in Darwin, Rebecca 17 graduate students participated in a Lawton was awarded the Danielle workshop entitled Talking science with Simmons Award for 2009, while the media, organised by the Centre’s Emily Howells won the Vicki Harriott Student Committee. The workshop was Memorial Student Prize for the presented by Econnect Communications

34 ARC Centre of Excellence for Coral Reef Studies  Trends in the ARC Centre’s training activities 2005 to 2009

200 2005 180 2006 160 2007 140 2008 2009 120 100 80

Number of students 60 40 20 0 Postgraduate Multi-Institutional Graduates/Honours Completions Supervisors students enrolled

 The ARC Centre’s international network of graduate students. In 2009, 102 overseas students, representing half of the Centre’s current enrolments, came to Australia from 39 countries.

2009 annual report 35 2009 Student members of the ARC Centre of Excellence for Coral Reef Studies

Country Student University Thesis Title CoE Supervisor/s of Origin

Rene Abesamis JCU, Silliman Philippines Demographic connectivity of reef fish populations Prof G Russ, Prof G Jones University in the Philippines. (PhD)

David Abrego JCU, AIMS Mexico Temporal and environmental influences on the Prof B Willis, Dr M van early establishment and maintenance of coral- Oppen, Prof S Connolly Symbiodinium symbioses. (PhD awarded)

Vanessa Adams JCU USA Incorporating economic factors into systematic Prof R Pressey, conservation planning. (PhD) Prof T Hughes

Siham Afatta UQ Indonesia Human impacts, resilience and management Dr K Anthony, challenges for Indonesian coral reefs: Prof O Hoegh-Guldberg Karimunjawa National Park case study. (MSc)

Campbell Allen UQ Australia Australian eco-informatic tools for coral reef Prof O Hoegh-Guldberg ecology. (MSc)

Jorge Alvarez-Romero JCU Mexico Cross-system threats and competing values Prof R Pressey, in coastal and marine conservation planning: Dr N Ban, Dr J Kool an integrated land-sea approach to prioritize conservation actions in the Gulf of California. (PhD)

Shelley Anthony JCU, AIMS USA White Syndrome Disease and colony mortality in Prof B Willis captive Indo-Pacific corals. (PhD)

Stephen Ban JCU Canada Investigating resilience and spatial responses Prof R Pressey, of coral reef ecosystems to climate change and Dr N Graham, associated stressors. (PhD) Prof S Connolly

Lissa Bar UQ, JCU Australia Measuring the effectiveness of marine protected Prof R Pressey areas. (PhD)

Christopher Bartlett JCU USA Marine conservation in Vanuatu. (PhD) Dr J Cinner

Brian Beck UQ, JCU USA Palaeoecological dynamics of coral communities Prof J Pandolfi, along a disturbance gradient, Solomon Islands. Prof S Connolly (PhD)

Roger Beeden JCU New How healthy is the Great Barrier Reef in a Prof B Willis Zealand warming world? (PhD)

Victor Beltran-Ramirez JCU Mexico Molecular aspects of the fluorescent protein Prof D Miller homologues in Acropora millepora. (PhD)

Dorothea Bender UQ Germany Impacts of climate change on macroalgae and Dr G Diaz-Pulido, their interactions with coral reef organisms. (PhD) Dr S Dove

Rose Berdin ANU Philippines Late Quaternary Palaeoclimate history of the Prof M McCulloch northern Indo-Pacific warm pool from raised coral reefs in the Philippines. (PhD awarded)

Duan Biggs JCU, CSIR South Africa Resilience of reef-based tourism to climate Prof T Hughes, Dr J Cinner South Africa, change and disturbance. (PhD) Emory University USA, University of Canterbury NZ

Teressa Bobeszko JCU Australia The role of carbonic anhydrase in the coral- Dr W Leggat, dinoflagellate symbiosis. (PhD) Prof D Yellowlees

Lynda Boldt JCU Australia Symbiodinium photosynthetic genes and the Dr W Leggat, effect of varying environmental conditions on Prof D Yellowlees photosynthetic processes. (PhD)

Roberta Bonaldo JCU Brazil The ecosystem role of parrotfishes. (PhD) Prof D Bellwood, Prof S Connolly

36 ARC Centre of Excellence for Coral Reef Studies Country Student University Thesis Title CoE Supervisor/s of Origin

Pim Bongaerts UQ Netherlands Ecological significance of deep, light-dependent Prof O Hoegh-Guldberg coral communities. (PhD)

Mary Bonin JCU USA Causes and consequences of habitat Prof G Jones, Dr G Almany specialization in coral reef fish communities. (PhD)

Madeleine Bottrill UQ, JCU United Evaluating the effectiveness of conservation Prof R Pressey Kingdom planning: when do plans work. (PhD)

Tom Brewer JCU, UQ Australia Linking sociological perspectives to coral reef Prof T Hughes, resources across scales. (PhD) Prof R Pressey, Dr J Cinner, Dr S Foale, Prof J Pandolfi

Kate Bromfield UQ, CSIRO Australia Neogene corals of the Indo-Pacific. (PhD Prof J Pandolfi awarded)

Rohan Brooker JCU New Reproduction and ecology of the harlequin Prof G Jones, Zealand filefish, Oxymonacanthus longirostris, and the Prof P Munday implications of climate change. (MSc)

Michael Cappo JCU, AIMS Australia Spatial patterns of demersal vertebrate Prof M Kingsford assemblages in inter-reef waters. (PhD)

Alexandra Carter JCU Australia The effects of no-take zoning, region and year on Dr M McCormick, reproductive output of the common coral trout, Prof G Russ Plectropomus leopardus. (PhD)

Paulina Cetina-Heredia JCU, AIMS Mexico Modelling physical and biological processes Prof S Connolly driving laval transport and supply in reef systems. (PhD)

Neil Chan JCU, UQ Malaysia Modelling the effects of pH, temperature and Prof S Connolly, flow on calcification of reef corals. (PhD) Dr K Anthony

Rowan Chick JCU Australia Stock enhancement of local populations of Prof M Kingsford blacklip abalone Haliotis rubra in New South Wales, Australia. (PhD)

Chia-Miin Chua JCU Malaysia Effects of elevated temperature and increased Dr A Baird, Dr W Leggat, acidity on the early life history of coral. (PhD) Prof T Hughes

Tara Clark UQ, AIMS Australia Dating and mapping historical changes in Great Prof J Pandolfi Barrier Reef coral communities. (PhD)

Philippa Cohen JCU Australia The contribution of locally-managed marine areas Dr S Foale, Prof T Hughes to food security of Solomon Islands. (PhD)

Darren Coker JCU, DEC in New The role of live coral in moderating key ecological Dr M Pratchett, WA, AIMS Zealand processes for coral reef fishes. (PhD) Dr N Graham

Andrew Cole JCU, DEC in Australia The effect of chronic fish predation on Dr M Pratchett, WA scleractinian corals. (PhD) Prof G Jones

Melissa Cowlishaw JCU Australia Determinants of home range and territorial Prof G Jones, behaviour in coral fishes: roles of body size, Dr M McCormick habitat structure and population density. (PhD)

Peter Cowman JCU Ireland Dating the evolutionary origins of trophic novelty Prof D Bellwood in coral reef fishes. (PhD)

Alicia Crawley UQ Australia The synergistic effect of rising ocean temperature Dr S Dove, Dr S Dunn and acidification on coral reef ecosystems. (PhD)

Vivian Cumbo JCU, AIMS Australia Thermal tolerance in corals: the role of the Dr A Baird, Dr M van symbiont. (PhD) Oppen, Prof T Hughes

Kathryn Danaher JCU Australia Oceanography and the condition of plankton. Prof M Kingsford (PhD)

2009 annual report 37 Country Student University Thesis Title CoE Supervisor/s of Origin

Andrea de Leon ANU Australia Palaeoceanographic records of the Southern Prof M McCulloch Ocean: insights from the boron composition of biogenic silica. (PhD)

Jeffry Deckenback UQ, JCU, USA Maturation, turn-over, oligomerization, and Dr S Dove, Dr W Leggat Monash transport of pocilloporins. (PhD awarded)

Brynn Devine JCU USA Effects of ocean acidification on habitat selection Prof P Munday, in fish. (MSc) Prof G Jones

Ayax Diaz-Ruiz UQ Mexico The use of coral associated fauna as indicators of Prof O Hoegh-Guldberg, coral health. (PhD) Prof J Pandolfi

Danielle Dixson JCU USA Use of olfactory cues for settlement site selection Prof P Munday, Prof G in coral reef fishes. (PhD) Jones, Dr M Pratchett

Juan Pablo D’Olivo ANU Mexico Environmental and climate variability in seawater Prof M McCulloch pH reconstructed from Boron isotopes in corals from the Pacific Ocean. (PhD)

Jennifer Donelson JCU, CSIRO Australia Climate change and the future for coral reef Prof P Munday, fishes: impacts and adaptation. (PhD) Dr M McCormick

Christopher Doropoulos UQ Australia Climate change effects on the recruitment and Dr Guillermo Diaz-Pulido succession of algae and corals from the Great Barrier Reef. (PhD)

Maxi Eckes UQ Germany How do coral reef fish protect themselves from Dr S Dove solar ultraviolet radiation? (PhD)

Udo Engelhardt UQ Australia Community-level ecological responses of coral Prof O Hoegh-Guldberg reef biota to mass coral bleaching events. (PhD)

Richard Evans JCU Australia No-take marine protected areas: abundance, Prof G Russ, Prof G Jones biomass, batch fecundity and genetic connectivity of target species on the Great Barrier Reef. (PhD awarded)

Michael Fabinyi ANU, JCU Australia Fishing for fairness: poverty, morality and marine Dr S Foale resource regulation in the Calamianes Islands, Philippines. (PhD awarded)

Kar Hei (James) Fang UQ China The synergistic effects of ocean warming and Dr S Dove, acidification on growth and bioerosion capacity of Prof O Hoegh-Guldberg the marine sponge Cliona orientalis, on the Great Barrier Reef, Australia. (PhD)

Pepito (Sonny) ANU, JCU Philippines Political engagements in marine protected area Dr S Foale Fernandez governance in northeastern Liloilo, Philippines. (PhD)

Rebecca Fox JCU United Ecosystem function of rabbitfishes F( :Siganidae) Prof D Bellwood Kingdom on the Great Barrier Reef, Australia. (PhD)

Matthew Fraser JCU Australia Dynamics of egg predation at tropical fish Dr M McCormick, spawning sites. (PhD) Prof G Jones

Irene Fuertes Jerez JCU Spain Characterization of microsatellite loci for Prof G Russ, Prof G Jones Epinephelus quoyanus (epinephelinae): preparing to measure connections from no-take to fished areas of the Great Barrier Reef. (MAppSc)

Naomi Gardiner JCU Australia Habitat specialization, co-occurrence and resting Prof G Jones site fidelity in cardinalfish on coral reefs. (PhD)

Chris Goatley JCU United The ecological role of sediments on coral reefs. Prof D Bellwood Kingdom (PhD)

38 ARC Centre of Excellence for Coral Reef Studies Country Student University Thesis Title CoE Supervisor/s of Origin

Alonso Gonzalez- JCU Mexico Cryptobenthic reef fish ecology in the Great Prof D Bellwood Cabello Barrier Reef, Australia. (PhD)

Luis Gonzalez Reynoso JCU, Griffith Mexico Mechanisms of stress inhibition of reproduction Dr M McCormick University in fish. (PhD)

Lauretta Grasso ANU, JCU Australia Transcriptome analysis of development, with a Prof D Miller focus on metamorphosis, in the coral Acropora millepora. (PhD awarded)

Erin Graham JCU USA Energetics of coral larvae and its implications for Prof B Willis, Prof S dispersal. (PhD) Connolly, Dr A Baird

Jessica Haapkyla JCU, AIMS Finland Impacts and drivers of coral disease in Indo- Prof B Willis Pacific reefs. (PhD)

Andrew Halford JCU Australia Disturbance, habitat structure and coral reef fish Prof G Jones communities. (PhD)

David Harris UQ Australia Ecology of high latitude populations of Prof O Hoegh-Guldberg Pomacentrus coelestis. (PhD)

Hugo Harrison JCU, University France Larval recruitment dynamics and the genetic Prof G Jones, Prof G Russ, of Perpignan structure of coral reef fish populations in marine Dr S Planes protected networks. (PhD)

Meegan Henderson UQ Australia Microbial ecology of coral disease: the use of Prof O Hoegh-Guldberg molecular techniques in understanding bacterial community shifts. (PhD awarded)

Christina Chemtai Hicks JCU United The interplay between economic values and Prof T Hughes, Prof R Kingdom societal settings in coral reef governance. (PhD) Pressey, Dr J E Cinner

Jean-Paul Hobbs JCU Australia Isolation, endemism and the structure of coral Prof G Jones, Prof P reef fish communities on islands. (PhD) Munday

Andrew Hoey JCU Australia Algal-fish interactions on coral reefs. (PhD) Prof D Bellwood, Prof G Russ

Thomas Holmes JCU Australia Selectivity of predation on newly settled tropical Dr M McCormick reef fish. (PhD)

Emily Howells JCU, AIMS Australia Genetic resilience of Symbiodinium populations: Prof B Willis, Dr L Bay, the role of coral endosymbionts in reef adaptation Dr M van Oppen to climate change. (PhD)

Stephanie Januchowski JCU USA Towards stream classifications for conservation Prof R Pressey planning: a Wet Tropics region case study. (PhD)

Jacob Johansen JCU Denmark Energetics of habitat choice in planktivorous coral Prof G Jones, reef fishes. (PhD) Prof D Bellwood

Charlotte Johansson JCU, AIMS Sweden Managing coral reefs - the importance of working Prof D Bellwood with functional groups to conserve ecosystem resilience. (PhD)

David Jones JCU Australia Predicting the distribution of two venomous Prof M Kingsford, cubozoans (Carukia barnesi and Chironex fleckeri) Prof G Russ using population genetic structure. (PhD)

Jung Ok Kang ANU Korea Anthropogenic increase of atmospheric carbon Prof M McCulloch dioxide and ocean acidification and global warming: implications for long-term changes in the calcification rate of coral reefs. (PhD)

Rucha Karkarey JCU India Using northern and southern Great Barrier Reef Prof S Connolly green turtle (Chelonia mydas) nesting data as a proxy to estimate abundance of the remote Coral Sea nesting population. (MAppSci)

Brent Knack JCU Australia Cell adhesion factors in Cnidarians. (PhD) Prof D Miller, Dr W Leggat

2009 annual report 39 Country Student University Thesis Title CoE Supervisor/s of Origin

Valeriya Komyakova JCU Russia Habitat characteristics as the determinants of Prof G Jones, the local diversity and structure of coral reef fish Prof P Munday communities. (MSc awarded)

Narinratana UQ Thailand The taxonomy and systematics of the genus Prof O Hoegh-Guldberg Kongjandtre Favia from Thai waters. (PhD)

Charlotte Kvennefors UQ, JCU Sweden Host-microbe interactions in reef-building corals. Dr W Leggat, (PhD awarded) Prof O Hoegh-Guldberg

Joleah Lamb JCU USA Effects of offshore tourist pontoons on coral Prof B Willis disease prevalence in the Cairns and Whitsunday sectors of the Great Barrier Reef Marine Park. (MAppSc)

Angela Lawton UQ USA The effects of micro-scale variation on the Prof O Hoegh-Guldberg, photosynthetic productivity of the symbiotic algae Dr S Dove of reef building corals. (PhD)

Rebecca Lawton JCU, KAUST New Geographic variation in the ecology of Dr M Pratchett, Dr L Bay, Zealand butterflyfishes and resilience to large scale Prof T Hughes disturbances. (PhD)

Helene Le Grand JCU, AIMS France Development of coral bioindicators to detect Prof B Willis changes in water quality on inshore reefs of the Great Barrier Reef. (MAppSc)

Carine Lefevre JCU France The ecology of cryptobenthic reef fishes. (PhD) Prof D Bellwood

Anne Leitch JCU, CSIRO Australia Social resilience to climate change: the adaptive Prof T Hughes capacity of local government. (PhD)

Anais Kimberley Lema JCU, AIMS Mexico/ Nitrogen fixing bacteria associated with corals of Prof B Willis France the Great Barrier Reef. (MSc)

Tove Lemberget JCU Norway Importance of body condition and growth to larval Dr M McCormick, survival of a Caribbean lizardfish. (PhD) Prof G Jones

Vetea Liao JCU French Direct effect of temperature on growth and body Dr M Pratchett Polynesia condition of the coral reef fish Acanthochromis polyacanthus. (MAppSc)

Raechel Littman JCU, AIMS USA The dynamics of bacterial populations associated Prof B Willis with corals and the role of bacterial pathogens in coral bleaching. (PhD)

Adrian Lutz JCU, AIMS Switzerland Coenzyme Q and Plastoquinone redox balance as Prof D Miller, a physiological determinant of oxidative stress in Dr M van Oppen coral algal symbiosis. (PhD)

Matt Lybolt UQ USA Causes of change in coastal ecosystems: past, Prof J Pandolfi present and future. (PhD)

Thomas Mannering JCU United Do marine reserves augment recruitment in Prof G Jones Kingdom nearby fished areas? (MSc awarded)

Jeffrey Maynard U. Melbourne, USA Climate-change processes affecting coral reef Dr K Anthony UQ ecology. (PhD)

Dominique McCowan JCU USA Bleaching susceptibility of corals: a hierarchy of Dr M Pratchett, Dr A Baird, causes and consequences. (PhD) Prof T Hughes

Amelie Menchenin JCU France Early life history of Epinephelus quoyanus. Prof G Jones, Prof G Russ (MAppSc)

Luiz- Felipe Mendes-de- JCU, AIMS Brazil Studies on secondary production of zooplankton Prof M Kingsford Gusmao in tropical seas and aquaculture. (PhD)

Vanessa Messmer JCU, U. France Causes and consequences of declining fish Prof G Jones, Perpignan biodiversity in coral reefs. (PhD) Prof P Munday

40 ARC Centre of Excellence for Coral Reef Studies Country Student University Thesis Title CoE Supervisor/s of Origin

Rachael Middlebrook UQ Australia Determining thermal threshold dynamics and Dr S Dove, Dr K Anthony, variability in reef building corals. (PhD) Prof O Hoegh-Guldberg

Gabrielle Miller JCU Australia Impact of pH on fish development. (PhD) Prof P Munday, Dr M McCormick

Morena Mills JCU Brazil Implementation opportunity in systematic Prof R Pressey, conservation planning. (PhD) Dr N Ban, Dr S Foale

Matthew Mitchell JCU United Antipredator defence through chemical alarm Dr M McCormick Kingdom cues - how common amongst tropical marine fishes? (PhD)

Roshni Narayan UQ Canada Holocene to recent changes in the benthic Prof J Pandolfi foraminifera communities of subtropical Moreton Bay, Queensland and potential indicators for monitoring sediment/water quality in estuarine environments. (PhD)

Crystal Neligh JCU USA Links between metabolism, growth and Dr M McCormick performance (MSc)

Daisie Ogawa JCU USA Synergistic effects of ocean acidification and Dr W Leggat, elevated temperature on carbon-concentrating Prof D Yellowlees mechanisms and energy transfer in the coral holobiont. (PhD)

Juan Carlos Ortiz UQ Venezuela Eco-physical dynamics of the Heron Island coral Prof O Hoegh-Guldberg reef. (PhD)

Cathie Page JCU Australia Ecology and biology of coral diseases on the Prof B Willis, Prof T Great Barrier Reef. (PhD awarded) Hughes

Allison Paley JCU, AIMS USA Genetic diversity, bleaching sensitivity and colour Prof B Willis, polymorphisms of a common reef-building coral, Dr M van Oppen Acropora millepora, on the Great Barrier Reef, Australia. (MSc)

Caroline Palmer JCU, United The basic biological mechanisms of scleractinian Prof B Willis Newcastle Kingdom immune defences involved in wound healing and University disease mitigation. (PhD)

Christine Pam JCU Australia Social responses to change on small islands in Dr S Foale Micronesia. (PhD)

Joe Pollock JCU , AIMS, USA Phylogeography of the coral pathogen, Vibrio Prof B Willis College of coralliilyticus, and the development of a qPCR- Charleston based diagnostic assay for its detection. (MSc)

Mary Portwood JCU USA Influence of marine protected areas on Prof G Jones invertebrate communities. (MAppSc)

Eneour Puill-Stephan JCU, AIMS France Self-nonself recognition and chimerism in Prof B Willis, Acropora millepora. (PhD) Dr M van Oppen

Paola G. Rachello- UQ Italy Constructing long-term proxy records of historical Prof J Pandolfi Dolmen changes in marine mollusc assemblages in tropical and subtropical Queensland region (Australia). (PhD)

Jean-Baptiste Raina JCU, AIMS France Coral-associated bacteria and their role in the Prof B Willis biogeochemical cycle of sulphur. (PhD)

Ana Redondo- UQ, AIMS Spain Implications of climate change for the Dr K Anthony, Rodriguez oceanography of the Great Barrier Reef Prof O Hoegh-Guldberg ecosystem. (PhD)

Ruth Reef UQ, JCU Israel The effect of temperature on the accumulation Prof O Hoegh-Guldberg, and repair of UV damage in zooxanthellae and Dr W Leggat, Dr S Dove corals. (PhD awarded)

2009 annual report 41 Country Student University Thesis Title CoE Supervisor/s of Origin

Alejandro Reyes JCU Colombia Cellular mechanisms of coral calcification. (PhD) Prof D Miller

Catalina Reyes UQ Colombia The role of elevated CO2 scenarios on bioerosion Dr S Dove, of coral reef ecosystems. (PhD) Dr G Diaz-Pulido, Prof O Hoegh-Guldberg

Maria Catalina Reyes- UQ Colombia Effects of climate change on bioerosion of reef Dr S Dove, Nivia carbonates. (PhD) Dr G Diaz-Pulido

Claire Reymond UQ, AIMS Australia Modern evolutionary and palaeoecology of Prof J Pandolfi foraminifera from the Great Barrier Reef: establishing a baseline. (PhD)

Zoe Richards JCU, AIMS Australia Characteristics of rare and common corals: Prof D Miller, Prof B Willis, implications for conservation. (PhD) Dr M van Oppen

Alma Ridep-Morris JCU Palau Dynamics of coral diseases on Palauan reefs and Prof B Willis, Prof G Jones the role of marine protected areas in mitigating their impacts (MSc)

Jairo Rivera Posada JCU Colombia Pathogenesis in crown-of-thorns starfish Dr M Pratchett, Prof T (Acanthaster planci). (PhD) Hughes, Dr T Ainsworth

George Roff UQ United Historical ecology of coral communities from the Prof J Pandolfi, Kingdom inshore Great Barrier Reef, Australia. (PhD) Prof O Hoegh-Guldberg

Pablo Saenz-Agudelo JCU , Colombia Demography and connectivity in coral reef fish Prof G Jones University of populations as revealed by parentage analysis. Perpignan (PhD)

Yui Sato JCU, AIMS Japan Dynamics of a black band disease outbreak. Prof B Willis (MSc)

Shio Segi ANU, JCU Japan Living under threat: depletion, development and Dr S Foale marine protected areas in the lives of small-scale fishers in the Philippines. (PhD)

Francois Seneca JCU, AIMS, Monaco The molecular stress response in a model Prof D Miller, ANU scleractinian coral: Acropora millepora. (PhD) Dr M van Oppen

Michael Short JCU Australia The recovery of coral reefs following ship Prof B Willis, Prof G Jones grounding disturbances. (MSc)

Jennifer Smith JCU Canada Influence of patch dynamics on coral reef fishes Prof G Jones, on the southern GBR. (MSc) Dr M McCormick

Jessica Stella JCU, Australian USA Climate impacts on non-coral reef invertebrates. Prof G Jones, Dr M Museum (PhD) Pratchett, Prof P Munday

Meir Sussman JCU, AIMS Israel A molecular approach to the study of coral Prof B Willis diseases. (PhD awarded)

Jill Sutton ANU Canada Southern ocean nutrients and climate change: Prof M McCulloch insights from isotopic and elemental signatures of diatoms and sponges. (PhD)

Chun Hong Tan JCU Malaysia Environmental controls and evolutionary Dr A Baird, Dr M Pratchett, constraints on growth and reproduction in corals. Dr L Bay (PhD)

Michelle Templeman JCU Australia The role of jellyfish in cycling contaminants Prof M Kingsford in the marine environment and their utility as biomonitors. (PhD)

Loic Thibaut JCU, France Resilience in coral reef and model ecosystems. Prof S Connolly, Université (PhD) Prof T Hughes Pierre et Marie Curie

42 ARC Centre of Excellence for Coral Reef Studies Country Student University Thesis Title CoE Supervisor/s of Origin

Lucija Tomljenovic JCU Croatia Charcterisation of the TTC4 gene family. (PhD Prof D Miller awarded)

Gergely Torda JCU, AIMS Hungary Assessment of ecological connectivity in corals: Dr M van Oppen, implications for their recovery from major Prof B Willis perturbations and their potential to adapt to climate change. (PhD)

Mélanie Trapon JCU France Ongoing disturbances and further shifts in Dr M Pratchett, Dr L Penin, community structure among coral assemblages Prof G Jones at Moorea, French Polynesia. (MAppSc)

Lubna Ukani JCU India Characterisation of DNA methylation systems in Prof D Miller, Dr W Leggat Acropora and other lower animals. (PhD)

Svetlana Ukolova JCU Russia Signalling molecules in coral development. (PhD) Prof D Miller, Dr W Leggat

Annamieke Van Den UQ, JCU Australia Characterisations of genes, proteins, and the Dr S Dove, Dr W Leggat, Heuvel regulatory pathways involved in nitrogen uptake Prof D Yellowlees and the assimilation in Acropora aspera and its symbiont Symbiodinium sp. (PhD)

Cameron Veal UQ Australia Meso-and micro-scale light fields around shallow Prof O Hoegh-Guldberg, coral reefs. (PhD) Dr K Anthony, Dr S Dove

Ana Cecilia Villacorta JCU Peru Selective mortality during early life stages of Dr M McCormick, Rath sprats. (MSc) Dr M Meekan

Piero Visconti JCU, University Italy Incorporating biodiversity processes and dynamic Prof R Pressey La Sapienza, threats in systematic conservation planning. (PhD) Rome, Italy

Marcelo Visentini- JCU, Brazil Taxonomic and phylogenic trends among Prof D Miller Kitahara Smithsonian azooxanthellate corals, using morphological and Institute molecular aspects. (PhD)

Stefan Walker JCU Australia The socio-biology of life history transitions and Dr M McCormick, lifetime fecundity in a tropical haremic reef fish. Prof P Munday (PhD)

Patricia Warner JCU, AIMS USA Reproductive ecology and population genetic Prof B Willis, approaches to assessing connectivity of the Dr M van Oppen brooding coral, Seriatopora hystrix. (PhD)

Christine Weaver JCU USA Competition between two damselfishes. Dr M McCormick (MAppSc)

Rebecca Weeks JCU United Approaches to designing marine protected area Prof G Russ Kingdom networks in the Philippines. (PhD)

Yvonne Weiss JCU Germany The immune system of Acropora millepora: Prof D Miller, Dr W Leggat, identification and characterisation of candidate Dr T Ainsworth genes. (PhD)

Colin Wen JCU Taiwan Recruitment hotspots and their role in the ecology Prof G Jones, Dr M and management of large exploited predatory Pratchett, Dr G Almany fishes. (PhD)

Amelia Wenger JCU USA Effects of sedimentation and turbidity on Prof G Jones, planktivorous fishes. (MSc) Dr M McCormick

David Williamson JCU Australia Fishery effects and benefits of marine protected Prof G Russ, Prof G Jones areas within the Great Barrier Reef Marine Park. (PhD awarded)

Huibin Zou JCU China The characterisation of selenium containing Prof D Miller, protein families in coral Acropora millepora. (PhD) Dr T Ainsworth

2009 annual report 43 Media and Public Outreach

The ARC Centre seeks to inform the University of Western Australia’s in the Coral Triangle region attracted the wider community of its research public lecture series. considerable media coverage during the outcomes through the media and ƒƒ During October and November, Mike World’s Ocean Conference in Manado, through public awareness activities. In Kingsford gave a series of public Indonesia in May 2009. Over 900 media 2009, Centre personnel participated in lectures at the University of Bergen stories were generated during the week 45 public outreach programs, reaching (Norway), University of Copenhagen long conference (see p.46). audiences locally, nationally and (Denmark) and the University of internationally. Examples include: Uppsala (Sweden). The Centre’s website caters for multiple audiences, providing information, access ƒƒ Ove Hoegh-Guldberg participated in ƒƒ Researchers from the ARC Centre of to resources, research services, and a Q&A session at the international Excellence teamed with Google to downloads of research, teaching and launch in Copenhagen of the movie populate the GBR section of Google educational tools. The site received documentary A Sea Change: imagine Earth’s Ocean with information about 4.5 million web hits in 2009, a six-fold a world without fish. the reef and human impacts on it. increase over the past 4 years. It ranks ƒƒ In Kimbe Bay, Papua New Guinea, ƒƒ The Centre hosted its 2-day national first of 20.2 million websites found in a Glenn Almany led a series of symposium and public forum in Google search for “coral research”. discussions with local communities Brisbane on the 6th – 7th August that own, manage and depend on In 2009, the Centre’s educational ƒƒ Under the Queensland Scientists in coral reefs about climate change, resources web pages were further School program, Line Bay, hosted overfishing and the value of marine developed to cater for the demand an information booth about threats protected area networks in mitigating by school children for information on to the Great Barrier Reef at the their impacts and the importance of coral reefs. In collaboration with the Mundingburra State School 125th year understanding connectivity to design Australian Academy of Science, a new anniversary fete. a resilient network. NOVA topic, Science for sustainable ƒƒ At the invitation of the Royal ƒƒ In April, Josh Cinner participated reefs, was developed and launched on Australasian College of Surgeons, in a public forum on Beyond the the Academy’s website. This resource John Pandolfi presented a lecture obituaries: success stories in marine provides the latest science on coral Countdown to extinction: Can coral conservation at the Smithsonian reefs in a format readily accessible for reefs survive? Institute in Washington DC. secondary school teachers, students ƒƒ Terry Hughes presented a and parents. The Centre’s highly public lecture in Brisbane on As part of our communications strategy popular webinar series continued in coral reef resilience, part of a the Centre has developed a robust 2009 with the addition of 35 new talks lecture series run by the National media strategy in consultation with under the theme, Securing the Future Climate Change Adaptation Julian Cribb, our media advisor. Julian of Coral Reefs. These videos range Facility, at Griffith University. converts sometimes esoteric science from short, highly topical presentations ƒƒ In association with the Queensland into everyday language and delivers our on issues of interest to a general branch of the Australian Academy research findings to a diverse Australian audience to longer videos showcasing of Science, the Centre hosted a and international audience. the latest, leading-edge science for a public forum in Townsville, with scientifically informed audience. The presentations from six Fellows of the In 2009, the ARC Centre produced 39 Centre also developed a new website Academy, including Terry Hughes and media releases, generating 2190 media for the 2012 International Coral Reef Academy medallist Sean Connolly, to stories that reached local, national and Symposium which will be launched in showcase the growing international international audiences. Five hundred March 2010. During 2010, the Centre’s profile of Queensland scientists. and eighty-four news articles and website will be redesigned to enhance commentaries were on the web, in access to our research services and ƒƒ Malcolm McCulloch presented a addition to 71 television and 296 radio information, and to improve navigability. lecture Shaping the Future Climate reports, 1073 newspaper and 166 Change: Sceptics Denial as part of magazine articles. The Centre’s research

44 ARC Centre of Excellence for Coral Reef Studies Examples of the Centre’s ABC local and national news, Coral BayJournal, Moreton Bay corals get the 2,190 media hits in 2009 can’t escape the heat, 7/5/09, M spotlight, 6/8/09, J Pandolfi McCulloch Sunday Mail, Scientists find Nemo all at include: The Jakarta Post, Oceans key in climate sea, 9/8/09, P Munday New Scientist, Acid oceans no laughing change battle, 14/5/09, O Hoegh- Courier Mail, ’TimTams’ of the reef go matter for clownfish, 2/2/09, P. Guldberg missing, 25/8/09, D Bellwood Munday The Reef and Marine Aquarium Cairns Sun, $14m reef forum coup, BBC News, Australian scientists have magazine, The Lazarus Reef: 26/8/09, ARC Centre rebounding bleached Acropora corals found a new, unexpected impact of Malaysia Sun, Man-made crises recorded off Australia, May/June ocean acidification, 4 /2/09, P Munday outrunning our ability to deal with 09, K Anthony, M Hoogenboom, R Australian Story, ABC television. The heat them, 12/9/09, T Hughes Middlebrook of the moment, 9/2/09, O Hoegh- Australian R&D Review, World at a Sydney Morning Herald, Scientists Guldberg tipping point, October 2009, T warn acid is killing oceans, 2/6/09, T The Australian, Barrier Reef lands in Hughes Hughes Google Net, 11/2/09, D Bellwood 7.30 report, ABC TV, Feature- coral The Hindu, Failed policies, corruption CNN.com/Asia, Beating poverty would calcification, 10/10/09, J Lough, A leading to overfishing, 23/6/09, J save coral reef fish, 9/2/09, J Cinner Crawley, S Dove Cinner Bush Telegraph, ABC Radio National, Townsville Bulletin, Bullied to death, World News, World’s corals face danger Fat corals make better survivors 7/11/09, M McCormick interview, 10/3/09, K Anthony as global warming whips up powerful storms, 24 June 2009, J Mallela Reuters, Great Barrier Reef survival Conservation Magazine, Saving Nemo, ‘requires 25% CO cut’, 17/11/09, T Africa Geographic, On the social scale, 2 24/3/09, G Jones Hughes July 09, J Cinner Lateline, ABC television, interview with ARD German public radio network, Townsville Bulletin, Happiness doesn’t Margot O’Neill, 30/3/09, O Hoegh- interview with Bernd Musch have to cost the Earth, 11/7/09, S Guldberg Borowska, 2/12/09, O Hoegh- Foale The Guardian, UK, Damaged Barrier Reef Guldberg Australian Geographic, News: turf wars, coral makes ‘spectacular’ recovery, Seoul Times, Scientists call for ‘ocean 14/7/09, L Penin 22/4/09, G Diaz Pulido parks’ to protect seas, 8/12/09, B Discovery Channel, Stress gives fish ScienceBlog, Humans ‘damaging the Pressey wonky ears, 28/4/09, M McCormick oceans’, 30/7/09, M Kingsford Solomon (Islands) Star, Markets deplete The Age, Scientists to unlock Great fish stocks here, 29/4/09, T Brewer Barrier Reef genome, 30/7/09, D Miller

2009 annual report 45 Photo by Pim Bongaerts

Australian News AUSTRALIA: Scientist Pushes For Coral Triangle Action Written by Stephen de Tarczynski

MELBOURNE, Jul 7 (IPS) - While Australia remains “The initiative is new and it’s wonderful to see it, committed to playing an ongoing role in assisting the six but Australian scientists see this as an opportunity nations of the Coral Triangle Initiative (CTI) to protect their to ramp-up an existing engagement. It’s not as marine environments, a leading scientist here says that an if we’re starting from scratch,” says Hughes. Australian-style of management in the triangle will not work. Additionally, of the Centre’s current batch of 155 PhD “There is no single recipe for how to manage a reef well students, 95 are from the immediate region. Australia and the Great Barrier Reef model is not exportable to a was quick to pledge an initial AUD$2 million to fund poor country,” says Professor Terry Hughes, director of critical projects within the CTI - part of the USD$300 the highly-regarded Australian Research Council Centre million to be provided by the Global Environment of Excellence for Coral Reef Studies. The Centre is a Facility, the Asian Development Bank, the United States partnership of several leading universities and statutory and other partners. The Rudd government describes the bodies - located at James Cook University in Townsville. first phase of this as an “ongoing plan” to back the CT6.

“Australia is very much the lucky country when it “This investment will focus on areas where we can make comes to having the resources to manage reefs and the greatest contribution by sharing our knowledge and to pay for science and reef management,” he says. directly supporting capacity building in marine biodiversity conservation, sustainable fisheries, protecting vulnerable “There’s a huge contrast between Australian investment marine species and community empowerment,” said in science and reef management compared to almost Peter Garrett, the country’s environment minister. anywhere else in the world because most coral reef countries in the tropics are developing countries and Australia’s role as a supporter of the CT6 stems from a just don’t have the resources that we do,” he adds. request sent to it by Indonesian President Susilo Bambang Yudhoyono at a CTI meeting in Bali in Dec. 2007. He asked for But the signing of the declaration of the Coral Triangle Australian technical expertise to aid in protecting the triangle. Initiative on Coral Reefs, Fisheries and Food Security at the CTI summit in Manado, Indonesia in May indicates Hughes told IPS that Australia is compelled to act. that where the political will exists, less-affluent nations can “Australia has a capacity that, in my opinion, obligates it also undertake action to protect their marine environments to be a major player in the Coral Triangle region,” he said. for the benefit of current and future generations. While he supports the view that the threat faced by Indonesia, Malaysia, the Philippines, East Timor, Papua the inhabitants of the triangle’s coastal areas requires New Guinea and the Solomon Islands - the so-called a multilateral approach, the diversity of marine Coral Triangle Six (CT6) - have committed to cooperate environments within the Coral Triangle means that a to preserve the biologically diverse yet highly-populated one-size-fits-all solution to management is not viable. Coral Triangle, an area which covers some 5.7 million square kilometers in Southeast Asia and Melanesia. “You need to tailor-make the management style to what will work on the ground in the different regions,” says Australia is currently involved in researching marine Hughes. Written by Stephen de Tarczynski environments in the triangle and in the Pacific region,

with the ARC Centre of Excellence for Coral Reef Studies working already in the Philippines, Indonesia, Article extract, reproduced with thanks to Australian the Solomon Islands and Papua New Guinea. News website www.australia.to

46 ARC Centre of Excellence for Coral Reef Studies © Giles Winstanley / pelagicon.com

International Coral Reef Symposium 2012

The ARC Centre and James Cook on major themes including climate Committee (chaired by the Symposium University are honoured to have been change, reef ecology, conservation Convenor, Terry Hughes), linked to sub- invited by the International Society planning, fish and fisheries, genomics, committees responsible for fundraising for Reef Studies to host the 12th management tools, the Coral Triangle (led by David Yellowlees), and developing International Coral Reef Symposium Initiative and the human dimension of the scientific program (chaired by Terry (ICRS) in Australia in 2012. The ICRS is coral reefs. Done). Two other sub-committees for the world’s largest and most important overseeing the proceeding publications coral reef meeting, bringing together Activities at ICRS 2012 will include a and for field trips will be established in coral reef scientists, educators, graduate comprehensive science program, a trade 2010. The committee membership, listed students, resource managers and policy exhibition, and field trips both before on the Symposium website, is global. makers. The 12th ICRS is expected to and after the Symposium to the Heron We sincerely thank everyone who has attract approximately 2,500 delegates Island, Lizard Island and Orpheus Island volunteered their expertise and support. from 80 countries to the Cairns Research Stations. Exciting and culturally Convention Centre, from 9th–13th July significant Australian social events and Our objective is for ICRS 2012 to be 2012. A First Announcement was made the Symposium banquet will provide carbon-neutral, and we are actively in 2009 to inform potential delegates additional networking opportunities for pursuing innovative ways to reduce of the dates and venue for the next delegates to develop collaborations and carbon emissions. ICRS and also to direct them to the partnerships to increase international Symposium’s new website, at capacity in coral reef research, education Eliza Glasson www.icrs2012.com. and environmental management. Conference Co-ordinator ICRS 2012 will attract an extensive ARC Centre of Excellence international media contingent, and the for Coral Reef Studies ICRS 2012 will provide the international ARC Centre expects to host some 100 James Cook University science community with a platform to journalists, whose stories will increase Townsville QLD 4811 increase global knowledge and interest awareness of coral reef science across Australia in coral reefs, as well as the opportunity the world. Phone: +61 7 4781 4844 to showcase innovative science, and Fax: +61 7 4781 3015 the latest developments in coral reef In developing ICRS 2012, the ARC Email: [email protected] conservation and management. Close to Centre has established an Executive 2,000 talks and posters will be presented

2009 annual report 47 “The ARC Centre, too, is highly ambitious... in its determination to remain at the cutting edge of world science... and its commitment to drive forward the national and international agenda on the sustainable use and management of coral reefs.”

Her Excellency, Ms Penelope Wensley, the Governor of Queensland. Opening the ARC Centre’s annual symposium, Securing Coral Reef Futures, Brisbane, August 2009.

48 ARC Centre of Excellence for Coral Reef Studies © Giles Winstanley / pelagicon.com Symposium 2010

© Giles Winstanley / pelagicon.com

A highlight of the ARC Centre’s 2010 among the most developed in the world, Society’s collection from Captain James calendar will be hosting an inter-academy and every year close to 200 international Cook’s exploration of Australia, as symposium on coral reefs, at the Shine scientists travel to the Great Barrier Reef well as historic items of significance Dome in Canberra on October 7-8th. to pursue their research. to marine science from Australian The Centre’s annual symposia are museums and private collections. an important feature of our outreach 2010 is also the International Year of activities. 2010 will be a particularly Biodiversity. It is therefore fitting that The Following the Canberra events, a UK- special event as we will be presenting Royal Society is taking the opportunity Australia Frontiers of Science meeting the conference in partnership with to recognize the special importance of sponsored by The Royal Society and the Australian Academy of Science the world’s coral reefs as part of its 350th the Australian Academy of Science will and The Royal Society, which is anniversary. Celebrations will comprise be held in Perth, from 13th-19th October. celebrating its 350th anniversary. The four major events: the 2-day symposium, Future leaders in marine science will Canberra symposium will incorporate a public forum and an exhibition at present the latest advances in their fields, presentations by members of both the National Museum of Australia in learn from each other about research national academies and the ARC Centre Canberra, and a Frontiers of Science developments in other marine science of Excellence for Coral Reef Studies, to meeting to be held in Perth. disciplines and explore opportunities for celebrate the birth, development and collaboration. Early career researchers emergence of coral reef sciences. The Public Forum will be held in the from the ARC Centre of Excellence, National Museum of Australia on Australian Postdoctoral Fellows Tracy The Royal Society has a long history of the evening of 7th October. It will be Ainsworth and Natalie Ban, have been involvement with research on the Great hosted by a science celebrity, with selected by the Australian Academy Barrier Reef. In 1928 they sponsored C. researchers presenting short talks of Science to represent Australia on M. Yonge to lead an expedition to the to a general audience. The National the organising committee for this Lowe Isles in northern Queensland. This Museum of Australia will host a international meeting. was the world’s first detailed scientific special commemorative exhibition study of coral and coral reefs. Less to coincide with the Public Forum than 100 years later, Australian coral and Symposium. The exhibition will reef science and reef management are feature artifacts from The Royal

2009 annual report 49 National Benefit Case Study

Case Study 1: Improved protection for the Coral Sea

The Coral Sea is bounded to the south zone is the best approach for protecting on expert interviews and on the existing by the 24th parallel, by New Caledonia, these pelagic and migratory species operating costs for the Great Barrier Reef Vanuatu and the Solomon Islands to the because they cannot be protected Marine Park. The resulting management east, Papua New Guinea and Solomon inside small reserves.” The practicality estimates for the Coral Sea indicate Islands to the north, and Queensland to of this statement was confirmed by that a single large marine reserve is less the west. It has a very rich biodiversity economic research undertaken by expensive to manage than multiple-use and is one of the few places remaining members of the Centre’s Program areas of equivalent size with a 30% on Earth where large pelagic fishes 6 on Conservation Planning (p.26). no-take component. Regardless of the (tuna, billfish and sharks) have not yet Consideration of management costs method used, the difference between been severely depleted. Importantly, it is important for several reasons. First, the costs of a 30% versus 100% no- also provides a refuge for some critically resources must be available for effective, take scenarios is the same: it is about endangered species including the long-term management to ensure 1.6 times more expensive to manage Hawksbill and Green turtles. It therefore effective conservation. Second, costs of a multiple-use area than the same area constitutes an extremely valuable management can be considerable, and with 100% protection. resource with outstanding conservation should therefore be explicitly addressed values. Consequently, the ARC Centre in the site design and selection In May 2009, the Coral Sea was declared of Excellence for Coral Reef Studies process. Third, current management as a Conservation Zone by the Hon. supports the establishment of the Coral budgets are rarely sufficient to achieve Peter Garrett, the Federal Minister for Sea as one of the world’s largest marine all their objectives. Incorporating the Environment, Heritage and the Arts. protected areas. management costs from the outset The new Conservation Zone constitutes of any planning exercise is critical. 972,000 km2 of Australian waters and Researchers in the ARC Centre seabed from directly east of the Great have recommended to the Federal In collaboration with Queensland Barrier Reef Marine Park out to the edge Government that the whole Coral Sea National Parks and Wildlife Service, Bob of Australia’s Exclusive Economic Zone. should become a no-fishing area to Pressey, Vanessa Adams and Natalie Ban Minister Garrett said that “The Coral protect its immense environmental addressed a key question that had not Sea Conservation Zone will protect this and heritage values from escalating been considered – here or elsewhere environmentally significant area from overfishing and climate change. There – of whether there was a significant increasing pressures while the national is overwhelming evidence, generated difference in the estimated management marine bioregional planning process is by the ARC Centre and elsewhere, that cost for different zoning proposals for undertaken, with a final plan scheduled the world’s marine ecosystems have the Coral Sea. Specifically, what is for completion in 2010”. been seriously degraded by overfishing, the difference in management costs pollution and global warming. Eleven between multiple use zones versus a percent of land habitats have been single large no-take area? designated as parks to conserve their biodiversity and the ecosystem services The Centre’s researchers developed they provide to people. In contrast, less two novel approaches for estimating than 0.1 per cent of the world’s oceans the management costs for a Coral Sea are fully protected. Marine Protected Area (MPA). They first examined the current operational In a media interview published worldwide budgets for existing Commonwealth in 2009, ARC Centre researcher MPAs to identify key indicators of John Pandolfi stated that F“ ishing management costs. The second activities in the Coral Sea contribute to approach identified management significant declines of sharks, turtles requirements for the Coral Sea, and and seabirds. A single large no-take estimated costs for these activities based

50 ARC Centre of Excellence for Coral Reef Studies Sample publications: Lough, JM (2007). Interdecadal conservation. Trends in Ecology & climate variability in the Coral Sea Evolution 24(7): 360-369. Almany, G, Connolly, S, Heath, D, since 1708 A.D. Palaeogeography, Hughes, TP (2009). Seascape patterns Hogan, J, Jones, G, McCook, L, Palaeoclimatology, Palaeoecology and dynamics of coral reefs. pp Mills, M, Pressey, R and Williamson, 248(1-2): 190-201 482-487. In The Princeton Guide to D (2009). Connectivity, biodiversity Game, ET, Grantham, HS, Hobday, AJ, Ecology. S. A. Levin (Ed.). Princeton conservation and the design of Pressey, RL, Lombard, AT, Beckley, Press, Princeton. marine reserve networks for coral LE, Gjerde, K, Bustamante, R, reefs. Coral Reefs 28(2): 339-351. Possingham, HP and Richardson, Calvo, E, Marshall, JF, Pelejero, C, AJ (2009). Pelagic protected areas: McCulloch, MT, Gagan, MK and The missing dimension in ocean

145° 151° 154° 157° 160° 163° 166° 169° PAPUA NEW GUINEA Guadalcanal 9° Port Moresby 3000 New Guinea m Eastern Fields SOLOMON 2000 m 4 00 0 Nupani Santa Cruz Ashmore Reef m San Cristobal 00 m Torres Strait m 30 ISLANDS 00 20 5000 m Islands 0 m 6000 m 00 Nende C 3 7000 m m 000 m m 6000 5 Bamaga 3000 m 7000 Rossel m m Tagula 3000 4000 Utupua 2 0 m 00 m 7 00 40 0 0

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0 0 0 nautical miles 200 4 ANTARCTICA DAVID E. CHANDLER Map reproduced with thanks to the Pew Foundation

2009 annual report 51 Media Release Photo by Simon Foale Scientists call for ‘ocean parks’ to protect seas

An international team of scientists has called for the argued they would be difficult and costly to enforce and creation of marine protected areas in the open oceans to manage in the ever-changing ocean environment. protect the world’s sea life from growing damage and loss “However my colleagues and I consider that recent caused by overexploitation, pollution and other human advances in conservation science, oceanography and impacts. fisheries science can provide the necessary evidence, tools “Pelagic ecosystems now face a multitude of threats and information to operate these ‘ocean parks’ for the including overfishing, pollution, climate change, conservation of marine species that live in the high seas. eutrophication, mining and species introductions,” the The scientists argue ocean protected areas should be researchers warn in the journal Trends in Ecology and seen as simply another form of marine protected area, Evolution (TREE). These threats can act together to cause except that they will extend in three dimensions – across far greater damage to marine food chains, fish stocks and the surface and deep into the water itself. ecosystems. They note that on the high seas, there is no single global “Mobile pelagic species also suffer from the cumulative body with the authority to establish protected areas or to impact of sublethal stressors. Chronic exposure to chemical regulate access to and use of an area for more than one and acoustic pollution from shipping, military activities purpose. However they say progress can be made through or oil and gas exploration and exploitation can lead to Regional Fisheries Management Organizations, the immunosuppression and reproductive failure in marine International Maritime Organisation and by individual mammals,” they add. countries doing more to protect the outer parts of their 200 The high seas provide almost 80 per cent of humanity’s mile sovereign territories. fish supplies, carry out half the photosynthesis (conversion By reducing the cumulative impact of human activities of solar energy to sustain life) that takes place on the planet on the world’s oceans, MPAs can help to mitigate the and, through their ability to absorb CO , are a dominant 2 severity of particular threats that cannot be directly influence over the speed and extent of climate change. controlled: “We believe that pelagic MPAs have now come “It is clear from declines in many species that there of age as an important tool in the planet’s last frontier of is inadequate protection for pelagic biodiversity and conservation management.” ecosystems,” the researchers from Australia, South Africa and Poland say. Game, ET, Grantham, HS, Hobday, AJ, Pressey, RL, “Fewer protected areas exist in the open ocean than in Lombard, AT, Beckley, LE, Gjerde, K, Bustamante, R, any other major ecosystem on Earth,” explains Professor Possingham, HP and Richardson, AJ (2009). Pelagic Bob Pressey of the ARC Centre of Excellence for Coral protected areas: The missing dimension in ocean Reef Studies, a co-author of the article. conservation. Trends in Ecology & Evolution 24(7): “Although there is growing support for the idea of 360-369. marine protected areas in the open oceans, critics have 19 October 2009

52 ARC Centre of Excellence for Coral Reef Studies A new ISI Web of Science analysis of journal publications and citations identifies the ARC Centre of Excellence for Coral Reef Studies as the premier climate change research institution in Australia, with three Centre researchers ranked among the top 20 researchers in the world for total number of citations on climate change papers. www.sciencewatch.com/ana/fea/pdf/09novdecFea.pdf

2009 annual report 53 © Giles Winstanley / pelagicon.com National Benefit Case Study

Case Study 2: Informing governments on responding to Climate Change

The 2009 United Nations climate change Malcolm McCulloch and Terry Hughes contributed to the briefing, under the summit in Copenhagen attracted >100 joined colleagues from Brazil, Canada, auspices of the Federation of Australian world leaders, including the Prime China, Germany, New Zealand, Mexico, Scientific and Technological Societies. Minister of Australia. The ecological, Japan, and Sweden in 2009 to produce social and economic consequences an Inter-Academy statement on ocean The ARC Centre contributed senior of climate change for coral reefs in acidification. The statement, timed in personnel to the team that drafted the Australia and throughout the tropics are advance of the Copenhagen United National Climate Change Adaptation critical issues that pervade all of the ARC Nations Framework Convention on Research Plan for Marine Biodiversity Centre’s research programs. The Great Climate Change (UNFCCC) negotiations, and Resources. Subject to Ministerial Barrier Reef alone contributes $5.4 billion summarizes the current state of the approval, the national plan provides a annually to the Australian economy – $5.1 science, and is aimed at policy-makers. framework to guide research funding billion from the tourism industry; $153 In September, Deputy Director, Ove decisions, and identifies the research million from recreational activity; and Hoegh-Guldberg provided Congressional required over the next 5-7 years to inform $139 million from commercial fishing. briefings on climate change and ocean policy development and management of acidification, in Washington DC. In marine resources. The plan focuses on The ARC Centre of Excellence for Coral October, the ARC Centre’s Director aquaculture, commercial and recreational Reef Studies is a global leader in climate provided a plenary talk on climate fisheries, conservation, and tourism. change research, producing so far well change, adaptation and coral reefs, at the over 500 papers since 2005 on this 2009 ASEAN Conference on Biodiversity Sample 2009 publications: broad inter-disciplinary topic. In 2009, ISI in Singapore, preceding the ASEAN Brierley, AS and Kingsford, MJ (2009). Web of Science analysed 28,000 journal Ministerial Meeting on the Environment. Impacts of climate change on marine articles on climate change research organisms and ecosystems. Current published world-wide over the past In Australia, the Federal and Queensland Biology 19: 602-614. decade. From this vast data-set, Web environment ministers acknowledged Cinner, JE, McClanahan, TR, Graham, of Science-Science Watch identified the key research provider role of the NAJ, Pratchett, MS, Wilson, SK the most-cited institutions and authors ARC Centre, the Australian Institute of and Raina, J-B (2009). Gear-based globally. Among the leading institutions, Marine Science, and the Commonwealth fisheries management as a potential James Cook University – headquarters Scientific and Industrial Research adaptive response to climate change of the ARC Centre of Excellence for Organization, in their formal response and coral mortality. Journal of Applied Coral Reef Science - is ranked 2nd in to the 2009 Great Barrier Reef Outlook Ecology 46: 724-732. the world in terms of impact, measured Report. The report is a legislative de Freitas, DM, Kininmonth, S and as citations per paper in climate change requirement, presented every 5 years Woodley, S (2009). Linking science research. Among the top papers of the to both Houses of the Australian and management in the adoption of decade, the most highly-cited climate- Parliament. The inaugural 2009 report sensor network technology in the change publication led by an Australian provides a summary of many of the Great Barrier Reef coast, Australia. author is a 2003 Science paper by Centre ARC Centre’s research findings, and Computers, Environment and Urban Director, Terry Hughes and colleagues, will inform policy and management Systems 33(2): 111-121. entitled “Climate Change, Human decisions. In Western Australia, Deputy Impacts, and the Resilience of Coral Director Malcolm McCulloch provided McCook, L, Almany, G, Berumen, M, Reefs”. According to Web of Science, a series of briefings to the Western Day, J, Green, A, Jones, G, Leis, three Australians rank among the top 20 Australian Department of Environment J, Planes, S, Russ, G, Sale, P and researchers in the world for the number and Conservation. In November, the Thorrold, S (2009). Management of citations their climate change papers Centre was a major contributor to a under uncertainty: Guide-lines for have received - ARC Centre members briefing on emission reduction targets incorporating connectivity into the Ove Hoegh-Guldberg, Terry Hughes and and the Great Barrier Reef, provided to protection of coral reefs. Coral Reefs John Pandolfi. Australian Members of Parliament and 28(2): 353-366 Senators, in Parliament House, Canberra. Rockstrom, J, and 28 co-authors (2009). The ARC Centre engages with many The ARC Centre’s Director and two A safe operating space for humanity. end-users of climate change research, Deputy Directors, along with Partner Nature 461: 472-475. in Australia and globally. For example, Investigator, Janice Lough from the Australian Academy of Science Fellows Australian Institute of Marine Science,

54 ARC Centre of Excellence for Coral Reef Studies Photo by Simon Foale Media Release Nemo “won’t be coming home”

Nemo, the lovable clownfish of movie fame, may be shown that baby fish can discriminate between seawater unable to find his way home as the world’s oceans acidify from reefs surrounding vegetated islands versus seawater due to human-derived carbon emissions. from reefs without islands. This is what enables many of the baby clownfish to find their way back to the reef where Fish lose the sense of smell that guides them home they were hatched”, says co-author Geoff Jones. when sea water becomes more acidic – with potentially devastating consequences for sea life, an international In normal sea water nemos are strongly attracted to team of scientists has discovered. scents from anemones on their home reefs and tropical rainforest trees on nearby land – but avoid the smell of Like many reef and coastal fish, Nemos are swept off swamp trees or tropical grasses. their home reef into the open ocean as tiny babies and use their acute sense of smell to find their way back again. Nemos reared in slightly more acidic water were attracted to a range of environmental smells, including The researchers tested clownfish raised in normal and those they normally avoided and that indicated a habitat slightly more acidic seawater to see what effect it had on less suited to their needs. Nemos reared in seawater at pH their sense of smell. To their dismay they found that the 7.6 showed no response to scent cues at all. fish, normally acutely sensitive to different smells in the

water, became confused when the water they were raised “Our results show for the first time that elevated CO2 in was more acidic than usual. and reduced seawater pH can affect the behavioural decisions of marine organisms during critical stages “This is a disturbing finding, because the tiny larvae of of their life-history. In this case, acidification disrupted many coastal fish probably rely on scent cues in the water the olfactory mechanism by which clownfish larvae to help locate adult habitat. Any disruption to their ability discriminate between cues that may be useful for locating to navigate could have far-reaching implications for the suitable adult habitat and other cues that could lead larvae future of these fish populations.” says lead author Prof to unsuitable settlement sites. Philip Munday of the ARC Centre of Excellence for Coral Reef Studies. “Disruption to this process would have significant consequences for the replenishment of adult populations Ocean acidification, caused by the absorption of human- and could lead to declines of many coastal species,” they released carbon dioxide (CO ) at the ocean surface, is 2 conclude. now recognized as a serious threat to marine ecosystems, the researchers from James Cook, Moscow and Oslo universities say. Munday, PL, Dixson, DL, Donelson, JM, Jones, GP, “Global ocean pH is estimated to have dropped by Pratchett, MS, Devitsina, GV and Daving, KB (2009). 0.1 units since preindustrial times and is projected to fall Ocean acidification impairs olfactory discrimination another 0.3-0.4 units by 2100 due to current and future and homing ability of a marine fish. Proceedings of the

CO2 emissions.” National Academy of Sciences 106(6): 1848-1852. “Orange clownfish – or nemos - mostly live on oceanic 4 February 2009 reefs surrounding vegetated islands and research has

2009 annual report 55 publications

The ARC Centre of Excellence for Coral Citations of the Centre’s publications Caldeira, K, Knowlton, N, Eakin, Reef Studies produced 224 publications continue to grow, increasing nearly 5-fold CM, Iglesias-Prieto, R, Muthiga, in 2009, continuing the rapid growth in since 2004. Twenty-five researchers N, Bradbury, RH, Dubi, A and output exhibited since 2004. According were each cited >200 times in 2009, Hatziolos, ME (2007). Coral Reefs to ISI Web of Science, the ARC Centre nine of the Centre members had >500 Under Rapid Climate Change and remains the first-ranked institution citations, and three had >1000 citations Ocean Acidification. Science 318: globally for both the number of journal in the 12-month reporting period. 1737-1742. publications and citations in coral reef ƒƒ Pratchett MS, Munday PL, science. The average Impact Factor for  Summed citations to members of Wilson SK, Graham NAJ, Cinner all 203 journal articles published in 2009 the ARC Centre of Excellence each JE, Bellwood DR, Jones GP, was 4.2. year for 2004-2009 Polunin NVC, McClanahan TR 16000 (2008) Effects of climate-induced Fifty-three of the 2009 articles are 14000 coral bleaching on coral-reef in journals with Impact Factors fishes - ecological and economic 12000 greater than four, including top-tier consequences. Oceanography journals such as Science, Nature, 10000 and Marine Biology: An Annual PNAS and Current Biology. 8000 Review 46:251-296 6000 ƒƒ ISI Essential Science Indicators  Number of publications by members 4000 2005 identified four Research Fronts in 2004 of the ARC Centre of Excellence Number of citations 2000 2009 that highlight the Centre’s 2006 2007 2008 2009 for 2004-2009 0 research. A research front is a group Year of highly cited papers, referred to 250 as core papers, in an emerging topic defined by a cluster analysis. League table achievements 200 Seventeen core papers in these in 2009 include: Research Fronts including 7 in 150 Science, Nature and PNAS, were co- ƒƒ Three Program Leaders in the authored by G. Almany, D. Bellwood, 100 Centre are recognized by ISI as C. Folke, N. Graham, O. Hoegh- Highly Cited Researchers in Earth Guldberg, T. Hughes, G. Jones, M. 50 Sciences (Malcolm McCulloch) Kingsford, M. McCormick, S. Planes, Number of publications 2004 2005 2006 2007 2008 2009 and Ecology/Environment (Terry 0 M. Pratchett, B. Pressey, R. Steneck, Hughes and Bob Pressey). Year S. Wilson, and D. Yellowlees. ƒƒ The Faculty of 1000 Biology The Centre’s research outputs were highlighted six of the ARC Centre’s published in a total of 90 journals, publications for review in 2009. spanning many fields of research. ƒƒ ISI Essential Science Indicators For example, the titles of these identified two of the Centre’s journals refer to each of the following recent articles as Hot Papers, which disciplines: archaeology, biochemistry, received an unusually high number of botany, conservation biology, ecology, citations within 2 years of publication: evolution, fisheries, immunology, modelling, oceanography, paleobiology, ƒƒ Hoegh-Guldberg, O, Mumby, petrology, photobiology, physiology, PJ, Hooten, AJ, Steneck, RS, genomics, geochemistry, social science, Greenfield, P, Gomez, E, Harvell, systematics, and many more. CD, Sale, PF, Edwards, AJ,

56 ARC Centre of Excellence for Coral Reef Studies publications list

Books processes, causes and Lough (Eds.). Springer, Berlin D, Carstens, BC, Chu, consequences. pp1-5. In Heidelberg. KH, Cubeta, MA, Cuda, [1] van Oppen, MJH and Lough, Coral Bleaching. M. J. H. [15] van Oppen, MJH and Lough, JP, Cui, ZX, Datnoff, LE, JM (2009). Coral bleaching: van Oppen and J. M. Lough Davila, JA, Davis, ES, patterns, processes, causes (Eds.). Springer, Berlin JM (2009). Synthesis: Coral bleaching - patterns, Davis, RM, Diekmann, and consequences 178pp. Heidelberg. OE, Eizirik, E, Fargallo, JA, Springer, Berlin Heidelberg. processes, causes and [9] McClanahan, TR, Weil, E, consequences. pp175-176. Fernandes, F, Fukuda, H, Cortés, J, Baird, AH and In Coral Bleaching. M. J. Gale, LR, Gallagher, E, Gao, Ateweberhan, M (2009). H. van Oppen and J. M. YQ, Girard, P, Godhe, A, Goncalves, EC, Gouveia, Book Sections Consequences of coral Lough (Eds.). Springer, Berlin bleaching for sessile reef Heidelberg. L, Grajczyk, AM, Grose, [2] Cinner, JE, McClanahan, TR, organisms. pp121-138. In MJ, Gu, ZF, Hallden, C, Abunge, C and Wamukota, Coral Bleaching. M. J. H. Harnstrom, K, Hemmingsen, AW (2009). Human van Oppen and J. M. Lough AH, Holmes, G, Huang, dimensions of conserving (Eds.). Springer, Berlin Journal Articles CH, Huang, CC, Hudman, Kenya’s coral reefs. In Heidelberg. SP, Jones, GP, Kanetis, L, [16] Abrego, D, van Oppen, Karunasagar, I, Keyghobadi, Advances in coastal ecology: MJH and Willis, BL (2009). People, processes and [10] Pratchett, MS, Wilson, SK, N, Klosterman, SJ, Klug, PE, Graham, NAJ, Munday, Highly infectious symbiont Koch, J, Koopman, MM, ecosystems in Kenya. J. dominates initial uptake in Hoorweg and N. A. Muthiga PL, Jones, GP and Polunin, Koppler, K, Koshimizu, E, NVC (2009). Coral bleaching coral juveniles. Molecular Krumbock, S, Kubisiak, T, (Eds.). African Studies Centre, Ecology 18(16): 3518-3531. Leiden, Netherlands. and consequences for Landis, JB, Lasta, ML, Lee, motile reef organisms: [17] Abrego, D, van Oppen, CY, Li, QQ, Li, SH, Lin, RC, [3] Connolly, SR (2009). past, present and uncertain MJH and Willis, BL (2009). Liu, M, Liu, N, Liu, WC, Macroecological theory future effects. pp139-158. Onset of algal endosymbiont Liu, Y, Loiseau, A, Luan, and the analysis of species In Coral Bleaching. M. J. specificity varies among WS, Maruthachalam, KK, richness gradients. pp279- H. van Oppen and J. M. closely related species of McCormick, HM, Mellick, 309. In Marine Macroecology. Lough (Eds.). Springer, Berlin Acropora corals during early R, Monnahan, PJ, Morielle- J. D. Witman and K. Roy Heidelberg. ontogeny. Molecular Ecology Versute, E, Murray, TE, (Eds.). The University of [11] Pressey, RL, Watts, ME, 18(16): 3532-3543. Narum, SR, Neufeld, K, de Chicago Press, Chicago. Nova, PJG, Ojiambo, PS, Barrett, TW and Ridges, [18] Adjeroud, M, Michonneau, [4] Eakin, CM, Lough, JM and MJ (2009). The C-Plan Okamoto, N, Othman, AS, F, Edmunds, P, Chancerelle, Overholt, WA, Pardini, R, Heron, SF (2009). Climate conservation planning Y, de Loma, T, Penin, L, variability and change: system: origins, applications, Paterson, IG, Patty, OA, Thibaut, L, Vidal-Dupiol, Paxton, RJ, Planes, S, Porter, monitoring data and evidence and possible futures. J, Salvat, B and Galzin, for increased coral bleaching pp211-234. In Spatial C, Pratchett, MS, Puttker, T, R (2009). Recurrent Rasic, G, Rasool, B, Rey, O, stress. pp41-67. In Coral conservation prioritization: disturbances, recovery Riegler, M, Riehl, C, Roberts, Bleaching. M. J. H. van Quantitative methods and trajectories, and resilience JMK, Roberts, PD, Rochel, Oppen and J. M. Lough computational tools. A. of coral assemblages on a (Eds.). Springer, Berlin Moilanen, K. A. Wilson and south central Pacific reef. E, Roe, KJ, Rossetto, M, Heidelberg. H. P. Possingham (Eds.). Coral Reefs 28(3): 775-780. Ruzzante, DE, Sakamoto, T, Saravanan, V, Sarturi, [5] Ferguson, KH (2009). That’s Oxford University Press, Oxford, UK. [19] Ainsworth, TD and Hoegh- CR, Schmidt, A, Schneider, not a reef, now that’s a reef: Guldberg, O (2009). Bacterial MPC, Schuler, H, Serb, JM, a century of (re)placing the [12] Souza Junior, WC and communities closely Serrao, ETA, Shi, YH, Silva, Great Barrier Reef. pp223- Fidelman, PIJ (2009). The associated with coral tissues A, Sin, YW, Sommer, S, 236. In ECOSEE: Image, Technopolitics of water vary under experimental Stauffer, C, Strussmann, Rhetoric, and Nature. S. I. in Brazil. pp195-211. In and natural reef conditions CA, Subbarao, KV, Syms, C, Dobrin and S. Morey (Eds.). Governança da água no and thermal stress. Aquatic Tan, F, Tejedor, ED, Thorrold, State University of New York Brasil. W. C. Ribeiro (Ed.). Biology 4(3): 289-296. SR, Trigiano, RN, Trucco, Press, New York. Annablumme Press, Brazil. MI, Tsuchiya-Jerep, MTN, [20] Almany, G, Connolly, S, Vergara, P, van de Vliet, MS, [6] Hughes, TP (2009). [13] Turner, WR and Pressey, Heath, D, Hogan, J, Jones, Wadl, PA, Wang, AM, Wang, Confronting the global decline RL (2009). Building and G, McCook, L, Mills, M, of coral reefs. pp140-166. In implementing systems of Pressey, R and Williamson, HX, Wang, RX, Wang, XW, Loss of Coastal Ecosystems. conservation areas. pp538- D (2009). Connectivity, Wang, Y, Weeks, AR, Wei, C. Duarte (Ed.). BBVA 547. In The Princeton guide biodiversity conservation and FW, Werner, WJ, Wiley, Foundation, Madrid. to ecology. S. Levin (Ed.). the design of marine reserve EO, Williams, DA, Wilkins, Princeton University Press, networks for coral reefs. RJ, Wisely, SM, With, KA, [7] Hughes, TP (2009). Seascape Wu, DH, Yao, CT, Yau, C, patterns and dynamics of Princeton. Coral Reefs 28(2): 339-351. Yeap, BK, Zhai, BP, Zhan, coral reefs. pp482-487. In The [14] van Oppen, MJH, Baker, Princeton Guide to Ecology. [21] Almany, GR, De Arruda, MP, XJ, Zhang, GY, Zhang, SY, AC, Coffroth, MA and Arthofer, W, Atallah, ZK, Zhao, R, Zhu, LF and Mol S. A. Levin (Ed.). Princeton Willis, BL (2009). Bleaching Press, Princeton. Beissinger, SR, Berumen, Ecol, R (2009). Permanent resistance and the role of ML, Bogdanowicz, SM, genetic resources added to [8] Lough, JM and van Oppen, algal endosymbionts. pp83- Brown, SD, Bruford, MW, molecular ecology resources MJH (2009). Introduction: 102. In Coral Bleaching. M. Burdine, C, Busch, JW, database 1 May 2009- coral bleaching - patterns, J. H. van Oppen and J. M. Campbell, NR, Carey, 31 July 2009. Molecular

2009 annual report 57 Ecology Resources 9(6): [31] Ban, NC and Klein, [41] Bonaldo, R and Bellwood, D in groups of the humbug 1460-1466. CJ (2009). Spatial (2009). Dynamics of parrotfish damselfish Dascyllus socioeconomic data as a grazing scars. Marine Biology aruanus: small, similar-sized [22] Anthony, KRN, 156(4): 771-777. Hoogenboom, MO, cost in systematic marine individuals may be close kin. Maynard, JA, Grottoli, AG conservation planning. [42] Bonin, M, Srinivasan, M, Molecular Ecology 18(22): and Middlebrook, R (2009). Conservation Letters 2(5): Almany, G and Jones, G 4707-4715. Energetics approach to 206-215. (2009). Interactive effects of [51] Cantin, N, van Oppen, M, predicting mortality risk from [32] Ban, NC, Picard, CR and interspecific competition and Willis, B, Mieog, J and Negri, environmental stress: a case Vincent, ACJ (2009). microhabitat on early post- A (2009). Juvenile corals study of coral bleaching. Comparing and integrating settlement survival in a coral can acquire more carbon Functional Ecology 23(3): community-based and reef fish. Coral Reefs 28(1): from high-performance algal 539-550. science-based approaches 265-274. symbionts. Coral Reefs [23] Baird, AH, Bhagooli, R, to prioritizing marine areas [43] Bonin, MC, Munday, PL, 28(2): 405-414. Ralph, PJ and Takahashi, S for protection. Conservation McCormick, MI, Srinivasan, [52] Carpenter, SR, Folke, C, (2009). Coral bleaching: the Biology 23(4): 899-910. M and Jones, GP (2009). Scheffer, M and Westley, role of the host. Trends in [33] Ban, NC and Vincent, ACJ Coral-dwelling fishes F (2009). Resilience: Ecology & Evolution 24(1): (2009). Beyond marine resistant to bleaching but not accounting for the 16-20. reserves: exploring the to mortality of host corals. noncomputable. Ecology and approach of selecting areas Marine Ecology Progress Society 14(1). [24] Baird, AH, Bhalla, RS, Series 394: 215-222. Kerr, AM, Pelkey, NW where fishing is permitted, [53] Carter, AB, Williams, AJ and and Srinivas, V (2009). Do rather than prohibited. PLoS [44] Botsford, L, White, J, Russ, GR (2009). Increased mangroves provide an ONE 4(7): e6258. Coffroth, M, Paris, C, accuracy of batch fecundity effective barrier to storm [34] Bartlett, CY, Manua, C, Planes, S, Shearer, T, estimates using oocyte surges? Proceedings of Cinner, J, Sutton, S, Jimmy, Thorrold, S and Jones, G stage ratios in Plectropomus the National Academy R, South, R, Nilsson, (2009). Connectivity and leopardus. Journal of Fish of Sciences 106(40): J and Raina, J (2009). resilience of coral reef Biology 75(3): 716-722. E111-E111. metapopulations in marine Comparison of outcomes [54] Carwardine, J, Klein, CJ, of permanently closed and protected areas: matching [25] Baird, AH, Birrel, CL, empirical efforts to predictive Wilson, KA, Pressey, RL Hughes, TP, McDonald, periodically harvested coral and Possingham, HP (2009). reef reserves. Conservation needs. Coral Reefs 28(2): A, Nojima, S, Page, CA, 327-337. Hitting the target and Pratchett, MS and Yamasaki, Biology 23(6): 1475-1484. missing the point: target- H (2009). Latitudinal variation [35] Bartlett, CY, Pakoa, K and [45] Bottrill, MC, Joseph, LN, based conservation planning in reproductive synchrony Manua, C (2009). Marine Carwardine, J, Bode, in context. Conservation in Acropora assemblages: reserve phenomenon in the M, Cook, C, Game, ET, Letters 2(1): 4-11. Japan vs. Australia. Galaxea Grantham, H, Kark, S, Linke, Pacific Islands. Marine Policy [55] Cinner, J, Fuentes, M and 11(2): 101-108. 33(4): 673-678. S, McDonald-Madden, E, Pressey, RL, Walker, S, Randriamahazo, H (2009). [26] Baird, AH and Guest, JR [36] Bay, LK, Ulstrup, KE, Wilson, KA and Possingham, Exploring social resilience (2009). Spawning synchrony HP (2009). Finite in Madagascar’s marine in scleractinian corals: Nielsen, HB, Jarmer, H, Goffard, N, Willis, BL, Miller, conservation funds mean protected areas. Ecology and comment on Mangubhai triage is unavoidable. Trends Society 14(1). & Harrison (2008). Marine DJ and Van Oppen, MJH (2009). Microarray analysis in Ecology & Evolution 24(4): [56] Cinner, JE (2009). Migration Ecology Progress Series 183-184. 374: 301-304. reveals transcriptional and coastal resource use in plasticity in the reef building [46] Brewer, TD, Cinner, JE, Papua New Guinea. Ocean [27] Baird, AH, Guest, JR and coral Acropora millepora. Green, A and Pandolfi, JM & Coastal Management Willis, BL (2009). Systematic Molecular Ecology 18(14): (2009). Thresholds and 52(8): 411-416. and biogeographical patterns 3062-3075. multiple scale interaction of in the reproductive biology of [57] Cinner, JE (2009). The [37] Bellwood, DR and Meyer, environment, resource use, middle path: avoiding scleractinian corals. 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UV-induced DNA damage Meekan, MG, Lawler, IR conservation: moving Eight microsatellite loci for in coral planulae. Journal and Bradshaw, CJA (2009). beyond malthus. Current the Irukandji syndrome- of Experimental Biology Aerial survey as a tool Biology 19(3): R117-R119. causing carybdeid jellyfish, 212(17): 2760-2766. to estimate whale shark Carukia barnesi (Cubozoa, abundance trends. Journal [196] Stockwell, B, Jadloc, Cnidaria). Molecular Ecology [180] Reef, R, Kaniewska, P and of Experimental Marine CRL, Abesamis, RA, Resources 9(2): 670-672. Hoegh-Guldberg, O (2009). Biology and Ecology 368(1): Alcala, AC and Russ, GR Coral skeletons defend 1-8. (2009). Trophic and benthic [172] Planes, S, Jones, GP and against ultraviolet radiation. responses to no-take Thorrold, SR (2009). Larval PLoS ONE 4(11): e7995. [188] Rowat, D, Speed, CW, marine reserve protection dispersal connects fish Meekan, MG, Gore, MA in the Philippines. 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Estimating ONE 4(2): e4511. juvenile Diplodus vulgaris connectivity in marine and D. sargus in the [182] Reyes-Bermudez, A and populations: An empirical [198] Tanner, JE, Hughes, TP Mediterranean. Aquatic Miller, D (2009). In vitro evaluation of assignment and Connell, JH (2009). Biology 6(1-3): 153-158. culture of cells derived from tests and parentage analysis Community-level density larvae of the staghorn coral under different gene flow dependence: an example [174] Pratchett, MS, Schenk, Acropora millepora. Coral scenarios. Molecular from a shallow coral TJ, Baine, M, Syms, C Reefs 28(4): 859-864. Ecology 18: 1765-1776. assemblage. Ecology 90(2): and Baird, AH (2009). 506-516. Selective coral mortality [183] Rockström, J, Steffen, [190] Sampayo, EM, Dove, associated with outbreaks W, Noone, K, Persson, Å, S and Lajeunesse, TC [199] Underwood, JN, Smith, of Acanthaster planci L. Chapin, FS, Lambin, EF, (2009). 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2009 annual report 63 Recognition of Excellence by Centre Members

The scientific achievements of many Nature Conservancy. Her project is Kingdom will allow him to forge members of the ARC Centre of entitled “Conservation objectives new collaborations across the ARC Excellence for Coral Reef Studies were to minimize the impacts of climate Centre’s nodes in Australia. Other recognised during 2009 through awards change on the Great Barrier Reef”. successes in latest ARC Fellowship and peer-recognition. Examples include: ƒƒ The book The Great Barrier Reef rounds include Glenn Almany, edited by Ove Hoegh-Guldberg, Andrew Baird (Future Fellowships), ƒƒ The Australian Academy of Science Pat Hutchings and Mike Kingsford and Natalie Ban and Nick Graham recognised the achievements was awarded a Commendation (Australian Postdoctoral Fellowships). of two of the Centre’s program Certificate for a Zoological Text ƒƒ At James Cook University, several leaders. Malcolm McCulloch was at the 2009 Whitley Awards of the Centre’s researchers were awarded the Jaeger Medal for hosted by the Royal Zoological recognised within the University: Research in Earth Science for the Society of New South Wales. ƒƒ Terry Hughes and Bob Pressey contribution throughout his career ƒƒ Three of the Centre’s Fellows were were appointed as Distinguished to “the study of the solid earth selected by the Australian Academy Professors in September. This and environmental issues”. Sean of Science for International Science new title is bestowed on leading Connolly won the Fenner Medal Linkages – Science Academies researchers who have achieved for Research in Biology. This is Program funding. John Pandolfi extraordinary levels in their awarded for distinguished research (UQ), Tracy Ainsworth (JCU), Andrew chosen fields. by an early career researcher Baird (JCU) will visit the University of under the age of 40. Sean was ƒƒ Morgan Pratchett won the JCU California, University of Hawaii and recognised for his “research Supervisor of the Year award in Academia Sinica respectively under on the processes influencing the early career category. this scheme. population dynamics, ecological ƒƒ Philip Munday, Morgan Pratchett interactions and biodiversity”. ƒƒ Professor Peter Mumby was and Nick Graham won the JCU awarded one of the Australian ƒƒ Australian Postdoctoral Fellow, Vice-Chancellor Excellence Award Research Council’s inaugural Natalie Ban, won the inaugural for Research and Supervision. Laureate Fellowships in late 2009. Bommies Award of the Great Barrier Peter’s move to Australia from the Reef Foundation along with her University of Exeter in the United associate Eddie Game from The

Courtesy of the Australian Academy of Science © Irene Dowdy

 Professor Sean Connolly was awarded the Fenner Medal for Research in Biology by the Australian Academy of Science

64 ARC Centre of Excellence for Coral Reef Studies Courtesy of the Australian Academy of Science © Irene Dowdy

Professor Malcolm McCulloch was awarded the Jaeger Medal for Research in Earth Science by the Australian Academy of Science

2009 annual report 65 Performance Measures

Research findings

Measure Target 2009 Outcome 2009

Number of publications (p.56) 145 224

Publications in journals with an impact factor > 4 38 53

Number of citations (p.56) 6500 14194

Invitations to provide plenary addresses at international 30 43 conferences

Invitations to provide review articles 35 42

Number and nature of commentaries about the Centre’s 850 2190 achievements

Awards, prizes or recognition (p.64) 17 26

Research training and professional education

Measure Target 2009 Outcome 2009

Number of postgraduates enrolled (p.34) 120 over 5 years 159 enrolled in 2009

Number of postgraduate completions 70 over 5 years 25

Number of Honours students 60 over 5 years 15 enrolled in 2009

Number of professional workshops 14 18

Participation in professional workshops 20 37

Number and level of graduate student courses and 10 16 workshops in the priority area(s)

66 ARC Centre of Excellence for Coral Reef Studies International, national and regional links and networks

Measure Target 2009 Outcome 2009

Number of international visitors 65 79

45 researcher participations Number of national and international Working Groups 16 in 20 working groups

Number of visits to overseas laboratories and research 50 58 facilities

Membership of national and international boards and advisory 40 57 committees

Number of cross-institutional publications 95 161

Number of multi-institutional supervisory arrangements of 50 57 graduate students

Commercialisation: Number of internationally funded students 20 over 5 years 57 Number of consultancies and contract research 5 23

Number of government, industry and business briefings 30 82

Number of Centre trained/ing personnel in knowledge / 5 5 technology transfer and commercialization

Public awareness programs: Website hits 1.5 million 4.5 million Public awareness presentations 12 45

Organisational support

Measure Target 2009 Outcome 2009

Annual cash contributions from Collaborating Organisations $1.36m $2.2m

Annual in-kind contributions from Collaborating Organisations $3.2m $5.7m

Number of new Organisations recruited to or involved in the Centre 5 5

Level and quality of infrastructure provided to the Centre $1.07m $1.1m

Annual cash contributions from other organisations $0.26m $2.3m

2009 annual report 67 Performance Measures

Governance

Measure Target 2009 Outcome 2009

Senior representation from all nodes. Breadth and experience of the members Representation of eminent international See page 7 of the Advisory Board researchers. Members with commercial and business links

2 Centre Advisory Board meetings p.a. Frequency and effectiveness of Advisory 4 Scientific Management Committee See page 7 Board meetings meetings p.a.

Strategic Plan reviewed and The Centre’s progress against endorsed by the Centre Advisory the plan will be formally reported Quality of the Centre strategic plan Board. Ongoing performance to the Advisory Board and be against plan reviewed at Scientific renewed in light of outcomes Management Committee meetings

Effectiveness of arrangements to manage 1. Meetings of the Scientific 1. All nodes and research programs Centre nodes Management Committee where represented at Scientific each node and program is Management Committee meetings represented 2. Monthly nodal leader phone or video 2. Regular nodal and program leader conferences meetings held

3. Annual rotational visits to the nodes 3. There were 24 cross-nodal visits in 2009. Additionally, members travelled to Brisbane for the Centre’s annual meeting and symposium.

4. Annual research retreats for all 4. Research planning meetings were Centre participants held by each research program

5. Annual research program planning 5. Cross-nodal attendance at all meetings with cross-nodal research planning meetings attendance

6. Number of co-supervisory 6. 57 arrangements for students

7. Number of multi-nodal seminar and 7. 40 discussion groups

The adequacy of the Centre’s Key International benchmarking to The Centre is ranked #1 in the world for Performance Measures research in top international citations and outputs in coral reef science marine research centres.

68 ARC Centre of Excellence for Coral Reef Studies National Benefit

Measure Target 2009 Outcome 2009

100% increase on 2004 benchmark by 2010 2.5 times the number of publications in the 2004 benchmark 4.8 times the number of citations in the 2004 benchmark Measures of expansion of Australia’s capability in the 34 briefings to government, business and 82 briefings priority area(s) industry groups

17 cross-nodal publications 30 cross-nodal publications

90 cross-institutional publications 161 cross-institutional publications

Case studies of economic, 2 to be highlighted in the annual report and 39 Media Releases social, cultural or distributed to media agencies See page 50 environmental benefits

2009 annual report 69 Financial Statement

ARC Centre of Excellence for Coral Reef Studies Statement of Operating Income and Expenditure for year ended 31 December 2009

2008 2009

Income $ $

ARC Centre Grant $2,598,470 $2,651,090

ARC Fellowships 789,965 932,744

ARC Discovery 71,418

ARC Linkages 150,000

ARC Networks 30,000

Host Institutions cash support 1,709,282 2,266,972

Local Government

State Government 117,000 119,965

Commonwealth Government other grants 356,000 408,423

International and other contracts 297,900 571,923

Total Income $5,868,617 $7,202,535

Expenditure

Salaries 3,710,607 3,829,430

Equipment 326,790 526,204

Travel 1,144,558 1,236,948

Research maintenance and consumables 1,133,984 1,087,630

Scholarships 54,112 153,077

Public outreach and administration 45,523 171,776

Total Expenditure $6,415,573 $7,005,065

Surplus (Deficit) $(546,956) $197,470

70 ARC Centre of Excellence for Coral Reef Studies Financial Status

With the announcement of the extension of the ARC Centre of Excellence to 2013 the operating cash and in-kind operating budget for the ARC Centre of Excellence for 2005-2013 currently totals $97m, more than triple the 2005 funding outlook. The chart below indicates the budgeted level of income from the various funding sources.

ARC Centre cash and inkind funding outlook 2005-2013 – Total funding $97m

Industry partners & contracts $7m, 7% UWA $1m, 1% ANU $2m, 2% UQ $4m, 4% ARC CoE $23m, 24%

JCU $42m, 44%

ARC Fellowships $7m, 7%

ARC Other $3m, 3% State Commonwealth Government Government / Other $3m, 3% $5m, 5%

2009 annual report 71 Acknowledgements

The ARC Centre of Excellence for Coral Reef Studies thanks the following organisations and partners for their ongoing support:

ƒƒ American Australian Association ƒƒ New Zealand Marsden Fund ƒƒ Australian Academy of Science ƒƒ Packard Foundation ƒƒ Australian Institute of Marine Science ƒƒ PADI Foundation ƒƒ Australian Coral Reef Society ƒƒ Project AWARE Foundation ƒƒ Australian Geographical Society ƒƒ Queensland Conservation Council ƒƒ Australian Museum ƒƒ Queensland Department of Premier and Cabinet ƒƒ Beijer Institute for Ecological Economics ƒƒ Queensland Department of Primary Industries ƒƒ Centre National de la Recherche Scientifique ƒƒ Queensland Department of Employment, Economic ƒƒ Conservation International Development & Innovation ƒƒ Department of Environment, Water, Heritage and the Arts ƒƒ Queensland Parks & Wildlife Service ƒƒ Ecological Society of Australia ƒƒ Resilience Alliance ƒƒ Environmental Futures Network ƒƒ Royal Swedish Academy of Science ƒƒ European Commission ƒƒ Stockholm Resilience Centre ƒƒ German Federal Ministry for the Environment, Nature ƒƒ The Nature Conservancy Conservation and Nuclear Safety ƒƒ United Nations University ƒƒ Government of the Republic of Indonesia ƒƒ University of Delaware ƒƒ Great Barrier Reef Foundation ƒƒ University of Maine ƒƒ Great Barrier Reef Marine Park Authority ƒƒ University of Perpignan ƒƒ Griffith University ƒƒ Western Australian Department of Commerce ƒƒ Hassall and Associates Pty Ltd ƒƒ Western Australian Department of Environment and ƒƒ Ian Potter Foundation Conservation ƒƒ IDP Education Australia ƒƒ Western Indian Ocean Marine Science Association ƒƒ Lizard Island Research Station ƒƒ Wildlife Conservation Society ƒƒ MacArthur Foundation ƒƒ Wildlife Preservation Society of Australia ƒƒ Marine and Tropical Sciences Research Facility ƒƒ World Bank Global Environment Facility Coral Reef Targeted Research Program ƒƒ National Geographic Society ƒƒ World Wide Fund for Nature ƒƒ Network in Genes and Environment in Development

Report design and layout by Zephyrmedia (www.zephyrmedia.com.au)

72 ARC Centre of Excellence for Coral Reef Studies ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland 4811 AUSTRALIA

Phone: +61 7 4781 4000 Fax: +61 7 4781 6722 Email: [email protected]

www.coralcoe.org.au